title: Liver cholesterol pool4 Affy

description: No additional data.


title: Staphylococcus aureus_hypochlorite_10min_replicate2

status: Public on Aug 01 2007

type: RNA

city: Singapore

first: Matthew

middle: Wook

last: Chang

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

description: Hypochlorite treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

label: Biotin

molecule: total RNA

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_hypochlorite

label_protocol: Approximately 12 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated S. aureus cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.  Then, we added 4.4mM hypochlorite immediately after OD600 reached 0.8.

extract_protocol: Total RNA was isolated after 10 min incubation with hypochlorite using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: hypochlorite (4.4mM)

tag: NCTC 8325 Wild type


title: Staphylococcus aureus_hypochlorite_10min_replicate3

description: Hypochlorite treatment


title: Liver cholesterol pool2 Affy

status: Public on Nov 27 2007

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: No additional data.

hyb_protocol: After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.

scan_protocol: MIcroarrays were scanned using a laser scanner (Affymetrix).

data_processing: Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).

label: biotin

organism: Mus musculus

source_name: liver, high cholesterol diet

label_protocol: All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.

growth_protocol: Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle. Seven days prior treatment they were on 1% (w/w) cholesterol diet (Provimi Kliba SA, Kaiseraugst, CH).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.

treatment_protocol: Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.

tag: Strain

tag: Gender

value: male

tag: Age

value: 9 - 12 weeks

tag: Tissue

value: liver

tag: Treatment

value: vehicle only (5% DMSO in corn oil)

tag: Diet

value: 1% cholesterol diet


title: Liver control pool4 Affy

description: No additional data.

source_name: liver, untreated

growth_protocol: Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.


title: P32_exPKO_pancreas

city: University Park

first: Douglas

last: Cavener

state: PA

address: 301 Life Sciences Building

department: Biology

country: USA

institute: Penn State University

description: standard Affymetrix protocol

data_processing: Affymetrix Microarray Suite 5.1

tag: pancreatic acinar cell-specific knockout of the Perk gene; mixed genetic background; postnatal day 32; total pancreas; pooled two mouse cDNA samples equally to generate cRNA.


title: P16_exPKO_pancreas_rep2

description: standard Affymetrix protocol

tag: pancreatic acinar cell-specific knockout of the Perk gene; mixed genetic background; postnatal day 16; total pancreas; replicate mouse #2.


title: P16_exPKO_pancreas_rep1

description: standard Affymetrix protocol

tag: pancreatic acinar cell-specific knockout of the Perk gene; mixed genetic background; postnatal day 16; total pancreas; replicate mouse #1.


title: Spleen Listeria infected 9d rep2

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

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 Pro3.0 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 (normalised log2 infected/non-infected ratio) column contains the log2 ratio of the result file after normalisation

source_name: Spleen infected 9d

label_protocol:
Channel 1 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: Sub-lethal dose L. monocytogenes

value: 4-5 weeks

value: female

tag: RNA pool

source_name: Spleen non-infected


title: Spleen Listeria infected 9d rep3

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


title: P32_WT_pancreas

description: standard Affymetrix protocol

tag: wild-type control (littermates) of "P32_exPKO_pancreas"; mixed genetic background; postnatal day 32; total pancreas; pooled two mouse cDNA samples equally to generate cRNA.


title: Spleen Listeria infected 9d rep1


title: Spleen Listeria infected 9d rep4


title: P16_WT_pancreas_rep1

description: standard Affymetrix protocol

tag: wild-type control (littermate) of "P16_exPKO_pancreas"; mixed genetic background; postnatal day 16; total pancreas; replicate mouse #1.


title: P19_exPKO_pancreas

description: standard Affymetrix protocol

tag: pancreatic acinar cell-specific knockout of the Perk gene; mixed genetic background; postnatal day 19; total pancreas; pooled two mouse cDNA samples equally to generate cRNA.


title: Spleen Listeria infected 4h rep2

source_name: Spleen infected 4h


title: Spleen Listeria infected 3d rep1

source_name: Spleen infected 3d


title: Spleen Listeria infected 1d rep1

source_name: Spleen infected 1d


title: Spleen Listeria infected 1d rep2


title: Spleen Listeria infected 3d rep2


title: Spleen Listeria infected 4h rep1


title: Spleen Listeria infected 2d rep4

source_name: Spleen infected 2d


title: Spleen Listeria infected 5d rep2

source_name: Spleen infected 5d


title: Patient 1_Control Myocardium

status: Public on Jul 01 2007

city: Bad Krozingen

first: Thomas

middle: G

last: Nuehrenberg

state: Baden-Württemberg

address: Südring 15

department: Klinik für Kardiologie II

institute: Universitäts-Herzzentrum Freiburg • Bad Krozingen

description: mRNA isolation, cDNA synthesis, and PCR amplification were performed as described by Klein (PMID: 11923846) and Zohlnhöfer (PMID: 11245643, 11389852)

hyb_protocol: The array was prehybridized overnight in the presence of 50 microg/mL Escherichia coli DNA, 50 microg/mL pbluescript, and 15 microg/mL herring sperm DNA in DigEasyHyb buffer (Roche) at 44°C. The denatured, labeled probe was added to the hybridization solution and incubated for 48 hours. The array was washed according to the manufacturer’s protocol and then adding 2 final washes in 0.1xsaline-sodium citrate/0.1% sodium dodecyl sulfate for 30 minutes at 68°C. Detection of filter-bound probes was performed according to the digoxigenin detection system (Roche).

scan_protocol: The developed film was scanned and analyzed using the Array Vision software (Imaging Research Inc). Background was subtracted, and signals were normalized to 9 housekeeping genes present on each filter, whereby the average of the signals of the housekeeping genes was set to 1 and the background to zero.

data_processing: normalized to housekeeping genes

label: DIG-labeled cDNA

molecule: polyA RNA

organism: Homo sapiens

source_name: myocardial biopsy from normal area on PET

label_protocol: 25 ng of each amplified cDNA were labeled with digoxigenin-11-dUTP (Roche) during PCR in the presence of 50 micromol/L digoxigenin-11-dUPT, 300 micromol/L dTTP, and other dNTPs at a final concentration of 350 micromol/L.

extract_protocol: Frozen tissue was lysed, and Dynabeads Oligo (dT)25 were added for 30 minutes. Afterward, beads were alternately washed in wash buffer-1 (50 mmol/L Tris-HCl [pH 8.3], 75 mmol/L KCl, 3 mmol/L MgCl2, 10 mmol/L dithiothreitol [DTT], and 0.5% Igepal) and wash buffer-2 (50 mmol/L Tris-HCl [pH 8.3], 75 mmol/L KCl, 3 mmol/L MgCl2, 10 mmol/L DTT, and 0.5% Tween-20). mRNA was reverse-transcribed in First Strand Buffer (Gibco), 0.01 mol/L

tag: Angina

value: yes

tag: Hypertension

tag: Smoking

tag: Diabetes

value: IDDM

tag: Dyslipidemia


title: Spleen Listeria infected 3d rep3

tag: Age

tag: Gender


title: Spleen Listeria infected 5d rep1


title: Spleen Listeria infected 4d rep2

source_name: Spleen infected 4d


title: P19_WT_pancreas

description: standard Affymetrix protocol

tag: wild-type control (littermates) of "P19_exPKO_pancreas"; mixed genetic background; postnatal day 19; total pancreas; pooled two mouse cDNA samples equally to generate cRNA.


title: Patient 1_Hibernating Myocardium

source_name: myocardial biopsy from mismatch area on PET


title: Patient 5_Control Myocardium

value: no


title: Spleen Listeria infected 5d rep4


title: Spleen Listeria infected 4d rep4


title: Spleen Listeria infected 4d rep3


title: Patient 6_Control Myocardium


title: Spleen Listeria infected 2d rep2


title: P16_WT_pancreas_rep2

description: standard Affymetrix protocol

tag: wild-type control (littermate) of "P16_exPKO_pancreas"; mixed genetic background; postnatal day 16; total pancreas; replicate mouse #2.


title: Patient 3_Control Myocardium


title: Spleen Listeria infected 4d rep1


title: Spleen Listeria infected 2d rep3


title: Spleen Listeria infected 2d rep1


title: Spleen Listeria infected 5d rep3


title: Patient 5_Hibernating Myocardium


title: Patient 6_Control Myocardium_Hu1.2II


title: Patient 4_Control Myocardium

extract_protocol:
Frozen tissue was lysed, and Dynabeads Oligo (dT)25 were added for 30 minutes. Afterward, beads were alternately washed in wash buffer-1 (50 mmol/L Tris-HCl [pH 8.3], 75 mmol/L KCl, 3 mmol/L MgCl2, 10 mmol/L dithiothreitol [DTT], and 0.5% Igepal) and wash buffer-2 (50 mmol/L Tris-HCl [pH 8.3], 75 mmol/L KCl, 3 mmol/L MgCl2, 10 mmol/L DTT, and 0.5% Tween-20). mRNA was reverse-transcribed in First Strand Buffer (Gibco), 0.01 mol/L
DTT, 0.25% Igepal, 50 micromol/L CFL5c-Primer [59-(CCC)5 GTC TAG A (NNN)2-39], 0.5 mmol/L dNTP, and 200 U Superscript II (Gibco) in 20-microL reactions. After 45 minutes at 44°C, beads were washed with tailing wash buffer (50 mmol/L KH2PO4 [pH 7.0], 1 mmol/L DTT, and 0.25% Igepal), and the tailing reaction was performed in a volume of 10-microL containing 4 mmol/L MgCl2, 0.1 mmol/L DTT, 0.2 mmol/L dGTP, 10 mmol/L KH2PO4, and 10 U terminal deoxynucleotide transferase (MBI Fermentas).
cDNA was amplified by PCR in buffer 1 (Expand Long Template, Roche), 3% deionized formamide, 1.2 micromol/L CP2-Primer [59-TCA GAA TTC ATG (CCC)5-39], 350 micromol/L dNTP, and 4.5 U DNAPolymerase-Mix (Roche) in a total volume of 50 microL. The PCR reaction was performed for 20 cycles of 94°C for 15 s, 65°C for 30 s, and 68°C for 2 minutes; followed by 20 cycles of 94°C for 15 s, 65°C for 30 s, 68°C for 2 minutes and 30 s plus 10 s per cycle; and a final extension of 68°C for 7 minutes.


title: Patient 4_Hibernating Myocardium


title: Patient 5_Control Myocardium_Hu1.2II


title: Patient 2_Control Myocardium


title: Patient 3_Control Myocardium_Hu1.2II


title: Patient 2_Hibernating Myocardium


title: Patient 3_Hibernating Myocardium


title: Patient 5_Hibernating Myocardium_Hu1.2II


title: Patient 4_Hibernating Myocardium_Hu1.2II


title: Patient 2_Hibernating Myocardium_Hu1.2II


title: Patient 3_Hibernating Myocardium_Hu1.2II


title: Patient 4_Control Myocardium_Cardio


title: Patient 1_Control Myocardium_Hu1.2II


title: Patient 5_Control Myocardium_Cardio


title: Patient 6_Control Myocardium_Cardio


title: Patient 1_Hibernating Myocardium_Hu1.2II


title: Patient 3_Control Myocardium_Cardio


title: Patient 1_Control Myocardium_Cardio


title: Patient 4_Control Myocardium_Hu1.2II


title: Patient 3_Hibernating Myocardium_Cardio


title: Patient 5_Hibernating Myocardium_Cardio


title: Patient 2_Hibernating Myocardium_Cardio


title: Patient 2_Control Myocardium_Cardio


title: Patient 2_Control Myocardium_Hu1.2II


title: Patient 4_Hibernating Myocardium_Cardio


title: Patient 5_Hibernating Myocardium_Ca1.2


title: Patient 4_Control Myocardium_Ca1.2


title: Patient 6_Control Myocardium_Ca1.2


title: Patient 1_Hibernating Myocardium_Cardio


title: Patient 4_Hibernating Myocardium_Ca1.2


title: Patient 2_Control Myocardium_Ca1.2


title: Patient 5_Control Myocardium_Ca1.2


title: Patient 3_Control Myocardium_Ca1.2


title: Patient 2_Hibernating Myocardium_Ca1.2


title: Patient 3_Hibernating Myocardium_Ca1.2


title: Patient 1_Control Myocardium_Ca1.2


title: Patient 1_Hibernating Myocardium_Ca1.2


title: MCF7/ADR_100Cell_rep2

status: Public on Jun 01 2007

city: Shanghai

first: Guohong

last: Hu

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health

data_processing: Microarrays were scanned with a GenePix 4000 scanner (Axon Instruments, Foster City, CA). The resultant images were digitized with the software Genepix Pro (version 4.0) provided with the scanner. The mean values of the signals from the duplicate spots of each probe were used for analysis. The background signal was determined by using negative controls and was subtracted from the samples signals. For the comparative expression analysis of the cell lines MCF-7 and MCF-7/AdrR, the arrays were normalized by Lowess smoothing.

source_name: MCF7/AdrR cells

tag: Cell Line

value: MCF7, Adromycin resistent


title: MCF7

source_name: cell line MCF7, 100 cells

tag: breast cancer line MCF7


title: MCF7/ADR_singleCell

source_name: MCF7/AdrR line, single cell

value: MCF7,Adromycin resistent

tag: Amount

value: single cell RNA


title: MCF7/ADR_100cells_rep1

source_name: Breast cancer line MCF7/AdrR

tag: Cell line

value: Breast cancer MCF7, Adromycin resistent


title: BG02 HAIF p10

status: Public on Jun 24 2007

city: Athens

first: Tom

last: Schulz

state: GA

address: 111 Riverbend Rd

institute: Novocell

description: Comparison of gene expression in human embyronic  stem cells grown in MEF-CM or defined media conditions

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Raw data for each sample was output using the Illumina BeadStudio software

label: Biotin-Labeled cRNA

source_name: Human embryonic stem cell line BG02, 10 passages in DC-HAIF media

label_protocol: Illlumina RNA amplification kit, according to the manufacturer’s protocol

growth_protocol:
BG02 cells were maintained in DC-HAIF media conditions for 10 passages.
DC-HAIF consisted of DMEM/F12 (Invitrogen), 2% fatty acid-free Cohn’s fraction V BSA (Serologicals), 1x Nonessential amino acids, 50 U/ml Penicillin, 50 µg/ml Streptomycin, 50 µg/ml Ascorbic Acid, 10 µg/ml bovine or human Transferrin, 0.1 mM β−ME (all from Invitrogen), 1x Trace Elements A, B & C (Mediatech), 10 ng/ml HRG1β (Peprotech), 10 ng/ml ActA (R&D Systems), 200 ng/ml LR3-IGF1 (JRH Biosciences), and 8 ng/ml FGF2 (Sigma or R&D Systems).  HESCs were cultured in DC-HAIF on growth factor depleted Matrigel (BD Biosciences) diluted 1:200.  Near-confluent hESC cultures were passaged by treating with 10 mg/ml (~2000 U/ml) Collagenase IV for three minutes, washing with 0.2% BSA in DMEM/F12, and gentle scraping to lift and break up the colonies. Colony pieces were centrifuged at 200g, aspirated, gently resuspended in DC-HAIF and typically split 1:3 to new plates.

extract_protocol: Trizol reagent (Invitrogen, Inc.)

treatment_protocol: No Treatment

tag: BG02 cell line, karyotypically normal, male


title: BG03 CM p35

scan_protocol: Refer to the Illumina Gene Expression System Manual

source_name: Human embryonic stem cell line BG03, 35 passages in MEF-CM

growth_protocol: BG03 cells were maintained in standard MEF-CM conditions for 35 passages. See Xu et all Nat Biotechnol 19, 971-974 (2001).

tag: BG03 cell line, karyotypically normal, female


title: Mycoplasma gallisepticum Rlow attached to MRC-5 vs broth grown replicate#3

status: Public on May 20 2007

city: Storrs

first: Steven

last: Geary

state: CT

address: 61 North Eagleville Rd

department: Pathobiology

institute: University of Connecticut

description: Rlow grown in broth vs Rlow attached to MRC-5 cells replicate #3

hyb_protocol: Microarray slide blocked (with 1%BSA, 1%SDS in 1xSSC) for 45 min at 42C, samples combined and resuspended in hybridization buffer (MWG Biotech), hybridized O/N at 42C

scan_protocol: Image scanned so ratio of overall signal F635/overall signal F532=1

data_processing: Data collected using GenePix 4, normalized and analyzed using Bayesian Analysis of Gene Expression (BAGEL) software

organism: Mycoplasmoides gallisepticum str. R

source_name: Rlow attached to MRC-5 cells

label_protocol: Labeled with cy5 using the Amino Allyl Labeling kit according to protocol

extract_protocol: MRC-5 monolayer with attached mycoplasmas lysed with TRIzol according to protocol, DNase-treated, eukaryotic RNA removed using MICROBEnrich kit (Ambion), reverse-transcribed using Amino Allyl Labeling kit (Ambion)

treatment_protocol: Rlow p15 culture grown to mid-log phase, centrifuged, resuspended in Hayflicks complete medium, incubated with washed MRC-5 cells for 1 hr, supernatant removed

tag: Mycoplasmas attached to MRC-5 cells for 1 hr

source_name: Rlow grown in broth culture

label_protocol: Labeled using Amino Allyl Labeling kit according to protocol

extract_protocol: Culture centrifuged, RNA extracted using TRIzol according to protocol, DNase-treated, reverse-transcribed using Amino Allyl Labeling kit according to protocol

treatment_protocol: Rlow p15 culture grown to mid-log phase

tag: Mycoplasma grown in broth culture (reference sample)


title: Mouse Young Bone Marrow YM2

city: Seattle

first: Denise

last: Mauldin

state: WA

address: 1100 Fairview Ave N D4-100

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Mouse Young Bone Marrow YM2 from castrated mouse hybridized against YM2 from matched Sham-operated mouse

scan_protocol: Image intensity data were extracted and analyzed using GenePix 4.0 microarray scanner and GenePix Pro Microarray Image Analyis (Axon).

data_processing: Lowess normalization of microarray data was performed using GeneSpring software (Agilent).  Statistical Analysis of Microarrays (SAM) software was used to determine genes that showed statistically significant differences.

source_name: Bone Marrow YM2 from Young Sham-operated Mouse

label_protocol: Purified cDNA from bone and bone marrow of treated or age-matched control mice was labeled with either Cy3 or Cy5 monoreactive fluors (Amersham Life Sciences).

extract_protocol: Total RNA was isolated from pulverized bone using TRIZOL® (Invitrogen, Carlsbad, CA) and cleaned with RNeasy® kit (Qiagen, Valencia, CA).  For each sample, 30 µg of total RNA was reverse transcribed into aminoallyl dUTP (Sigma-Aldrich) incorporated cDNA.

tag: Mouse Young Bone Marrow YM2 Sham-operated Specimen ID

value: YM2 Age:17 weeks Tissue type:Bone Marrow Control:Sham-operated Treatment:Castrated at 7 weeks Category:Young

source_name: Bone Marrow YM2 from Young Castrated at 7 weeks Mouse

tag: Mouse Young Bone Marrow YM2 Specimen ID


description: Mouse Testosterone Replacement Bone Marrow T1 from castrated mouse hybridized against T1 from matched Placebo mouse

source_name: Bone Marrow T1 from Testosterone Replacement Castrated at 7 weeks Mouse

tag: Mouse Testosterone Replacement Bone Marrow T1 Specimen ID

source_name: Bone Marrow T1 from Testosterone Replacement Placebo Mouse

tag: Mouse Testosterone Replacement Bone Marrow T1 Placebo Specimen ID:T1 Age:17 weeks Tissue type:Bone Marrow Control:Placebo Treatment:Castrated at 7 weeks Category:Testosterone Replacement


title: Mycoplasma attached to host cells microarray replicate #4

description: Rlow grown in broth vs Rlow attached to MRC-5 cells replicate #4

source_name: Mycoplasmas grown in broth culture

tag: Rlow grown in broth culture (reference sample)

source_name: Mycoplasmas attached to MRC-5 cells

tag: Rlow p15 attached to MRC-5 human lung fibroblast cells for 1 hr


description: Mouse Testosterone Replacement Bone Marrow T2 from castrated mouse hybridized against T2 from matched Placebo mouse

source_name: Bone Marrow T2 from Testosterone Replacement Placebo Mouse

tag: Mouse Testosterone Replacement Bone Marrow T2 Placebo Specimen ID

value: T2 Age:17 weeks Tissue type:Bone Marrow Control:Placebo Treatment:Castrated at 7 weeks Category:Testosterone Replacement

source_name: Bone Marrow T2 from Testosterone Replacement Castrated at 7 weeks Mouse

tag: Mouse Testosterone Replacement Bone Marrow T2 Specimen ID


title: Mouse Young Bone Marrow YM1

description: Mouse Young Bone Marrow YM1 from castrated mouse hybridized against YM1 from matched Sham-operated mouse

source_name: Bone Marrow YM1 from Young Castrated at 7 weeks Mouse

tag: Mouse Young Bone Marrow YM1 Specimen ID

source_name: Bone Marrow YM1 from Young Sham-operated Mouse

tag: Mouse Young Bone Marrow YM1 Sham-operated Specimen ID:YM1 Age:17 weeks Tissue type:Bone Marrow Control:Sham-operated Treatment:Castrated at 7 weeks Category:Young


title: Mouse Young Bone YB2

description: Mouse Young Bone YB2 from castrated mouse hybridized against YB2 from matched Sham-operated mouse

source_name: Bone YB2 from Young Castrated at 7 weeks Mouse

tag: Mouse Young Bone YB2 Specimen ID

source_name: Bone YB2 from Young Sham-operated Mouse

tag: Mouse Young Bone YB2 Sham-operated Specimen ID:YB2 Age:17 weeks Tissue type:Bone Control:Sham-operated Treatment:Castrated at 7 weeks Category:Young


title: BG02 HAIF p32

source_name: Human embryonic stem cell line BG02, 32 passages in DC-HAIF media

label_protocol: Illlumina RNA amplification kit, according to the manufacturers protocol

growth_protocol:
BG02 cells were maintained in DC-HAIF media conditions for 32 passages.
DC-HAIF consisted of DMEM/F12 (Invitrogen), 2% fatty acid-free Cohns fraction V BSA (Serologicals), 1x Nonessential amino acids, 50 U/ml Penicillin, 50 g/ml Streptomycin, 50 g/ml Ascorbic Acid, 10 g/ml bovine or human Transferrin, 0.1 mM ??ME (all from Invitrogen), 1x Trace Elements A, B & C (Mediatech), 10 ng/ml HRG1? (Peprotech), 10 ng/ml ActA (R&D Systems), 200 ng/ml LR3-IGF1 (JRH Biosciences), and 8 ng/ml FGF2 (Sigma or R&D Systems).  HESCs were cultured in DC-HAIF on growth factor depleted Matrigel (BD Biosciences) diluted 1:200.  Near-confluent hESC cultures were passaged by treating with 10 mg/ml (~2000 U/ml) Collagenase IV for three minutes, washing with 0.2% BSA in DMEM/F12, and gentle scraping to lift and break up the colonies. Colony pieces were centrifuged at 200g, aspirated, gently resuspended in DC-HAIF and typically split 1:3 to new plates.


title: Mouse Young Bone YB1

description: Mouse Young Bone YB1 from castrated mouse hybridized against YB1 from matched Sham-operated mouse

source_name: Bone YB1 from Young Castrated at 7 weeks Mouse

tag: Mouse Young Bone YB1 Specimen ID

source_name: Bone YB1 from Young Sham-operated Mouse

tag: Mouse Young Bone YB1 Sham-operated Specimen ID:YB1 Age:17 weeks Tissue type:Bone Control:Sham-operated Treatment:Castrated at 7 weeks Category:Young


title: Mouse Old Bone Marrow OBM2

description: Mouse Old Bone Marrow OBM2 from castrated mouse hybridized against OBM2 from matched Sham-operated mouse

source_name: Bone Marrow OBM2 from Old Sham-operated Mouse

tag: Mouse Old Bone Marrow OBM2 Sham-operated Specimen ID

value: OBM2 Age:59 weeks Tissue type:Bone Marrow Control:Sham-operated Treatment:Castrated at 7 weeks Category:Old

source_name: Bone Marrow OBM2 from Old Castrated at 7 weeks Mouse

tag: Mouse Old Bone Marrow OBM2 Specimen ID


title: Mouse Old Bone Marrow OBM3

description: Mouse Old Bone Marrow OBM3 from castrated mouse hybridized against OBM3 from matched Sham-operated mouse

source_name: Bone Marrow OBM3 from Old Castrated at 7 weeks Mouse

tag: Mouse Old Bone Marrow OBM3 Specimen ID

source_name: Bone Marrow OBM3 from Old Sham-operated Mouse

tag: Mouse Old Bone Marrow OBM3 Sham-operated Specimen ID:OBM3 Age:59 weeks Tissue type:Bone Marrow Control:Sham-operated Treatment:Castrated at 7 weeks Category:Old


description: Mouse Testosterone Replacement Bone Marrow T3 from castrated mouse hybridized against T3 from matched Placebo mouse

source_name: Bone Marrow T3 from Testosterone Replacement Castrated at 7 weeks Mouse

tag: Mouse Testosterone Replacement Bone Marrow T3 Specimen ID

source_name: Bone Marrow T3 from Testosterone Replacement Placebo Mouse

tag: Mouse Testosterone Replacement Bone Marrow T3 Placebo Specimen ID:T3 Age:17 weeks Tissue type:Bone Marrow Control:Placebo Treatment:Castrated at 7 weeks Category:Testosterone Replacement


title: Mouse Old Bone Marrow OBM1

description: Mouse Old Bone Marrow OBM1 from castrated mouse hybridized against OBM1 from matched Sham-operated mouse

source_name: Bone Marrow OBM1 from Old Castrated at 7 weeks Mouse

tag: Mouse Old Bone Marrow OBM1 Specimen ID

source_name: Bone Marrow OBM1 from Old Sham-operated Mouse

tag: Mouse Old Bone Marrow OBM1 Sham-operated Specimen ID:OBM1 Age:59 weeks Tissue type:Bone Marrow Control:Sham-operated Treatment:Castrated at 7 weeks Category:Old


title: Rlow grown in broth vs Rlow attached to MRC-5 rep#2

description: Second replicate of five in dataset

hyb_protocol: Microarray slide blocked (with 1%BSA, 1%SDS in 1x SSC) for 45 min at 42C, samples combined and resuspended in MWG hybridization buffer, hybridized O/N at 42C

scan_protocol: Slide scanned so overall signal F635/signal F532=1

data_processing: Scanned in GenePix 4, analysed as part of entire data set using Bayesian Analysis of Gene Expression

source_name: Rlow grown in broth

label_protocol: Labeled with Amino Allyl Labeling kit according to protocol

extract_protocol: Rlow grown to mid-log phase, centrifuged, extracted with TRIzol according to protocol, DNase-treated, reverse-transcribed using the Amino Allyl Labeling kit

treatment_protocol: Rlow p15 grown to mid-log phase

tag: Mycoplasma grown to mid-log phase in broth culture

source_name: Rlow attached to MRC-5

label_protocol: Labeled using Amino Allyl Labeling kit (Ambion) according to protocol

extract_protocol: Monolayer lysed with TRIzol, DNase-treated, eukaryotic RNA removed using MICROBEnrich kit (Ambion), reverse-transcribed using Amino Allyl Labeling kit (Ambion)

treatment_protocol: Rlow p15 grown to mid-log phase, centrifuged, resuspended in Hayflicks complete medium, incubated with washed MRC-5 monolayer for 1 hr, supernatant removed

tag: Rlow attached to MRC-5 human lung fibroblasts for 1 hr


title: Rlow grown in broth vs Rlow attached to MRC-5 rep#1

description: first replicate of five in data set

hyb_protocol: Microarray slide blocked (with 1%BSA, 1%SDS in 1xSSC) for 45 min at 42C, labeled samples combined and resuspended in hybridization buffer supplied by MWG Biotech, incubated O/N at 42C

scan_protocol: Scanned to ratio of overall signal in cy3/signal in cy5 =1

data_processing: Scanned and recorded with GenePix 4, later normalized and analyzed with other replicates using Bayesian Analysis of Gene Expression (BAGEL) software

extract_protocol: Monolayer of MRC-5 and attached mycoplasma lysed with TRIzol, DNase-treated, eukaryotic RNA removed with MICROBEnrich kit (Ambion), reversed-transcribed and labeled using Amino Allyl Labeling kit (Ambion)

treatment_protocol: Mycoplasma grown to mid-log phase, centrifuged, resuspended in Hayflicks broth, incubated with washed MRC-5 lung fibroblasts for 1 hr

tag: Mycoplasma gallisepticum strain R p15 attached to MRC-5 human lung fibroblasts

source_name: Rlow grown in broth culture

label_protocol: Labeled using Amino Allyl Labeling Kit (Ambion) according to protocol

extract_protocol: Mycoplasma grown to mid-log phase, centrifuged, extracted with TRIzol according to protocol, reverse-transcribed using Amino Allyl Labeling Kit

treatment_protocol: Mycoplasma grown to mid-log phase

tag: Mycoplasma grown to mid-log phase


title: BG02 CM p64

source_name: Human embryonic stem cell line BG02, 64 passages in MEF-CM

growth_protocol: BG02 cells were maintained in standard MEF-CM conditions for 64 passages. See Xu et all Nat Biotechnol 19, 971-974 (2001).

tag: BG02 cell line, karyotypically normal, male


title: Mycoplasma gallisepticum Rlow grown in broth vs Rlow attached to MRC-5 replicate #5

source_name: Mycoplasma gallisepticum Rlow attached to MRC-5

tag: Mycoplasmas attached to MRC-5 human lung fibroblasts

source_name: Mycoplasma gallisepticum strain R grown in broth (reference)

tag: Mycoplasma gallisepticum strain Rlow p15 grown in broth culture


title: pGIT8.1 + NO2

status: Public on May 18 2007

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: Successful pathogens must be able to protect themselves against reactive nitrogen species generated either as part of host defence mechanisms, or as products of their own metabolism. The regulatory protein, NsrR (a member of the Rrf2 family of transcription factors), plays key roles in this stress response. Microarray analysis was utilised to reveal the full role of NsrR. Regulation by NsrR is known to be extremely sensitive to repressor titration by NsrR-binding sites provided on a multicopy plasmid. Transformation of an nsrR+ strain with plasmid pGIT1, which carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation. As a control, pGIT8 carries the same promoter fragment, but a 1 bp deletion mutation in the NsrR binding site eliminates repressor titration in vivo. Strain MG1655 transformed with pGIT8 was grown anaerobically and RNA was isolated from early exponential phase cultures grown in the presence of nitrite. A pool of RNA from the control strain (MG1655 transformed with pGIT8 and grown in the absence of nitrite) was included as a common reference.

hyb_protocol: Prior to hybridization, the slides were treated with the background-reducing Pronto! Pre-Soak System (Corning Life Sciences). The slides were incubated for 20 min in prewarmed Universal Pre-Soak solution at 42 °C and washed twice in 0.1xSSC, 0.1% SDS for 30 s at room temperature. Slides were immediately transferred into prewarmed prehybridization solution (5xSSC, 0.1% SDS, and 0.1% bovine serum albumin) and incubated for 2–4 h at 42 °C. The microarray slides were finally washed at room temperature once in 0.1xSSC, 0.1% SDS for 1 min and twice in 0.1xSSC for 30 s, briefly dipped in water and then ethanol, and dried by centrifugation for 5 min at 800xg. For each experiment, equal quantities (80 pmol) of each Cy5- and Cy3-labeled cDNA were added to a final volume of 80 microlitre of hybridization solution containing 25% formamide, 10 mg of bovine serum albumin (fraction V) per ml, 5xSSC (1xSSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% SDS, 8 micrograms of poly(A), and 1xDenhardt’s solution. The cDNA probes were denatured at 95 °C for 3 min and hybridized for 16 h at 42 °C in an Advalytix Hyb station. After hybridization was complete, the slides were washed in an Advalytix Wash station with 2xSSC, 0.1% SDS at 42 °C, followed with 0.1xSSC, 0.1% SDS at room temperature, and finally twice in 0.1xSSC at room temperature. The microarray slides were dried by centrifugation for 5min at 800g.

scan_protocol: Slide was scanned at 532 and 630 nm by using a Genepix 4000A scanner (Axon Instruments, Union City, CA).

data_processing: Data was analysed using GeneSpring

organism: Escherichia coli

source_name: pGIT8 + NO2

label_protocol: 20 ug total RNA was converted to Cy5-labelled cDNA using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE Healthcare) according to manufacturer’s instructions. Amino-allyllabelled nucleotides were incorporated into the cDNA by reverse transcription of the total RNA, followed by a direct chemical coupling of Cy5 NHS-dye esters to the amino-allyl-labelled cDNAs

extract_protocol: An RNeasy midikit was used to prepare total RNA according to the manufacturer’s instructions (QIAGEN Ltd.). Any contaminating DNA was removed using a DNAase column kit (QIAGEN Ltd).

treatment_protocol: 15 ml of culture was mixed with 30 ml of RNAprotect bacterial reagent (QIAGEN Ltd).

tag: Strain

value: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter) Growth:Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide + 2.5 mM sodium nitrite

label_protocol: 20 ug total RNA was converted to Cy3-labelled cDNA using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE Healthcare) according to manufacturer’s instructions. Amino-allyllabelled nucleotides were incorporated into the cDNA by reverse transcription of the total RNA, followed by a direct chemical coupling of Cy5 NHS-dye esters to the amino-allyl-labelled cDNAs

value: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter) Growth:Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide Pool of eight independent cultures


title: Mouse Young Bone Marrow YM3

description: Mouse Young Bone Marrow YM3 from castrated mouse hybridized against YM3 from matched Sham-operated mouse

source_name: Bone Marrow YM3 from Young Castrated at 7 weeks Mouse

tag: Mouse Young Bone Marrow YM3 Specimen ID

source_name: Bone Marrow YM3 from Young Sham-operated Mouse

tag: Mouse Young Bone Marrow YM3 Sham-operated Specimen ID:YM3 Age:17 weeks Tissue type:Bone Marrow Control:Sham-operated Treatment:Castrated at 7 weeks Category:Young


title: pGIT8.4 + NO2

value: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter) Growth:Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide + .5 mM sodium nitrite


title: Mouse Young Bone YB3

description: Mouse Young Bone YB3 from castrated mouse hybridized against YB3 from matched Sham-operated mouse

source_name: Bone YB3 from Young Sham-operated Mouse

tag: Mouse Young Bone YB3 Sham-operated Specimen ID

value: YB3 Age:17 weeks Tissue type:Bone Control:Sham-operated Treatment:Castrated at 7 weeks Category:Young

source_name: Bone YB3 from Young Castrated at 7 weeks Mouse

tag: Mouse Young Bone YB3 Specimen ID


title: pGIT1.2

description:
Successful pathogens must be able to protect themselves against reactive nitrogen species generated either as part of host defence mechanisms, or as products of their own metabolism. The regulatory protein, NsrR (a member of the Rrf2 family of transcription factors), plays key roles in this stress response. Microarray analysis was utilised to reveal the full role of NsrR.
Regulation by NsrR is known to be extremely sensitive to repressor titration by NsrR-binding sites provided on a multicopy plasmid. Transformation of an nsrR+ strain with plasmid pGIT1, which carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation. As a control, pGIT8 carries the same promoter fragment, but a 1 bp deletion mutation in the NsrR binding site eliminates repressor titration in vivo. Strain MG1655 transformed with either pGIT1 was grown anaerobically and RNA was isolated from early exponential phase cultures grown in the absence of nitrite.  A pool of RNA from the control strain (MG1655 transformed with pGIT8 and grown in the absence of nitrite) was included as a common reference.

hyb_protocol: solution at 42 °C and washed twice in 0.1xSSC, 0.1% SDS for 30 s at room temperature. Slides were immediately transferred into prewarmed prehybridization solution (5xSSC, 0.1% SDS, and 0.1% bovine serum albumin) and incubated for 2–4 h at 42 °C. The microarray slides were finally washed at room temperature once in 0.1xSSC, 0.1% SDS for 1 min and twice in 0.1xSSC for 30 s, briefly dipped in water and then ethanol, and dried by centrifugation for 5 min at 800xg. For each experiment, equal quantities (80 pmol) of each Cy5- and Cy3-labeled cDNA were added to a final volume of 80 microlitre of hybridization solution containing 25% formamide, 10 mg of bovine serum albumin (fraction V) per ml, 5xSSC (1xSSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% SDS, 8 micrograms of poly(A), and 1xDenhardt’s solution.

label_protocol:
20 ug total RNA was converted to Cy5-labelled cDNA
using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE
Healthcare) according to manufacturer’s instructions. Amino-allyllabelled
nucleotides were incorporated into the cDNA by reverse
transcription of the total RNA, followed by a direct chemical coupling
of Cy5 NHS-dye esters to the amino-allyl-labelled
cDNAs

value: MG1655 pGIT1 (carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation) Growth:Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide

label_protocol:
20 ug total RNA was converted to Cy3-labelled cDNA
using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE
Healthcare) according to manufacturer’s instructions. Amino-allyllabelled
nucleotides were incorporated into the cDNA by reverse
transcription of the total RNA, followed by a direct chemical coupling
of Cy3 NHS-dye esters to the amino-allyl-labelled
cDNAs


title: pGIT8.3 + NO2


title: pGIT8.2 + NO2

value: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter) Growth:Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide +2.5 mM sodium nitrite


title: pGIT1.3


title: pGIT1.1 + NO2

description:
Successful pathogens must be able to protect themselves against reactive nitrogen species generated either as part of host defence mechanisms, or as products of their own metabolism. The regulatory protein, NsrR (a member of the Rrf2 family of transcription factors), plays key roles in this stress response. Microarray analysis was utilised to reveal the full role of NsrR.
Regulation by NsrR is known to be extremely sensitive to repressor titration by NsrR-binding sites provided on a multicopy plasmid. Transformation of an nsrR+ strain with plasmid pGIT1, which carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation. As a control, pGIT8 carries the same promoter fragment, but a 1 bp deletion mutation in the NsrR binding site eliminates repressor titration in vivo. Strain MG1655 transformed with either pGIT1 was grown anaerobically and RNA was isolated from early exponential phase cultures grown in the presence of nitrite.  A pool of RNA from the control strain (MG1655 transformed with pGIT8 and grown in the absence of nitrite) was included as a common reference.

source_name: pGIT1 + NO2

tag: Pool of eight independent cultures


title: pGIT1.4


title: pGIT1.1


title: pGIT1.3 + NO2

value: MG1655 pGIT1 (carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation) Growth:Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide +2.5 mM sodium nitrite


title: Case 2 2005061510

status: Public on May 01 2007

type: genomic

city: Leuven

first: Helena

last: Pospisilova

address: Herestraat 49

department: Department of Human Genetics

country: Belgium

institute: Catholic University Leuven

description: Comparison between individual with B-cell malignancy vs normal individual

hyb_protocol: Probe preparation and preblocking of the slide were performed as described by Fiegler et al. (2003). Equal amounts (200 pmol) of Cy5- and Cy3-labeled probe were combined with 100 ug Cot-1 DNA followed by an ethanol precipitation. Resuspension of the pellet was done in hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween 20, 2 x SSC, and 10 mM Tris HCl, pH 7.5) containing 400 ug yeast tRNA to hybridize a spotting area of 24 x 60 mm. The slide was blocked with 50 ug Cot-1 DNA and 300 ug salmon sperm DNA dissolved in 60 ul hybridization buffer. Blocking solution and probe mixture were denaturated for 10 min in a water bath at 75°C. Blocking solution was then placed on the slide covered with a coverslip (24 x 60 mm) and placed in a humid chamber. Meanwhile, the probe was placed at 37°C for preannealing. After 1 hr of blocking, the coverslip was removed and probe was placed on the slide. After placing a coverslip (24 x 60 mm), the slide was placed in a humid chamber saturated with 20% formamide and 2 x SSC. Hybridization was allowed to take place for two nights at 37°C. Posthybridization washes were performed as described by Fiegler et al. (2003). The coverslip was removed by placing the slide in PBS with 0.05% Tween 20, followed by a 10- min wash in a fresh solution of PBS/Tween 20 at room temperature, 30 min in 50% formamide/2 x SSC at 42°C, and 10 min in PBS/0.05% Tween 20 at room temperature. Slides were spin dried at 1000 rpm for 5 min. See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22

scan_protocol: Array slides were scanned with a GenePix 4000B scanner and hybridization signals were evaluated using GenePixPro 3.0 image analysis software.

data_processing: All data analysis was performed with Excel. Spot intensities were corrected for local background, and only spots with signal intensities at least two fold above background signal intensities were included in the final analysis. For each clone, a ratio of Cy5 to Cy3 fluorescence intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of the autosomes followed by the 2D normalization. Normalized ratios of the duplicates were averaged and a log2 value was calculated. Precise localizations of clones spotted on the array were obtained from the Ensemble database (www.ensembl.org/Homo_sapiens). The Normalized ratio is not included in the submitted raw data.

molecule: genomic DNA

source_name: 66/M bone marrow

label_protocol: The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy5-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

extract_protocol: Genomic DNA was extracted from a bone marrow using standard procedures.

tag: age

value: 66, Gender:male, tissue:bone marrow

source_name: control DNA

label_protocol: The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy3-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

extract_protocol: Genomic DNA was extracted from a peripheral blood using standard procedures.

tag: normal individual, Tissue

value: peripheral blood


title: Case 3 2005061502

source_name: 65/M peripheral blood

value: 65, Gender:male, tissue:peripheral blood


title: pGIT1.4 + NO2


title: Case 28 2005092011(B)

hyb_protocol: Probe preparation and preblocking of the slide were performed as described by Fiegler et al. (2003). Equal amounts (150 pmol) of Cy5- and Cy3-labeled probe were combined with 50 ug Cot-1 DNA followed by an ethanol precipitation. Resuspension of the pellet was done in hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween 20, 2 x SSC, and 10 mM Tris HCl, pH 7.5) containing 200 ug yeast tRNA to hybridize a spotting area of 24 x 24 mm. The slide was blocked with 17 ug Cot-1 DNA and 100 ug salmon sperm DNA dissolved in 20 ul hybridization buffer. Blocking solution and probe mixture were denaturated for 10 min in a water bath at 75°C. Blocking solution was then placed on the slide covered with a coverslip (24 x 24 mm) and placed in a humid chamber. Meanwhile, the probe was placed at 37°C for preannealing. After 1 hr of blocking, the coverslip was removed and probe was placed on the slide. After placing a coverslip (24 x 24 mm), the slide was placed in a humid chamber saturated with 20% formamide and 2 x SSC. Hybridization was allowed to take place for two nights at 37°C. Posthybridization washes were performed as described by Fiegler et al. (2003). The coverslip was removed by placing the slide in PBS with 0.05% Tween 20, followed by a 10- min wash in a fresh solution of PBS/Tween 20 at room temperature, 30 min in 50% formamide/2 x SSC at 42°C, and 10 min in PBS/0.05% Tween 20 at room temperature. Slides were spin dried at 1000 rpm for 5 min. See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22

source_name: 74/M bone marrow

value: 74, gender:male, tissue:bone marrow


title: Case 33 2005092003(B)

source_name: 64/F bone marrow

value: 64, gender:female, tissue:bone marrow


title: Case 32 2005092012(A)

source_name: 72/M bone marrow

value: 72, gender:male, tissue:bone marrow


title: Case 1 2005061506

source_name: 59/M lymph node

extract_protocol: Genomic DNA was extracted from a lymph node using standard procedures.

value: 59, Gender:male, tissue:lymph node


title: Case 31 2005092011(A)


title: pGIT1.2 + NO2

value: MG1655 pGIT1 (carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation)

tag: Growth

value: Anaerobic to early exponential growth

tag: Media:Minimal salts + 20 mM trimethylamine-N-oxide +2.5 mM sodium nitrite

value: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter)


title: Case 35 2005092004(B)

source_name: 55/F peripheral blood

value: female, gender:female, tissue:peripheral blood


title: Case 25 2005092010(B)

source_name: 82/M bone marrow

value: 82, gender:male, tissue:bone marrow


title: Case 34 2005092007(A)

source_name: 58/F lymph node

value: 58, gender:female, tissue:lymph node


title: Case 29 2005092007(B)

data_processing: All data analysis was performed with Excel. Spot intensities were corrected for local background, and only spots with signal intensities at least two fold above background signal intensities were included in the final analysis. For each clone, a ratio of Cy5 to Cy3 fluorescent intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of the autosomes followed by the 2D normalization. Normalized ratios of the duplicates were averaged and a log2 value was calculated. Precise localizations of clones spotted on the array were obtained from the Ensemble database (www.ensembl.org/Homo_sapiens). The Normalized ratio is not included in the submitted raw data.

source_name: 83/F bone marrow

value: 83, gender:female, tissue:bone marrow


title: Case 23 2005092009(B)

source_name: 66/M lymph node

value: 66, gender:male, tissue:lymph node


title: Case 27 2005092004(A)

source_name: 52/M bone marrow

value: 52, gender:male, tissue:bone marrow


title: Case 8 2005092009(A)

source_name: 80/F lymph node

value: 80, Gender:female, tissue:lymph node


title: Expression in spo11Y135F strain at meiosis 4 hr

status: Public on Apr 10 2007

city: Kisarazu

first: Kazuto

last: Kugou

state: Chiba

address: 2-6-7 KazusaKamatatri

department: Department of Frontier Research

country: Japan

institute: Kazusa DNA Research Institute

description: Gene expression data from diploid cells in prophase.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip YG-S98. GeneChips were washed and stained using EukGE-WS1 ver3 protocol in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.  The comparison with GSM153627 was performed with MAS 5.0 using Affymetrix default analysis settings.  See Comparison data table on Series GSE6620 record.

organism: Saccharomyces cerevisiae

source_name: 4 hrs after transfer into sporulation medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown on a YPD plate for 2 days at 30C. The cells were grown to a density of 4.0x10^7 cells/ml at 30C in SPS presporulation medium (0.5% yeast extract, 1% peptone, 0.17% yeast nitrogen base w/o amino acid and ammonium sulfate, 1% potassium acetate, 0.5% ammonium sulfate, usual level fo amino acids, 50 mM potassium phthalate buffer pH 5.0, and antifoam). The cells were suspended in sporulation medium (1% potasium acetate, 1/5 level of amino acids, and polypropylene glycol) to a density of 2x10^7 cells/ml, and incubated for 4 hrs at 30C for sporulation.

extract_protocol: Total RNA was prepared using glass beads and RNeasy Maxi Kit (QIAGEN). mRNA was isolated the total RNA using Oligotex-dT30 (TaKaRa). These processes were performed according to the manufacturer's instructions.

treatment_protocol: Cells were washed twice with water, frozen in liquid nitrogen, and stored at -80C.

tag: strain

tag: background

tag: genotype


title: Case 21 2005061507

hyb_protocol: e preparation and preblocking of the slide were performed as described by Fiegler et al. (2003). Equal amounts (200 pmol) of Cy5- and Cy3-labeled probe were combined with 100 ug Cot-1 DNA followed by an ethanol precipitation. Resuspension of the pellet was done in hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween 20, 2 x SSC, and 10 mM Tris HCl, pH 7.5) containing 400 ug yeast tRNA to hybridize a spotting area of 24 x 60 mm. The slide was blocked with 50 ug Cot-1 DNA and 300 ug salmon sperm DNA dissolved in 60 ul hybridization buffer. Blocking solution and probe mixture were denaturated for 10 min in a water bath at 75°C. Blocking solution was then placed on the slide covered with a coverslip (24 x 60 mm) and placed in a humid chamber. Meanwhile, the probe was placed at 37°C for preannealing. After 1 hr of blocking, the coverslip was removed and probe was placed on the slide. After placing a coverslip (24 x 60 mm), the slide was placed in a humid chamber saturated with 20% formamide and 2 x SSC. Hybridization was allowed to take place for two nights at 37°C. Posthybridization washes were performed as described by Fiegler et al. (2003). The coverslip was removed by placing the slide in PBS with 0.05% Tween 20, followed by a 10- min wash in a fresh solution of PBS/Tween 20 at room temperature, 30 min in 50% formamide/2 x SSC at 42°C, and 10 min in PBS/0.05% Tween 20 at room temperature. Slides were spin dried at 1000 rpm for 5 min. See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22

source_name: 72/F bone marrow

value: 72, gender:female, tissue:bone marrow


title: Case 9 2005092013(B)

source_name: 73/M bone marrow

value: 73, Gender:male, tissue:bone marrow

value: peripheral blood


title: Case 15 2005092005(A)

source_name: 82/F bone marrow

value: 82, Gender:female, tissue:bone marrow


title: Expression in rad50delta strain at meiosis 4 hr


title: Expression in mre11delta strain at meiosis 4 hr

extract_protocol: Total RNA was prepared using Trizol reagent (Invitrogen). mRNA was isolated the total RNA using Oligotex-dT30 (TaKaRa). These processes were performed according to the manufacturer's instructions.


title: Case 22 2005092008(B)

source_name: 75/F peripheral blood

value: 75, gender:female, tissue:peripheral blood

source_name: control DNA


title: Case 24 2005092010(A)

source_name: 59/M bone marrow

value: 59, gender:male, tissue:bone marrow


title: Case 17 2005092002(B)

source_name: 84/M lymph node

value: 57, Gender:male, tissue:lymph node


title: Expression in wild type strain at meiosis 4 hr

value: wt


title: Case 30 2005092006(B)

source_name: 71/M lymph node

value: 71, gender:male, tissue:lymph node


title: Case 26 2005061509

source_name: 56/M bone marrow

value: 56, gender:male, tissue:bone marrow


title: PCRamplified_Siliques_Stage comparison_slideAV34_LabellingRep1

status: Public on Apr 02 2007

city: Dunedin

first: Robert

last: Day

state: Otago

address: Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: Our aim was to identify which stand alone amplification protocol performed best in our lab when the starting amount of total RNA was limited by comparison to conventional hybridisations. RNA was isolated from siliques during early (2-5 DAP) and late (6-10 DAP) stages of development. To help identify major alterations in the array data due to our target preparation protocols, the late stage RNA sample was spiked with 10% early stage sample (90%-late). In the absence of compression, the signals from the genes only expressed in the early sample should not be more than 10-fold higher than those obtained from the late sample. Conversely, the late sample should display a full range of differential expression. This design should result in the unamplified MA plots (plots of differential expression against intensity) having a distinctive asymmetrical shape. The two same RNA populations were used as the basis for all labellings and hybridisations. Duplicate target preparations (amplifications and labelling or just labelling) of the Early silique sample were hybridised against a single preparation of the 90% late silique sample for each treatment.

hyb_protocol: Pre-wash and BSA pre-hybridisation: Slides were pre-washed in 0.2% SDS for 2 mins and then washed twice in MilliQ (MQ) water. The slides were then placed in a 50mL Falcon tube containing fresh MQ water and incubated in a water bath for 20 mins at 50°C. Slides were then pre-hybridised in buffer containing 4x SSC, 0.5% SDS and 5% w/v bovine serum albumin (BSA, Sigma) at 42°C for 45 mins. Slides were then washed 5 times with MQ water at room temperature to remove BSA residue. Prior to hybridisation, the slides were dried by centrifuged at 5800 rpm. Hybridisation: Hybridisations were carried out under LifterSlips (Erie scientific) placed over the region of the slide containing the array.  A mix of SlideHyb buffer 1 (Ambion) and the labelled probes were then injected under the lifterslip. The arrays were then placed in a humidified hybridisation chamber (Corning) and hybridised over night in a 55°C water bath. Post-hybridisation: The slides were removed from the hybridisation chamber and washed at 55°C for 8 mins with agitation in 50mL Falcon tubes containing 2x SSC, 0.1% SDS. The slides were then moved to new 50mL Falcon tubes and washed with constant agitation in 1x SSC, 0.1% SDS at room temperature for a further 6 mins.   This procedure was repeated with a solution containing 0.5x SSC and then 0.1x SSC before the slides were dried by centrifugation at 5800 rpm.

scan_protocol: Scanning: Slide scanning was carried out using an Axon 4000B dual colour scanner running GenePix 4.1 software  (Axon instruments).

data_processing:
Genepix files were normalised by implementing elements of the SNOMAD gene
analysis tools (http://pevsnerlab.kennedykrieger.org/snomadinput.html) at a local
level using an splus script. This involved global mean normalisation, local mean
normalisation across the array surface and local mean normalisation across the
element signal intensity.

organism: Arabidopsis thaliana

source_name: Siliques 2-5 DAP bio rep1 labelling rep1

label_protocol: 50 ng total RNA was subjected to reverse transcription using superscript III reverse transcriptase (Invitrogen) and amplified dsDNA was prepared following the methods described in Petalidis et al (Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA: Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003, 31:e142), with the exception that the entire cDNA sample was used in the amplification reaction. To determine the optimal number of cycles required for generating products during the exponential phase of the PCR reaction PCR products from parallel runs were visualised after 15, 18, 21 and 24 cycles on a 1.2% agarose gel. When the yield of PCR product stops increasing with more cycles, the reaction has reached its plateau. The optimal number of cycles for the amplification is one cycle fewer than is needed to reach the plateau; in our case 20 cycles. Amino-allyl dNTPs were incorporated by Klenow and the free Cy dyes (Amersham Biosciences) were coupled to the target dsDNA as described in the Superscript Indirect labelling kit manual (Invitrogen).

extract_protocol: Tissues were ground to a fine powder in liquid nitrogen using a pestle and mortar. Total RNA was isolated from the samples using Concert Plant RNA Purification Reagent (Invitrogen) following the manufacturers’ large-scale extraction protocol. Aliquots of these samples were further purified using Qiagen RNeasy columns integrating the manufacturers’ optional on column DNase step.

tag: Developing siliques 2-5 DAP from Arabidospsis thaliana (Col)

source_name: Siliques 90% 6-10 DAP, 10% 2-5 DAP bio rep1 labelling rep1

tag: Developing siliques from Arabidospsis thaliana (Col). RNA was isolated from siliques during early (2-5 DAP) and late (6-10 DAP) stages of development. To help identify major alterations in the array data due to our target preparation protocols, the late stage RNA sample was spiked with 10% early stage sample (90%-late).


title: IVTamplified_Siliques_Stage comparison_slideAV41_LabellingRep2

data_processing:
Genepix files were normalised by implementing elements of the SNOMAD gene analysis tools (http://pevsnerlab.kennedykrieger.org/snomadinput.html) at a local
level using an splus script. This involved global mean normalisation, local mean normalisation across the array surface and local mean normalisation across the element signal intensity.

source_name: Siliques 2-5 DAP bio rep1 labelling rep2

label_protocol: 5µg of total RNA was amplified using the Message Amp II amino-allyl aRNA kit (Ambion) following the manufacturers’ instructions. Amino-allyl UTPs were incorporated into the IVT reaction and coupled to Cy dyes (Amersham Biosciences) following the kits recommendations. All labelled aRNA targets were fragmented prior to hybridisation using Ambion fragmentation reagent following the manufacturers’ protocol (Ambion).


title: Unamplified_Siliques_Stage comparison_slideAV39_LabellingRep2

label_protocol: 30 µg of total RNA was reverse transcribed and labelled using the Superscript Indirect labelling kit (Invitrogen).


title: Case 4 2005092005(A)

source_name: 57/M peripheral blood

value: 57, Gender:male, tissue:peripheral blood


title: 2xIVTamplified_Siliques_Stage comparison_slideAV36_LabellingRep1

label_protocol: 50ng of total RNA was amplified using the Message Amp II amino-allyl aRNA kit (Ambion) following the manufacturers’ instructions. Two rounds of amplification were used an amino-allyl UTPs were incorporated into the second IVT reaction and coupled to Cy dyes (Amersham Biosciences) following the kits recommendations. All labelled aRNA targets were fragmented prior to hybridisation using Ambion fragmentation reagent following the manufacturers’ protocol (Ambion).


title: IVTamplified_Siliques_Stage comparison_slideAV40_LabellingRep1


title: PCRamplified_Siliques_Stage comparison_slideAV35_LabellingRep2


title: Endosperm_LCM_4DAP_slideBG12_rep3dyeswap

description: We hybridised whole silique total RNA against Endosperm total RNA obtained by laser capture microdissection.

scan_protocol: Scanning: Slide scanning was carried out using an Axon 4000B dual colour scanner running GenePix 4.1 software (Axon instruments).

data_processing:
Genepix files were normalised by implementing elements of the SNOMAD gene analysis tools (http://pevsnerlab.kennedykrieger.org/snomadinput.html) at a local level using an splus script. This involved global mean normalisation, local mean
normalisation across the array surface and local mean normalisation across the element signal intensity.

source_name: Siliques 4DAP rep1

label_protocol:
100ng of total RNA underwent a two round IVT amplification using the Message Amp II amino-allyl aRNA kit (Ambion) following the manufacturers’ instructions. Amino-allyl UTPs were incorporated into the second IVT reaction and coupled to Cy dyes (Amersham Biosciences) following the kits recommendations. All labelled aRNA targets were fragmented prior to hybridisation using Ambion fragmentation reagent
following the manufacturers’ protocol (Ambion).

extract_protocol: Total RNA was obtained from the tissue scrape samples using the Picopure RNA isolation kit (Arcturus) with optional on column DNase step (Qiagen). The purified total RNA was quantified using the Ribogreen RNA quantification kit (Invitrogen) according to the manufacturers’ instructions.

tag: Developing siliques 4DAP. Prepared for LCM and mounted on glass slides. Tissue was scraped from the slide and used for RNA extraction.

extract_protocol: Total RNA was obtained from the endosperm sample using the Picopure RNA isolation kit (Arcturus) with optional on column DNase step (Qiagen). The purified total RNA was quantified using the Ribogreen RNA quantification kit (Invitrogen) according to the manufacturers’ instructions.

tag: Developing siliques 4DAPwere prepared for LCM and mounted on glass slides. Endosperm was isolated from the sample using the Arcturus LM200 Pixcell II laser capture microdissection system.


title: Endosperm_LCM_4DAP_slideBG9_rep1


title: Endosperm_LCM_4DAP_slideBG11_rep2dyeswap


title: 2xIVTamplified_Siliques_Stage comparison_slideAV37_LabellingRep2


title: Unamplified_Siliques_Stage comparison_slideAV38_LabellingRep1


title: Endosperm_LCM_4DAP_slideBG10_rep2


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069789B rep 3

status: Public on Apr 01 2007

first: John

last: Leigh

department: Microbiology

institute: University of Washington

description: Biological replicate 3 of 3. Cultures grown at rapid speed where compared to those under slow growth, both under phosphate limitation

hyb_protocol: 100-120 pmol of Cy3 and Cy5 labeled cDNA where mixed, dried, resuspended in hybridization buffer (Agilent), boiled 3 min, 30 sec on ice, placed on the slide, covered with a coverslip and incubated at 42 C for 14-16 hours in the dark. Slides where washed in 1xSSC + 0.2% SDS then 0.1xSSC + 0.2% SDS at 54 C, washed with 0.1xSSC at room temp then rinsed with water and dried under nitrogen gas.

scan_protocol: Scanned on a Perkin-Elmer Scan-Array Express Images where quantified using TIGR spotfinder

data_processing: Background subtraction followed by LOESS normalization using S+ array analyzer

organism: Methanococcus maripaludis

source_name: Total RNA from Methanococcus maripaludis grown with 0.15 mM phosphate at 0.19 per hour dilution rate

label_protocol: A variation of aminoallyl cDNA labeling (Ambion), 5-10 ug of total RNA was incubated with 4 ug of random decamers at 75 C for 7 min, reverse transcibed in the presence of 0.15mM aminoallyl UTP for 2 hours at 42 C,the RNA hydrolyzed by NaOH at 65 C for 15 min, neutralized with HEPES, percipitated and resuspended in coupling buffer, NHS-Cy5 was used to couple Cy5 to the aminoallyl UTP, and the reaction cleaned up with minelute columns

growth_protocol: cells were grown in chemostats in McCas media with 0.15 mM phosphate at 0.19 per hour dilution rate

extract_protocol: Qiagen RNeasy

tag: grown at rapid speed under phosphate limitation

source_name: Total RNA from Methanococcus maripaludis grown with 0.15 mM phosphate at 0.042 per hour dilution rate

label_protocol: A variation of aminoallyl cDNA labeling (Ambion), 5-10 ug of total RNA was incubated with 4 ug of random decamers at 75 C for 7 min, reverse transcibed in the presence of 0.15mM aminoallyl UTP for 2 hours at 42 C,the RNA hydrolyzed by NaOH at 65 C for 15 min, neutralized with HEPES, percipitated and resuspended in coupling buffer, NHS-Cy3 was used to couple Cy3 to the aminoallyl UTP, and the reaction cleaned up with minelute columns

growth_protocol: cells were grown in chemostats in McCas media with 0.15 mM phosphate at 0.042 per hour dilution rate

tag: grown at slow speed under phosphate limitation


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069789A rep 3


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000070024Blow rep 1

description: Biological replicate 1 of 3. Cultures grown at rapid speed where compared to those under slow growth, both under phosphate limitation

scan_protocol: Scanned on a Perkin-Elmer Scan-Array Express at a low gain setting Images where quantified using TIGR spotfinder


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069789Alow rep 3


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069789Blow rep 3


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069786Alow rep 2

description: Biological replicate 2 of 3. Cultures grown at rapid speed where compared to those under slow growth, both under phosphate limitation


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069790A rep 3


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000070023Blow rep 1


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069790B rep 3


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069786Blow rep 2


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069787Blow rep 2


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069790Blow rep 3


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000070023Alow rep 1


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069790Alow rep 3


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000070024Alow rep 1


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069787B rep 2


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069787A rep 2


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069787Alow rep 2


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069786B rep 2


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000070024B rep 1


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000070024A rep 1


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000069786A rep 2


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000070023B rep 1


title: Rapid speed under phosphate limitation vs. slow speed under phosphate limitation slide 3000070023A rep 1


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070036B rep 3

description: Biological replicate 3 of 3. Cultures grown at rapid speed where compared to those under slow growth, both under hydrogen limitation

scan_protocol: Scanned on a Molecular Dynamics Gen III array scanner Images where quantified using TIGR spotfinder

source_name: Total RNA from Methanococcus maripaludis grown with 29 ml/min dihydrogen at 0.2 per hour dilution rate

growth_protocol: cells were grown in chemostats in McCas media gassed with 29 ml/min dihydrogen at 0.2 per hour dilution rate

tag: grown at rapid speed under hydrogen limitation

source_name: Total RNA from Methanococcus maripaludis grown with 8 ml/min dihydrogen at 0.042 per hour dilution rate

growth_protocol: cells were grown in chemostats in McCas media with 8 ml/min dihydrogen at 0.042 per hour dilution rate

tag: grown at slow speed under hydrogen limitation


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070040B rep 2

description: Biological replicate 2 of 3. Cultures grown at rapid speed where compared to those under slow growth, both under hydrogen limitation


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070037B rep 3


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070037A rep 3


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070036A rep 3


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070042A rep 1

description: Biological replicate 1 of 3. Cultures grown at rapid speed where compared to those under slow growth, both under hydrogen limitation


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070040A rep 2


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070042B rep 1


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070041B rep 1


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070038B rep 2


title: Hydrogen limitation vs. phosphate limitation slide 3000070248A rep 3

description: Biological replicate 3 of 4. Cultures grown under hydrogen limitation where compated to those grown under phosphate limitation

source_name: Total RNA from Methanococcus maripaludis grown with 20 ml/min dihydrogen

growth_protocol: cells were grown in chemostats in McCas media gassed with 20 ml/min dihydrogen

tag: grown under hydrogen limitation

source_name: Total RNA from Methanococcus maripaludis grown under 15 mM phosphate

growth_protocol: cells were grown in chemostats in McCas media with 15 mM phosphate

tag: grown under phosphate limitation


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070041A rep 1


title: Hydrogen limitation vs. phosphate limitation slide 3000070035B rep 4

description: Biological replicate 4 of 4. Cultures grown under hydrogen limitation where compated to those grown under phosphate limitation


title: Hydrogen limitation vs. phosphate limitation slide 3000070254A rep 1

description: Biological replicate 1 of 4. Cultures grown under hydrogen limitation where compated to those grown under phosphate limitation


title: Hydrogen limitation vs. phosphate limitation slide 3000070253B rep 1


title: Hydrogen limitation vs. phosphate limitation slide 3000070254B rep 1


title: Hydrogen limitation vs. phosphate limitation slide 3000070035A rep 4


title: Hydrogen limitation vs. phosphate limitation slide 3000070249B rep 2

description: Biological replicate 2 of 4. Cultures grown under hydrogen limitation where compated to those grown under phosphate limitation


title: Hydrogen limitation vs. phosphate limitation slide 3000070247B rep 3


title: Hydrogen limitation vs. phosphate limitation slide 3000070249A rep 2


title: Hydrogen limitation vs. phosphate limitation slide 3000070034B rep 4


title: Hydrogen limitation vs. phosphate limitation slide 3000070247A rep 3


title: Hydrogen limitation vs. phosphate limitation slide 3000070250B rep 2


title: Hydrogen limitation vs. phosphate limitation slide 3000070250A rep 2


title: Hydrogen limitation vs. phosphate limitation slide 3000070248B rep 3


title: Hydrogen limitation vs. phosphate limitation slide 3000070253A rep 1


title: Hydrogen limitation vs. phosphate limitation slide 3000070034A rep 4


title: Rapid speed under Hydrogen limitation vs. slow speed under hydrogen limitation slide 3000070038A rep 2


title: Hydrogen limitation vs. leucine limitation slide 3000070033A rep 4

description: Biological replicate 4 of 4. Cultures grown under hydrogen limitation where compated to those grown under leucine limitation

source_name: Total RNA from Methanococcus maripaludis grown under 15 mM leucine

growth_protocol: cells were grown in chemostats in McCas media with 15 mM leucine

tag: grown under leucine limitation


title: Hydrogen limitation vs. leucine limitation slide 3000070033B rep 4


title: Hydrogen limitation vs. leucine limitation slide 3000070032A rep 4


title: Hydrogen limitation vs. leucine limitation slide 3000070240B rep 3


title: Hydrogen limitation vs. leucine limitation slide 3000070240A rep 3


title: Hydrogen limitation vs. leucine limitation slide 3000070239B rep 3


title: Hydrogen limitation vs. leucine limitation slide 3000070032B rep 4


title: Hydrogen limitation vs. leucine limitation slide 3000070259B rep 2


title: Hydrogen limitation vs. leucine limitation slide 3000070258B rep 2


title: Hydrogen limitation vs. leucine limitation slide 3000070239A rep 3


title: Hydrogen limitation vs. leucine limitation slide 3000070259A rep 2


title: Hydrogen limitation vs. leucine limitation slide 3000070261A rep 1


title: Hydrogen limitation vs. leucine limitation slide 3000070261B rep 1


title: Hydrogen limitation vs. leucine limitation slide 3000070258A rep 2


title: Human_soft tissue tumor_NCCS098

city: Tokyo

first: Hitoshi

last: Ichikawa

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

description: NCCS098, male, Malignant fibrous histiocytoma

hyb_protocol: Target cRNA preparation from total RNA, hybridization to the microarray, washing and staining with a Single Stain procedure and scanning were all carried out according to the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the GeneArray scanner GA2500 (Agilent).

data_processing: The expression value (Signal) of each probe set was calculated using GeneChip Operating Software (GCOS) ver. 1.3 (Affymetrix), so that the mean of expression values in each experiment was set at 100 to adjust for minor differences between experiments.

source_name: Soft tissue tumors - Malignant fibrous histiocytoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, rev 1, Affymetrix).

extract_protocol: Tumor samples were obtained at the time of surgical excision and cryopreserved in liquid nitrogen until use. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: Sampling site:mets


title: Human_soft tissue tumor_NCCS104

description: NCCS104, male, Malignant fibrous histiocytoma

tag: Sampling site:primary


title: Human_soft tissue tumor_NCCS099

description: NCCS099, female, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS103

description: NCCS103, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS097

description: NCCS097, female, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS102

description: NCCS102, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS105

description: NCCS105, female, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS094

description: NCCS094, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS089

description: NCCS089, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS090

description: NCCS090, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS100

description: NCCS100, male, Malignant fibrous histiocytoma


title: Hydrogen limitation vs. leucine limitation slide 3000070260A rep 1


title: Human_soft tissue tumor_NCCS095

description: NCCS095, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS096

description: NCCS096, male, Malignant fibrous histiocytoma


title: Hydrogen limitation vs. leucine limitation slide 3000070260B rep 1


title: Human_soft tissue tumor_NCCS101

description: NCCS101, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS087

description: NCCS087, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS088

description: NCCS088, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS092

description: NCCS092, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS086

description: NCCS086, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS091

description: NCCS091, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS082

description: NCCS082, female, Fibrosarcoma

source_name: Soft tissue tumors - Fibrosarcoma


title: Human_soft tissue tumor_NCCS084

description: NCCS084, male, Fibrosarcoma


title: Human_soft tissue tumor_NCCS093

description: NCCS093, male, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS085

description: NCCS085, female, Malignant fibrous histiocytoma


title: Human_soft tissue tumor_NCCS079

description: NCCS079, male, Malignant peripheral nerve sheath tumor

source_name: Soft tissue tumors - Malignant peripheral nerve sheath tumor

tag: Histology:Malignant peripheral nerve sheath tumor


title: Human_soft tissue tumor_NCCS083

description: NCCS083, female, Fibrosarcoma


title: Human_soft tissue tumor_NCCS078

description: NCCS078, male, Malignant peripheral nerve sheath tumor


title: Human_soft tissue tumor_NCCS080

description: NCCS080, female, Malignant peripheral nerve sheath tumor


title: Human_soft tissue tumor_NCCS081

description: NCCS081, female, Fibrosarcoma


title: Human_soft tissue tumor_NCCS073

description: NCCS073, male, Leiomyosarcoma

source_name: Soft tissue tumors - Leiomyosarcoma


title: Human_soft tissue tumor_NCCS075

description: NCCS075, female, Leiomyosarcoma


title: Human_soft tissue tumor_NCCS074

description: NCCS074, female, Leiomyosarcoma


title: Human_soft tissue tumor_NCCS067

description: NCCS067, male, Myxofibrosarcoma

source_name: Soft tissue tumors - Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS068

description: NCCS068, male, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS064

description: NCCS064, female, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS066

description: NCCS066, male, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS071

description: NCCS071, male, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS060

description: NCCS060, female, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS072

description: NCCS072, male, Leiomyosarcoma


title: Human_soft tissue tumor_NCCS062

description: NCCS062, male, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS063

description: NCCS063, female, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS059

description: NCCS059, male, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS077

description: NCCS077, female, Leiomyosarcoma


title: Human_soft tissue tumor_NCCS070

description: NCCS070, male, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS058

description: NCCS058, female, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS069

description: NCCS069, female, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS057

description: NCCS057, male, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS065

description: NCCS065, female, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS051

description: NCCS051, unknown, Dedifferentiated liposarcoma

source_name: Soft tissue tumors - Dedifferentiated liposarcoma

tag: Histology:Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS054

description: NCCS054, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS055

description: NCCS055, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS061

description: NCCS061, male, Myxofibrosarcoma


title: Human_soft tissue tumor_NCCS053

description: NCCS053, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS056

description: NCCS056, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS049

description: NCCS049, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS047

description: NCCS047, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS050

description: NCCS050, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS052

description: NCCS052, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS048

description: NCCS048, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS044

description: NCCS044, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS045

description: NCCS045, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS043

description: NCCS043, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS046

description: NCCS046, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS041

description: NCCS041, unknown, Well-differentiated liposarcoma

source_name: Soft tissue tumors - Well-differentiated liposarcoma


title: Human_soft tissue tumor_NCCS035

description: NCCS035, female, Myxoid liposarcoma

source_name: Soft tissue tumors - Myxoid liposarcoma

tag: Histology:Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS037

description: NCCS037, unknown, Lipoma

source_name: Soft tissue tumors - Lipoma


title: Human_soft tissue tumor_NCCS038

description: NCCS038, unknown, Lipoma


title: Human_soft tissue tumor_NCCS040

description: NCCS040, unknown, Well-differentiated liposarcoma


title: Human_soft tissue tumor_NCCS039

description: NCCS039, unknown, Well-differentiated liposarcoma


title: Human_soft tissue tumor_NCCS036

description: NCCS036, unknown, Lipoma


title: Human_soft tissue tumor_NCCS031

description: NCCS031, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS029

description: NCCS029, male, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS032

description: NCCS032, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS033

description: NCCS033, male, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS030

description: NCCS030, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS025

description: NCCS025, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS034

description: NCCS034, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS042

description: NCCS042, unknown, Dedifferentiated liposarcoma


title: Human_soft tissue tumor_NCCS028

description: NCCS028, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS026

description: NCCS026, male, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS027

description: NCCS027, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS024

description: NCCS024, male, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS023

description: NCCS023, male, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS020

description: NCCS020, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS019

description: NCCS019, male, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS022

description: NCCS022, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS016

description: NCCS016, male, Synovial sarcoma

source_name: Soft tissue tumors - Synovial sarcoma

tag: Histology:Synovial sarcoma


title: Human_soft tissue tumor_NCCS017

description: NCCS017, female, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS018

description: NCCS018, male, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS010

description: NCCS010, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS012

description: NCCS012, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS011

description: NCCS011, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS015

description: NCCS015, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS014

description: NCCS014, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS013

description: NCCS013, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS021

description: NCCS021, male, Myxoid liposarcoma


title: Human_soft tissue tumor_NCCS009

description: NCCS009, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS007

description: NCCS007, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS005

description: NCCS005, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS003

description: NCCS003, male, Synovial sarcoma


title: Human_soft tissue tumor_NCCS006

description: NCCS006, female, Synovial sarcoma


title: Human_soft tissue tumor_NCCS004

description: NCCS004, male, Synovial sarcoma


title: Human_soft tissue tumor_NCCS002

description: NCCS002, male, Synovial sarcoma


title: E. histolytica strain HM1 replicate 3

status: Public on Mar 01 2007

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

description: Trophozoites after long term axenic growth. Isolated mid-log phase

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: GCOS scaling only- target 500

organism: Entamoeba histolytica

source_name: Trophozoites grown in TYI

label_protocol: SPIA

tag: Strain

tag: Media

value: TYI

tag: Long term axenic growth


title: Human_soft tissue tumor_NCCS001

description: NCCS001, female, Synovial sarcoma


title: E. histolytica strain 200:NIH replicate 1

label_protocol: Affymetrix single amplification


title: E. histolytica strain Rahman replicate 1

value: Rahman


title: E. histolytica strain Rahman replicate 3


title: E. histolytica strain Rahman replicate 2


title: E. histolytica strain HM1 +5AzC 3 day

description: Trophozoites after 3-day treatment with 23 micromolar 5-Azacytidine

value: TYI +5-Azacytidine

tag: 3-day treatment with 5-Azacytidine


title: E. histolytica strain HM1 +5AzC 7 day

description: Trophozoites after 7-day treatment with 27 micromolar 5-Azacytidine

tag: 7-day treatment with 5-Azacytidine


title: SLIDE 13: wild type vs PerR mutant

city: St. Louis

first: Michael

last: Caparon

state: MO

address: 660 S. Euclid Ave.

department: Dept. of Molecular Microbiology

institute: Washington University School of Medicine

description: Wild type strain versus PerR mutant strain in mid-logarithmic phase of growth

hyb_protocol: The tagged cDNAs from the appropriate samples were mixed and then allowed to hybridize with the array using a commercial buffer (MWG) at 42°C overnight. Following washing using 2× SSC, 0.2% SDS, at 65°C to remove unhybridized cDNAs, the detection reagents (Cyanine 3 and Cyanine 5 3DNA dendrimers, Genisphere) were added with incubation at 65°C for 3 h. Unbound detection reagents were removed by washing.

scan_protocol: Slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer) to detect Cy3 and Cy5 fluorescence.

data_processing: What is submitted is the raw output of Scanarray. VALUE = log2 (test/ref)

organism: Streptococcus pyogenes

source_name: Streptococcus pyogenes, PerR mutant, mid-logarithmic phase of growth

label_protocol: Synthesis and labelling of cDNA used a commercial kit (3DNA Array 900, Genisphere).

growth_protocol: Overnight growth in THY medium was diluted 1:100 in fresh THY medium followed by incubation at 37°C to the mid-logarithmic phase (OD600=0.300) of growth

extract_protocol: Total RNA was isolated using glass beads (Lysing Matrix A, Q/BioGene) and a high-speed reciprocating shaking device (FP-120, Savant Instruments). RNA was further purified (RNeasy Mini Kit for RNA clean up, Qiagen) and contaminating DNA was removed by DNase. Total RNA concentration was calculated using absorbance at 260 nm.RNA was further analyzed by a fluorescent assay involving electrophoretic separation of RNA (Agilent 2100 Bioanalyzer), and rejected if the electropherogram (a diagram of fluorescence over time) showed degradation of RNA

tag: Streptoccocus pyogenes strain HdeltaPerR (PerR mutant derived form the wild type strain HSC5) grown in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY medium) to mid-logarithmic phase of growth

source_name: Streptocococcus pyogenes, wild type strain, mid-logarithmic phase of growth

tag: Streptoccocus pyogenes strain HSC5 (Wild type) grown in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY medium) to mid-logarithmic phase of growth


title: 1000cGY replicate 2

city: Durham

first: Holly

middle: Kloos

last: Dressman

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University Medical Center

data_processing: Data was analysed with GeneSpring 7 data software package (Silicon Genetics). Each data set was filtered based on 1.5X background, thus there are missing data ( ) and normalised using  Lowess intensity-dependent normalisation.

source_name: 1000cGY replicate 2

growth_protocol: no growth protocol

extract_protocol: Briefly, 5 x 106 MNCs were pelleted and total RNA was isolated using the RNAeasy minispin column

tag: MNCs were plelleted and total RNA was isolated via RNAeasy minispin column

source_name: Stratagene Universal Mouse reference

treatment_protocol: No treatment


title: Post Irradiation patient 25

description: No treatment

data_processing: Data was analysed with GeneSpring 7 data software package (Silicon Genetics). Each data set filtered out probes that were below 1.5X background was normalised using  Lowess intensity-dependent normalisation, then data was put into PAM and missing values were imputed.

source_name: Post Irradiation patient

treatment_protocol: 150-200 cGy of total body irradiation

tag: Mononuclear cells (MNCs) were collected from each patient’s PB and RNA extracted via Qiagen RNAeasy kits

source_name: Stratagene Universal Human reference


title: Post Irradiation patient 23

description: No treatment


title: 1000cGY replicate 6

source_name: 1000cGY replicate 6


title: Post Irradiation patient 21

description: No treatment


title: Post Irradiation patient 20

description: No treatment


title: 1000cGY replicate 5

source_name: 1000cGY replicate 5


title: Post Irradiation patient 18

description: No treatment


title: Post Irradiation patient 27

description: No treatment


title: 1000cGY replicate 4

source_name: 1000cGY replicate 4


title: 1000cGY replicate 7

source_name: 1000cGY replicate 7


title: Post Irradiation patient 24

description: No treatment


title: Post Irradiation patient 12

description: No treatment


title: Post Irradiation patient 17

description: No treatment


title: Post Irradiation patient 22

description: No treatment


title: Post Irradiation patient 13

description: No treatment


title: Post Irradiation patient 19

description: No treatment


title: Post Irradiation patient 16

description: No treatment


title: sok2-yap6 rep3

city: Bar Harbor

first: Gregory

last: Carter

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Gene expression from yeast cells

data_processing: Data was normalized using BioConductor RMA

source_name: Yeast colonies after 10 hr growth

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: 10hr growth on Synthetic low-ammonium dextrose media (SLAD) with uracil and histidine

tag: Genotype

value: G85 with yap6::NatMX4 sok2::bcKanMX4


title: 1000cGY replicate 3

source_name: 1000cGY replicate 3


title: Post Irradiation patient 14

description: No treatment


title: Post Irradiation patient 11

description: No treatment


title: Human_soft tissue tumor_NCCS008

description: NCCS008, male, Synovial sarcoma


title: sok2-yap6 rep2

description: Gene expression from yeast cells


title: Post Irradiation patient 9

description: No treatment


title: Post Irradiation patient 10

description: No treatment


title: Post Irradiation patient 7

description: No treatment


title: Post Irradiation patient 8

description: No treatment


title: sok2-yap6 rep1

description: Gene expression from yeast cells


title: sfl1-yap6 rep3

description: Gene expression from yeast cells

value: G85 with yap6::NatMX4 sfl1::bcKanMX4


title: sfl1-yap6 rep2

description: Gene expression from yeast cells


title: sfl1-yap6 rep1

description: Gene expression from yeast cells


title: yap6 rep2

description: Gene expression from yeast cells

value: G85 with yap6::NatMX4


title: cup9-yap6 rep2

description: Gene expression from yeast cells

value: G85 with yap6::NatMX4 cup9::bcKanMX4


title: Post Irradiation patient 4

description: No treatment


title: yap6 rep1

description: Gene expression from yeast cells


title: cup9-yap6 rep3

description: Gene expression from yeast cells


title: sok2-skn7 rep3

description: Gene expression from yeast cells

value: G85 with sok2::bcKanMX4 skn7::bcKanMX4


title: cup9-yap6 rep1

description: Gene expression from yeast cells


title: Post Irradiation patient 5

description: No treatment


title: Pre Irradiation patient 32

description: No treatment

source_name: Pre Irradiation patient

treatment_protocol: no IR treatment


title: sok2-skn7 rep2

description: Gene expression from yeast cells


title: Post Irradiation patient 6

description: No treatment


title: Post Irradiation patient 1

description: No treatment


title: Post Irradiation patient 2

description: No treatment


title: sok2-skn7 rep1

description: Gene expression from yeast cells


title: Pre Irradiation patient 33

description: No treatment


title: Pre Irradiation patient 30

description: No treatment


title: Post Irradiation patient 3

description: No treatment


title: Pre Irradiation patient 31

description: No treatment


title: sfl1-skn7 rep3

description: Gene expression from yeast cells

value: G85 with sfl1::bcKanMX4 skn7::bcKanMX4


title: Post Irradiation patient 26

description: No treatment


title: Pre Irradiation patient 29

description: No treatment


title: Post Irradiation patient 15

description: No treatment


title: sfl1-skn7 rep2

description: Gene expression from yeast cells


title: sfl1-skn7 rep1

description: Gene expression from yeast cells


title: sfl1-sok2 rep3

description: Gene expression from yeast cells

value: G85 with sfl1::bcKanMX4 sok2::bcKanMX4


title: yap6 rep3

description: Gene expression from yeast cells


title: sfl1-sok2 rep1

description: Gene expression from yeast cells