title: bsu_glnTreated_2h_2_3

status: Public on Sep 09 2009

city: Shanghai

first: Hui

last: Yu

address: No.100, Rd. Qinzhou

country: China

institute: Shanghai Center for Bioinformation Technology

hyb_protocol: Hybridization was performed in an Agilent Microarray Hybridization Chamber (G2534A) for 16 h at 65°C at rotation of 10 rpm.

scan_protocol: Scanned on an Agilent G2505B US80803205 scanner

data_processing: Feature extraction and image analysis software (Feature Extraction Software; Agilent Technologies) was used to locate and delineate every spot in the array, to integrate each spot's intensity, and to normalize data using the Lowess method. Spots with flag value of non-zero or a signal-to-noise ratio smaller than 2.6 were masked in normalization.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: B.subtilis, 2 h after being treated by Glutamine.

label_protocol: Agilent Quick Amp Kit (Agilent Technologies) was used to synthesize cDNA from total RNA samples of 2 g and subsequently produce the amino allyl modified cRNA according to the supplier's manual, except using amino allyl-dUTP (Ambion). In the next step, the amino allyl labeled cRNA of 4 g is coupled with the monoreactive succinimide ester derivative of a Cy dye (GE healthcare, PA13105 or PA15100).

growth_protocol: Bacteria was inoculated in LB medium (10 g tryptone, 5 g yeast extract, and 10 g NaCl per liter of distilled H2O), grown for 16 h at 37 °C and 200 rpm. The seed culture was used to inoculate in a an aerobic chemostat culture in a 5-L fermentor with a working volume of 2 L on the adapted medium (2g (NH4)2SO4, 7g K2HPO4, 3g KH2PO4, 1g sodium citrate, 0.2g MgSO4•7H2O, 5g glucose per liter of distilled H2O). The culture was allowed to grow in batch mode for 7-8 h before the feed pump and effluent pump were turned on to start the chemostat.

extract_protocol: Total RNAs were isolated from culture samples by using the Trizol reagent (Gibco BRL, Cleveland, OH) according to the standard protocols.

treatment_protocol: At the age of 70 h, the steady-state chemostat culture was perturbed by the addition of amino acid (valine, glutamate, or glutamine) to the fermentor so that amino acid concentration was suddenly increased to about 1.8 g/l, 3.3 g/l, or 4.6 g/l (15.4 mM, 22.4 mM, or 31.5 mM)

value: Glutamine

tag: elongationtime

value: 2 h

source_name: B.subtilis, not treated with any amino acid.

value: no treatment


title: 10071_normal control_rep2

status: Public on Sep 15 2009

type: RNA

city: Portland

first: Grover

middle: C

last: Bagby

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Dept. of Medicine

country: USA

institute: Oregon Health & Science University

description: Hybridization date: 07/26/02; Array lot: 2003960

hyb_protocol: The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 16 hours at 45⁰C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 400s (Affymetrix, Santa Clara, CA) running standard Affymetrix fluidics script.

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Agilent G2500 GeneArray Scanner (Agilent Technologies, Santa Clara, CA). The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.

data_processing: The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: normal low-density bone marrow cells

label_protocol: Each total RNA sample was labeled and amplified following the recommended protocol in the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 2 (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf). Using 4 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (IDT, Coralville, IA). Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation. In the second step, the cDNA was converted to labeled cRNA (the target) using T7 RNA polymerase in the presence of biotinylated UTP and CTP (Enzo, Farmingdale, NY). Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) and was followed by an ethanol precipitation of the labeled target. The target was fragmented to produce a uniform distribution of short cRNAs. 10µg each of fragmented target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.

extract_protocol: Heparinized bone marrow aspiration samples were obtained from patients and normal volunteers after obtaining informed consent. Low-density marrow cells were isolated using Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ), then total RNA was extracted immediately using the RNeasy Mini Kit (QIAGEN, Valencia, CA). RNA was concentrated to approximately 1 ug/ul by precipitation with 3M sodium acetate, pH 5.2, 5 ug of linear polyacrylamide (Sigma, St. Louis, MO), and 2.5 volumes of 100% ethanol. Final RNA pellets were dissolved in nuclease-free water.

tag: disease state

value: normal

tag: cell type

value: low-density bone marrow cells

tag: gender

value: F

tag: age

tag: fa complementation group


title: bsu_valTreated_30min_Val.1_2

source_name: B.subtilis, 30 min after being treated by Valine.

tag: treatment

value: Valine

value: 30 min


title: bsu_gluTreated_2h_1_3

source_name: B.subtilis, 2 h after being treated by Glutamate.

value: Glutamate


title: bsu_glnTreated_30min_2_2

source_name: B.subtilis, 30 min after being treated by Glutamine.


title: bsu_valTreated_8h_Val.1_4

source_name: B.subtilis, 8 h after being treated by Valine.

value: 8 h


title: bsu_gluTreated_30min_1_2

source_name: B.subtilis, 30 min after being treated by Glutamate.


title: 10051_normal control_rep1


title: bsu_gluTreated_24h_1_4

source_name: B.subtilis, 24 h after being treated by Glutamate.


title: bsu_valTreated_5min_rep2_Val.2_1

description:
bsu_valTreated_5min_rep2_Val.2_1
Two biological replicates were perfomed for Val-5min treatment. This is replicate 2.

source_name: B.subtilis, 5 min after being treated by Valine (rep 2).

value: 5 min


title: bsu_glnTreated_24h_2_4

source_name: B.subtilis, 24 h after being treated by Glutamine.


title: bsu_glnTreated_5min_2_1

source_name: B.subtilis, 5 min after being treated by Glutamine.


title: Lame 19

status: Public on Sep 01 2009

city: Nouzilly

first: Joel

last: Gautron

address: UR83 Recherches avicoles

country: France

institute: INRA

description: Twenty micrograms of total RNA from various regions of oviduct were used to produce fluorescently labelled cDNA with the Superscript Indirect cDNA Labelling System (Invitrogen, USA). After synthesis and purification, the cDNA was assessed with a Nanodrop ND 1000 (Nanodrop, Nyxor biotech, France). cDNA was used to perform fluorescent dye coupling reaction. The dye incorporation rate was assessed with a Nanodrop ND 1000. Only cDNA-probes with frequency of incorporation (Dye molecules/1000 bases) > 11.4 were used for hybridization.

hyb_protocol: All microarrays slides were prehybridized using 100 µL of DIG easy buffer (Roche) in humidified chambers for 1 hr at 42°C. Slides were then washed with distilled water for 10 min with mild agitation. The hybridization solution contained 80 µl of DIG easy buffer, 2.5 µl of yeast tRNA, 2.5 µl DNA salmon sperm (10µg/ µl) and 2 µl PolyA RNA (1µg/µl). An equal amount of Alexa 555- and Alexa 647-labelled cDNA probes from two samples was added to the mixture, which was denatured at 100°C for 2 min. The mixture of Alexa® 555 and Alexa 647® labeled samples was pipetted onto the slides, which were covered with a Lifter cover slips in hybridization chambers and the microarray hybridized for 16 hr at 42°C. The slides were washed in 0.2X saline sodium citrate (SSC) buffer and 0.1% sodium dodecyl sulfate (SDS) for 15 min at 42°C. The slides were washed a second time with 0.2x SSC for 15 min at room temperature. Finally, the slides were rinsed with distilled water and dried by centrifugation.

scan_protocol: Microarray slides were scanned at 532 nm for Alexa® 555 and 635 nm for Alexa® 647 using a GenePix 4000B microarray scanner. The GenePix Pro 6.0 software was used to acquire the fluorescent images, align the spots, quantify their intensity and finally export GenePix report (GPR) files containing spot intensity raw data. The GPR files were stored in the BioArray Software Environment (BASE) of SIGENAE (Système d'Information du projet d'Analyse des Genomes des Animaux d'Elevage) for further processing and analysis.

data_processing: The identification of differentially expressed genes was performed using anapuce package. Spot intensities were calculated using the median value that was logarithm transformed (log2). A normalization consisting of global locally-weighted regression (LOWESS) was applied on the overall intensity log ratio to remove the bias due to fluorescence incorporation. A block effect was also corrected by subtracting the median value of the block. Differential analysis was performed on data where at least four repeated expressions by gene were available. The gene variance was a mixture model by using the varmixt method. On both dataset, unilateral statistical t-test was performed according to varmixt method. Taking into account that all tests were simultaneous, P-values were adjusted by a Benjamini-Hochberg (BH) multiple testing procedures, to control False Discovery Rate to less than 0.05.

label: Alexa Fluor 555

organism: Gallus gallus

source_name: Poule IsaBrown 35 stade 17:10

label_protocol: The methods for generating fluorescently labelled cDNA were performed according to the procedure recommended by the manufacturer (Invitrogen, USA). Twenty micrograms of total RNA from various regions of oviduct were used to produce fluorescently labelled cDNA with the Superscript Indirect cDNA Labelling System (Invitrogen, USA). After synthesis and purification, the cDNA was assessed with a Nanodrop ND 1000 (Nanodrop, Nyxor biotech, France). cDNA was used to perform fluorescent dye coupling reaction. The experimental design used a dye switch procedure in which half of samples were labelled with Alexa 555 fluorescent probe and the other half using Alexa 647 (Fisher Scientific BioBLock, France). The dye incorporation rate was assessed with a Nanodrop ND 1000. Only cDNA-probes with frequency of incorporation (Dye molecules/1000 bases) > 11.4 were used for hybridization.

extract_protocol: Total RNA was extracted from frozen tissue samples using a commercial kit (RNeasy mini kit, Qiagen, France) and simultaneously treated with DNase (RNase-free DNase set, Qiagen, France) according to the manufacture procedure. RNA concentrations were measured by absorption at 260 nm. The integrity of RNA was electrophoretically evaluated on a 1% agarose gel and using an agilent 2100 bio analyzer (Agilent technology, USA). Only RNA samples with a 28S/18S ratio > 1.3 were considered as good enough quality and used for hybridization experiments.

value: magnum

label: Alexa Fluor 647

value: uterus


title: bsu_valTreated_5min_rep1_Val.1_1

description:
bsu_valTreated_5min_rep1_Val.1_1
Two biological replicates were perfomed for Val-5min treatment. This is replicate 1.

source_name: B.subtilis, 5 min after being treated by Valine (rep 1).


title: Lame 39

source_name: Poule 46 IsaBrown stade 16h46

source_name: Poule IsaBrown 46 stade 16h46


title: EPC2-hTERT_Hypoxia_Exp2_rep2

city: Philadelphia

first: Hiroshi

last: Nakagawa

state: PA

address: 415 Curie Blvd.

department: Gastroenterology Division

institute: University of Pennsylvania

hyb_protocol: Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions

scan_protocol: Scanning of Affymetrix chips were performed according manufacturer's instructions

data_processing: .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the hypoxia-exposed cell experiments

source_name: esophageal epithelial cells (keratinocytes)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: EPC2-hTERT cells were grown under normoxic conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.

extract_protocol: RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: EPC2-hTERT cells were exposed to either 21% O2 (normoxia) or 0.2% O2 (severe hypoxia) for 24 hrs. in experiment 1 (Exp 1) and either  21% O2 (normoxia) or 1% O2 (moderate hypoxia) for 24 hrs. in experiment 2 (Exp 2).

tag: cells

value: epithelial cells (keratinocytes)

tag: genotype

value: hTERT-immortalized, non-transformed


title: EPC2-hTERT_Normoxia_Exp2_rep2


title: Lame 26

source_name: Poule IsaBrown 49 stade 18:02

source_name: Poule IsaBrown 49 stade 18h02


title: Lame 5

source_name: Poule Isabrown 56 stade 17h50

source_name: Poule IsaBrown 56 stade 17h50


title: 10101_normal control_rep4

source_name: normal low-density bone marrow cells

value: M


title: Lame 16

source_name: Poule IsaBrown 38 stade 17h57


title: EPC2-hTERT_Hypoxia_Exp2_rep1


title: Lame 8

source_name: Poule IsaBrown 27 stade 16h43


title: Lame 24

source_name: Poule IsaBrown 19 stade 17h59

source_name: Poule ISA BRown 19 stade 17h59


title: Lame 14

source_name: Poule IsaBrown 54 stade 17h43


title: EPC2-hTERT_ Normoxia_ Exp1_rep1


title: EPC2-hTERT_Normoxia_Exp1_rep2


title: EPC2-hTERT_Hypoxia_Exp1_rep2


title: bsu_valTreated_2h_Val.1_3

source_name: B.subtilis, 2 h after being treated by Valine.

source_name: B.subtilis, not treated with any amino acid.


title: bsu_gluTreated_5min_1_1

source_name: B.subtilis, 5 min after being treated by Glutamate.


title: EPC2-hTERT_Hypoxia_Exp1_rep1


title: Cplx_Boar2_E0_lot186_04

city: NOUZILLY

first: JEAN-LUC

last: GATTI

address: Unité Mixte de Recherche :  INRA - CNRS (UMR 6175) -  Université François Rabelais de Tours - Haras nationaux

department: PHASE

hyb_protocol: After stripping (3 hours 68°c, 0.1X SSC, 0.2% SDS), hybridizations were carried out as previously described [Bertucci F et al, Hum Mol Genet 1999], with minor modifications. Arrays were prehybridized for 4 hours at 65°C in hybridization solution (5X Denhardt's, 5X SSC, 0.5% SDS). Arrays were then incubated with the corresponding denatured labeled cDNA for 18 h at 65°C in hybridization solution. After 3 washes (1 hours 68°C, 0.1X SSC, 0.2% SDS), they were exposed to phosphor-imaging plates (24 or 48 hours) before scanning using a FUJI BAS 5000 (Fujifilm France, St. Quentin en Yvelines, France).

scan_protocol: Arrays were scanned using a FUJI BAS 5000 (Fujifilm France, St. Quentin en Yvelines, France).

data_processing: Each array image was inspected using AGScan software [Cathelin R et al, Bioinformatics 2007, Lopez F et al, BMC Genomics 2004] to eliminate (flag) "bad" spots and artifacts (dust, etc.) from the analysis. Signal intensities were then automatically quantified. Spots for which the vector oligonucleotide data had intensities lower than a cut-off value established as a mean level intensity of water control spots plus 3 times the standard error deviation were excluded from analysis. This cut-off value was calculated for each microarray independently. Then data corresponding of all hybridizations (vector and labeled cDNA) were log2-transformed, normalized by the median of intensities by block then by array. Finally, signal processing was performed using vector oligonucleotide data to correct the relative amount of cDNA present in each spot.

organism: Sus scrofa

source_name: Male Reproductive Tract

label_protocol: Labelled cDNA probes were prepared from 5microg of RNA by simultaneous reverse transcription and labeling for 2 hours at 42°C in the presence of 30microCi alpha 33P-dCTP, 2.4microM dCTP, 0.4mM each dATP, dTTP, dGTP, 40 units RNasin® Ribonuclease Inhibitor (Promega, Charbonnières-les-Bains, France) and 200 units MMLV SuperScript RNase H-reverse transcriptase (Gibco-BRL, Cergy Pontoise, France) in 30microL final volume.

extract_protocol: Frozen tissue (150 to 200 mg) was homogenized in 2 ml of Tri-Reagent (Sigma, St Quentin Fallavier, France) using an Ultra-Turrax. The RNA extraction was performed according to the manufacturer's instructions with small modifications. A second extraction was performed on the aqueous phase to optimize the RNA quality. For all samples, RNA quantity and quality were measured by absorbance ratio at 260/280 nm (NanoDrop, Thermo Fisher Scientific, Villebon-sur-Yvette, France) and the integrity of the RNAs was determined by both standard agarose gels and RNA-chip gel system using an Agilent Bioanalyzer (Agilent Technologies, Massy, France). Only samples passing these tests were kept and for sample that failed, extraction was redone on a different piece of sample in order to meet these criteria of quality.

tag: microarray type

value: Probe

tag: male reproductive tract

value: Epididymal zone 0

value: Large White


title: Cplx_Boar1_VE_lot186_35

value: Efferent ducts


title: Cplx_Boar1_E0_lot186_31


title: Cplx_Boar1_E6_lot186_30

value: Epididymal zone 6


title: Cplx_Boar2_Testis_lot186_15

value: Testicle


title: EPC2-hTERT_Normoxia_Exp2_rep1


title: Cplx_Boar2_VD_lot186_62

value: Deferent duct


title: Cplx_Boar1_Testis_lot186_38


title: Cplx_Boar1_E1_lot186_47

value: Epididymal zone 1


title: Cplx_Boar2_E4_lot186_58

value: Epididymal zone 4


title: Cplx_Boar3_E0_lot186_21

value: Large White_Landrace (3/4_1/4)


title: Cplx_Boar1_E8/9_lot186_18

value: Epididymal zone 8/9


title: Cplx_Boar1_E4_lot186_33


title: Cplx_Boar2_E3_lot186_23

value: Epididymal zone 3


title: Cplx_Boar2_E8/9_lot186_26


title: Cplx_Boar2_E7_lot186_57

value: Epididymal zone 7


title: Cplx_Boar3_E1_lot186_39


title: Cplx_Boar1_E7_lot186_28


title: Cplx_Boar2_E2_lot186_52

value: Epididymal zone 2


title: Cplx_Boar3_E2_lot186_54


title: Cplx_Boar2_E1_lot186_07


title: Cplx_Boar1_E2_lot186_44


title: Cplx_Boar2_E6_lot186_37


title: Cplx_Boar1_VD_lot186_60


title: Cplx_Boar1_E3_lot186_17


title: Cplx_Boar2_VE_lot186_42


title: Cplx_Boar1_E5_lot186_41

value: Epididymal zone 5


title: Cplx_Boar3_E6_lot186_10


title: Cplx_Boar3_E5_lot186_19


title: Cplx_Boar3_E4_lot186_45


title: Cplx_Boar3_VD_lot186_05


title: Cplx_Boar3_E8/9_lot186_09


title: Cplx_Boar3_Testis_lot186_16


title: Cplx_Boar3_E3_lot186_24


title: Cplx_Boar4_E2_lot186_27


title: Yeast W303 SSD1-V cell cycle_110 min

city: Seattle

first: lihong

last: li

state: WA

address: 1100 Fairview Ave N.

department: Basic Science

institute: Fred Hutchinson Cancer Research Center

description: Transcript profiling of yeast W303 SSD1-V cell cycle.

hyb_protocol: Cy5-labeled cDNA from each timepoint was mixed with Cy3-labeled control cDNA, and hybridized to yeast cDNA microarrays

scan_protocol: Arrays were scanned using an Axon Instruments GenePix4000B scanner, and image analysis was performed using GenePix Pro microarray acquisition and analysis software.

data_processing: LOWESS normalized using agilent software (Genespring 7).

organism: Saccharomyces cerevisiae

source_name: Yeast W303 SSD1-V, cell cycle, time point 110 min

label_protocol: Thirty micrograms of total RNA was used for cDNA synthesis. The cDNA was coupled to Cy5 using an amino-allyl dye-coupling procedure (http://cmgm.stanford.edu/pbrown/protocols/aadUTPCouplingProcedure.htm). RNA from an asynchronous population of W303a cells was used as a control, and its cDNA was labeled with Cy3 dye.

growth_protocol: Cells were grown in YEPD medium to early log phase before arrest by alpha factor. For the yeast asynchronous population control, cells were grown overnight to an OD of 0.6 in YEPD before harvest.

extract_protocol: RNA extractions initiated by spinning down and wash cell pellet with 1 ml cold RNA buffer. Freeze cell pellet in dry ice, then thaw cells, resuspend in 100-120 µl ice cold RNA-buffer. Add 1/2 volume of acid washed glass beads, vortex at highest level 3 min in cold room. Add 450 µl RNA-buffer-SDS (RT), vortex briefly, add 450 µl equilibrated Phenol, vortex at highest level 3 min in cold room. Spin full speed 10 min, transfer upper phase to fresh tube, add 300 µl equilibrated Phenol, vortex, add 300 µl Chloroform, vortex, spin 2 min, extract upper phase once again with Chloroform. Add 20 µl 4 M NaCl, 1 ml Ethanol, precipitate 30 min at -20 to -80 °C. Spin full speed 10 min, wash pellet with 150 µl 70 % Ethanol, air dry pellet, resuspend in 30-50 µl H2O.

treatment_protocol: Cells were arrested with alpha factor, and released into YEPD to get a synchronized population. Cells were sampled every 10 min after release.

tag: strain

tag: background

tag: time point

value: 110 min

source_name: Yeast asynchronous culture

treatment_protocol: None.


title: Cplx_Boar2_E5_lot186_20


title: Cplx_Boar4_E5_lot186_40


title: Cplx_Boar4_E3_lot186_06


title: Cplx_Boar4_E8/9_lot186_43


title: Cplx_Boar4_E7_lot186_13


title: Yeast W303 SSD1-V cell cycle_120 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 120 min

value: 120 min


title: Cplx_Boar4_E1_lot186_08

value: Probe


title: Cplx_Boar4_E4_lot186_66


title: Yeast W303 SSD1-V cell cycle_90 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 90 min

value: 90 min


title: Cplx_Boar4_E6_lot186_03


title: Cplx_Boar4_VD_lot186_55


title: Yeast W303 SSD1-V cell cycle_80 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 80 min

value: 80 min


title: Vector_lot186_05

hyb_protocol: Microarrays were hybridized with a 33P-labeled 19-mer oligonucleotide over-night at 42°C in 1 ml of hybridization solution (5X SSC, 5X Denhardt's, 05%SDS). After washes, arrays were exposed over-night to radioisotopic-sensitive imaging plates.

source_name: 19 mer-oligonucleotide (CACTATAGGGAATTTGGCC which matches a sequence present at the extremity of each PCR product)

label_protocol: A first hybridization was performed using a 33P-labelled 19-mer oligonucleotide (CACTATAGGGAATTTGGCC), which matches a sequence present at the extremity of each PCR product to estimate the amount of cDNA dropped on each spot. Only membranes with a good pattern of spotting were retained and were attributed at random for the hybridization with the 33P-cDNA from the tissues.

value: Vector


title: Vector_lot186_06


title: Cplx_Boar4_Testis_lot186_14


title: Yeast W303 SSD1-V cell cycle_100 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 100 min

value: 100 min


title: Vector_lot186_04


title: Vector_lot186_10


title: Vector_lot186_13


title: Vector_lot186_09


title: Cplx_Boar4_VE_lot186_61

value: Efferent ducts


title: Vector_lot186_07


title: Vector_lot186_08


title: Vector_lot186_03


title: Yeast W303 SSD1-V cell cycle_60 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 60 min

value: 60 min


title: Vector_lot186_17


title: Yeast W303 SSD1-V cell cycle_30 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 30 min

value: 30 min


title: Cplx_Boar4_E0_lot186_34

value: Epididymal zone 0


title: Vector_lot186_15


title: Yeast W303 SSD1-V cell cycle_50 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 50 min

value: 50 min


title: Vector_lot186_16


title: Yeast W303 SSD1-V cell cycle_40 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 40 min

value: 40 min


title: Vector_lot186_14


title: Yeast W303 SSD1-V cell cycle_70 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 70 min

value: 70 min


title: Cplx_Boar3_E7_lot186_48

value: Epididymal zone 7

value: Large White_Landrace (3/4_1/4)


title: Yeast W303 SSD1-V cell cycle_10 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 10 min

value: 10 min


title: Vector_lot186_34


title: Vector_lot186_41


title: Vector_lot186_35


title: Vector_lot186_39


title: Vector_lot186_30


title: Vector_lot186_28


title: Vector_lot186_27


title: Vector_lot186_45


title: Vector_lot186_24


title: Vector_lot186_21


title: Vector_lot186_19


title: Vector_lot186_20


title: Vector_lot186_33


title: Vector_lot186_37


title: Vector_lot186_44


title: Vector_lot186_38


title: Vector_lot186_18


title: Vector_lot186_40


title: Vector_lot186_26


title: Vector_lot186_23


title: Vector_lot186_31


title: Yeast W303 SSD1-V cell cycle_0 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 0 min

value: 0 min


title: Vector_lot186_42


title: Vector_lot186_47


title: Vector_lot186_43


title: Vector_lot186_48


title: Vector_lot186_55


title: Vector_lot186_61


title: Vector_lot186_60


title: Yeast W303 SSD1-V cell cycle_20 min

source_name: Yeast W303 SSD1-V, cell cycle, time point 20 min

value: 20 min


title: Vector_lot186_54


title: Vector_lot186_58


title: Vector_lot186_52


title: Vector_lot186_57


title: Vector_lot186_66


title: Vector_lot186_62


title: Vector_lot186_63


title: 19544274

status: Public on Aug 31 2009

type: genomic

city: Helsinki

first: Anna-Kaarina

last: Jarvinen

address: Biomedicum Helsinki 2U, Tukholmankatu 8

country: Finland

institute: Mobidiag

description:
PCR negative control (water)
* Negative by manual analysis, gridding problem

hyb_protocol: All incubation steps except that of the last precipitation reaction were performed under continuous agitation of 550 rpm at 25°C. Briefly, a first a prewash with 500 µl of water from 30 to 55°C for 5 to 10 minutes was done. Hybridization at 55°C for 10 minutes, of 1 ul of the biotinylated target and 99 ul hybridization buffer (250 mM Na2HPO4, 4.5% SDS, 1mM EDTA, 1xSSC) took place on a microarray. When hybridization control oligonucleotides were included, they were added to the hybridization buffer. After hybridization, the microarray was washed in 500 µl of 0.2xSCC at 20°C for 5 minutes. Incubation with 100 µl of blocking buffer (2% milk powder, 6xSSPE, 0.005% Triton-X100) was performed for 5 minutes at 30°C. Then 100 µl of 1:5000 dilution of streptavidin-conjugated horseradish peroxidase in PBS was applied for 10 minutes at 30°C followed by a similar washing step as described above. Finally, 100 µl of 3, 3′, 5, 5′-tetramethylbenzidine (TMB) analog (Seramun Grün; Seramun Diagnostica, Germany) was added for the precipitation reaction at 25°C for 10 minutes.

scan_protocol: Microarray images were generated by ATR-01 Reader (Clondiag).

data_processing:
The array images were analyzed with the Prove-it™ Advisor software (Mobidiag, Finland, www.mobidiag.com). The software performed image analyses and result reporting, including the identification of the bacterial targets and the evaluation of the control probes. This took place automatically without user involvement in adjusting any of the parameters. The target identifications were made by software using multiple parameters such as signals from the probe oligonucleotides on the array. These were interpreted using built-in rules and parameters specific for each assay type. All the probes for a specific bacterial target were required to be positive for that target to be classified as positively identified, except for the CNS probes of which only 2 of 4 specific oligonucleotides were required to be positive. If both CNS and S. epidermidis probes in the analyses were positive, only S. epidermidis was reported due to its identification by species-specific probes. The original array layout contained spots, which were not included in the final probe panel.
The software reports signal intensities as  percentages between 0-100%. The scanner gives 8-bit images. Median signal intensity reported in the data table (these are the raw data). The processed data are composed of ORGANISM NAME or NEGATIVE answers depending if the pathogen is detected in the sample or not.  The processed data  are linked as a supplementary file on the Series GSE17221 record.

molecule: genomic DNA

organism: unidentified

source_name: water

label_protocol: The PCR reaction mixture contained 1 uM of gBF primer mixture (Metabion, Germany), 1 uM of biotin-labeled gBR primer mixture (Metabion, Germany), 0.165 µM of SaurF primer (Metabion, Germany), 0.165 µM of biotin-labeled SaurR primer (Metabion, Germany), 0.25 µM of mecAF primer (Metabion, Germany), 0.25 µM biotin-labeled mecAR primer (Metabion, Germany), 1x Hot Start Taq® PCR buffer (Qiagen, Germany), in which the final concentration MgCl2was 2.0 mM, 300 uM of each of dNTP (Finnzymes, Finland), 1.5 g/l BSA (EuroClone, Italy), 0.125 U/ul Hot Start Taq® DNA polymerase (Qiagen, Germany), 1.5 ul of isolated DNA, and water to bring the total volume to 15 ul. In the blood culture dataset, 1.5 ul of PCR control template was added in the reaction and the equivalent amount of water was reduced. A negative control, i.e., sterile water was included in each test series. All the reverse primers were biotinylated at their respective 5′-end. The PCR was performed using a Mastercycler® epgradient S thermal cycler (Eppendorf, Germany). The following PCR program was used: a denaturation step at 95°C for 15 minutes, 36 cycles of 10 seconds at 96°C, 35 seconds at 52°C, 10 seconds at 72°C, 5 cycles of 5 seconds at 96°C, 30 seconds at 65°C, 5 cycles of 5 seconds at 96°C and finally 30 seconds at 68°C. After the PCR, the success of the amplification of double-stranded DNA and single-stranded DNA was ascertained by gel electrophoresis using a 2% agarose gel containing SYBR® Green II (Invitrogen, USA) or using Agilent BioAnalyzer (Agilent Technologies, USA).

growth_protocol: Blood samples were drawn into aerobic and anaerobic blood culture bottles (BacT/Alert®, bioMérieux, France) and were incubated in the blood culturing equipment BacT/ALERT 3 D (bioMérieux) for up to 5 or 6 days, at which time they were reported as negative when no sign of micro-organism growth was detected. If during the cultivation period possible growth was observed by the blood culturing instrument, it was identified and reported according to CLSI guidelines.

extract_protocol: The DNA was extracted using an automated nucleic acid extraction instrument Nuclisens® easyMAG™ (bioMérieux, France) according to the manufacturer’s protocol (Generic 1.0.6).  The elution volume was 55 µl.

tag: organism detected in blood culture

tag: organism detected using array

value: Negative


title: 19544273

description: no additional information

source_name: Blood culture


title: 19544259

description: no additional information

value: coagulase-negative staphylococci (CNS)


title: 19544262

description: no additional information


title: 19544265

description: no additional information


title: 19544275

description: no additional information


title: 19544264

description: no additional information


title: 19544271

description: no additional information


title: 19544261

description: no additional information


title: 19544263

description: no additional information


title: FRIK2000 Cy5 rep2 vs EDL933 pool Cy3

city: Lubbock

first: Scot

last: Dowd

state: TX

address: 4321 Marsha Sharp Fwy

department: MBRI

institute: MBRI

hyb_protocol: Labeled cDNA was hybridized to the Agilent microarrays using the Gene Expression Hybridization kit (Agilent Technologies Inc.) following manufacturer’s protocols. Arrays were washed with Gene Expression Wash Buffer kit (Agilent Technologies Inc.)

scan_protocol: Microarray images were captured using a Genepix 4000B (Molecular Devices Corporation, Union City, CA) laser scanner and images processed using Genepix 6.0 software (Molecular Devices Corporation).

data_processing: Microarray data analyses were performed using Acuity 4.0 software. Slides were normalized using standard ratio-based methods. Data were analyzed based upon Log ratio (635/532) values. Genes were included in the final dataset that exhibit significance based upon a very conservative FDR less than 2.5% [27] and at least 2.0-fold comparative regulation.

organism: Escherichia coli

source_name: RNA from late log phase E coli FRIK2000 rep 2

label_protocol: label star kit with random nonamers

extract_protocol: late log phase grown e coli 966 into RNAprotect solution, RNA extracted with qiagen RNA bacteria kits

tag: isolate

value: bovine isolate of e coli o157:H7 FRIK2000 lineage II

source_name: RNA from late log phase E coli EDL933 pooled reference

extract_protocol: late log phase grown e coli EDL933 into RNAprotect solution, RNA extracted with qiagen RNA bacteria kits

value: clinical isolate e coli o157:H7 lineage I


title: FRIK2000 Cy3 rep1 vs EDL933 pool Cy5

source_name: RNA from late log phase E coli FRIK2000 rep 1


title: 19544257

description: no additional information


title: FRIK966 Cy3 rep3 vs EDL933 pool Cy5

source_name: RNA from late log phase E coli FRIK966 rep 3

value: bovine isolate of e coli o157:H7 FRIK966 lineage II


title: FRIK966 Cy5 rep4 vs EDL933 pool Cy3

source_name: RNA from late log phase E coli FRIK966 rep 4


title: FRIK966 Cy3 rep1 vs EDL933 pool Cy5

source_name: RNA from late log phase E coli FRIK966 rep 1


title: Ago2 knockout mouse mature oocyte#2

city: Cambridge

first: Fuchou

last: Tang

state: Cambridgeshire

address: Tennis Court Road

department: Wellcome Trust/Cancer Research UK Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
The Ago2 floxed mice were mated with Zp3-Cre transgenic mice to obtain [Ago2F/F, Zp3-Cre] conditional knockout females
Gene expression data from single cell (AGo2 knockout mouse oocyte) using Applied Biosystems AB1700 Whole Genome Microarray

hyb_protocol: Hybridization was performed according to Applied Biosystems Chemiluminescence Detection Kit Protocol (PN 4339627) using 10 ug fragmented cRNA

scan_protocol: Image was captured using CCD camera came with AB1700 Microarray Analyzer

data_processing: Quantile normalization was performed separately for knockout and wild-type samples. The normalization was performed using ABarray bioconductor package

label: digoxigenin

organism: Mus musculus

source_name: Ago2 knockout mouse mature oocyte

label_protocol: Digoxigenin labeled cRNA was prepared according to Applied Biosystems nanoamp RT-IVT protocol

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

value: Ago2 knockout

value: mature oocyte

tag: replicate


title: FRIK2000 Cy3 rep3 vs EDL933 pool Cy5

source_name: RNA from late log phase E coli FRIK2000 rep 3


title: FRIK2000 Cy5 rep4 vs EDL933 pool Cy3

source_name: RNA from late log phase E coli FRIK2000 rep 4


title: FRIK966 Cy5 rep2 vs EDL933 pool Cy3

source_name: RNA from late log phase E coli FRIK966 rep 2


title: 19544272

description: no additional information


title: 19544533

description: no additional information

value: Escherichia coli


title: 19544534

description: no additional information

value: Salmonella enteritidis


title: 19544535

description: no additional information


title: 19544529

description: no additional information


title: 19544537

description: no additional information


title: 19544536

description: no additional information


title: 19544280

description: no additional information


title: 19544276

description: no additional information

value: Klebsiella pneumoniae


title: 19544278

description: no additional information

value: Diphtheroid


title: 19544310

description: no additional information

value: Staphylococcus epidermidis

value: Staphylococcus epidermidis+mecA


title: 19544319

description: no additional information

value: Streptococcus pyogenes (A)

value: Streptococcus pyogenes


title: 19544318

description: no additional information

value: Streptococcus pneumoniae


title: 19544312

description: no additional information

value: Escherichia coli, Streptococcus viridans


title: 19544317

description: no additional information


title: 19544316

description: no additional information

value: Negative


title: 19544315

description: no additional information

value: Bacteroides fragilis group


title: 19544277

description: no additional information

value: coagulase-negative staphylococci (CNS)

value: mecA


title: 19544306

description: no additional information


title: 19544279

description: no additional information


title: 19544307

description: no additional information

value: Pseudomonas aeruginosa


title: 19544314

description: no additional information


title: 19544301

description: no additional information


title: 19544304

description: no additional information


title: 19544303

description: no additional information


title: 19544282

description: no additional information

value: Streptococcus viridans


title: 19544283

description: no additional information


title: 19544284

description: no additional information


title: 19544509

description: no additional information

value: Staphylococcus aureus


title: 19544511

description: no additional information


title: 19544514

description: no additional information


title: 19544516

description: no additional information

value: Escherichia coli


title: 19544505

description: no additional information


title: 19544525

description: no additional information


title: 19544524

description: no additional information


title: 19544515

description: no additional information


title: 19544502

description: no additional information


title: 19544504

description: no additional information


title: 19544528

description: no additional information


title: 19544512

description: no additional information

value: Streptococcus agalactiae (B)

value: Streptococcus agalactiae


title: 19544508

description: no additional information


title: 19544526

description: no additional information


title: 19544519

description: no additional information


title: 19544507

description: no additional information

value: Propionibacter sp


title: 19544517

description: PCR negative control (water)


title: 19544522

description: no additional information


title: 19544521

description: no additional information


title: 19544523

description: no additional information


title: 19544281

description: PCR negative control (water)


title: 19544527

description: no additional information


title: 19544424

description: PCR negative control (water)


title: 19544503

description: no additional information


title: 19544510

description: no additional information


title: 19544425

description: no additional information


title: 19544428

description: no additional information


title: 19544437

description: no additional information

value: Enterococcus faecium


title: 19544436

description: no additional information


title: 19544432

description: no additional information


title: 19544430

description: no additional information


title: 19544431

description: no additional information


title: 19544435

description: no additional information


title: 19544433

description: no additional information

value: Bacillus sp


title: 19544429

description: no additional information


title: 19544434

description: no additional information


title: 19544442

description: no additional information

value: Enterococcus sp


title: 19544439

description: no additional information

value: Enterococcus faecalis


title: 19544404

description: no additional information


title: 19544440

description: no additional information


title: 19544406

description: no additional information


title: 19544407

description: no additional information

value: Staphylococcus epidermidis

value: Staphylococcus epidermidis+mecA


title: 19544408

description: PCR negative control (water)

value: Negative


title: 19544400

description: no additional information


title: 19544441

description: no additional information


title: 19544403

description: no additional information


title: 19544401

description: no additional information


title: 19544410

description: no additional information


title: 19544438

description: no additional information


title: HEK2

first: Christian

last: Metallo

state: MA

address: 77 Mass. Ave.

department: Chemical Engineering

institute: Massachusetts Institute of Technology

description: hEKs obtained from H9 differentiation experiment 2 and maintained in DSFM

hyb_protocol: Hybridization was performed by the Gene Expression Center at UW-Madison, following the standard operating protoco of NimbleGen. See www.nimblegen.com.

scan_protocol: Scanning was performed by the Gene Expression Center at UW-Madison, following the standard operating protoco of NimbleGen. See www.nimblegen.com.

data_processing: RMA-normalization was performed on the entire set of samples

source_name: Differentiated H9 hES cells

label_protocol: Labeling was performed by the Gene Expression Center at UW-Madison, following the standard operating protoco of NimbleGen. See www.nimblegen.com.

growth_protocol: Differentiated hES cells and PFKs were cultured in Defined Serum-free Keratinocyte Medium (DSFM; Invitrogen)

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at Gene Expression Center at the University of Wisconsin-Madison.

treatment_protocol: Differentiated cells were treated with 1uM retinoic acid for 7 days in hES cell medium (no bFGF) before subculture and maintenance in DSFM.  See Metallo et al. Stem Cells 2008 for details.

value: differentiated H9 hES cells

tag: induction agent

value: Retinoic acid

tag: culture medium

value: DSFM (Invitrogen)


title: HEK3

description: hEKs obtained from H9 differentiation experiment 3 and maintained in DSFM

tag: cell type


title: 19544416

description: no additional information

value: Klebsiella pneumoniae, Streptococcus sanguis

value: Klebsiella pneumoniae


title: 19544392

description: no additional information


title: 19544391

description: no additional information


title: 19544413

description: no additional information

value: Streptococcus pneumoniae


title: 19544394

description: no additional information

value: coagulase-negative staphylococci (CNS)


title: 19544393

description: no additional information

value: Fusobacterium nucleatum, Micromonas micros


title: 19544411

description: no additional information

value: Streptococcus viridans


title: 19544255

description: no additional information


title: 19544419

description: no additional information

value: Fusobacterium necrophorum


title: 19544248

description: no additional information


title: 19544418

description: no additional information

value: Enterobacter cloacae


title: 19544420

description: no additional information


title: 19544417

description: no additional information


title: 19544396

description: no additional information

value: Enterococcus faecium


title: 19544398

description: no additional information


title: PFK3

description: PFKs obtained from Invitrogen and maintained in DSFM

source_name: Primary foreskin keratinocytes

value: primary foreskin keratinocytes


title: 19544395

description: no additional information

value: Staphylococcus haemolyticus


title: 19544390

description: no additional information


title: 19544414

description: no additional information


title: 19544246

description: PCR negative control (water)


title: 19544397

description: no additional information


title: PFK1


title: PFK2


title: HEK1

description: hEKs obtained from H9 differentiation experiment 1 and maintained in DSFM


title: 19544247

description: no additional information


title: 19544240

description: no additional information

value: Enterococcus faecalis


title: 19544245

description: no additional information

value: Staphylococcus epidermidis

value: Staphylococcus epidermidis+mecA


title: 19544234

description: no additional information

value: Negative


title: 19544243

description: no additional information

value: Micrococcus sp


title: 19544235

description: no additional information


title: 19544233

description: no additional information


title: 19544232

description: no additional information


title: 19544239

description: no additional information


title: 19544228

description: no additional information


title: 19544229

description: no additional information


title: 19544224

description: no additional information

value: Escherichia coli


title: 19544250

description: no additional information


title: 19544238

description: no additional information

value: Staphylococcus aureus


title: 19544221

description: no additional information

value: Enterococcus casseliflavus


title: 19544241

description: no additional information


title: 19544230

description: no additional information


title: 19544242

description: no additional information


title: 19544225

description: no additional information


title: 19544227


title: 19544207

description: no additional information


title: 19544206

description: no additional information


title: 19544222

description: no additional information


title: 19544244

description: no additional information


title: 19544231

description: no additional information

value: Propionibacter sp


title: 19544236

description: no additional information


title: 19544209

description: no additional information

value: Streptococcus pneumoniae


title: 19544210

description: no additional information


title: 19544214

description: no additional information


title: 19544215

description: no additional information


title: 19544213

description: no additional information


title: 19544446

description: no additional information

value: Streptococcus agalactiae (B)

value: Streptococcus agalactiae


title: 19544212

description: no additional information


title: 19544444

description: no additional information

value: Salmonella paratyphi A


title: 19544445

description: no additional information


title: 19544211

description: no additional information

value: Fusobacterium necrophorum


title: 19544447

description: no additional information

value: Streptococcus pyogenes (A)


title: 48h 31.5C rep3

city: Thuwal

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description:
pooled reference of coral larvae raised at three temperatures (27.5C, 29C, 31.5C) of12, 24, 36, 48 hours after fertilization
coral larvae raised at 31.5C for 48 hours after fertilization
coral larvae raised for 12 hours at 27.5C hybridized against pooled reference

hyb_protocol: Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25mM HEPES, and 3x SSC. The hybridization mixtures were boiled for 2min at 99°C then allowed to cool at room temperature for 5 minutes. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63°C. Microarrays were washed twice in 0.6x SSC and 0.01% SDS followed by a rinse in 0.06x SSC and dried via centrifugation.

scan_protocol: Slides were immediately scanned using an Axon 4000B scanner.

data_processing: Spot intensities were extracted, background subtracted, and block-wise lowess normalized using TIGR Spotfinder 2.2.4 (Saeed et al., 2003). Duplicated spots were averaged over the median of intensities.

organism: Orbicella faveolata

source_name: common reference

label_protocol: 1 µg of total RNA was amplified using the MessageAmp II aRNA kit (Ambion). For cDNA synthesis, 3 µg of aRNA per sample were primed with 3.5 nmol random pentadecamer for 10min at 70°C. Reverse transcription (RT) lasted for 2 hours at 42°C using a master mix containing a 3:2 ratio of aminoallyl-dUTP to TTP. Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10 uL 0.5M EDTA and 10 uL 1M NaOH for 15min at 65°C. After hydrolysis, RT reactions were cleaned using the MinElute Cleanup kit (Qiagen). Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 17uL DMSO, and the coupling reactions lasted for 2hr at room temperature in the dark. Dye-coupled cDNAs were cleaned using the MinElute Cleanup kit (Qiagen).

extract_protocol: Total RNA of coral larvae was isolated using Qiazol (Qiagen) according to manufacturer’s instructions. Larvae were homogenized for 2 minutes using a Mini-Beadbeater (Biospec) with 0.1 mm and 0.55 mm silica beads to disrupt cellular structures. RNA pellets were cleaned further with RNeasy Mini columns (Qiagen).

tag: sample

value: pooled reference

tag: developmental stage

value: coral larvae

tag: growth protocol

value: raised at 31.5C

tag: age

value: 48 hours after fertilization


title: 48h 31.5C rep1


title: 48h 31.5C rep2


title: 19544449

description: no additional information


title: 48h 29C rep1

description:
pooled reference of coral larvae raised at three temperatures (27.5C, 29C, 31.5C) of12, 24, 36, 48 hours after fertilization
coral larvae raised at 29C for 48 hours after fertilization
coral larvae raised for 12 hours at 27.5C hybridized against pooled reference

value: raised at 29C


title: 19544450

description: no additional information

value: Streptococcus pneumoniae +mecA


title: 48h 29C rep3


title: 19544452

description: no additional information

value: Staphylococcus epidermidis

value: Staphylococcus epidermidis+mecA


title: 48h 27.5C rep2

description:
pooled reference of coral larvae raised at three temperatures (27.5C, 29C, 31.5C) of12, 24, 36, 48 hours after fertilization
coral larvae raised at 27.5C for 48 hours after fertilization
coral larvae raised for 12 hours at 27.5C hybridized against pooled reference

value: raised at 27.5C


title: 19544451

description: no additional information

value: Staphylococcus aureus


title: 48h 27.5C rep1


title: 48h 29C rep2


title: 19544448

description: no additional information


title: 12h 31.5C rep3

description:
pooled reference of coral larvae raised at three temperatures (27.5C, 29C, 31.5C) of12, 24, 36, 48 hours after fertilization
coral larvae raised at 31.5C for 12 hours after fertilization
coral larvae raised for 12 hours at 27.5C hybridized against pooled reference

value: 12 hours after fertilization


title: 48h 27.5C rep3


title: 19544172

description: PCR negative control (water)

value: Negative


title: 12h 31.5C rep2


title: 19544170

description: no additional information


title: 12h 31.5C rep1


title: 19544173

description: no additional information


title: 12h 29C rep3

description:
pooled reference of coral larvae raised at three temperatures (27.5C, 29C, 31.5C) of12, 24, 36, 48 hours after fertilization
coral larvae raised at 29C for 12 hours after fertilization
coral larvae raised for 12 hours at 27.5C hybridized against pooled reference


title: 19544155

description: no additional information


title: 12h 29C rep2


title: 19544187

description: no additional information


title: 19544189

description: no additional information

value: Escherichia coli


title: 19544186

description: no additional information


title: 12h 29C rep1


title: 12h 27.5C rep1

description:
pooled reference of coral larvae raised at three temperatures (27.5C, 29C, 31.5C) of 12, 24, 36, 48 hours after fertilization
coral larvae raised at 27.5C for 12 hours after fertilization
coral larvae raised for 12 hours at 27.5C hybridized against pooled reference


title: 12h 27.5C rep2

description:
pooled reference of coral larvae raised at three temperatures (27.5C, 29C, 31.5C) of12, 24, 36, 48 hours after fertilization
coral larvae raised at 27.5C for 12 hours after fertilization
coral larvae raised for 12 hours at 27.5C hybridized against pooled reference


title: 19544190

description: no additional information

value: Enterococcus faecalis


title: 19544156

description: no additional information

value: Streptococcus viridans


title: 12h 27.5C rep3


title: 19544158

description: no additional information


title: 19544193

description: no additional information


title: 19544191

description: no additional information

value: Klebsiella oxytoca


title: 19544154

description: no additional information


title: 19544188

description: no additional information


title: 19544192

description: no additional information


title: Cplx_Boar3_VE_lot186_63

source_name: Male Reproductive Tract

value: Probe

value: Efferent ducts

tag: genotype

value: Large White_Landrace (3/4_1/4)


title: 19544161

description: no additional information


title: 19544159

description: no additional information

value: Candida albicans


title: 19544194

description: no additional information


title: 19544157

description: no additional information


title: 19544162

description: no additional information


title: 19544163

description: no additional information

value: Bacillus sp


title: 19544160

description: no additional information


title: 19544175

description: PCR negative control (water)


title: 19544178

description: no additional information


title: 19544184

description: no additional information


title: 19544179

description: no additional information


title: 19544077

description: no additional information


title: 19544177

description: no additional information


title: 19544081

description: no additional information


title: 19544083

description: no additional information

value: Enterococcus faecalis+mecA


title: 19544176

description: no additional information


title: 19544180

description: no additional information

value: Enterococcus faecium


title: 19544101

description: no additional information

value: Streptococcus pyogenes (A)

value: Streptococcus pyogenes


title: 19544102

description: no additional information

value: Stenotrophomonas maltophilia


title: 19544100

description: no additional information

value: Pseudomonas-like gram- rod


title: 19544084

description: no additional information


title: 19544082

description: no additional information

value: Streptococcus betahemolytic group C


title: 19544080

description: no additional information


title: 19544079

description: no additional information

value: Staphylococcus epidermidis


title: 19544099

description: no additional information


title: 19544098

description: no additional information


title: 19544075

description: no additional information


title: 19544076

description: no additional information

value: Staphylococcus epidermidis+mecA


title: 19544183

description: no additional information

value: Negative


title: Aid-GFP positive LPS+IL4-stimulated splenic B cells (2)

status: Public on Aug 15 2009

city: Los Angeles

first: Markus

last: Müschen

state: CA

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description: Aid-GFP-Reporter Spleen

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: GCOS 1.3

label: Biotin

source_name: Aid-GFP-Reporter Spleen

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

tag: Aid-GFP-Reporter Spleen


title: Aid-GFP negative LPS+IL4-stimulated splenic B cells (2)

description: Aid-GFP-Reporter Spleen

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)


title: Aid-GFP negative LPS+IL4-stimulated splenic B cells (1)

description: Aid-GFP-Reporter Spleen


title: BCR-ABL1 Aid-GFP-positive(1)

description: BCR-ABL1 Aid-GFP-Reporter BM

source_name: BCR-ABL1 Aid-GFP-Reporter BM

tag: BCR-ABL1 Aid-GFP-Reporter BM


title: Aid-GFP positive LPS+IL4-stimulated splenic B cells (1)

description: Aid-GFP-Reporter Spleen


title: BCR-ABL1 Aid-GFP-positive(2)

description: BCR-ABL1 Aid-GFP-Reporter BM


title: BCR-ABL1 Aid-GFP-negative(2)

description: BCR-ABL1 Aid-GFP-Reporter BM


title: BCR-ABL1 Aid-GFP-negative(1)

description: BCR-ABL1 Aid-GFP-Reporter BM


title: MCF-7 + miRctrl + vehicle, biological rep2

status: Public on Aug 04 2009

city: Toulouse

first: Stephan

last: Vagner

address: 20-24 Rue du Pont St Pierre

department: Institut Claudius Regaud

institute: INSERM U563

description:
n/a
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: miR Ctrl + vehicle

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: MCF-7 cells were maintained in DMEM supplemented with 5% fetal calf serum at 37°C, 5% CO2 in a humidified atmosphere.

extract_protocol: Trizol (Invitrogen) was used to extract total RNA from 1X PBS-rinsed cells.

treatment_protocol: MCF-7 cells plated at 30% of confluence were grown 3 days in DMEM w/o red phenol and supplemented with 5% of dextran-coated charcoal-treated fetal calf serum. At day 3, 5 nM of indicated miRNA were transfected with INTERFERin (PolyPlus Transfection) and stimulated with 10 nM of 17-beta-estradiol( E2). Total RNA were extracted 48 h after E2 stimulation.

tag: cell line


title: MCF-7 + miRctrl + E2, biological rep2

source_name: miR Ctrl + E2


title: SMM-NaCl-GB_3

status: Public on Aug 01 2009

city: Greifswald

first: Leif

last: Steil

address: Friedrich-Ludwig-Jahn Str. 15A

department: Genetics and Functional Genomics

country: Germany

institute: University of Greifswald

hyb_protocol: Prehybridization was carried out in 5 ml of hybridization solution (5x Denhardt solution, 5x SSC [1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 2% sodium dodecyl sulfate [SDS], 100 µg of denatured herring sperm DNA [Sigma]/ml) for 2 h at 65°C. Hybridization was performed for 20 h at 65°C in 5 ml of hybridization solution containing the labeled cDNA probe that had been heated to 98°C for 2 min. After hybridization, arrays were washed twice with 200 ml of 2x SSC and 0.1% (wt/vol) SDS for 5 min at room temperature and twice with 200 ml of 0.2x SSC and 0.1% (wt/vol) SDS for 20 min at 65°C.

scan_protocol: The arrays were exposed for 2 and 4 days to storage phosphor screens (Molecular Dynamics, Sunnyvale, Calif.) and scanned with a Storm 840/860 PhosphorImager (Molecular Dynamics) at a resolution of 50 µm and a color depth of 16 bits.

data_processing: Data analysis followed a three-step procedure. First, ArrayVision software (version 6.1; Imaging Research, St. Catherine's, Ontario, Canada) was used for the quantification of the hybridization signals after direct import of the phosphorimager files. The analysis yielded the artifact-removed volumes and background values, calculated from the median of lines surrounding each group of eight spots on the array. These data were then used in a second step in Microsoft Excel, calculating for every spot on the array a quality score that reflected the ratio between the signal intensity and the background intensity. This quality score was utilized to identify the hybridization signals close to the detection limit, thereby avoiding artificially high induction ratios for those genes. Data normalization and analysis were performed in a third step using GeneSpring (version 7.3.1; Agilent Technologies).

organism: Bacillus subtilis

source_name: bacterial culture

label_protocol: For cDNA synthesis, 2 µg of total RNA was mixed with 4 µl of a commercially available primer mix (Sigma-Genosys Ltd.) and 3 µl of 10× hybridization buffer (100 mM Tris [pH 7.9], 10 mM EDTA, 2.5 M KCl) in a total volume of 30 µl. The sample was heated to 95°C for 10 min and subsequently cooled to 42°C for primer annealing. Reverse transcription was performed in a total volume of 60 µl with SuperScript II reverse transcriptase and [alpha -33P]dCTP in the appropriate buffer for 1 h (Life Technologies, GmbH, Karlsruhe, Germany). After addition of 2 µl of 1% sodium dodecyl sulfate (SDS), 2 µl of 0.5 M EDTA (pH 8.0), and 6 µl of 3 M NaOH, the remaining RNA was hydrolyzed by incubation at 65°C for 30 min and at room temperature for 15 min. Prior to ethanol precipitation, the cDNA solution was neutralized with 20 µl of 1 M Tris (pH 8.0) and 6 µl of 2 N HCl. After a wash with 70% ethanol the pellet was carefully dried and resolved in 100 µl of distilled water. Labeling efficiency was determined with a liquid scintillation counter. This study was performed with Panorama B. subtilis gene arrays from Sigma-Genosys Ltd., which carry duplicate spots of PCR products representing 4,107 currently known B. subtilis genes.

growth_protocol: The Bacillus subtilis sigB mutant strain BLOB22 was grown in Spizzien minimal medium (SMM) to an OD 578nm of 1.0.

extract_protocol: Total RNA was isolated from nitrogen frozen cells using acidic phenol/chloroforn/Isoamyl alcohol extraction.

treatment_protocol: SMM; (ii) SMM with 1 mM glycine betaine, (iii) SMM with 0.7 M NaCl and (iv) SMM with 0.7 M NaCl and 1 mM glycine betaine.

tag: strain

tag: genome/variation

value: sigB mutant

tag: medium

value: Spizzien minimal medium

tag: medium supplement

value: 0.7 M NaCl, 1 mM glycine betaine


title: MCF-7 + miRctrl + E2, biological rep1


title: CGH data from AID WT2 vs AID KO BCR-ABL1 mouse leukemia cells

description: Standard Agilent protocols (performed by MOgeneLC)

data_processing:
Aberration Algorithm:  ADM-2
Threshold: 6.0
Centralization: ON
Bin Size: 10
Centralization Threshold: 6.0
Fuzzy Zero: ON
Combine Replicates (Intra Array): OFF
Combine Replicates (Inter Array): OFF
Genome: mm8
Aberration Filters:   minProbes = 3 AND minAvgAbsLogRatio = 0.2 AND maxAberrations = 100 AND percentPenetrance = 0
Feature Level Filters:   gIsSaturated = true OR rIsSaturated = true OR gIsFeatNonUnifOL = true OR rIsFeatNonUnifOL = true
Array Level Filters: NONE
Expand Non Unique Probes: OFF
Genomic Boundaries: Not Applied

source_name: KO MIG

extract_protocol: Invitrogen  Genomic DNA Mini Kit

value: AID KO BCR-ABL1

value: leukemia cells

source_name: WT MIG2

value: AID WT BCR-ABL1


title: CGH data from AID WT3 vs AID KO BCR-ABL1 mouse leukemia cells

hyb_protocol: Standard Agilent protocols (performed by MOgeneLC)

data_processing:
Software:Agilent DNA Analytics 4.0
Settings:
Aberration Algorithm:  ADM-2
Threshold: 6.0
Centralization: ON
Bin Size: 10
Centralization Threshold: 6.0
Fuzzy Zero: ON
Combine Replicates (Intra Array): OFF
Combine Replicates (Inter Array): OFF
Genome: mm8
Aberration Filters:   minProbes = 3 AND minAvgAbsLogRatio = 0.2 AND maxAberrations = 100 AND percentPenetrance = 0
Feature Level Filters:   gIsSaturated = true OR rIsSaturated = true OR gIsFeatNonUnifOL = true OR rIsFeatNonUnifOL = true
Array Level Filters: NONE
Expand Non Unique Probes: OFF
Genomic Boundaries: Not Applied

source_name: WT MIG3


title: MCF-7 + miR26a + E2, biological rep3

source_name: miR26a + E2


title: MCF-7 + miRctrl + vehicle, biological rep3


title: MCF-7 + miR26a + E2, biological rep2


title: SMM-NaCl_2

value: 0.7 M NaCl


title: MCF-7 + miRctrl + vehicle, biological rep1


title: MCF-7 + miR26a + E2, biological rep1


title: MCF-7 + miRctrl + E2, biological rep3


title: SMM-NaCl-GB_1


title: SMM-NaCl-GB_2


title: SMM-NaCl_1


title: SMM-GB_3

value: 1 mM glycine betaine


title: CGH data from AID WT1 vs AID KO BCR-ABL1 mouse leukemia cells

scan_protocol: Standard Agilent protocols (performed by MOgeneLC)

source_name: WT MIG1


title: SMM-GB_1


title: Neonatal day3-4

city: Lund

first: Stefan

last: Jovinge

address: Klinikgatan 26

country: Sweden

institute: Lund Strategic Center for Stem Cell Biology and Cell Therapy

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: mouse cardiomyocyte

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: eGFP α-MHC  on DBA

value: Neonatal day3-4

tag: tissue

value: heart


title: Adult 10 weeks

value: Adult 10 weeks+


title: ED11-12 embryonic cardiomyocytes


title: SMM-GB_2


title: SMM_3


title: SMM_2


title: SMM-NaCl_3


title: SMM_1


title: Input-Replicate 4

first: Russ

middle: P

last: Carstens

address: 411 Hill Pavilion, 380 S. University Ave.

department: Medicine

institute: University Of Pennsylvania School of Medicine

description: no additional information

data_processing: Raw data exported from Illumina's BeadStudio software.  The normalization was simply a log2 transformation as implemented with Partek Genomics Suite v. 6.4.  The log2 transformed data were then subject to further statistical analysis.

source_name: Differentiated mouse MPC-5 podocyte cell line

label_protocol: 650ng of purified total RNA from four replicates each of input control extract or eluted sample were single-round amplified and biotin-labeled using the Ambion Message-Amp II-Biotin Enhanced RNA amplification kit (Applied Biosystems) according to manufacturer’s instructions.

growth_protocol: MPC-5 cells were propogated based on the recommendations in the original manuscript.

extract_protocol: RNAs were harevsted with Trizol and qualtiy control was performed with the Agilent Bioanalyzer to confirm intact RNA prior to analysis

treatment_protocol:
The MPC-5 cell lines were stably expressing the Wilm's Tumor protein (+KTS) isoform carrying a modified TAP tag. A fraction of each extract (Input samples) was saved and the remaining extract was applied to a sepharose IgG column, washed, and eluates were harvested after addition of TEV protease and elution in microbiospin columns.
MPC-5 cells were transferred from 33 to 37 degrees for 14 days prior to extract preparation.  Four input and four eluate samples were then used to harvest RNA using Trizol.

value: MPC-5 podocyte cell line

tag: fraction

value: input (control)


title: Eluate-Replicate 4

description: no additional information

value: eluate


title: Input-Replicate 1

description: no additional information


title: Input-Replicate 3

description: no additional information


title: Eluate-Replicate 1

description: no additional information


title: 5-BX12, non-BRCA1/2 mutation associated breast tissue

city: Parkville

first: Jane

middle: E

last: Visvader

state: Victoria

address: 1G Royal Parade

department: Victorian Breast Cancer Research Consortium

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Labeled cRNA (1.5 μg) was prepared for hybridization to Illumina HumanWG-6 V3 (R1) BeadChips.

scan_protocol: After washing, we coupled the chips with Cy3 and scanned them in an Illumina BeadArray Reader.

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed used the lumi and limma packages of the Bioconductor open-source software project (http://www.bioconductor.org). The raw intensities were normexp background corrected with offset 16, quantile normalized, then log2-transformed.

source_name: Mammary tissue

label_protocol: We labeled up to 500 ng with the Total Prep RNA amplification kit (Ambion).

growth_protocol: Not applicable

extract_protocol: RNA from sorted cell populations were prepared with the RNeasy Micro kit (Qiagen). RNA quality was ascertained using the Agilent Bioanalyser 2100 with the NanoChip protocol.

treatment_protocol: Not applicable

value: Preneoplastic breast tissue

tag: gender

value: female

tag: mutation

value: non-BRCA1/2 mutation

tag: hybridization date

tag: beadchip barcode

tag: beadchip section

value: E


title: Eluate-Replicate 2

description: no additional information


title: 11-B21, BRCA1 mutation associated breast tissue

value: D


title: Input-Replicate 2

description: no additional information


title: Eluate-Replicate 3

description: no additional information


title: 71-18-C9, Normal breast tissue

value: Normal

value: F


title: 68-12-BX7, non-BRCA1/2 mutation associated breast tissue


title: 7-BX14, non-BRCA1/2 mutation associated breast tissue

value: C


title: 64-5-B15, BRCA1 mutation associated breast tissue

value: A


title: 70-17-C7, Normal breast tissue


title: 67-11-BX5, non-BRCA1/2 mutation associated breast tissue


title: 12-B22, BRCA1 mutation associated breast tissue


title: 10-B20, BRCA1 mutation associated breast tissue


title: 72-21-BX3, non-BRCA1/2 mutation associated breast tissue


title: 3-BX10, non-BRCA1/2 mutation associated breast tissue


title: 2-BX9, non-BRCA1/2 mutation associated breast tissue


title: 72-23-C3, Normal breast tissue


title: 62-3-B13, BRCA1 mutation associated breast tissue


title: 66-7-BX1, non-BRCA1/2 mutation associated breast tissue


title: 69-16-C6, Normal breast tissue


title: 63-4-B14, BRCA1 mutation associated breast tissue

value: B


title: BRP Induction 60 minutes against 45 minutes

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

description:
Gene expression of E.coli culture at different timepionts related to BRP-induction were analyzed and compared to samples before induction.
The RNA used for microarray experiments was obtained by cultivation of the strain E. coli MG1655 ara bearing the plasmid pBAD-LppBRP-His6phoAbla. E. coli MG1655 ara is the total sequenced wild type MG1655 where the araB – gene was totally and the araD – gene partially deleted. The strain is not able to utilize arabinose as carbon source. Induction of the pBAD-promoter with arabinose will stay constant during cultivation. On the plasmid pBAD-LppBRP-His6phoAbla the gene for the mature bacteriocin release protein (BRP) from CloDF13 fused with the signal sequence of Lpp, the major lipoprotein, is transcribed from the BAD – promoter of the arabinose operon. For analytical reasons, the BRP is fused with a 6-histidine tag. Two proteins, the alkaline phosphatase PhoA and ß-lactamase Bla, controlled by an in E. coli constitutive promoter (ß-glucanase from Bacillus amyloliquefaciens) are expressed as secretion reporters.

hyb_protocol: The cDNA pellet is solved in salt-based hybridisation buffer (Ocimum, Indianapolis, USA), denatured for 3 minutes at 95°C and subsequently Top-Block (Sigma, Taufkirchen, Germany) is added to a concentration of 2mg/ml. Differently labelled cDNAs (Cy5/Cy3) are hybribidized (42°C over night) simultaneously in one experiment to the same array according to the slide manufacter`s recommendations.

scan_protocol: The microarrays were scanned by the Axon 4000 B Scanner, image intensity data were extracted and analyzed using with Gene Pix Pro 6.0™ software.

data_processing:
The scanning process of the hybridized chips included a fourteen-fold scan of each chip at different settings, altering both PMT and laser power settings. The following primary analysis served as a quantification method and is performed with the Gene Pix Pro 6.0™ (Molecular Devices, Sunnyvale, USA) software tool.
The secondary analysis is subsequently conducted using the data from the primary analysis. Therefore, data from different scans is first searched for saturation effects, which are eliminated. A locally weighted linear regression (Lowess) has been employed as a normalization method in order to account for intensity-dependent effects. Due to the lacking gene replicates on the commercial whole genome array, a t-test could not be applied. Instead, the quotients of respectively two states have been calculated for the assessment of the regulation. A absolute value of log-ratio (to base2) higher than 1 is used as criteria for a regulated gene.

source_name: E.coli 60 minutes after BRP induction

label_protocol: 50µg of total RNA is converted into cDNA and labelled with Cy5-dCTP (Perkin Elmer, Waltham, USA) using Total Script reverse transkriptase (OLS, Hamburg, Germany). The RNA template is removed with an alkaline treatment at 65°C for 10 minutes and cDNA is purified using the PCR-Purification Kit (Qiagen, Hilden, Germany). Concentration and labelling efficiency of the cDNA is subsequently tested in the Nanodrop ND 1000 spectrophotometer (PEQLAB, Erlangen, Germany) and the aqueos phase is removed in a speed-vac.

growth_protocol: The strain was cultivated in 5L defined medium with glycerol as carbon source in a 7L (total) MBR-bioreactor. When the OD at 600 nm reached a value of around 5, the BAD – promoter was induced by adding 1g per litre and OD arabinose to the medium. Samples were taken at –10, 0, 2, 5, 10, 20, 30, 45 and 60 minutes related to point of induction.

extract_protocol: Total RNA is extracted from 10^9 cells by phenol-chloroform extraction and ethanol precipitation with 5M NaCl. Subsequently a DNAse I digest at 37°C for 30 minutes and an additional phenol-chloroform extraction step is performed. Integrity of the total RNA is electrophoretically confirmed using the Agilent 2100 Bioanalyzer.

treatment_protocol: Total RNA is extracted from 10^9 cells by phenol-chloroform extraction according to Sambrook et al. and ethanol precipitation with 5M NaCl. Subsequently a DNAse I digest at 37°C for 30 minutes and an additional phenol-chloroform extraction step is performed. Integrity of the total RNA is electrophoretically confirmed using the Agilent 2100 Bioanalyzer.

tag: time point

value: 60 minutes related to point of BRP induction

source_name: E.coli 45 minutes after BRP induction

label_protocol: 50µg of total RNA is converted into cDNA and labelled with Cy3-dCTP (Perkin Elmer, Waltham, USA) using Total Script reverse transkriptase (OLS, Hamburg, Germany). The RNA template is removed with an alkaline treatment at 65°C for 10 minutes and cDNA is purified using the PCR-Purification Kit (Qiagen, Hilden, Germany). Concentration and labelling efficiency of the cDNA is subsequently tested in the Nanodrop ND 1000 spectrophotometer (PEQLAB, Erlangen, Germany) and the aqueos phase is removed in a speed-vac.

value: 45 minutes related to point of BRP induction


title: BRP Induction -10 minutes against 60 minutes

source_name: E.coli -10 minutes after BRP induction

value: -10 minutes related to point of BRP induction

extract_protocol: Total RNA is extracted from 10^9 cells by phenol-chloroform extraction according to Sambrook et al. and ethanol precipitation with 5M NaCl. Subsequently a DNAse I digest at 37°C for 30 minutes and an additional phenol-chloroform extraction step is performed. Integrity of the total RNA is electrophoretically confirmed using the Agilent 2100 Bioanalyzer.


title: BRP Induction 45 minutes against 30 minutes

source_name: E.coli 30 minutes after BRP induction

value: 30 minutes related to point of BRP induction


title: 61-2-B12, BRCA1 mutation associated breast tissue


title: BRP Induction 10 Minutes against 5 Minutes

source_name: E.coli 10 minutes after BRP induction

value: 10 minutes related to point of BRP induction

source_name: E.coli 5 minutes after BRP induction

value: 5 minutes related to point of BRP induction


title: BRP Induction 5 minutes against 2 minutes

source_name: E.coli 2 minutes after BRP induction

value: 2 minutes related to point of BRP induction


title: E.coli 2 minutes after BRP induction

source_name: E.coli 0 minutes after BRP induction

value: 0 minutes related to point of BRP induction


title: BRP Induction 30 minutes against 20 minutes

source_name: E.coli 20 minutes after BRP induction

value: 20 minutes related to point of BRP induction


title: BRP Induction 20 minutes against 10 minutes


title: Genomic response analysis of E.coli during coexpression of a bacteriocin release protein


title: 76-28-C8, Normal breast tissue

value: Preneoplastic breast tissue

value: female


title: RT24_DH2 rat

first: ke

last: wang

address: 151 Libing Road

institute: Shanghai Biochip Co., Ltd.

description: Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

hyb_protocol: After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42?  for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1 SSC/0.2 SDS(50°C), 0.1 SSC/0.2%SDS(50°C) and 0.1 SSC(room temperature) before scanning.

scan_protocol: Axon GenePix 4000B

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal

organism: Rattus norvegicus

source_name: the tissue of dorsal horn (DH) of the fifth and sixth lumbar (L5 and L6) of experimental restraint stress rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65 ? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received restrain for 50 min, nociceptive testing and returned to home cages for 24 hours was labeled with Cy3.

extract_protocol: Total RNA was prepared using Trizol reagent (Invitrogen,USA), and further purified with a QIAGEN RNeasy Kit

value: Sprague-Dawley

tag: stress

value: restrain for 50 min, nociceptive testing and returned to home cages for 24 hours before sacrificed.

tag: tissue type

value: dorsal horn

source_name: the tissue of DH of control rats

value: none (sacrificed after stayed in their home cages without receiving restraint stress and nociceptive testing)


title: RT24_PAG3 rat

source_name: the tissue of periaqueductal gray (PAG) of experimental restraint stress rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65 ? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received restrain for 50 min, nociceptive testing and returned to home cages for 24 hours was labeled with Cy3.

value: periaqueductal gray

source_name: the tissue of PAG of control rats


title: RT24_DH1 rat


title: RT24_PAG5 rat


title: RT24_DH5 rat


title: RT24_PAG2 rat


title: RT24_DH3 rat


title: RT24_DH4 rat


title: RT24_PAG4 rat


title: Meg-01 Runx1 ko #2 vs. Meg-01 negative control #2 + orientation

city: Detroit

first: Yubin

last: Ge

state: MI

address: 110 East Warren Ave.

institute: Karmanos Cancer Institute

description: no additional information

hyb_protocol: Microarrays were hybridized using 0.75 ug of Alexa 555 labeled aRNA and 0.75 ug of Alexa 647 labeled aRNA. Agilent's SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 h at 60 °C. After hybridization, the slides were washed per Agilent's SSPE wash protocol.

scan_protocol: Scanned on an Agilent G2505A scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1) and protocol GE2-v5_95_Feb07

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and Linear+LOWESS normalization.

source_name: Meg-01 negative transfection control #2

label_protocol: RNA samples were amplified and labeled using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit per the vendor's protocol (Epicentre, Madison, WI, USA). Five micrograms of each aminoallyl-aRNA sample were fluorescently labeled using Alexa 555 or 647 by incubating with an amine-reactive dye conjugate for 1 h at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA, USA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

growth_protocol:
The Meg-01 AMkL cell line was obtained from the American Type Culture Collection (Manassas, VA, USA). The parental and the engineered sublines were cultured in RPMI 1640 with 10% fetal bovine serum (FBS, Hyclone, Logan, UT) and 2 mM L-glutamine, plus 100 U/ml penicillin and 100 µg/ml streptomycin, in a 37 °C humidified atmosphere containing 5% CO2/95% air.
AML1 shRNA lentivirus clones were purchased from the RNAi Consortium (Sigma-Aldrich, St Louis, MO). Meg-01 cells were infected by shRNA lentivirus clones. After selection with puromycin, infected Meg-01 cells were plated in soft agar. Colonies were isolated, expanded and tested for RUNX1 expression by Western blotting and real-time RT-PCR. Two colonies (designated Meg-01 RUNX1 1-1 and RUNX1 1-2, respectively) were selected for loss of RUNX1 gene expression and used for further study. A pool of cells from the negative control transduction was used as the control (designated Meg-01 Negative).

extract_protocol: Total RNAs were extracted from the samples using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA).

tag: transfection protocol

value: control

source_name: Meg-01 Runx1 KO #2

value: Runx1 knockout


title: RT24_PAG1 rat

city: Shanghai


title: RT24_Arc5 rat

source_name: the tissue of arcuate nucleus (Arc) of experimental restraint stress rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65 ? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each Arc which come from rats received restrain for 50 min, nociceptive testing and returned to home cages for 24 hours was labeled with Cy3.

value: arcuate nucleus

source_name: the tissue of Arc of control rats


title: RT24_Arc4 rat


title: Meg-01 Runx1 ko #1 vs. Meg-01 negative control #1 + orientation

description: no additional information

source_name: Meg-01 negative transfection control #1

source_name: Meg-01 Runx1 KO #1


title: Meg-01 Runx1 ko #1 vs. Meg-01 negative control #1 - orientation

description: no additional information


title: Meg-01 Runx1 ko #2 vs. Meg-01 negative control #2 - orientation

description: no additional information


title: RT1_PAG5 rat

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65 ? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received restrain for 50 min, nociceptive testing and returned to home cages for 1 hours was labeled with Cy3.

value: restrain for 50 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.


title: 19544538

description: no additional information

source_name: Blood culture

label_protocol: The PCR reaction mixture contained 1 uM of gBF primer mixture (Metabion, Germany), 1 uM of biotin-labeled gBR primer mixture (Metabion, Germany), 0.165 µM of SaurF primer (Metabion, Germany), 0.165 µM of biotin-labeled SaurR primer (Metabion, Germany), 0.25 µM of mecAF primer (Metabion, Germany), 0.25 µM biotin-labeled mecAR primer (Metabion, Germany), 1x Hot Start Taq® PCR buffer (Qiagen, Germany), in which the final concentration MgCl2was 2.0 mM, 300 uM of each of dNTP (Finnzymes, Finland), 1.5 g/l BSA (EuroClone, Italy), 0.125 U/ul Hot Start Taq® DNA polymerase (Qiagen, Germany), 1.5 ul of isolated DNA, and water to bring the total volume to 15 ul. In the blood culture dataset, 1.5 ul of PCR control template was added in the reaction and the equivalent amount of water was reduced. A negative control, i.e., sterile water was included in each test series. All the reverse primers were biotinylated at their respective 5′-end. The PCR was performed using a Mastercycler® epgradient S thermal cycler (Eppendorf, Germany). The following PCR program was used: a denaturation step at 95°C for 15 minutes, 36 cycles of 10 seconds at 96°C, 35 seconds at 52°C, 10 seconds at 72°C, 5 cycles of 5 seconds at 96°C, 30 seconds at 65°C, 5 cycles of 5 seconds at 96°C and finally 30 seconds at 68°C. After the PCR, the success of the amplification of double-stranded DNA and single-stranded DNA was ascertained by gel electrophoresis using a 2% agarose gel containing SYBR® Green II (Invitrogen, USA) or using Agilent BioAnalyzer (Agilent Technologies, USA).

tag: organism detected in blood culture

value: Streptococcus bovis (D)

tag: organism detected using array

value: Negative


title: RT1_DH4 rat

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65 ? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received restrain for 50 min, nociceptive testing and returned to home cages for 1 hours was labeled with Cy3.

tag: strain


title: RT1_DH2 rat


title: RT1_DH1 rat


title: RT1_DH3 rat


title: RT1_PAG4 rat


title: RT1_DH5 rat


title: RT1_PAG3 rat


title: RT1_Arc3 rat

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65 ? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each Arc which come from rats received restrain for 50 min, nociceptive testing and returned to home cages for 1 hours was labeled with Cy3.


title: RT24_Arc3 rat


title: RT24_Arc2 rat


title: RT1_Arc5 rat


title: RT1_PAG2 rat


title: RT1_PAG1 rat


title: RT1_Arc2 rat


title: RT24_Arc1 rat


title: wildtype_Mmt-inoculated_rep2_a

city: Sainte-Foy

first: Armand

last: Séguin

state: Quebec

department: Laurentian Forestry Centre

country: Canada

institute: Natural Resources Canada

description:
Gene expression data from infected tissues with Melampsora medusae f. sp. tremuloidae (Mmt).
Processed with Mmt-inoculated WRKY23-RNAi plants.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Fluidics protocol EukGE_WS2v5_450.

scan_protocol: GeneChip scanner.

data_processing: Robust Multichip Average (RMA) via FlexArray software package (http://genomequebec.mcgill.ca/FlexArray).

organism: Populus tremula x Populus alba

source_name: wildtype leaf discs, Mmt-inoculated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wildtype and WRKY23-RNAi plants of Populus tremula x P. alba clone INRA 717 1-B4 were grown in a mixture of peatmoss, vermiculite and turface (4:2:1) with a photoperiod of 16-h day/8-h night at 24°C/20°C.  Melampsora medusae f. sp. tremuloidae (Mmt) were maintained on Populus tremuloides according to Boyle et al., 2005 [Boyle B, Hamelin RC, Seguin A (2005) In vivo monitoring of obligate biotrophic pathogen growth by kinetic PCR. Applied and Environmental Microbiology 71: 1546-1552].

extract_protocol: Total RNA were extracted from frozen leaf tissues according to Chang et al., 1993 [Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 11: 113-116] and were purified on RNeasy columns (RNeasy Plant Mini Kit, Qiagen). Following a DNase I treatment (Qiagen), 10 μg of total RNA from each biological sample were used for each microarray experiment.

treatment_protocol: Leaf discs (2-cm diameter) prepared from leaf LPI9 (leaf plastochron index) of 1-m tall plants were inoculated on the abaxial side with Melampsora medusae f. sp. tremuloidae (Mmt) urediniospores suspended in 0.01% tween at a density of 500 spores per cm2. After inoculation, discs were kept on wet paper in petri dishes and incubated in a growth chamber at 18°C with a 16-h photoperiod until sample collection at 5 dpi.

value: Leaf discs from fully expanded leaf LPI9 (leaf plastochron index)

tag: genotype

value: wildtype


title: WRKY23-RNAi_Mmt-inoculated_rep1

description: Gene expression data from infected tissues with Melampsora medusae f. sp. tremuloidae (Mmt).

source_name: WRKY23-RNAi leaf discs, Mmt-inoculated


title: Slide 216 Ewe 2091 and 15

city: College Station

first: Thomas

last: Spencer

address: 442 Kleberg Center

department: Animal Science

institute: Texas A&M University

description: One array is included in one slide.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit (Genisphere Inc., Hatfield, PA) using dual channel design with dye-swapping.  Microarray slides were prepared by placing them approximately 6-8 cm above a 50oC water bath for 10 sec followed by snap drying on a heat block at 65oC for 5 sec and then allowing them to cool at room temperature for 1 min; this process was repeated four times for each slide.  Slides were then UV crosslinked at 1800 J.  Following UV crosslinking, slides were washed in 1% SDS (Ambion, Austin, TX) for 5 min on a gently rotating platform, rinsed twice in nuclease free water (Invitrogen), and subsequently washed for 3 min in 100% ethanol with gentle agitation.  Slides were then placed in 50 ml conical tubes and dried by centrifugation at <1000 X g for 4 min.  Dried slides were stored in a light-tight slide box until hybridization.  At the time of hybridization, 130 μl of concentrated cDNA (combined samples) was mixed with 2 μl LNA dT blocker, 118 μl nuclease free water, and 250 μl 2X Enhanced Hybridization Buffer (Genisphere) and denatured at 80ºC for 10 min.  An Agilent gasket slide was utilized for the first hybridization step.  Following assembly of the hybridization chamber, slides were hybridized at 58oC for 16 h.  Slides were washed and dried according to manufacturer’s instructions, and a second hybridization reagent containing the capture reagents was made according to instructions.  All subsequent steps were performed under minimal light conditions.  Dried slides were then hybridized with 50 μl of the 3DNA hybridization mix, coverslipped, placed in a humidified 50 ml conical tube and hybridized at 58oC for 4 h in the dark.  Following removal of coverslips, slides were washed and dried according to manufacturer’s instructions.

scan_protocol: Arrays were scanned at 5 μm resolution on a GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and images were saved in the TIFF format.  Auto photomultiplier tube (PMT) settings were selected and adjusted so that the ratio of overall intensities between two channels (Cy3 and Cy5) was 0.95 to 1.05.  The signal intensities of all spots on each image were quantified by Genepix Pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analysis.

data_processing: The signal intensity of each probe was divided by that of negative control to filter the genes which were not expressed.  Signal intensities were normalized by LOWESS within the R statistics package.  To correct for background signal, median signal intensity and median background intensity was used to normalize the data by LOWESS.  A mixed model that included the fixed effects of dye (Cy3 and Cy5) as well as random effects of slide and array was used to analyze the normalized data by SAS (SAS Institute, Cary, NC).  Comparisons were conducted as follows: day 9 CO vs day 9 P4; day 9 CO vs day 12 CO; and day 12 CO vs day 12 P4.  P-value and fold changes between each comparison for each gene were calculated.  False discovery rate (FDR) was calculated by R program according to Benjamini and Hochberg's method.  The P-value and FDR was set at 0.05 for statistical analyses to identify differentially expressed genes.

organism: Ovis aries

source_name: Ovis aries endometrium ewe 2091 day 12 corn oil treated

label_protocol: Preparation of cDNA was performed according to the manufacturer’s instructions.  Briefly, endometrial total RNA (9 µg) from each ewe (n=5 per day and treatment) was reverse-transcribed with Superscript II (Invitrogen, Carlsbad, CA) with the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labeling reagents.  Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was co-hybridized with a cDNA sample from the opposite treatment for direct comparison of differences between treatments.

extract_protocol: Total cellular RNA was isolated from frozen ipsilateral endometrium using Trizol reagent (Gibco-BRL, Bethesda, MD) according to manufacturer’s instructions. The quantity and quality of total RNA was determined by spectrometry and Agilent BioAnalyzer 2100 (Agilent, Palo Alto, CA) using the RNA 6000 Nano Labchip kit (Agilent), respectively in accordance with the manufacturer’s instructions. Endometrial RNA was subsequently processed through an RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol: Ewe was bred at estrus (day 0) and received daily exogenous injections of corn oil vehicle from days 1.5 to 12 post-mating.

value: endometrium

tag: developmental stage

value: day 12 of pregnanacy

tag: treatment

value: corn oil vehicle

source_name: Ovis aries endometrium ewe 15 day 12 progesterone treated

treatment_protocol: Ewe was bred at estrus (day 0) and received daily exogenous injections of progesterone (25 mg in corn oil vehicle) from days 1.5 to 12 post-mating.

value: progesterone in corn oil vehicle


title: Slide 218 Ewe 3225 and 3148

description: One array is included in one slide.

source_name: Ovis aries endometrium ewe 3225 day 12 corn oil treated

tag: tissue

source_name: Ovis aries endometrium ewe 3148 day 12 progesterone treated


title: WRKY23-RNAi_Mmt-inoculated_rep3


title: RT1_Arc1 rat

value: Sprague-Dawley


title: RT1_Arc4 rat


title: Slide 217 Ewe 2680 and 3202

description: One array is included in one slide.

source_name: Ovis aries endometrium ewe 2680 day 12 progesterone treated

source_name: Ovis aries endometrium ewe 3202 day 12 corn oil treated


title: wildtype_Mmt-inoculated_rep1_a


title: wildtype_Mmt-inoculated_rep3_a


title: WRKY23-overexpressor_Mmt-inoculated_rep1

source_name: WRKY23-overexpressor leaf discs, Mmt-inoculated

growth_protocol: Wildtype and WRKY23-overexpressor plants of Populus tremula x P. alba clone INRA 717 1-B4 were grown in a mixture of peatmoss, vermiculite and turface (4:2:1) with a photoperiod of 16-h day/8-h night at 24°C/20°C.  Melampsora medusae f. sp. tremuloidae (Mmt) were maintained on Populus tremuloides according to Boyle et al., 2005 [Boyle B, Hamelin RC, Seguin A (2005) In vivo monitoring of obligate biotrophic pathogen growth by kinetic PCR. Applied and Environmental Microbiology 71: 1546-1552].

treatment_protocol: Leaf discs (2-cm diameter) prepared from leaf LPI9 (leaf plastochron index) of 1-m tall plants were inoculated on the abaxial side with Melampsora medusae f. sp. tremuloidae (Mmt) urediniospores suspended in 0.01% tween at a density of 500 spores per cm2 or were mock-inoculated with 0.01% tween (control). After inoculation, discs were kept on wet paper in petri dishes and incubated in a growth chamber at 18°C with a 16-h photoperiod until sample collection at 5 dpi.


title: WRKY23-RNAi_Mmt-inoculated_rep2


title: Slide 213 Ewe 4141 and 4184

description: One array is included in one slide.

source_name: Ovis aries endometrium ewe 4141 day 9 corn oil treated

treatment_protocol: Ewe was bred at estrus (day 0) and received daily exogenous injections of corn oil vehicle from days 1.5 to 9 post-mating.

value: day 9 of pregnanacy

source_name: Ovis aries endometrium ewe 4184 day 9 progesterone treated

treatment_protocol: Ewe was bred at estrus (day 0) and received daily exogenous injections of progesterone (25 mg in corn oil vehicle) from days 1.5 to 9 post-mating.