title: N2a_22L vers Mock_rep7

city: München

first: Christian

last: Bach

address: Trogerstr. 30

institute: TU München

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro6.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: N2a_22L_Passage 18

tag: N2a_Mock_Passage 18


title: N2a_22L vers Mock_rep3

status: Public on Feb 22 2008

type: RNA

country: Germany

molecule: total RNA

organism: Mus musculus


title: H. pylori Kx1 infecting mGEPs, biological rep2

city: Saint Louis

first: Marios

last: Giannakis

state: MO

address: 4444 Forest Park Blvd.

department: Developmental Biology

country: USA

institute: Washington University in Saint Louis

description: Gene expression data from a Helicobacter pylori isolate associated with ChAG infecting gastric epithelial progenitor cells

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on GeneChips Hp-AG78a520172F. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GS300

data_processing: See methods of Helicobacter pylori Evolution during Progression from Chronic Atrophic Gastritis to Gastric Cancer and its Impact on Gastric Stem Cells Giannakis M et al, 2008 PNAS

label: biotin

organism: Helicobacter pylori

source_name: H. pylori isolate Kx1 infecting mouse gastric epithelial progenitor cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Bacterial cells were grown to log phase in BB medium and then added to mGEPs cells in RPMI 1640 medium supplemented with 10% FBS at 37C or just RPMI 1640 medium supplemented with 10% FBS at 37C (no mGEP cells)

extract_protocol: Qiagen RNeasy mini-prep kit.

treatment_protocol: After 24h of infection, medium and non-attached bacteria were washed off and the bacterial and mammalian cells harvested by trypsinization (5mins at 37C). Following neutralization with ice-cold medium, and a PBS wash, cells were flash frozen in liquid nitrogen

tag: Bacterial cells


title: H. pylori Kx2 infecting mGEPs, biological rep2

description: Gene expression data from a Helicobacter pylori isolate associated with cancer infecting gastric epithelial progenitor cells

source_name: H. pylori isolate Kx2 infecting mouse gastric epithelial progenitor cells


title: H. pylori Kx2, biological rep1

description: Gene expression data from a Helicobacter pylori isolate associated with cancer grown in cell media

source_name: H. pylori isolate Kx2 grown in cell media for 24h


title: H. pylori Kx1, biological rep2

description: Gene expression data from a Helicobacter pylori isolate associated with ChAG grown in cell media

source_name: H. pylori isolate Kx1 grown in cell media for 24h


title: H. pylori Kx1, biological rep1


title: H. pylori Kx2 infecting mGEPs, biological rep1


title: H. pylori Kx2, biological rep2


title: N2a_22L vers Mock_rep5


title: H. pylori Kx1 infecting mGEPs, biological rep3


title: N2a_22L vers Mock_rep6


title: MG1655 delta yncC colony 37C

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from colony cells of E. coli K-12  MG1655 delta yncC after 15 hours of growth in LB plates at 37ºC

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: Channel 1

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181)

growth_protocol: Bacteria from frozen glycerols was used to streak plates of fresh LB medium  for forming colonies. After incubation for 15 h at 37°C a single colony was re streaked in fresh LB plates, regrowth 15 h at 37°C and after the growth about 0.05 g of the colony cultures on LB plate were quickly transferred to 2-mL collection tubes and frozen at -80°C, later the cells were broken with ca bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: N2a_22L vers Mock_rep4


title: N2a_22L vers Mock_rep8


title: MG1655 WT colony 37C

description: RNA extracted from colony cells of E. coli K-12  MG1655 wild type after 15 hours of growth in LB plates at 37ºC

extract_protocol: Bacteria from frozen glycerols was used to streak plates of fresh LB medium  for forming colonies. After incubation for 15 h at 37°C a single colony was re streaked in fresh LB plates, regrowth 15 h at 37°C and after the growth about 0.05 g of the colony cultures on LB plate were quickly transferred to 2-mL collection tubes and frozen at -80°C, later the cells were broken with ca bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: H. pylori Kx1 infecting mGEPs, biological rep1


title: N2a_22L vers Mock_rep1


title: N2a_22L vers Mock_rep2


title: first analysis of pair #2 Sirt1 knock-out versus control testis

city: Honolulu

first: rich

last: allsopp

state: HI

address: 651 Ilalo St

department: anatomy & reprod biol

institute: university of hawaii

hyb_protocol: slides were blocked with prehybridization solution at 42C for 30 minutes. Prehybridization solution 20x SSC 75 ml (3x) 10% SDS 5 ml (0.1%) BSA (Sigma, A9647) 1 g (0.2%) ddH2O to 420 ml filter and store at room temperature Slides were then hybridized in hybridization solution, containing a mixture of the channel 1 and 2 labeled probes, at 42C overnight. Hybridization solution contained 4X SSC plus 25% formamide, and 0.01% SDS. The next day, slides were washed in 0.5XSSC plus 0.01% SDS (low stringency), then 0.06XSSC, twice, all at room temp

scan_protocol: slides were scanned using a GenePix 4000b Microarray Scanner (Molecular Devices). Data was analyzed using GenePix Pro 6.0 and Acuity 4.0 softwares.

data_processing: raw data was normalized using a ratio based method, where the ratio of the means was made equal to 1 for all features, excluding flagged features.

source_name: testis, Sirt1 knock-out

label_protocol: reverse transcription starting from 20 ug input RNA

extract_protocol: whole testis from 1 mouse were finely cut with sterile scalpel, then lysed in Trizol reagent. Total RNA was then isolated according to manufacturers protocol.

treatment_protocol: no treatment

tag: strain

value: Sirt1 knock out, age:8 week old gender:male

source_name: testis, Sirt1 heterozygote


title: cDNA spotted array, Sirt1 KO/Het pair #1, replicate 2

value: mouse  gender:male  age:8 weeks

value: mouse  gender:male  age:8 weeks  sibling to animal used in channel #1


title: cDNA spotted array, Sirt1 KO/Het pair #1, replicate 3 dye swap

label_protocol: reverse transcription, starting from 20 ug input RNA

value: Sirt1 heterozygous

tag: gender

value: male

tag: age

value: 8 weeks

tag: note, this animal was sibling to animal used in channel 1


title: 3d_ctrl_vs_0d_3_FD

status: Public on Feb 21 2008

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: Solanum lycopersicum cv. Moneymaker tomato plants were grown for 4 weeks in greenhouse conditions (16h/8h light/darkness, 27 °C).  L. esculentum was randomly sorted into two groups of 16 plants each and a third reference group of 6 plants.  All plants were contained individually in mesh bags.  One group of 16 plants was infested with 25 female adult tomato psyllids that were 2-3 days old per plant.   The other two groups of 16 and 6 plants were not infested (healthy control, and reference pool).  After 3 days, the adults were removed from the infested plants to allow for egg eclosion and eventually nymphal development.  In this study, leaves infested and healthy plants were harvested for RNA extraction at 0, 3, 11, and 17 days after infestation with tomato psyllids. The reference pool was harvested on day 0.   Tissue (all-leaflets) from at least three plants per group was collected, flash frozen in liquid nitrogen and pooled for each time point (0, 3, 11 and 17 days after infestation) to represent treatments for before feeding (0 d), adult feeding and egg deposition (3 d), 1st and 2nd instar feeding (11 d) and 3rd to 5th instar feeding (17 d ), respectively.  The whole experiment was repeated three times (three biological replicates).   Plant tissues were ground using a cold mortar and pestle.  Total tomato leaf RNA was extracted using the hot-phenol protocol.  The RNA was precipitated, pooled, cleaned with a kit and stored at –80C. Two populations of single-stranded cDNAs will be generated from the aliquots and labeled with the cyanine Cy3 and Cy5 fluorophores.  RNA isolated from the reference pool (0 d) will be pooled from each replicate and will be labeled with Cy5; this is the reference sample for each hybridization.  RNA isolated from leaves infested with tomato psyllids and healthy uninfested plants from each time point will be query samples labeled with Cy3.    The two samples of labeled cDNA will be simultaneously hybridized to the same microarray.

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Solanum lycopersicum

source_name: LEY0049, Healthy plants 3d after infestation

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: Grown for 28 days in green house (16h/8h light/darkness, 35% humidity, 27C) in peat moss substrate

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: Healthy plants 3d after infestation

source_name: LEY0030, Reference Pool Healthy Plants 0d

treatment_protocol: Reference Pool Healthy Plants 0d

tag: Solanum lycopersicum, Leaves, Biotic stress control


title: replicate #2 of pair #2 Sirt1 knock-out versus control testis

value: Sirt1 knock out, age:8 week old gender:male sibling to animal used in

tag: channel #1


title: 17d_ctrl_vs_0d_3

source_name: LEY0051, Healthy plants 17d after infestation

treatment_protocol: Healthy plants 17d after infestation

tag: Solanum lycopersicum, Leaves, Biotic stress


title: first analysis of pair #1 Sirt1 knock-out versus control testis


title: Ptri-20hr-3

type: other

city: Raleigh

first: Ying-Hsuan

last: Sun

state: NC

address: 2500 Partners II, 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

description: 21 samples from 7 cold stress time point were analyzed, each cold stress time point contain three replicates. 0 hour cold stress treatment were used as control.

hyb_protocol: Labeled small RNAs were resuspended in hybridization buffer containing 12% formamide, 6x SSPE, and 0.5% SDS and applied to microarray chips.  Microarray chips were prehybridized in buffer containing 400 mM Na2HPO4 pH 7.0, 0.8% BSA, 0.5% SDS, and 12% formamide at 65oC for 10 min. Labeled targets were then applied to microarray chips and hybridized at 37oC for 3 h.

scan_protocol: Microarrays were scanned with 5 micron per pixel resolution using .

data_processing: Lu Shanfa, Ying-Hsuan Sun, Vincent Chiang. (2008). Stress-Responsive MicroRNAs in Populus. Plant Journal. In press, Detail information will be provided when available.

molecule: other

organism: Populus trichocarpa

source_name: Cold stress 4oC at dark for 20 hour

label_protocol: Small RNAs from 100 µg of total RNA were isolated using YM-100 microcon column (Millipore; http://www.millipore.com/) and concentrated to 5 µL and dephosphorylated with 2 units of shrimp alkaline phosphatase (Roche Diagnostics; http://www.roche-diagnostics.us/) in 50 mM Tris pH 8.5 and 5 mM MgCl2 at 37oC for 1 h. Reactions were terminated by incubating at 65oC for 15 min. Small RNA labeling and hybridization were based on the protocol of Thomson et al. (2004). Dephosphorylated small RNAs were then labeled by incubation with 500 ng 5'-phosphate-cytidyl-uridyl-Cy5-3' (Dharmacon; http://www.dharmacon.com/) and 20 units of T4 RNA ligase in 0.1 mM ATP, 50 mM HEPES pH 7.8, 3.5 mM DTT, 20 mM MgCl2, 10 mg ml-1 BSA, and 10% DMSO at 4oC for 2 h and cleaned up by ethanol precipitation and incubated overnight at -80 oC.

extract_protocol: Leaf, stem and root of each treated plant were harvest separately and mixed at equal

treatment_protocol: Plant were subjected to 4oC cold stress at dark.

tag: 3 month old tissue culture propagual. Eaually mixed leaf, stem, and root tissues .


title: Ptri-16hr-3

source_name: Cold stress 4oC at dark for 16 hour


title: Ptri-24hr-3

source_name: Cold stress 4oC at dark for 24 hour


title: Ptri-4hr-3

source_name: Cold stress 4oC at dark for 4 hour


title: 11d_ctrl_vs_0d_3

source_name: LEY0050, Healthy plants 11d after infestation

treatment_protocol: Healthy plants 11d after infestation


title: Ptri-12hr-3

source_name: Cold stress 4oC at dark for 12 hour


title: 3d_ctrl_vs_0d_3


title: Ptri-0hr-3

source_name: Cold stress 4oC at dark for 0 hour


title: Ptri-24hr-2


title: 17d_instar_feed_vs_0d_3

source_name: LEY0042, Tomato psyllid 3rd-5th instar feeding, 17d after infestation


title: Ptri-20hr-2


title: 11d_instar_feed_vs_0d_2

source_name: LEY0037, Tomato psyllid 1st-2nd instar feeding, 11d after infestation


title: 3d_ctrl_vs_0d_1

source_name: LEY0043, Healthy plants 3d after infestation


title: 3d_adult_feed_egg_dep_vs_0d_3

source_name: LEY0040, Tomato psyllid adult feeding and egg deposition, 3d after infestation


title: 11d_instar_feed_vs_0d_3

source_name: LEY0041, Tomato psyllid 1st-2nd instar feeding, 11d after infestation


title: 17d_ctrl_vs_0d_2

source_name: LEY0048, Healthy plants 17d after infestation


title: 17d_ctrl_vs_0d_1

source_name: LEY0045, Healthy plants 17d after infestation


title: 11d_ctrl_vs_0d_2

source_name: LEY0047, Healthy plants 11d after infestation


title: 3d_ctrl_vs_0d_2

source_name: LEY0046, Healthy plants 3d after infestation

source_name: LEY0030, Reference Pool Healthy Plants 0d


title: 0d_infest_vs_0d_3

source_name: LEY0039, Healthy plants control 0d after infestation


title: replicate #3 of pair #2 Sirt1 knock-out versus control testis dye swap

source_name: testis, Sirt1 knock-out

source_name: testis, Sirt1 heterozygote

value: Sirt1 knock out, age:8 week old gender:male  sibling to animal used in channel #1


title: Ptri-16hr-2

source_name: Cold stress 4oC at dark for 16 hour


title: 17d_instar_feed_vs_0d_2

source_name: LEY0038, Tomato psyllid 3rd-5th instar feeding, 17d after infestation


title: 3d_adult_feed_egg_dep_vs_0d_2

source_name: LEY0036, Tomato psyllid adult feeding and egg deposition, 3d after infestation


title: 11d_ctrl_vs_0d_1

source_name: LEY0044, Healthy plants 11d after infestation


title: 0d_infest_vs_0d_2

source_name: LEY0035, Healthy plants control 0d after infestation


title: Ptri-12hr-2

source_name: Cold stress 4oC at dark for 12 hour


title: Ptri-8hr-2

source_name: Cold stress 4oC at dark for 8 hour


title: PMNCs_total RNA Pool_3 weeks Intervention_Aliquot N2

city: Barcelona

first: MONTSERRAT

last: FITO COLOMER

address: DR.AIGUADER 88

country: Spain

institute: IMIM

description: esperiment 2

hyb_protocol: Microarrays were prehybridized during 1h at 55ºC. During prehybridization, 10 micrograms of DIG-labeled cRNA were fragmented and used for hybridization (55 ºC, 16 h, 100 rpm agitation), according to Applied Biosystems Chemiluminescence Detection Kit. Same manufacturer´s protocol was used for hybridization washes and for performing Antibody Binding (anti-digoxigenin-AP) and antibody washes. The next steps, chemiluminescent reaction and detection, were performed with only one microarray at a time and following manufactures´ procedures.

scan_protocol: Microarrays were scanned with the Applied Biosystems 1700 Chemiluminescent Analyzer and quantified using the AB1700 software

data_processing: The algorithm's quality metrics “flags” and the ratio of signal/noise were used, on each microarray, to quantify probe quality and detectability (1700 Chemiluminescent Microarray Analyzer Users Guide). Probes with a signal/noise ratio <3 and/or flags >5,000 were excluded. From the initial 32,878 probeset, 15,308 high-quality probes were kept, and their signal were normalized among arrays by using the quantile technique

label: DIG-UTP

organism: Homo sapiens

source_name: Periferal Blood Mononuclear cells

label_protocol: One microgram of total RNA was reverse-transcribed using T7-oligo (dT) primer. After first and second strand cDNA synthesis, the cDNA was purified and used for in vitro transcription (IVT) labeling with DIG-UTP, rendering labeled cRNA, according to the Applied Biosystems instructions for Chemiluminescent RT-IVT labeling kit V.2.0.

growth_protocol: Prior to the intervention, volunteers followed a one week washout period in which sunflower oil was provided as a source of fat for all purposes. During the first four days of the washout period, participants were asked to follow an antioxidant-controlled diet. Participants were allowed to eat per day less than: 2 pieces of fruit, 2 servings of vegetables or legumes, 2 cups of tea or coffee, and to avoid wine, beer, and olive oil consumption. During the last 3 days before, and on the intervention day, volunteers followed a strict low-phenolic compound diet., according to which  several foods, rich in phenolic compounds, were excluded from their diet (vegetables, legumes, fruit, juice, wine, coffee, tea, caffeine-containing soft drinks, beer, cacao, marmalade, olive oil and olives).

extract_protocol: Blood was collected at 8 a.m., at fasting state, prior to first (0 hours, pre-dose), 6 h after acute (50 ml (44 g) virgine olive oil) and at 8 a.m., at fasting state, after 3-weeks (25 ml (22 g) virgine olive oil per day) interventions. Periferal Blood Mononuclear Cells (PBMCs) were isolated within two hours after blood drawing using Vacuntainer CPT tubes (Beckton Dickinson, Franklin Lakes, NJ, USA) and following manufacturer´ instructions. Harvested PMNCs were preserved in 1 ml of Ultraspec solution (Biotecx Laboratories, Houston, TX, USA) and were stored at -80ºC prior to RNA extraction. Total RNA was extracted from Ultraspec preserved PMNCs following manufacturer´instructions. RNA concentration (A260) and RNA purity (A260/A280 and A260/A280 ratios) were estimated spectrometrically (NanoDrop® ND-1000, NanoDrop Technologies, USA). RNA integrity was assessed by micro capillary gel electrophoresis (Bioanalyzer, NanoChip, Agilent Technologies, Wilmington, DE, USA) and was estimated by both the rRNA ratio (28S/18S rRNA ratio) and the RIN value (RNA integrity number) using Agilent 2100 Expert Software . The purity of isolated individual RNA samples was greater than 1.8 by A260/A280 and 1.75 by A260/A280, with integrity values not lower than 1.7 and 8.5 by 28S/18S rRNA ratio and by RIN, respectively.The weight equivalents of individual total RNA samples corresponding to baseline, acute and to 3-week intervention were combined into three RNA pooles, respectively. The pooled RNA samples were concentrated using the Rneasy Mini Elute Cleanup system (Qiagen, Barcelona, Spain), till the required by microarray service concentration (0.1 μg/μl). The prepared RNA pools had purity not lower than 1.9 by both A260/A280 and A260/A280 ratios and the integrity was at score of 9.0 according to RIN.The aliquoted pooled and individual RNAs samples were stored at -80º C prior to use.

treatment_protocol: At first intervention day, at fasting state, 50 mL (44 g) of virgin olive oil were administered in a single dose (experiment 1), following this, volunteers continued with consumption of 25 ml (22 g) of virgin olive oil per day during 3 consequent weeks (experiment 2).

tag: total RNA pool

tag: 6 males

tag: 3-week intervention

tag: AGE

tag: 3 smokers + 3 non-smokers

tag: BMI


title: PMNCs_total RNA Pool_3 weeks Intervention_Aliquot N3

description: esperiment 2


title: Ptri-8hr-3


title: Ptri-4hr-2

source_name: Cold stress 4oC at dark for 4 hour


title: PMNCs_total RNA Pool_PostPrandial_Aliquot N3

description: experiment 1

tag: post prandial (6 hours)


title: 17d_instar_feed_vs_0d_1

source_name: LEY0034, Tomato psyllid 3rd-5th instar feeding, 17d after infestation


title: PMNCs_total RNA Pool_3 weeks Intervention_Aliquot N1

description: esperiment 2


title: Ptri-0hr-2

source_name: Cold stress 4oC at dark for 0 hour


title: Ptri-24hr-1

source_name: Cold stress 4oC at dark for 24 hour


title: Ptri-20hr-1

source_name: Cold stress 4oC at dark for 20 hour


title: Ptri-16hr-1


title: 3d_adult_feed_egg_dep_vs_0d_1

source_name: LEY0032, Tomato psyllid adult feeding and egg deposition, 3d after infestation

source_name: LEY0030, Reference Pool Healthy Plants 0d


title: Ptri-8hr-1


title: PMNCs_total RNA Pool_Wash Out_Aliquot N2

description: reference sample

tag: wash out


title: 11d_instar_feed_vs_0d_1

source_name: LEY0033, Tomato psyllid 1st-2nd instar feeding, 11d after infestation


title: 0d_infest_vs_0d_1

source_name: LEY0031, Healthy plants control 0d after infestation


title: PMNCs_total RNA Pool_PostPrandial_Aliquot N1

description: experiment 1


title: Cowpea_503-1_Stressed_Replicate2

city: RIVERSIDE

first: Sayan

last: Das

state: CA

address: 900 University Avenue

department: Botany and Plant Sc.

institute: University of California-Riverside

hyb_protocol: Biotin labelled cRNA was hybridized to an Affymetrix soybean genome array as recommended by Affymetrix (Affymetrix GeneChip Expression Analysis Technical Manual; Affymetrix Inc., Santa Clara, CA) at the Institute for Integrative Genome Biology Microarray Facility at the University of California, Riverside (http://www.genomics.ucr.edu).

scan_protocol: The GeneChip arrays were washed and then stained (SAPE, streptavidinphycoerythrin)on an Affymetrix Fluidics Station 400, followed by scanning on a Hewlett-Packard GeneArray scanner.

data_processing: The hybridization data were scanned for visible defects and then extracted using default settings and tabulated as CEL files using Affymetrix GeneChip Operating Software (GCOS 1.2). A global scaling factor of 500, a normalization value of 1, and default parameter settings were used for the soybean genome array.

organism: Vigna unguiculata

source_name: Cowpea young trifoliate leaves drought stressed, genotype IT93K-503-1

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (10 µg total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase.  A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY).

extract_protocol: Total RNA was isolated using TRIzol (Gibco BRL Life Technologies, Rockville, MD) reagent.  RNA was further purified using an RNeasy spin column (Qiagen, Chatsworth, CA) and an on-column DNase treatment.  RNA integrity was assessed prior to target preparation using RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: Cowpea genotype IT93K-503-1.  Tissue was isolated 14 days after planting. Tisuue type young trifolilate leaves. Plants were drought stressed by withholding watering.


title: Cowpea_503-1_UnStressed_Replicate2

source_name: Cowpea young trifoliate leaves under normal irrigation, genotype IT93K-503-1

tag: Cowpea genotype IT93K-503-1.  Tissue was isolated 14 days after planting. Tisuue type young trifolilate leaves. Plants were grown under normal irrigation.


title: Cowpea_503-1_Stressed_Replicate1

tag: Cowpea genotype IT93K-503-1. Tissue was isolated 14 days after planting. Tisuue type young trifolilate leaves. Plants were drought stressed by withholding watering.


title: Cowpea_CB46_Stressed_Replicate1

source_name: Cowpea young trifoliate leaves drought stressed, genotype CB46

tag: Cowpea genotype CB46.  Tissue was isolated 14 days after planting. Tisuue type young trifolilate leaves. Plants were drought stressed by withholding watering.


title: PMNCs_total RNA Pool_Wash Out_Aliquot N3

description: reference sample


title: Cowpea_CB46_Stressed_Replicate2


title: Cowpea_CB46_UnStressed_Replicate2

source_name: Cowpea young trifoliate leaves under normal irrigation, genotype CB46

tag: Cowpea genotype CB46.  Tissue was isolated 14 days after planting. Tisuue type young trifolilate leaves. Plants were grown under normal irrigation.


title: Rhesus macaque ileal loop study MK6 WT

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: whole tissue

hyb_protocol: Affymetrix protocol, O/N

scan_protocol: Affymetrix scanner 3000

data_processing: GCOS

label: phycoerythrin

organism: Macaca mulatta

source_name: ileum

label_protocol: Affymetrix One-cycle labeling protocol

extract_protocol: Trizol extraction protocol

tag: adult male


title: Ptri-12hr-1

source_name: Cold stress 4oC at dark for 12 hour


title: Rhesus macaque ileal loop study MK5 LB

description: whole tissue


title: Rhesus macaque ileal loop study MK6 LB

description: whole tissue


title: Acid shift 10 min rep 2

status: Public on Feb 20 2008

city: Gambier

first: Joan

middle: Lyn

last: Slonczewski

state: OH

address: 202 N. College Rd

department: Biology Dept

institute: Kenyon College

description: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of time versus change in external pH. Overnight cultures were diluted 1:500 in potassium-modified Luria-Bertani medium (LBK) buffered with 20 mM HOMOPIPES at 7.6. Bacteria were cultured in baffled flasks (less than 10% volume) with rotation at 225 rpm, incubated at 37°C to an optical density at 600 nm of 0.2. External pH was lowered to pH 5.5 by adding 840 µl of 1M HCl to 40 mls of culture within 5 seconds. Four samples were taken from each of  five replicate cultures, corresponding to time 0 (before HCl addition),1, 5, and 10 min post HCl addition.

hyb_protocol: Affymetrix standard procedures

data_processing: Affymetrix GCOS software

source_name: Escherichia coli K-12 W3110

label_protocol: Labeled cDNA was prepared and hybridized to Affymetrix Antisense E. coli arrays by standard procedures.

growth_protocol: E. coli K-12 strain W3110 was diluted 500- fold in potassium-modified Luria-Bertani medium (LBK) buffered with 20 mM HOMOPIPES at pH 7.6.  The cultures were rotated at 225 rpm at 37ºC.  Cultures were grown to an optical density at 600 nm of 0.2.  External pH was lowered to 5.5 with 1 M HCl.  Four samples were taken from each of five replicate cultures, corresponding to time 0 (before HCl addition),1, 5, and 10 min post HCl addition.

extract_protocol: RNA was isolated using 10% saturated phenol-ethanol solution and the RNeasy Kit.

treatment_protocol: Growth at pH 5.5 for 10 min

tag: Escherichia coli K-12 W3110


title: Cowpea_503-1_UnStressed_Replicate1


title: Ptri-0hr-1


title: Ptri-4hr-1


title: Acid shift 10 min rep 3


title: Rhesus macaque ileal loop study MK5 WT

description: whole tissue


title: Acid shift 10 min rep 5


title: Acid shift 10 min rep 4


title: Acid shift 5 min rep 2

treatment_protocol: Growth at pH 5.5 for 5 min


title: Acid shift 5 min rep 4


title: Acid shift 10 min rep 1


title: Acid shift 1 min rep 4

treatment_protocol: Growth at pH 5.5 for 1 min


title: Acid shift 5 min rep 1


title: Acid shift 1 min rep 3


title: Acid shift time 0 rep 3

treatment_protocol: Growth at  pH 7.6


title: Acid shift 1 min rep 5


title: Acid shift 5 min rep 5


title: Acid shift 5 min rep 3


title: Acid shift 1 min rep 2


title: Acid shift 1 min rep 1


title: Acid shift time 0 rep 4


title: Acid shift time 0 rep 2


title: LZ63 Normal Control 42 weeks

city: Denver

first: Robert

middle: S

last: Stearman

state: CO

address: 4200 E Ninth Ave

department: Medicine/Pulmonary

institute: UCHSC

description: Gene expression data from normal mouse lung tissue

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip MGU74Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method arbitrarily set to 500

source_name: A/J mouse (Jackson Labs) lung tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 to 5 microg total RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: Age matched Control, no treatment


title: Acid shift time 0 rep 5


title: Acid shift time 0 rep 1


title: Cowpea_CB46_UnStressed_Replicate1


title: LZ61 Normal Control 42 weeks


title: LZ62 Normal Control 42 weeks


title: AJ1 Normal Control 24 to 26 weeks


title: LZ25 Normal Control 42 weeks


title: LZ24 Normal Control 42 weeks


title: AJ2 Normal Control 24 to 26 weeks


title: AJ4 Normal Control 24 to 26 weeks


title: LZ2 Normal Control 24 to 26 weeks


title: LZ3 Normal Control 24 to 26 weeks


title: GRASP array Skin 24hr Post-Exposure Hofer Rep2

first: Melinda

last: Baerwald

address: One Shields Ave

hyb_protocol: Array Prewash: 1. 0.1% SDS for 5 minutes, repeat once 2. Filtered Milli-Q H20 (with DDT added) for 1 minute, repeat 4 times 3. Wash in near boiling water for 3 minutes 4. Immediately transfer to Sigma 4-15C centrifuge from Qiagen. Centrifuge for 2 minutes at 1500 RPM to dry. 5. Wash Erie Scientific mSeries lifterslips (25X60) in filtered water and dry with a Kimwipe to remove all traces of dust. Microarray Prehybridization: 1. Incubate microarray for 90 minutes in 5XSSC, 0.1% SDS, 3% BSA (Fraction V) at 49C. 2. Wash 3 time in Milli-Q H20 for 20 seconds 3. Dry slides immediately by centrifugation 514 x g for 5 minutes 4. Place the arrays into 49oC hybridization oven until hybridization Microarray Hybridization: 1. Thaw 2X Formamide hybridization buffer in 55C water bath for 10 minutes. Ensure it’s thoroughly mixed by inversion. 2. Combine 6.5 ug of each labeled target (26 ul total) + 4 ul LNA dT blocker + 30 ul of 2X formamide hybridization buffer. 3. Gently vortex in a microcentrifuge tube and briefly spin down. 4. Incubate at 80C for 10 minutes 5. Keep at 65C until loaded onto array 6. Place lifterslip on top of array. Slowly pipet hybridization solution onto array at a corner of the lifterslip so that solution slowly spreads out by capillary action. 7. Incubate overnight at 49C in a tightly sealed 50 ml conical tube with 250 ul RNase-free water in bottom of tube. Wrap in foil to ensure complete darkness. Post-hybridization Washes: Place arrays into staining trays. Perform all post-washes in foil- wrapped staining dishes in a dark room. 1. Heat 2X SSC/0.1% SDS to 49C 2. Place array into dish (no more than 4 slides per dish) and gently agitate tube for 10 minutes. Coverslip should float off. 3. Wash array (no coverslip) with 2X SSC/0.1% SDS (room temp) for 5 minutes, repeat once 4. Wash array 2X with 1X SSC (room temp) 5. Wash array 2X with 0.1X SSC (room temp) 6. Immediately transfer to Sigma 4-15C centrifuge from Qiagen. Orient slide so array surface is facing out in the centrifuge, label is down.  Centrifuge for 2 minutes at 1500 RPM to dry. 7. Place slides in dark until ready to scan. Signal will decrease with time so scan ASAP.

scan_protocol: Arrays were scanned using the Agilent G2565BA fluorescent scanner.

data_processing: Data were local background subtracted and normalized (LOWESS method) using Agilent's feature extraction software.

organism: Oncorhynchus mykiss

source_name: Rainbow trout (Hofer strain) skin exposed to M. cerebralis pathogen

label_protocol: RNA (starting amount: 750 ng) was amplified and indirect labeled according to the protocol provided with the Ambion Amino Allyl  MessageAmp II aRNA Amplification kit.

growth_protocol: Fish were reared in 15C flow-through well water for 9 weeks post-hatch.

extract_protocol:
RNA from caudal fin (posterior to peduncle), comprised largely of skin tissue, was extracted using the ABI Prism TransPrep system with the ABI Prism 6100 Nucleic Acid PrepStation according to manufacturer’s instructions.
RNA quality was determined using agarose gel electrophoresis. RNA concentration was determine using a ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: Each fish was exposed to 2,000 triactinomyxons (life stage of pathogen that infects salmonids) for one hour. Twenty four hours after initial exposure, fish was euthanized by overdose with benzocaine at 500 mg/L.

tag: Strain

value: Hofer Age:9 weeks old Tissue:Skin (caudal fin) Treatment:Exposed to 2,000 triactinomyxons per fish and tissue collected 24 hours after initial exposure.

source_name: Rainbow trout (Hofer strain) skin unexposed control

treatment_protocol: No treatments other than euthanized by overdose with benzocaine at 500 mg/L.

value: Hofer Age:9 weeks old Tissue:Skin (caudal fin) Treated identically to exposed fish other than lack of pathogen exposure.


title: GRASP array Skin 24hr Post-Exposure Trout Lodge Rep3

source_name: Rainbow trout (Trout Lodge strain) skin unexposed control

label_protocol: RNA (starting amount: 500 ng) was amplified and indirect labeled according to the protocol provided with the Ambion Amino Allyl  MessageAmp II aRNA Amplification kit.

value: Trout Lodge Age:9 weeks old Tissue:Skin (caudal fin) Treated identically to exposed fish other than lack of pathogen exposure.

source_name: Rainbow trout (Trout Lodge strain) skin exposed to M. cerebralis pathogen

value: Trout Lodge Age:9 weeks old Tissue:Skin (caudal fin) Treatment:Exposed to 2,000 triactinomyxons per fish and tissue collected 24 hours after initial exposure.


title: GRASP array Skin 24hr Post-Exposure Hofer Rep4

label_protocol: RNA (starting amount: 250 ng) was amplified and indirect labeled according to the protocol provided with the Ambion Amino Allyl  MessageAmp II aRNA Amplification kit.


title: GRASP array Skin 24hr Post-Exposure Hofer Rep1

label_protocol: RNA (starting amount: 800 ng) was amplified and indirect labeled according to the protocol provided with the Ambion Amino Allyl  MessageAmp II aRNA Amplification kit.

value: Hofer

tag: Age

value: 9 weeks old

tag: Tissue

value: Skin (caudal fin)

tag: Treated identically to exposed fish other than lack of pathogen exposure.

tag: Treatment

value: Exposed to 2,000 triactinomyxons per fish and tissue collected 24 hours after initial exposure.


title: GRASP array Skin 24hr Post-Exposure Trout Lodge Rep4

label_protocol: RNA (starting amount: 1000 ng) was amplified and indirect labeled according to the protocol provided with the Ambion Amino Allyl  MessageAmp II aRNA Amplification kit.


title: LZ22 Normal Control 42 weeks


title: cDNA Analysis of Fe Sufficient Hydroponic Conditions on NILs 199

city: Ames

first: Randy

last: Shoemaker

state: IA

address: 100 Osbourne Dr. G401

department: Agronomy

institute: Iowa State University

description: Slides weree hybridized in the Shoemaker Lab and scanned at the Microarray Core Facility at Iowa State University.

hyb_protocol: Arrays were hybridized at 42 degrees C. for 18 hours.  After overnight hybridization, arrays were washed (wash 1: 1X SSC, 0.2%SDS; wash2: 0.2X SSC, 0.2%SDS; wash 3: 0.1% SDS) to remove unbound cDNAs.  Slides were then centrifuged for 5 minutes to dry.

scan_protocol: Slides were scanned using a Pro Scan Array HT at the Center for Plant Genomics Microarray Facility at Iowa State University.  Resulting images were overlaid and spots identified by the ImaGene program.

data_processing: Differential Expression between iron efficient and iron inefficient samples was identified by a log ratio of positive or negative 2 using the GeneTraffic analysis program.

organism: Glycine max

source_name: Iron Sufficient Iron Inefficient IsoClark Roots

label_protocol: 90ug of RNA was combined with oligo dT for 10 min.  20uL 1X Buffer, 110mM DTT, 500uM low T dNTPs, 100uM Cy3, and 13u/uL SuperScriptII were incubated with RNA/Oligo dT mix for 2 hours at 42 degrees C.

extract_protocol: Total RNA was extracted using a modified phenol:chloroform extraction protocol described by Vodkin et al. BMC Genomics 2005.  Qiagen RNeasy kit provided further purification of the extracted total RNA

tag: Roots of iron inefficient soybeans grown under iron sufficient (100uM Fe(NO3)3) hydroponic conditions for 14 days.

source_name: Iron Sufficient Iron Efficient Clark Roots

label_protocol: 90ug of RNA was combined with oligo dT for 10 min.  20uL 1X Buffer, 110mM DTT, 500uM low T dNTPs, 100uM Cy5, and 13u/uL SuperScriptII were incubated with RNA/Oligo dT mix for 2 hours at 42 degrees C.

tag: Roots of iron efficient soybeans grown under iron sufficient (100uM Fe(NO3)3) hydroponic conditions for 14 days.


title: GRASP array Skin 24hr Post-Exposure Hofer Rep3


title: E14_ovary_rep2

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Chip ID=Mehmet-day14-1Female-230A-090403.  RNA from E-14 old rat ovaries

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: Auto-scale ON (1-1000).  Scaling = all probe sets.  The microarray image data were converted to numerical data with GeneChip Operating Software using a scaling to targed signal of 125.

organism: Rattus norvegicus

source_name: E14-day rat ovary

label_protocol: standard Affymetrix procedures

extract_protocol:
Animals were euthanized at E14-day of pregnancy, and embrionic ovaries were collected
Ovaries with the same age were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturer's instructions (Sigma, St. Louis, MO).  Two pooled independent RNA samples were analysed for each treatment group.

tag: ovaries dissected from E14-day old Sprague-Dawley rats


title: E16_ovary_rep1

description: Chip ID=Matt-E16-Ovary-230A-032905.  RNA from E-16 old rat ovaries

source_name: E16-day rat ovary

extract_protocol:
Animals were euthanized at E16-day of pregnancy, and embrionic ovaries were collected
Ovaries with the same age were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturer's instructions (Sigma, St. Louis, MO).  Two pooled independent RNA samples were analysed for each treatment group.

tag: ovaries dissected from E16-day old Sprague-Dawley rats


title: E14_ovary_rep1

description: Chip ID=Matt-E14-Ovary-230A-032905.  RNA from E-14 old rat ovaries


title: E16_testis_rep1

description: Chip ID=Anway-E16Testis-230A-111003.  RNA from E-16 old rat testis

source_name: E16-day rat testis

extract_protocol:
Animals were euthanized at E16-day of pregnancy, and embrionic testis were collected
Testis with the same age and treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturer's instructions (Sigma, St. Louis, MO).  Two pooled independent RNA samples were analysed for each treatment group.

tag: testis dissected from embryonic day 16 Sprague-Dawley rats


title: E13_ovary_rep2

description: Chip ID=Matt-E13Ovary-020705.  RNA from E-13 old rat ovaries

source_name: E13-day rat ovary

extract_protocol:
Animals were euthanized at E13-day of pregnancy, and embrionic ovaries were collected
Ovaries with the same age were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturer's instructions (Sigma, St. Louis, MO).  Two pooled independent RNA samples were analysed for each treatment group.

tag: ovaries dissected from E13-day old Sprague-Dawley rats


title: E16_ovary_rep2

description: Chip ID=Mehmet-E16Female-230A-072303.  RNA from E-16 old rat ovaries


title: cDNA Analysis of Fe Sufficient Hydroponic Conditions on NILs 200


title: E16_testis_rep2

description: Chip ID=Mehmet-E16Male-230A-072303.  RNA from E-16 old rat testis


title: E14_testis_rep2

description: Chip ID=Mehmet-day14-1Male-230A-090403.  RNA from E-14 old rat testis

source_name: E14-day rat testis

extract_protocol:
Animals were euthanized at E14-day of pregnancy, and embrionic testis were collected
Testis with the same age and treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturer's instructions (Sigma, St. Louis, MO).  Two pooled independent RNA samples were analysed for each treatment group.

tag: testis dissected from embryonic day 14 Sprague-Dawley rats


title: E14_testis_rep1

description: Chip ID=Anway-E14testis-230A-111003.  RNA from E-14 old rat testis


title: E13_ovary_rep1

description: Chip ID=Matt-E13-Ovary-052705.  RNA from E-13 old rat ovaries


title: E13_testis_rep2

description: Chip ID=Mehmet-E13-1-Male-230A-080603.  RNA from E-13 old rat testis

source_name: E13-day rat testis

extract_protocol:
Animals were euthanized at E13-day of pregnancy, and embrionic testis were collected
Testis with the same age and treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturer's instructions (Sigma, St. Louis, MO).  Two pooled independent RNA samples were analysed for each treatment group.

tag: testis dissected from embryonic day 13 Sprague-Dawley rats


title: E13_testis_cultured_rep2

description: Chip ID=Mehmet-E13CImale-230A-072303.  RNA from E-13 old rat testis cultured 3 days

source_name: E13-day rat testis cultured 3 days

extract_protocol: Testis with the same age and treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturer's instructions (Sigma, St. Louis, MO).  Two pooled independent RNA samples were analysed for each treatment group.

treatment_protocol: Animals were euthanized at E13-day of pregnancy, and embrionic testis were collected  and cultured in drops of medium on Millicell CM filters (Millipore, Bedford, MA, USA) floating on 0.4 ml of CMRL 1066 medium (Gibco BRL) supplemented with penicillin–streptomycin, insulin (10 µg/ml), L-glutamine (350 µM), transferrin (10 µg/ml), and BSA (0.01%). Media were changed on the second day of culture. Gonads were maintained in culture for 3 days and used for RNA collection.

tag: testis dissected from embryonic day 13 Sprague-Dawley rats and cultured for 3 days


title: E13_testis_rep1

description: Chip ID=Matt-E13Testis-012805.  RNA from E-13 old rat testis


title: Human Testis (Random)

city: Tsuruoka City

first: Yuki

last: Okada

address: Nipponkoku 403-1, Daihouji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

description: Custom oligo (60mer) microarray was manufactured by Agilent Technologies.

hyb_protocol: The protocols supplied by Agilent Technologies were used.

data_processing: The quantitations based on the images were performed using Feature Extraction software (Agilent Technologies). The same total RNA samples were labeled with single color Cy3, hybridized to the oligo DNA on the chip, and dye-normalized; the processed signals were obtained by using Feature Extraction software (Agilent Technologies). The custom oligo DNA microarray chip (microarray format: 11K) contained 2793 probes for 1486 pairs of exon-overlapping SATs. The data on all genes on the chip were used to enable the Feature Extraction software to produce the processed signals. For further analysis, the Cy3-labeled processed signal was used as the processed signal from the expression of a particular gene. The total mean signal on the human chip in each hybridization experiment was adjusted to 1491.6, so that the relative differences in gene expression could be compared among cell lines and tissues.

source_name: Human Testis

label_protocol: RNA was labeled with random nanomers, CyScribe First-Strand cDNA Labeling Kit(Amersham), according to the manufacturer’s protocols.

extract_protocol: Human testis total RNA was purchased from Ambion Inc.

tag: Human Testis


title: Human Heart (Random)

scan_protocol: The protocols supplied by Agilent Technologies were used.

source_name: Human Heart

extract_protocol: Human heart total RNA was purchased from Ambion Inc.

tag: Human Heart


title: Human Brain (Random)

source_name: Human Brain

extract_protocol: Human brain total RNA was purchased from Ambion Inc.

tag: Human Brain


title: GRASP array Skin 24hr Post-Exposure Trout Lodge Rep2

tag: Strain


title: Postnatal day 4 ovary cultured with AMH for 10 days, replicate 1

description: Chip ID=Eric-MIS-1-092805.  RNA from P4-day old rat ovaries cultured with AMH for 10 days, replicate 1

scan_protocol: chips were scanned using Agilent GeneArray Scanner G2500A

data_processing: Auto-scale ON (1-1000).  Scaling = all probe sets.  The microarray image data were converted to numerical data with GeneChip Operating Software using a scaling factor of 125, and then imported into the GeneSpring program (Agilent Technologies, Palo Alto, CA).

extract_protocol: About 10 ovaries with the same treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturer's instructions (Sigma, St. Louis, MO).  Two independent RNA samples were analysed for each treatment group.

treatment_protocol: Female day P4 rat pups were euthanized and rat ovaries were removed according to IACUC-approved animal use protocols.  Ovaries were placed in culture for ten days with treatment of 50ng/mL AMH.  Whole ovaries were cultured as previously described (Nilsson, Parrott et al. 2001) on floating filters (0.4 um Millicell-CM, Millipore, Bedford, MD) in 0.5 ml Dulbecco's Modified Eagle's Medium (DMEM)-Ham's F-12 medium (1:1, vol/vol) containing 0.1 % bovine serum albumin (BSA, Sigma, St. Louis, MO), 0.1% Albumax (Gibco BRL, Gaithersburg, MD), 27.5 ug/ml transferrin, 200 ug/ml insulin (human recombinant, Sigma), and 0.05 ug/ml L-ascorbic acid (Sigma) in a 4-well culture plate (Nunc plate, Applied Scientific, South San Francisco, CA). Medium was supplemented with penicillin and streptomycin to prevent bacterial contamination.

tag: ovaries dissected from 4-day old Sprague-Dawley rats and cleaned of ovarian bursa and cultured for 10 days with AMH


title: Human Liver (Random)

source_name: Human Liver

extract_protocol: Human liver total RNA was purchased from Ambion Inc.

tag: Human Liver


title: Human Fibroblast HF19 (Random)

source_name: Human Fibroblast HF19

extract_protocol: Total RNA was prepared from human fibroblast HF19 cells using Trizol reagent according to manufacturer’s instruction (Invitrogen).

tag: Human Fibroblast HF19


title: E13_testis_cultured_rep1

description: Chip ID=Anway-E13-Cult-230A-111003.  RNA from E-13 old rat testis cultured 3 days


title: GRASP array Skin 24hr Post-Exposure Trout Lodge Rep1

label_protocol: RNA (starting amount: 1000 ng) was amplified and indirect labelled according to the protocol provided with the Ambion Amino Allyl  MessageAmp II aRNA Amplification kit.

source_name: Rainbow trout (Hofer strain) skin exposed to M. cerebralis pathogen


title: K562 pan-H3 ChIP-chip

type: genomic

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description: crosslinked, MNase-digested chromatin was immunoprecipitated with an antibody to pan-H3 and compared with input DNA (crosslinked, MNase-digested) for assessing nucleosome positions.

hyb_protocol: Nimblegen Hybridization protocol (http://www.nimblegen.com)

scan_protocol: Arrays were scanned using AXON 5uM scanner

data_processing: Calculated log2 intensity ratios from raw intensity values

molecule: genomic DNA

source_name: K562 crosslinked, MNase-digested, pan-H3 ChIP

label_protocol: Nimblegen ChIP labeling protocol (http://www.nimblegen.com)

growth_protocol: Cells were grown in suspension in RPMI media with 10% fetal bovine calf serum

extract_protocol: see manuscript

treatment_protocol: Cells were grown untreated and were centrifuged for harvesting.

tag: 53 year old female derived chronic myuelogenous leukemia cells; human K562

source_name: K562 crosslinked, MNase-digested, input


title: Postnatal day 4 ovary cultured with AMH for 10 days, replicate 2

description: Chip ID=Eric-MIS-2-092805.  RNA from P4-day old rat ovaries cultured with AMH for 10 days, replicate 2


title: Human Testis (Oligo dT)

label_protocol: RNA was labeled using Fluorescent Direct Label Kits (oligo dT-primed labeling) (Agilent Technologies), according to the manufacturer’s protocols.


title: MNase digested vs. sonicated bare genomic DNA

description: MNase-digested bare genomic DNA compared with sonicated bare-genomic DNA for assessing MNase digestion bias.

source_name: K562 bare genomic MNase-digested

source_name: K562 bare genomic DNA sonicated


title: Postnatal day 4 ovary cultured for 10 days, replicate 2

description: Chip ID=Eric-C-2-070705.  RNA from P4-day old rat ovaries cultured for 10 days, replicate 2

treatment_protocol: Female day P4 rat pups were euthanized and rat ovaries were removed according to IACUC-approved animal use protocols.  Ovaries were placed in culture for ten days with no treatment (controls).  Whole ovaries were cultured as previously described (Nilsson, Parrott et al. 2001) on floating filters (0.4 um Millicell-CM, Millipore, Bedford, MD) in 0.5 ml Dulbecco's Modified Eagle's Medium (DMEM)-Ham's F-12 medium (1:1, vol/vol) containing 0.1 % bovine serum albumin (BSA, Sigma, St. Louis, MO), 0.1% Albumax (Gibco BRL, Gaithersburg, MD), 27.5 ug/ml transferrin, 200 ug/ml insulin (human recombinant, Sigma), and 0.05 ug/ml L-ascorbic acid (Sigma) in a 4-well culture plate (Nunc plate, Applied Scientific, South San Francisco, CA). Medium was supplemented with penicillin and streptomycin to prevent bacterial contamination.

tag: ovaries dissected from 4-day old Sprague-Dawley rats and cleaned of ovarian bursa and cultured for 10 days


title: K562 non-crosslinked mononucleosome

description: MNase-digested chromatinized DNA compared with MNase-digested bare-genomic DNA for nucleosome mapping.

source_name: K562 mononucleosome MNase-digested

source_name: K562 bare genomic DNA MNase-digested


title: K562 crosslinked mononucleosome (repeat2)

description: MNase-digested crosslinked chromatinized DNA compared with MNase-digested bare-genomic DNA for nucleosome mapping.

source_name: K562 mononucleosome crosslinked, MNase-digested


title: HeLa crosslinked mononucleosome

source_name: HeLa S3 mononucleosome crosslinked, MNase-digested

growth_protocol: Cells were grown in suspension in Joklik's modified MEM with 5% bovine calf serum

tag: 31 year old female epithelial cells from cervix; HeLa S3 cells

source_name: HeLa bare genomic, crosslinked, MNase digested


title: K562 crosslinked mononucleosome (repeat1)

source_name: K562 bare genomic crosslinked, MNase-digested


title: Human Liver (Oligo dT)


title: HeLa non-crosslinked mononucleosome

source_name: HeLa S3 mononucleosome MNase-digested

source_name: HeLa bare genomic, MNase digested


title: Postnatal day 4 ovary cultured for 10 days, replicate 1

description: Chip ID=Eric-C-1-070705.  RNA from P4-day old rat ovaries cultured for 10 days, replicate 1


title: Human Brain (Oligo dT)


title: K562 IgG ChIP-chip

description: crosslinked, MNase-digested chromatin was immunoprecipitated with an antibody to rabbit IgG and compared with input DNA (crosslinked, MNase-digested) for assessing nucleosome positions.

source_name: K562 crosslinked, MNase-digested, IgG ChIP


title: Mouse Brain (Random)

data_processing: The quantitations based on the images were performed using Feature Extraction software (Agilent Technologies). The mouse custom oligo DNA microarray chip (microarray format: 11K) contained 3896 probes that represented genes in 1948 exon-overlapping SAT (sense-antisense transcript) pairs. The same total RNA samples were reciprocally labeled with Cy3 or Cy5, hybridized to the oligo DNA on the chip, and dye-normalized. The data on all genes on the chip were used to enable the Feature Extraction software to produce the processed signals. The total mean signal on the mouse chip in each hybridization experiment was adjusted to a value of 4872.3.

source_name: Mouse Brain

extract_protocol: Total RNA was prepared from mouse brain using Trizol reagent according to manufacturer’s instruction (Invitrogen).

tag: Mouse Brain


title: CDNA Analysis of Fe Deficiency on NILs D07

description: Slides were hybridized at Iowa State University.  Scanning and data analysis was done at the University of Illinois.

hyb_protocol: Arrays were hybridized at 42 degrees for 18 hours.  After overnight hybridization, arrays were washed (wash 1: 1XSSC, 0.2%SDS; wash 2: 0.2XSSc, 0.2%SDS; wash 3: 0.1%SDS) to remove unbounds cDNAs.  Slides were then centrifuged for 5 min. to dry.

scan_protocol: Slides were scanned using ScanArray Express.  Resulting images were overlaid and spots identified by the ImaGene Program.

data_processing: Differential expression between the samples was identified by a federated ratio of above 2.0 or below 0.5 corresponding to a positive or negative two fold difference respectively between the two samples.

source_name: Fe Inefficient Roots

label_protocol: 90ug of RNA was combined with oligo dT for 10 min.  20uL 1XBuffer, 10mM DTT, 500uM low T dNTPs, 100um Cy dye and 13u/uL SuperScript II were incubated with RNA/Oligo dT mix for 2 hours at 42 degrees C.

extract_protocol: Total RNA extracted using the modified Phenol:Chloroform total RNA extraction described by Vodkin et al. BMC Genomics 2005.

tag: Roots of Fe Inefficient soybeans grown under 50 uM Fe(NO3)3 hydroponic conditions for 14 days.

source_name: Fe Efficient Roots

label_protocol: 90ug of RNA was combined with oligo dT for 10 min.  20uL 1X Buffer, 10mM DDTT, 500uM low T dNTPs, 100uM of Cy Dye, and 13 u/uL SuperScript II were incubated with RNA/Oligo dT mix for 2 hours at 42 degrees.

extract_protocol: Total RNA was extracted using a Modified Phenol:Chloroform extraction protocol described by Vodkin et. al BMC Genomics 2005.

tag: Roots of Fe Efficient soybeans grown under 50uM Fe(NO3)3 hydroponic conditions for 14 days.


title: Mouse Testis (Oligo dT)

source_name: Mouse Testis

extract_protocol: Total RNA was prepared from mouse testis using Trizol reagent according to manufacturer’s instruction (Invitrogen).

tag: Mouse Testis


title: Human Heart (Oligo dT)

source_name: Human Heart


title: Mouse Fibroblast NIH3T3 (Random)

source_name: Mouse Fibroblast NIH3T3

extract_protocol: Total RNA was prepared from mouse NIH3T3 cells using Trizol reagent according to manufacturer’s instruction (Invitrogen).

tag: Mouse Fibroblast NIH3T3


title: Mouse Liver (Random)

source_name: Mouse Liver

extract_protocol: Total RNA was prepared from mouse liver using Trizol reagent according to manufacturer’s instruction (Invitrogen).

tag: Mouse Liver


title: Human Fibroblast HF19 (Oligo dT)

source_name: Human Fibroblast HF19


title: CDNA Analysis of Fe Deficiency on NILs D06

tag: Roots of Fe Inefficient soybeans grown under 50uM Fe(NO3)3 hydroponic conditions for 14 days.


title: Mouse Heart (Oligo dT)

source_name: Mouse Heart

extract_protocol: Total RNA was prepared from mouse heart using Trizol reagent according to manufacturer’s instruction (Invitrogen).

tag: Mouse Heart


title: Mouse Liver (Oligo dT)


title: Stria Vascularis Control (Pendrin)-2

city: Manhattan

first: Philine

last: Wangemann

state: KS

address: 1600 Dension Avenue

department: Anatomy and Physiology

institute: Kansas State University

description: Stria Vascularis was isolated from the mouse cochlea, RNA was isolated and hybridized on Affymetrix mouse 430.2

data_processing: Raw data, normalized and scaled in GCOS

label: streptavidin

source_name: Stria Vascularis RNA

tag: Strain 129S6, Age 150 days, Tissue ear


title: cDNA Analysis of Fe Deficiency on NILs

description: Slides were hybridized at Iowa State University.  Slides were scanned and analyzed at the University of Illinois.

hyb_protocol: After 18 hour hybridization at 42 degrees, arrays were washed to remove unbound cRNAs (wash 1: 1XSSC, 0.2%SDS, wash 2: 0.2XSSC, 0.2%SDS, wash 3: 0.1%SDS).  Slides are then spun dry (5 min)

scan_protocol: Slides were scanned with ScanArray Express and resulting images were overlaid and spots identified by the ImaGene program.

data_processing: Differential expression between samples was identified by an analysis program developed at the University of Illinois using a Federated Ratio.  A federated ratio above 2.0 or below 0.5 corresponds to a positive or negative two fold difference.

label_protocol: 90ug of total RNA was combined with Oligo dT for 10min.  20uL of 1X Buffer, 10mM DTT, 500uM low T dNTPs, 100uM Cy3 and 13u/uL SuperScriptII were combined and incubated at 42 degrees for 2 hours.  The resulting labeled cRNA was hybridized to arrays at 42degrees for 18 hours

growth_protocol: Plants germinated in sterile vermiculite and transplanted to iron deficient hyroponics for 14 days before root tissue was harvested for experiments.

extract_protocol: Total RNA extracted from Roots of IsoClark plants by a modified Phenol:Chloroform Extraction (Vodkin et al BMC Genomics 2005).

treatment_protocol: Plants grown in iron deficient hydroponics for 14 days

tag: Roots of Iso Clark grown 14 days in 50uM Fe(NO3)3 hydroponics

tag: Roots of Fe Efficient Clark grown 14 days in 50uM Fe(NO3)3 hydroponics


title: Stria Vascularis Knockout (Pendrin)-2

tag: Strain 129S6, Age 150 days, Tissue Ear


title: Mouse Testis (Random)


title: Stria Vascularis Knockout (Pendrin)-3

description: Stria vascularis was isolated from the mouse cochlea, RNA was isolated and hybridized on Affymetrix mouse 430.2 chips

label: Streptavidin


title: Stria Vascularis Knockout (Pendrin)-1


title: Mouse Fibroblast NIH3T3 (Oligo dT)


title: Mouse Brain (Oligo dT)


title: Primary root_rep_168 998_Cy5_301x301

status: Public on Feb 16 2008

city: Bonn

first: Frank

last: Hochholdinger

state: BW

address: Katzenburgweg 1a

department: INRES - Crop Functional Genomics

institute: University of Bonn

description:
slide 998
998_Cy5_301x301

hyb_protocol: Microarray probe hybridization of spotted 12k maize cDNA microarray chips (GenII vB, GPL 1996; www.plantgenomics.iastate.edu/maizechip) representing 10,649 non-redundant gene fragments was conducted as described in Woll et al. (2005).

scan_protocol: Dried slides were scanned six times with an Array Scanner (Genetic MicroSystems, USA) for each channel (Cy3 and Cy5) with laser power settings fixed at 90%. A series of up to six scans for each channel, in ascending order of PMT gain, was performed at 10 mm resolution individually adjusted to overall spot intensities per array according to Piepho et al. (2006). ImaGene software (Biodiscovery, Marina Del Rey, CA, USA) was used to quantify the spot intensities on the slides by the use of the default settings.  ImaGene software (Biodiscovery, Marina Del Rey, CA, USA) was used to quantify the spot intensities on the slides by the use of the default settings.

data_processing: The experimental design for the microarray experiments was described in Keller et al. (2005). To combine data from different scanning intensities, a nonlinear latent regression model was applied (Piepho et al., 2006). After combining the signals of different scans, a loess regression was performed. To account for differences between arrays the median absolute deviations (MAD) of the slides were normalized. The normalized data was analysed by a linear mixed model for every gene. Effects that occur during hybridization (genotype, dye, slide) were considered as well as temporal and spatial effects that might affect the genetic material during cultivation in the phytochamber (Keller et al., 2005). The unbalancedness of the design was accounted for by the mixed model analysis. Pairwise contrasts between genotypes were estimated. Furthermore, linear contrasts between hybrid and parental mean were determined. The p-values of these contrasts based on Wald tests were adjusted for multiple testing by controlling the false discovery rate (FDR) at 5% using the procedure of Benjamini and Hochberg (1995). The analyses for this paper were generated using SAS software, Version 9. Linear model analyses were done by PROC MIXED, while the FDR adjustment was performed by PROC MULTTEST.

molecule: polyA RNA

organism: Zea mays

source_name: Maize primary root 3.5 dag

label_protocol: Reverse transcription of the mRNA to cDNA with concurrent incorporation of aminoallyl dUTPs as well as Cy3 and Cy5 labeling was performed according to Nakazono et al. (2003).

growth_protocol: Germination in a phytochamber at 26°C, with a 16 hours light, 8 hours dark cycle and 60% humidity in twice distilled water.

extract_protocol: For each biological replicate approximately 20 roots per germination roll and genotype were pooled and homogenized using the Micro-Dismembrator U (Sartorius AG, Göttingen, Germany). Isolation of total RNA with Trizol (Invitrogen, Carlsbad, CA, USA), followed by mRNA purification using Oligotex mRNA columns (Qiagen, Hilden, Germany) was performed according to the manufacturers´ instructions.

tag: genotype


title: Primary root_rep_169 999_Cy3_301x301

description:
slide 999
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title: Primary root_rep_164 996_Cy5_301x002

description:
slide 996
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title: Stria Vascularis Control (Pendrin)-3


title: Primary root_rep_166 997_Cy5_301x301

description:
slide 997
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title: Primary root_rep_163 996_Cy3_002x301

description:
slide 996
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title: Primary root_rep_165 997_Cy3_301x002

description:
slide 997
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title: Mouse Heart (Random)

extract_protocol: Total RNA was prepared from mouse heart cells using Trizol reagent according to manufacturer’s instruction (Invitrogen).


title: invdup15_1_vs_NA15724

status: Public on Feb 17 2008

city: Seattle

first: Heather

last: Mefford

address: 1705 NE Pacific St

department: Genome Sciences

institute: University of Washington

description: Hybridization on custom 2-plex oligo array. All steps carried out according to NimbleGen protocol.

hyb_protocol: per NimbleGen protocol

scan_protocol: Scanned on Axon scanner with GenePix, per NimbleGen protocol

data_processing: NimbleScan software, per protocol

source_name: LB300, inverted duplicated chr 15 sample

label_protocol: Labeled using random 9mer primers per Nimblegen protocol

extract_protocol: standard genomic DNA extraction protocol

tag: Patient LB300 with inverted duplicated chr15

extract_protocol: Gentra DNA extraction kit for genomic DNA from cell line

tag: reference male NA15724


title: IMR338M_vs_NA15724

source_name: IMR338M, 4-Mb deletion of 15q13

tag: Patient IMR338M with a 4-Mb deletion of 15q13


title: Primary root_rep_167 998_Cy3_301x002

description:
slide 998
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title: Primary root_rep_162 995_Cy5_002x301

description:
slide 995
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title: Primary root_rep_170 999_Cy5_301x002

description:
slide 999
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title: CMS7833_vs_NA15724

description: Custom Nimblegen chip, all steps per Nimblegen protocol. This patient was found to have a 15q13 deletion.

source_name: CMS7833, 15q13 deletion

extract_protocol: tandard genomic DNA extraction protocol

tag: Patient CMS7833 with 15q13 deletion


title: Primary root_rep_160 945_Cy5_005x250

description:
slide 945
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title: Primary root_rep_156 942_Cy5_005x250

description:
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title: Primary root_rep_157 944_Cy3_005x250

description:
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title: Primary root_rep_161 995_Cy3_301x002

description:
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title: Primary root_rep_159 945_Cy3_250x250

description:
slide 945
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title: Primary root_rep_155 942_Cy3_005x005

description:
slide 942
942_Cy3_005x005


title: CMS7906_vs_NA15724

source_name: CMS7906, 15q13 deletion

tag: Patient CMS7906 with 15q13 deletion


title: Stria Vascularis Control (Pendrin)-1

data_processing: Raw data , normalized and scaled in GCOS


title: Primary root_rep_152 932_Cy5_002x002

description:
slide 932
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title: 69/06_vs_NA15724

tag: Patient 69/06 with 15q13 deletion


title: 02961_vs_NA15724

tag: Patient 02961 with 15q13 deletion


title: CMS5826_vs_NA15724

source_name: CMS5826, 15q13 deletion

tag: Patient CMS5826 with deletion of 15q13


title: 543/06_vs_NA15724

tag: Patient 543/06 with 15q13 deletion


title: invdup15_2_vs_NA15724

description: Hybridization to custom oligo array targeting the PWS region on chr 15 (ultra high density). All steps carried out according to NimbleGen protocol.

source_name: inverted duplicated chr15 (2), total 4 copies

tag: individual with inverted duplicated chr15 (total 4 copies)


title: Primary root_rep_150 930_Cy3_002x301

description:
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title: Primary root_rep_143 924_Cy3_301x250

description:
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title: Primary root_rep_145 925_Cy3_301x301

description:
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title: Primary root_rep_154 941_Cy5_002x250

description:
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title: marker15_vs_NA15724

source_name: marker15, total 4 copies

tag: individual with chr15 marker chromosomes (total 4 copies)


title: Primary root_rep_158 944_Cy5_005x005

description:
slide 944
944_Cy5_005x005


title: Primary root_rep_153 941_Cy3_250x250

description:
slide 941
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title: PWSdeletion_vs_NA15724

source_name: PWSdel, deletion of Prader-Willi region on chr 15q11

tag: individual with deletion of Prader-Willi region on chr 15q11


title: Primary root_rep_148 929_Cy5_301x002

description:
slide 929
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title: Primary root_rep_140 922_Cy5_002x002

description:
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title: Primary root_rep_139 922_Cy3_301x002

description:
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title: Primary root_rep_134 919_Cy5_002x005

description:
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title: Primary root_rep_137 921_Cy3_002x301

description:
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title: Primary root_rep_141 923_Cy3_250x002

description:
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title: Primary root_rep_136 920_Cy5_301x250

description:
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title: Primary root_rep_135 920_Cy3_250x250

description:
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title: Primary root_rep_138 921_Cy5_002x002

description:
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title: Primary root_rep_129 917_Cy3_250x250

description:
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title: Primary root_rep_147 929_Cy3_002x002

description:
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title: Primary root_rep_130 917_Cy5_250x301

description:
slide 917
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title: Primary root_rep_131 918_Cy3_301x250

description:
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title: Primary root_rep_144 924_Cy5_301x301

description:
slide 924
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title: Primary root_rep_133 919_Cy3_005x002

description:
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title: Primary root_rep_146 925_Cy5_301x002

description:
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title: Primary root_rep_132 918_Cy5_250x250

description:
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title: Primary root_rep_142 923_Cy5_250x250

description:
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title: CMS5803_vs_NA15724

source_name: CMS5803, 15q13 deletion

tag: Patient CMS5803 with MR and seizures who has 15q13 deletion


title: Primary root_rep_151 932_Cy3_002x301

description:
slide 932
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title: Primary root_rep_126 561_Cy5_002x002

description:
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title: Primary root_rep_112 509_Cy5_250x002

description:
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title: Primary root_rep_127 916_Cy3_250x301

description:
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title: Primary root_rep_125 561_Cy3_002x301

description:
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title: Primary root_rep_149 930_Cy3_002x002

description:
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title: Primary root_rep_120 558_Cy5_002_002

description:
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title: Primary root_rep_121 559_Cy3_002x301

description:
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title: Primary root_rep_116 511_Cy5_002x002

description:
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title: Primary root_rep_111 509_Cy3_002x002

description:
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title: Primary root_rep_128 916_Cy5_301x301

description:
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title: Primary root_rep_113 510_Cy3_002x250

description:
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title: Primary root_rep_124 560_Cy5_250x002

description:
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title: Primary root_rep_122 559_Cy5_301x301

description:
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title: Primary root_rep_107 506_Cy3_002x002

description:
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title: Primary root_rep_114 510_Cy5_002x002

description:
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title: Primary root_rep_115 511_Cy3_250x002

description:
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title: Primary root_rep_119 558_Cy3_301x002

description:
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title: Primary root_rep_117 557_Cy3_301x301

description:
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title: Primary root_rep_108 506_Cy5_002x250

description:
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title: Primary root_rep_105 476_Cy3_002x002

description:
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title: Primary root_rep_106 476_Cy5_005x002

description:
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title: Primary root_rep_118 557_Cy5_002x301

description:
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title: Primary root_rep_123 560_Cy3_002x250

description:
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title: Primary root_rep_104 474_Cy5_002x002

description:
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title: Primary root_rep_109 508_Cy3_250x002

description:
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title: Primary root_rep_101 472_Cy3_002x005

description:
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title: Primary root_rep_102 472_Cy5_002x002

description:
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title: Primary root_rep_93 307_Cy3_301x301

description:
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title: Primary root_rep_98 309_Cy5_301x301

description:
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title: Primary root_rep_99 471_Cy3_002x005

description:
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title: Primary root_rep_100 471_Cy5_005x002

description:
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title: Primary root_rep_91 304_Cy3_301x301

description:
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title: Primary root_rep_92 304_Cy5_005x301

description:
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title: Primary root_rep_103 474_Cy3_005x002

description:
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title: Primary root_rep_88 301_Cy5_301x005

description:
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title: Primary root_rep_89 302_Cy3_301x005

description:
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title: Primary root_rep_87 301_Cy3_005x301

description:
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title: Primary root_rep_94 307_Cy5_005x301

description:
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title: Primary root_rep_95 308_Cy3_005x301

description:
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title: Primary root_rep_86 299_Cy5_301x005

description:
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title: Primary root_rep_81 297_Cy3_002x250

description:
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title: Primary root_rep_80 295_Cy5_002x250

description:
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title: Primary root_rep_110 508_Cy5_250x250

description:
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title: Primary root_rep_79 295_Cy3_250x002

description:
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title: Primary root_rep_84 298_Cy5_301x301

description:
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title: Primary root_rep_96 308_Cy5_005x005

description:
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title: Primary root_rep_97 309_Cy3_005x301

description:
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title: Primary root_rep_85 299_Cy3_301x301

description:
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title: Primary root_rep_82 297_Cy5_002x002

description:
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title: Primary root_rep_78 292_Cy5_250x002

description:
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title: Primary root_rep_90 302_Cy5_301x301

description:
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title: Primary root_rep_83 298_Cy3_301x005

description:
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title: Primary root_rep_76 291_Cy5_005x005

description:
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title: Primary root_rep_77 292_Cy3_250x250

description:
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title: Primary root_rep_73 290_Cy3_005x005

description:
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title: Primary root_rep_71 289_Cy3_301x005

description:
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title: Primary root_rep_75 291_Cy3_301x005

description:
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title: Primary root_rep_67 287_Cy3_005x301

description:
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title: Primary root_rep_72 289_Cy5_005x301

description:
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title: Primary root_rep_68 287_Cy5_005x005

description:
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title: Primary root_rep_65 274_Cy3_250x002

description:
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title: Primary root_rep_69 288_Cy3_005x005

description:
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title: Primary root_rep_66 274_Cy5_250x250

description:
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title: Primary root_rep_74 290_Cy5_301x005

description:
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title: Primary root_rep_60 61_Cy5_250x301

description:
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title: Primary root_rep_70 288_Cy5_005x301

description:
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title: Primary root_rep_55 59_Cy3_250x301

description:
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title: Primary root_rep_63 273_Cy3_002x250

description:
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title: Primary root_rep_59 61_Cy3_301x250

description:
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title: Primary root_rep_57 60_Cy3_005x002

description:
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title: Primary root_rep_56 59_Cy5_250x250

description:
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title: Primary root_rep_58 60_Cy5_005x005

description:
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title: Primary root_rep_64 273_Cy5_250x250

description:
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title: Primary root_rep_50 48_Cy5_250x250

description:
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title: Primary root_rep_54 58_Cy5_301x301

description:
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title: Primary root_rep_49 48_Cy3_250x005

description:
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title: Primary root_rep_47 46_Cy3_250x005

description:
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title: Primary root_rep_48 46_Cy5_005x250

description:
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title: Primary root_rep_46 44_Cy5_250x005

description:
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title: Primary root_rep_44 41_Cy5_301x250

description:
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title: Primary root_rep_45 44_Cy3_005x250

description:
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title: Primary root_rep_53 58_Cy3_301x250

description:
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title: Primary root_rep_43 41_Cy3_301x301

description:
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title: Primary root_rep_51 57_Cy3_301x301

description:
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title: Primary root_rep_52 57_Cy5_250x301

description:
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title: Primary root_rep_41 39_Cy3_301x250

description:
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title: Primary root_rep_39 38_Cy3_250x301

description:
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title: Primary root_rep_40 38_Cy5_250x250

description:
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title: Primary root_rep_38 37_Cy5_301x250

description:
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title: Primary root_rep_42 39_Cy5_301x301

description:
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title: Primary root_rep_35 36_Cy3_005_002

description:
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title: Primary root_rep_34 34_Cy5_005x250

description:
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title: Primary root_rep_32 33_Cy5_002x005

description:
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title: Primary root_rep_33 34_Cy3_250x250

description:
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title: Primary root_rep_30 31_Cy5_250x301

description:
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title: Primary root_rep_28 30_Cy5_002x250

description:
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title: Primary root_rep_36 36_Cy5_005x005

description:
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title: Primary root_rep_29 31_Cy3_301x301

description:
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title: Primary root_rep_27 30_Cy3_250x250

description:
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title: Primary root_rep_24 28_Cy5_250x250

description:
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title: Primary root_rep_21 27_Cy3_002x005

description:
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title: Primary root_rep_22 27_Cy5_005x005

description:
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title: Primary root_rep_26 29_Cy5_002x005

description:
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title: Primary root_rep_18 19_Cy5_250x005

description:
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title: Primary root_rep_20 26_Cy5_002x002

description:
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title: Primary root_rep_23 28_Cy3_250x005

description:
slide 28
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title: Primary root_rep_25 29_Cy3_002x002

description:
slide 29
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title: Primary root_rep_15 18_Cy3_005x250

description:
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title: Primary root_rep_16 18_Cy5_005x005

description:
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title: Primary root_rep_17 19_Cy3_005x005

description:
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title: Primary root_rep_31 33_Cy3_005x005

description:
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title: Primary root_rep_19 26_Cy3_002x005

description:
slide 26
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title: Primary root_rep_13 16_Cy3_250x250

description:
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title: Primary root_rep_12 15_Cy5_005x005

description:
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title: Primary root_rep_14 16_Cy5_250x005

description:
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title: Primary root_rep_10 4_Cy5_005x005

description:
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title: Primary root_rep_11 15_Cy3_250x005

description:
slide 15
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title: Primary root_rep_7 3_Cy3_005x005

description:
slide 3
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title: Primary root_rep_6 2_Cy5_002x005

description:
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title: Primary root_rep_9 4_Cy3_005x301

description:
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title: Primary root_rep_4 1_Cy5_005x005

description:
slide 1
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title: Primary root_rep_8 3_Cy5_301x005

description:
slide 3
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title: Primary root_rep_3 1_Cy3_005x002

description:
slide 1
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title: Primary root_rep_2 0_Cy5_301x005

description:
slide 0
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title: Primary root_rep_1 0_Cy3_005x301

description:
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title: sepsis patient #21

status: Public on Feb 15 2008

first: Judie

middle: Ann

last: Howrylak

address: 75 Francis Street

department: Pulmonary and Critical Care Medicine

institute: Brigham and Women's Hospital

description: patient with sepsis only

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: GCRMA

source_name: patient with sepsis only

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: plasma

tag: patient with sepsis only


title: sepsis patient #18

description: patient with sepsis only


title: sepsis patient #12

description: patient with sepsis only


title: sepsis patient #19

description: patient with sepsis only


title: sepsis patient #15

description: patient with sepsis only


title: sepsis patient #13

description: patient with sepsis only


title: sepsis patient #17

description: patient with sepsis only


title: sepsis patient #14

description: patient with sepsis only


title: sepsis patient #20

description: patient with sepsis only


title: sepsis patient #16

description: patient with sepsis only


title: Primary root_rep_5 2_Cy3_005x005

description:
slide 2
2_Cy3_005x005


title: sepsis patient #5

description: patient with sepsis only


title: sepsis patient #6

description: patient with sepsis only


title: sepsis patient #7

description: patient with sepsis only


title: sepsis patient #11

description: patient with sepsis only


title: sepsis patient #8

description: patient with sepsis only


title: sepsis patient #10

description: patient with sepsis only


title: sepsis patient #9

description: patient with sepsis only


title: sepsis patient #4

description: patient with sepsis only


title: sepsis patient #3

description: patient with sepsis only


title: Cell_4

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

country: France

institute: INSERM U1127-CNRS UMR7225-UPMC

description: Fourth single cell analysis in the microfluidic rotary mixer.

hyb_protocol: RNG-MRC_MM25k_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dessicator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt’s, 4x SSC and 0.1% SDS solution at 42°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes in 0.2X SSC and 5 minutes in 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.

scan_protocol: Microarray images were obtained using a ScanArray Gx scanner (Perkin Elmer) with laser power = 90% and PMT gain = 80%. Median signal and median local background intensities were extracted from the images using Mapix v2.2.4 software (Innopsys).

data_processing:
Intensity/background ratios were calculated for each spot in each experiment.
Features which were not interpretable in all the 4 single cells analyzed were excluded for further analysis. For comparing experiments, the sum of F/B values for each slide was then multiplied by a correcting factor so that the sum of the corrected ratios was equal in all experiments.

source_name: Fourth embryonic neuronal single cell

label_protocol:
Single cell was peristaltically pumped and trapped into the microfluidic device. The cell was then mixed with 1X 1st strand synthesis buffer, 5mM DTT, 1mM dNTPs, 0.1% NP40, 1µM 3’ SMART CDS primer IIA (5’AAGCAGTG-GTATCAACGCAGAGTACT30VN-3’), 1µM template switching primer (5’AAGCAGTGGTATCAACGCAGAGTACGCGGG-3’) and 140U Rtases Reverse-iT Blend (ABgene) and incubated at 37°C for 25 minutes.
cDNAs were amplified in the presence of 1X Advantage® 2 polymerase (BD Clontech) and 1.25µM 5’PCR primer (AAGCAGTGGTATCAACGCAGAGT) by TS-PCR : 95°C for 2 minutes then 40 cycles 95°C for 15s, 65°C for 30s and 68°C for 6 minutes, in a conventional PCR machine (9700, Applera).
After purification using the Qiaquick PCR prurification kit (Qiagen), amplified cDNAs were labelled with 20µM dUTP-Cy5 (GE Healthcare) and 100mM random hexamers (GE Healthcare) in the presence of 50U Klenow fragment (Ozyme) overnight at 37°C.

extract_protocol: CGE explants were dissected from embryonic mouse telencephalon and individual cells were dissociated in PBS

tag: Strain

value: OF1, Age :E14, Tissue :CGE


title: Cell_3

description: Third single cell analysis in the microfluidic rotary mixer.

source_name: Third embryonic neuronal single cell


title: Cell_2

description: Second single cell analysis in the microfluidic rotary mixer.

source_name: Second embryonic neuronal single cell


title: sepsis patient #2

description: patient with sepsis only


title: ALI patient #3

description: patient with Acute Lung Injury

source_name: patient with Acute Lung Injury

tag: patient with Acute Lung Injury


title: Primary root_rep_37 37_Cy3_250x301

description:
slide 37
37_Cy3_250x301

tag: genotype


title: Cell_1

description: First single cell analysis in the microfluidic rotary mixer.

source_name: First embryonic neuronal single cell


title: ALI patient #2

description: patient with Acute Lung Injury


title: sepsis patient #1

description: patient with sepsis only


title: Conventional_rep2

description: Second replicate of conventional experiment performed with 10pg total RNA in a 10µL in tube.

data_processing:
Intensity/background ratios were calculated for each spot in each experiment.
Features which were not interpretable in all the 9 experiments performed were excluded for further analysis. For comparing experiments, the sum of F/B values for each slide was then multiplied by a correcting factor so that the sum of the corrected ratios was equal in all experiments.

source_name: 10pg RNA, conventional experiment, replicate 2

label_protocol:
10pg of RNA were reverse-transcribed with 1µM of each following primer : Smart A (AAGCAGTGGTATCAACGCAGAGTACGCGGG) and 3’CDS (AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) and 140U Rtases Reverse-iT Blend (ABgene) in tube for 20 minutes at 37°C.
cDNAs were then amplified in the presence of 1.25µM 5’PCR primer (AAGCAGTGGTATCAACGCAGAGT) and 1X Advantage® 2 polymerase (Clontech) by TS-PCR : 95°C for 2 minutes then 40 cycles 95°C for 15s, 65°C for 30s and 68°C for 6 minutes, in a conventional PCR machine (9700, Applera).

extract_protocol: Total RNA was extracted from a wild-type forebrain and treated with DNAse using Nucleospin RNA L kit (Macherey-Nagel) according to the manusfacturer’s instructions.

value: B6.C3Sn, Gender:Female, Age :Adult, Tissue :forebrain


title: Microfluidic_rep1

description: First replicate of microlfuidic experiment performed with 10pg total RNA in a 7nL rotary mixer.

scan_protocol: Microarray images were obtained using  a ScanArray Gx scanner (Perkin Elmer) with laser power = 90% and PMT gain = 80%. Median signal and median local background intensities were extracted from the images using Mapix v2.2.4 software (Innopsys).

source_name: 10pg RNA, microfluidic experiment, replicate 1

label_protocol:
10pg of RNA were reverse-transcribed with 1µM of each following primer : Smart A (AAGCAGTGGTATCAACGCAGAGTACGCGGG) and 3’CDS (AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) and 140U Rtases Reverse-iT Blend (ABgene) in microfluidic device for 20 minutes at 37°C.
cDNAs were then amplified in the presence of 1.25µM 5’PCR primer (AAGCAGTGGTATCAACGCAGAGT) and 1X Advantage® 2 polymerase (Clontech) by TS-PCR : 95°C for 2 minutes then 40 cycles 95°C for 15s, 65°C for 30s and 68°C for 6 minutes, in a conventional PCR machine (9700, Applera).


title: ALI patient #13

description: patient with Acute Lung Injury


title: ALI patient #11

description: patient with Acute Lung Injury


title: ALI patient #12

description: patient with Acute Lung Injury


title: SNM library

type: MPSS

first: Blake

middle: C.

last: Meyers

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

description:
All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630).
The specific modifications to the method for the MPSS sequencing of small RNAs are described in the paper Lu et al. (Science 2005, 309:1567) .

data_processing: To determine the normalized abundance value for each signature in the library, we separately merged 2-step runs and 3-step runs to create a raw abundance count for each stepper. The average total number of signatures sequenced in all 2-step or for all 3-step runs was calculated within the library. The normalized abundance is the raw abundance count divided by the average total number of signatures for both of the steppers in the library, multiplied by 250,000 to obtain a "transcripts per quarter million" or TPM value. For each signature, only one normalized value is used - either the 2-step or 3-step normalized value, selected based on the higher of the sum of the 2-step or 3-step data across all libraries. The numbers in the VALUE column represent the average expression level of the corresponding signatures in the 2 libraries. More details are available in Meyers et al. (2004, Genome Research 14:1641).

organism: Oryza sativa

source_name: Germinating seedlings infected with Magnaporthe grisea (strain 70-15)]

extract_protocol: Total RNA was isolated using TRIzol reagent.

tag: Cultivar

value: Nipponbare


title: ALI patient #10

description: patient with Acute Lung Injury


title: Microfluidic_rep3

description: Third replicate of microlfuidic experiment performed with 10pg total RNA in a 7nL rotary mixer.

source_name: 10pg RNA, microfluidic experiment, replicate 3


title: Microfluidic_rep2

description: Second replicate of microlfuidic experiment performed with 10pg total RNA in a 7nL rotary mixer.

source_name: 10pg RNA, microfluidic experiment, replicate 2


title: ALI patient #9

description: patient with Acute Lung Injury


title: Conventional_rep3

description: Third replicate of conventional experiment performed with 10pg total RNA in a 10µL in tube.

source_name: 10pg RNA, conventional experiment, replicate 3


title: UNT library

source_name: Seedling control for ABA treatment


title: Control_rep1

description: First replicate of control experiment performed with 15µg total RNA without amplification.

source_name: 15µg RNA, control experiment, replicate 1

label_protocol: 15µg of total RNA were labelled by reverse-transcription in the presence of 7.5µM random hexamers (GE Healthcare), 250µM dUTP-Cy5 (GE Healthcare) and 100U Rtases Reverse-iT Blend (ABgene) overnight at 37°C.


title: Control_rep2

description: Second replicate of control experiment performed with 15µg total RNA without amplification.

source_name: 15µg RNA, control experiment, replicate 2


title: Conventional_rep1

description: First replicate of conventional experiment performed with 10pg total RNA in a 10µL in tube.

source_name: 10pg RNA, conventional experiment, replicate 1


title: ALI patient #8

description: patient with Acute Lung Injury


title: Control_rep3

description: Third replicate of control experiment performed with 15µg total RNA without amplification.

source_name: 15µg RNA, control experiment, replicate 3


title: ALI patient #7

description: patient with Acute Lung Injury


title: ALI patient #6

description: patient with Acute Lung Injury


title: ALI patient #4

description: patient with Acute Lung Injury


title: ABA library

source_name: Seedlings treated with ABA


title: ALI patient #5

description: patient with Acute Lung Injury


title: Aspergillus fumigatus treated with Amphotericin B replicate 1

status: Public on Feb 14 2008

city: San Jose

first: Jata

last: Shankar

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

description: Biological 1 of 2

hyb_protocol: Labeled cDNAs in hybridization buffer were mixed and heated at 94 C for 5 min before loading onto the array slides. Slides were covered with a 2450 mm glass cover slip (Erie Scientific Company, Portsmouth, New Hampshire, US) and kept in hybridization chamber (Corning, Saint Louis, Missouri, US) at 42 C for 16-18 h to prevent evaporation (http://pfgrc.tigr.org/protocols).

scan_protocol: Scanned in both Cy3 and Cy5 channels with AXON Instruments Scanner 4200 with a 10 µm resolution. Each of the signals was converted into a resolution of 16 bits per pixel.

data_processing: TIFF images were analyzed using GenePix Pro 6.0 software. The signal intensity value of each spot was subtracted with local background for each spot. Intensity based normalization by means was used as previously described by Foster, W. R., and R. M. Huber.  2002. Current themes in microarray experimental design and analysis. Drug Discov Today. 7(5):290-2.

organism: Aspergillus fumigatus

source_name: Aspergillus fumgatus grown alone in RPMI-1640 medium for 24hrs

label_protocol: Total RNA (7µg) from Afu alone or Afu treated with AMB (MIC50) was reverse transcribed separately using fluorescein labeled dCTP and biotin labeled dCTP from MICROMAX TSA labeling kits (Perkin Elmer, Wellesley, Massachusetts, US). Labeled cDNA was purified by isopropanol precipitation method as described in the MICROMAX TSA labeling kit. Each of the purified labeled cDNA was dissolved in 20 µl of hybridization buffer; 50 % formamide, 5× sodium citrate-sodium cholride (SSC), 0.1 % sodium dodecyl sulphate (SDS) and 300 µg salmon sperm DNA.

growth_protocol: Aspergillus fumigatus were harvested from Afu culture (after 72 h) on SDA in 3-L haffkine flask using 100 ml phosphate-buffered saline (PBS) with 0.05 % Tween 20 (PBST) and centrifuged at 10,000 rpm for 10 min. at 4 °C and washed with 25 ml PBS twice. Conidia were then allowed to swell in PBS containing Ca2+ and Mg2+ for 1 h followed by a viability count on SDA plates by hemocytometer and CFU count/ml. Afu Spores (1×106/ ml) were inoculated in 100 ml of RPMI-1640 medium (with L-glutamine with sodium bicarbonate) (Sigma, Saint Louis, Missouri, US) in culture flasks (225 cm2) alone or with AMB (MIC50) followed by incubation at 37 °C for 24 h (Axygen, Union City, California, US).

extract_protocol: DNA free total RNA was isolated from Afu using RNeasy plant mini kits (Qiagen GmbH, Hilden, Germany). A fumigatus frozen in -70 °C were grinded using mortar and pestle in the presence of liquid nitrogen (1.5 g, wet weight). The cell powder was suspended in 2 ml of RLT lysis buffer provided with RNeasy plant mini kit and centrifuged at 10,000 rpm for 2 min followed by further steps for isolation of total RNA as described in the kit protocol. Examination of total RNA by gel electrophoresis revealed prominent intact 26S and 18S ribosomal bands and no genomic DNA contamination. RNA concentration was determined spectrophotometer by measuring absorption at 260 nm in a Lambda Bio 20 UV-visible spectrophotometer (Perkin Elmer, Wellesley, Massachusetts, US).

tag: Afu Spores (1×106/ ml) were inoculated in 100 ml of RPMI-1640 medium (with L-glutamine with sodium bicarbonate) (Sigma, Saint Louis, Missouri, US) in culture flasks (225 cm2) alone at 37 °C for 24 h (Axygen, Union City, California, US). Afu were scraped from the culture flask and pelleted at 4 °C by centrifuging at 18,000 rpm for 15 min and kept at -70 °C for microarray experiment.

source_name: Aspergillus fumgatus grown for 24hrs in RPMI-1640 medium containing AmphotericinB

tag: Afu Spores (1×106/ ml) were inoculated in 100 ml of RPMI-1640 medium (with L-glutamine with sodium bicarbonate) (Sigma, Saint Louis, Missouri, US) in culture flasks (225 cm2) with Amphoterin B (MIC50= determined to be 0.125±0.008 µg/ml using MTT assay) followed by incubation at 37 °C for 24 h (Axygen, Union City, California, US). Afu treated with AMB were scraped from the culture flask and pelleted at 4 °C by centrifuging at 18,000 rpm for 15 min and kept at -70 °C.