title: DBY8268 30 min vs T0 - 5% EtOH #1

description: 5% EtOH Time-course in DBY8268


title: E18.5 brain, Meg3 knock-out, rep 7

status: Public on Dec 17 2010

type: RNA

city: Boston

first: Xun

last: Zhang

state: MA

address: 55 Fruit St Rm Bull 450

department: Neuroendocrine Unit

country: USA

institute: Massachusetts General Hospital

description: 262_1 KO

hyb_protocol: 20 µg of cRNA was fragmented and hybridized for 16H at 45ºC on Mouse 430 2.0 chips.  Chips were then washed and stained using the Affymetrix Fluidics Station 400

scan_protocol: Standard Affymetrix protocol

data_processing: Microarray data were analyzed using GeneSifter with a quality cut-off of 0.5 and a fold-change between groups of at least 1.2.  Raw data were normalized by median scaling of P-calls.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Brain from Meg3 knock-out E18.5 mouse embryo

label_protocol: Biotinylated cRNA was prepared from 5 µg total RNA using Affymetrix One-Cycle Target Labeling protocol (GeneChip Expression Analysis Technical Manual 1999-2004, Affymetrix)

extract_protocol: Extraction of total RNA was performed using the Qiagen RNeasy Lipid Tissue Kit according to the manufacturer's instructions.

tag: tissue

value: Whole Brain

tag: developemental stage

tag: genotype/variation

value: Meg3 knock-out


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-17B

city: Bethesda

first: Delong

last: Liu

state: MD

address: 10 Center Drive

institute: NHLBI/NIH

description:
CD133+ cells sorted from PB.
SG-17B

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 Plus 2.0 chips for 16 hours.

scan_protocol: Affymetrix GeneChip scanner.

data_processing: Intensities were pre-processed with MAS5.0, and further processed with variance stablization transformation ('S10').  26,123 probesets present in at least 2 out of 14 chips (4 healthy controls and 10 CAD baselines) were S10 transformed and analyzed.

organism: Homo sapiens

source_name: CAD patient, after 3 months of exercise

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

growth_protocol: CAD patients enrolled in a cardiac rehabilitation program consisting of 36 sessions of 60 minutes each, spaced over 3 months. Medical management was stable for at least a month prior to program participation and all patients were maintained on medications throughout the study as prescribed without change in preparation or dose.

extract_protocol: 32 ml of PB was used for isolation of CD133+ cells using fluorescence-actived cell sorting. Total RNA was extracted from CD133+ cells with an RNAqueous micro RNA isolation kit (Ambion, Austin, TX).  Cells were lysed in buffer containing guanidinium thiocyanate.

treatment_protocol: Cardivovascular examination and baseline testing were performed after an overnight fast (except for water). Symptom-limited treadmill exercise was performed using the modified Bruce protocal.  Healthy subjects of similar age and sex distribution were recruited for the study to serve as controls for baseline analysis.

value: peripheral blood

tag: cell type

value: CD133+ cells

tag: disease

value: coronary artery disease

tag: treatment

value: 3 months of exercise


title: DBY8268 45 min vs T0 - 5% EtOH

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

institute: University of Arkansas

description: 5% EtOH Time-course in DBY8268

hyb_protocol: As indicated in Gasch AP Methods in Enzymology 350: 393-414

scan_protocol: Arrays were scanned on an Axon 4000B scanner

data_processing: Data were extracted using GenePix 6.0.  Data were normalized by regional mean-centering as described by Lyne et al. 2003 BMC Genomics

label: Oyster 550 cyanine dye

organism: Saccharomyces cerevisiae

source_name: DBY8268 log growth

label_protocol: Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology 350: 393-414

growth_protocol: All cells were grown for at least 8 doublings in log phase in YPD medium at 30C.

extract_protocol: Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology 350: 393-414

treatment_protocol: For ethanol-shocked cells, ethanol was added to a final concentration of 5% (v/v).

tag: genotype

tag: protocol

value: DBY8268 log growth

label: Oyster cyanine 650 dye

source_name: DBY8268 45 min after 5% EtOH shock

value: DBY8268 45 min after 5% EtOH shock


title: M22 30 min vs T0 - 5% EtOH #1

description: 5% EtOH Time-course in M22

source_name: M22 log growth

value: M22 log growth

source_name: M22  30 min after 5% EtOH shock

value: M22  30 min after 5% EtOH shock


title: E18.5 brain, Meg3 knock-out, rep 5

description: 250_1 KO


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-9B

description:
CD133+ cells sorted from PB.
SG-9B


title: E18.5 brain, Meg3 knock-out, rep 4

description: 238_5 KO


title: E18.5 brain, Meg3 knock-out, rep 6

description: 250_3 KO


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-10B

description:
CD133+ cells sorted from PB.
SG-10B


title: DBY8268 15 min vs T0 - 5% EtOH

description: 5% EtOH Time-course in DBY8268

source_name: DBY8268 15 min after 5% EtOH shock

value: DBY8268 15 min after 5% EtOH shock


title: DBY8268 vs YPS163 #3

description: Comparison of DBY8268 and YPS163 during log phase growth

source_name: YPS163 log growth

value: YPS163 log growth


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-10A

description:
CD133+ cells sorted from PB.
SG-10A

source_name: CAD patient, baseline

value: baseline


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-9A

description:
CD133+ cells sorted from PB.
SG-9A


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-7B

description:
CD133+ cells sorted from PB.
SG-7B


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-8B

description:
CD133+ cells sorted from PB.
SG-8B


title: E18.5 brain, Meg3 knock-out, rep 3

description: 238_1 KO


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-8A

description:
CD133+ cells sorted from PB.
SG-8A


title: E18.5 brain, wild-type, rep 6

description: 262_2 WT

source_name: Brain from wild-type E18.5 mouse embryo

value: Wild-type


title: E18.5 brain, wild-type, rep 5

description: 250_4 WT


title: DBY8268 vs YPS163 #2


title: DBY8268 vs M22 #2

description: Comparison of DBY8268 and M22 during log phase growth


title: E18.5 brain, Meg3 knock-out, rep 2

description: 219_12 KO


title: DBY8268 vs M22 #3


title: DBY8268 vs YPS163 #1


title: E18.5 brain, Meg3 knock-out, rep 1

description: 148_15 KO


title: E18.5 brain, wild-type, rep 4

description: 250_2 WT


title: Endothelial cells from left and right iliac arteries rep 3 p2

status: Public on Dec 18 2010

city: Durham

first: Kelley

last: Burridge

state: NC

address: Rm 136 Hudson Hall

department: Biomedical Engineering

institute: Duke University

description: Endothelial cells from coronary and iliac arteries were harvested from four pigs and grown in culture out to passage 4.

hyb_protocol: • Make hybridization buffer fresh each time. • Add 38 ul hybridization buffer to 12 ul fragmented Cy Dye labeled aa-aRNA. • Add 1ul each poly dA and appropriate Cot-1 DNA. • Heat at 95ºC for 2 minutes and put on ice to cool down. • Mix well and load sample to the array slide with lifter cover slip. • Hybridize overnight in 42ºC water bath.

scan_protocol: Scanned by GenePix 4000B and quantified using GenePix software

data_processing: LOWESS normalized. Agilent GeneSpring GX was used.

organism: Sus scrofa

source_name: iliac endothelial cells

label_protocol: Messenger RNA was amplified using a MessageAmp II aRNA amplification kit (Ambion). Two rounds of amplification were performed, and aminoallyl-UTP was used in the final round to provide reactive groups for dye incorporation. The RNA samples were labeled with Cy5 dyes and reference RNA sample was labeled with Cy3 dyes.

growth_protocol: Endothelial cells were grown in EGM-2MV media.

extract_protocol: Qiagen RNeasy Micro kit following manufacturer's protocol

treatment_protocol: passage 2

tag: animal

value: iliac endothelial cells

source_name: reference RNA

value: aortic endothelial cells (passage 3)


title: DBY8268 vs M22 #1


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-7A

description:
CD133+ cells sorted from PB.
SG-7A


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-6B

description:
CD133+ cells sorted from PB.
SG-6B


title: SF1_ChIP_vs_input_2exps

type: genomic

city: London

first: Bruno

last: Ferraz-de-Souza

address: 30 Guilford St

department: Clinical & Molecular Genetics Unit

country: United Kingdom

institute: UCL Institute of Child Health

description: SF1 ChIP NCIH295R cells, 2 biological replicates

hyb_protocol: Samples were hybridised to GeneChip Human Promoter 1.0R Arrays (16 hours at 45°C) and stained using the GeneChip Hybridization, Wash and Stain Kit, following manufacturers instructions (all Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 3000 7G System (Affymetrix)

data_processing:
CisGenome was used to generate BAR, BED and COD files (BED file was generated from COD file).  Quantile normalization was applied prior to analysis, and a moving average (MA) statistic was computed for each probe based on a half-window size of 300 bp or 5 probes. Peaks were discarded if they contained less than five probes or were less than 100 base pairs in width. Peaks that were separated by less than 300 base pairs or 5 probes were merged. Peaks that had a left-tail false discovery rate >5% were discounted. The genomic coordinates of all regions were converted into coordinates based on NCBI genome build 36 (hg18) and mapped to neighboring transcriptional start sites (TSS).

fc.bar and ma.bar are generated by CisGenome. fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average (MA) statistic for each probe. File SF1_ChIP_MA3_annot_all.bed contains all 946 SF1 binding sites with MA>3.0. The COD files, generated by CisGenome to be opened using Excel, provide better details of these binding sites. SF1_ChIP_MA3_annot_all.cod has statistical details and location of all binsing sites, while SF1_ChIP_MA3_annot_neighb.cod has details of gene loci neighbouring these sites.

molecule: genomic DNA

label_protocol: Amplified DNA (7.5 μg) was fragmented and end-labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit, following manufacturers instructions (Affymetrix)

growth_protocol: NCI-H295R cells were maintained in 75 cm2 tissue culture flasks with 15 ml of DMEM:F12 supplemented with 2.5% Nu-Serum, 1% ITS+ Premix and 1% P/S. Upon 80-90% confluency (usually every 4 to 6 days), cells were washed with 5 ml PBS and detached from flask through incubation with 3 ml trypsin-EDTA at 37°C for 3 min. Trypsin was inactivated by the addition of 7 ml full medium and resuspended cells were replated at 1:10 dilution.

extract_protocol: Chromatin immunoprecipitation assays were performed using the ChIP-IT Express kit (Active Motif, Rixensart, Belgium) following the manufacturer’s instructions. NCI-H295R human adrenocortical tumor cells were fixed with 1% formaldehyde and subsequently sonicated in eight 20 sec pulses at 2 μm amplitude for 5 min (MSE Soniprep 150; Sanyo Gallenkamp, Loughborough, UK). Immunoprecipitation was carried out in aliquots of sheared chromatin from approximately 2,000,000 cells using 3 μg SF-1 antibody (07-618 from Upstate Millipore UK Ltd., Watford, UK) and aliquots of sheared chromatin were separated to serve as input DNA control. SF-1-immunoprecipitated DNA (50 ng) and respective input DNA were amplified by ligation-mediated PCR (LMPCR): chromatin was blunt-ended using T4 DNA Polymerase (New England Biolabs (NEB) UK Ltd., Hitchin, UK) and ligated to double-stranded linkers overnight (16C; NEB T4 DNA Ligase) [Long (5’-GCG GTG ACC CGG GAG ATC TGA ATT C-3’) and short (5’-GAA TTC AGA TC-3’) unidirectional oligonucleotides]. Linker-ligated chromatin was linearly amplified by PCR using 0.1 U Taq polymerase, 3 μM long oligonucleotide, 1 M betaine, 2.5 mM MgCl2 and 0.1 mM dNTP + dUTP mix (25% dATP, 25% dCTP, 25% dGTP, 20% dTTP and 5% dUTP).

treatment_protocol: no treatment (unstimulated)

tag: cell line

value: NCIH295R adrenal cells

tag: chip antibody

value: anti-SF-1 antibody

tag: chip antibody vendor

value: Upstate (Millipore)

tag: chip antibody catalog#


title: E18.5 brain, wild-type, rep 3

description: 238_4 WT

value: Whole Brain


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-6A

description:
CD133+ cells sorted from PB.
SG-6A

value: peripheral blood

value: CD133+ cells


title: E18.5 brain, wild-type, rep 2

description: 219_17 WT


title: E18.5 brain, wild-type, rep 1

description: 219_16 WT


title: HF-19323-(1)_Hind

status: Public on Dec 16 2010

city: South San Francisco

first: Jinfeng

state: CA

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Ninety normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=100k) and analyzed at the same time.  One CEL file for each set (Xba and Hind) with the median signal intensity across the set was selected as the reference array.   The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.

source_name: Ovarian tumor

label_protocol: Affymetrix 100K protocol

extract_protocol: A small piece of frozen tissue was removed from a sample of frozen tissue and incubated in a proteinase K digestion solution followed by cleanup using the Qiagen M48 robotics protocol.

value: primary ovarian tumor


title: HF-18770-(1)_Hind


title: HF-19081-(1)_Hind


title: HF-19328-(1)_Hind


title: HF-18405-(1)_Hind


title: HF-19083-(1)_Hind


title: HF-19330-(1)_Hind


title: HF-17782-(1)_Hind


title: HF-19073-(1)_Hind


title: HF-19319-(1)_Hind


title: HF-18389-(1)_Hind


title: HF-18774-(1)_Hind


title: HF-19077-(1)_Hind


title: HF-17953-(1)_Hind


title: HF-18401-(1)_Hind


title: HF-18399-(1)_Hind


title: HF-17786-(1)_Hind


title: HF-18395-(1)_Hind


title: HF-16154-(1)_Hind


title: HF-18393-(1)_Hind


title: HF-16280-(1)_Hind


title: HF-16150-(1)_Hind


title: HF-17788-(1)_Hind


title: HF-17778-(1)_Hind


title: HF-16277-(1)_Hind


title: HF-17780-(1)_Hind


title: HF-17528-(1)_Hind


title: HF-17532-(1)_Hind


title: HF-16903-(1)_Hind


title: HF-17060-(1)_Hind


title: HF-17531-(1)_Hind


title: HF-19073-(1)_Xba


title: HF-18389-(1)_Xba


title: HF-19319-(1)_Xba


title: HF-16897-(1)_Hind


title: HF-16899-(1)_Hind


title: HF-16902-(1)_Hind


title: HF-19328-(1)_Xba


title: HF-19330-(1)_Xba


title: HF-19077-(1)_Xba


title: HF-17525-(1)_Hind


title: HF-17953-(1)_Xba


title: HF-19081-(1)_Xba


title: HF-18774-(1)_Xba


title: HF-19083-(1)_Xba


title: HF-17782-(1)_Xba


title: HF-18405-(1)_Xba


title: HF-17786-(1)_Xba


title: HF-17780-(1)_Xba


title: HF-18770-(1)_Xba


title: HF-18399-(1)_Xba


title: HF-18401-(1)_Xba


title: HF-17060-(1)_Xba


title: HF-16280-(1)_Xba


title: HF-17788-(1)_Xba


title: HF-18395-(1)_Xba


title: HF-17778-(1)_Xba


title: HF-16902-(1)_Xba


title: HF-16277-(1)_Xba


title: HF-17531-(1)_Xba


title: HF-17532-(1)_Xba


title: HF-18393-(1)_Xba


title: HF-16899-(1)_Xba


title: HF-16901-(1)_Xba


title: HF-16903-(1)_Xba


title: HF-16154-(1)_Xba


title: HF-16150-(1)_Xba


title: CBE_ROM5-P1-2_S00935-N-FF_170310_GWS6

city: Cologne

first: martin

last: sos

address: Gleuelerstr. 50

country: Germany

institute: Max-Planck Institute for neurological research

description: hybridized to 6.0 SNP arrays

hyb_protocol: according to the manufacturers instructions

scan_protocol: arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: genotype calls were generated by the Birdseed algorithm (part of the Affymetrix powertools v 1.264.2.2 12.10.2009)

source_name: normal tissue

label_protocol: as per manufacturer

extract_protocol: Genomic DNA was extracted from cell lines using the PureGene kit

tag: disease state

value: normal tissue


title: CBE_ROM5-P1-2_S00941-N-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00934-N-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: HF-16897-(1)_Xba


title: HF-17528-(1)_Xba


title: HF-17525-(1)_Xba


title: CBE_ROM5-P1-2_S00944-N-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00943-N-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00933-N-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: Wild type (15 month) vs wild type (2.5 month)_VP_R1

city: Smithville

first: Dean

middle: G

last: Tang

state: TX

address: 1808 Park road 1C

department: Carcinogenesis

institute: U.T M. D. Anderson Cancer Center

description: The current array analysis was carried out to study the changes in the gene expression profile of 15 month old wild type mice ventral prostate (VP) compared to 2.5 month old wild type mice VP.

hyb_protocol: Manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF

scan_protocol: Scanning and data acquisition were performed using Agilent scanner and feature extraction software version A.7.5.1 (www.agilent.com).

data_processing: The data was acquired using Agilent's feature extraction software (version A.7.5.1) with inbuilt Lowess normalization feature and Logratio algorithms, for details visit www.agilent.com

source_name: wild type (2.5 month old) mice ventral prostate

label_protocol: labeling was done according to manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF

extract_protocol: Total RNA was extracted from combined ventral prostates of three 2.5 month old wild type mice after mincing with Biopulverizer (Biospec products) and using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

value: ventral prostate

tag: age

value: 2.5 month old

tag: genetic background

value: FVB

value: wild type

source_name: wild type (15 month old) mice ventral prostate

extract_protocol: Total RNA was extracted from combined ventral prostates of three 15 month old wild type mice after mincing with Biopulverizer (Biospec products) and using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

value: 15 month old


title: CBE_ROM5-P1-1_S00939-N-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00945-N-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00825-N-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00946-N-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00938-N-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: 15-LOX2 splice variant b transgenic (svb9) vs wild type (wt)_VP_R1

description: The current array analysis was carried out to study the changes in the gene expression profile of 2.5 month old 15-LOX2 splice variant b (sv-b) transgenic mice (line svb9) ventral prostate (VP) compared to age matched wild type mice VP.

scan_protocol: Scanning and data acquisition were performed using Agilent scanner and feature extraction software version  A.7.5.1 (www.agilent.com).

source_name: 15-LOX2 splice variant b transgenic (svb9, 2.5 month old) mice ventral prostate

extract_protocol: Total RNA was extracted from combined ventral prostates of three 2.5 month old svb9 mice after mincing with Biopulverizer (Biospec products) and using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

value: 15-Lipoxygenase 2 (15-LOX2) splice variant b (sv-b) transgenic mice (line svb9),


title: 15-LOX2 transgenic (fl26) vs wild type (wt)_VP_R2

description: The current array analysis was carried out to study the changes in the gene expression profile of 2.5 month old 15-LOX2 transgenic mice (line fl26) ventral prostate (VP) compared to age matched wild type mice VP.

source_name: 15-LOX2 transgenic (fl26, 2.5 month old) mice ventral prostate

extract_protocol: Total RNA was extracted from combined ventral prostates of three 2.5 month old fl26 mice after mincing with Biopulverizer (Biospec products) and using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

value: 15-Lipoxygenase 2 (15-LOX2) transgenic mice (line fl26),


title: 15-LOX2 splice variant b transgenic (svb9) vs wild type (wt)_VP_R2


title: CBE_ROM5-P1-1_S00830-N-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00829-N-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM18871B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM19099B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM19143B_200110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM19153B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM19137B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM18870B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00932-N-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM18912B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM18857B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_GM19153B_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM18508B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_GM18517C_200110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_GM19143B_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_GM19194B_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_GM19137B_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_GM18857B_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: Comparison cya mutant with wt under glucose-limited conditions (replicate 1)

city: Zürich

first: Alessandro

middle: Guido

last: Franchini

address: Universitätstrasse 16

country: Switzerland

institute: Swiss Federal Institute of Technology (ETH)

hyb_protocol: The purified cDNA was concentrated to 5 ul and was mixed with 120 ul hybridization buffer (MWGBiotech), heated to 95 °C for 3 min and cooled on ice for 3 min. The hybridization mixture was then added to the microarray slide and covered with a coverslip. The hybridization slide was incubated overnight at 42 °C. After the hybridization step the slide was washed three times, the first time for 5 min in 2x SSC/0.1% SDS, the second time for 5 min in 1x SSC, and finally for 5 min in 0.1x SSC. SSC buffer was prepared as a 20x solution containing 0.3 M sodium citrate and 3 M NaCl at pH 7.0. The slides were dried by centrifugation at room temperature for 2 min at 500 g.

scan_protocol: Microarray slides were scanned using an Affymetrix 428 Array Scanner. Spot intensities and corresponding background signals were quantified with the Affymetrix Jaguar software version 2.0.

data_processing: The data provided are the original data generated with the Jaguar software from the microarray images. The VALUEs reported represent normalized log10 (Cy5/Cy3) ratios for this experiment/sample. They were not normalized across all samples in the study.

organism: Escherichia coli K-12

source_name: control

label_protocol: CyScribe First-Strand cDNA Labelling Kit (Amersham Bioscience, Little Chalfont, England) was used to reversely transcribe mRNA into fluorescently labelled cDNA. Reverse transcription was performed using 25 ug total RNA (maximally in 10 ul) and 1 ml random nonamer primers. The volume of the assay mixture was adjusted to 11 ul with RNase-free water, then the assay mixture was incubated for 5 min at 70 °C, followed by incubation for 10 min at room temperature to allow the primers to anneal with the RNA. After cooling to room temperature, the reagents for the labelling reaction were added. After the addition of 4 ul 5x CyScript buffer, 2 ul 0.1 M DTT, 1 ul dNTP mixture, 1 ul 0.5 mM Cy3-labelled dCTP (Amersham Bioscience) and 1 ml CyScript reverse transcriptase (100 U/ul), the final reaction volume was 20 ul.

extract_protocol: Total RNA was isolated as described (Sambrook et al., 1989). The extracted RNA was checked for purity by gel electrophoresis and was quantified by measuring extinction spectrophotometrically at 260 nm.

tag: strain

value: wild-type

tag: condition

value: glucose limited

source_name: cya mutant

label_protocol: CyScribe First-Strand cDNA Labelling Kit (Amersham Bioscience, Little Chalfont, England) was used to reversely transcribe mRNA into fluorescently labelled cDNA. Reverse transcription was performed using 25 ug total RNA (maximally in 10 ul) and 1 ml random nonamer primers. The volume of the assay mixture was adjusted to 11 ul with RNase-free water, then the assay mixture was incubated for 5 min at 70 °C, followed by incubation for 10 min at room temperature to allow the primers to anneal with the RNA. After cooling to room temperature, the reagents for the labelling reaction were added. After the addition of 4 ul 5x CyScript buffer, 2 ul 0.1 M DTT, 1 ul dNTP mixture, 1 ul 0.5 mM Cy5-labelled dCTP (Amersham Bioscience) and 1 ml CyScript reverse transcriptase (100 U/ul), the final reaction volume was 20 ul.

value: cya mutant


title: Comparison cya mutant with wt under glucose-limited conditions (replicate 2)


title: Comparison rpoS mutant with wt under glucose-limited conditions (replicate 2)

source_name: rpoS mutant

value: rpoS mutant


title: Comparison rpoS mutant with wt under glucose-limited conditions (replicate 1)


title: CBE_ROM4-P4-2_GM18517C_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: Comparison rpoS mutant with wt under glucose-limited conditions (replicate 3)


title: Comparison cya mutant with wt under glucose-limited conditions (replicate 3)


title: CBE_ROM4-P4-2_GM18508B_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_GM18504B_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_GM19099B_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_GM12144C_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_GM18912B_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_GM18870B_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_GM18871B_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_GM19142B_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_GM18863B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_GM19194B_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_GM19142B_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_GM18504B_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_GM12144C_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: HF-19323-(1)_Xba

tag: tissue


title: CBE_ROM3-P1-3_GM18912B_091209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_GM19099B_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_GM19153B_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_GM19137B_031209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_GM18504B_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_GM18870B_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_GM18863B_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_GM19143B_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_GM18517C_031209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-3_GM18508B_091209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_GM18871B_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_GM18857B_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-3_GM19194B_091209_GWS6

description: hybridized to 6.0 SNP arrays


title: HF-16901-(1)_Hind


title: CBE_ROM5-P1-2_S00491-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays

source_name: adenocarcinoma of the lung

value: adenocarcinoma of the lung


title: CBE_ROM3-P1-2_GM12144C_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_GM19142B_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00490-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00492-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00489-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00466-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00488-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00487-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_GM18863B_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00211-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00203-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00205-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00206-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00190-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00207-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00183-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00485-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00494-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00180-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00493-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00176-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00467-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00172-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00470-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00197-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00202-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00192-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00191-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00194-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00201-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00002-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00737_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00170-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00171-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_464_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00735_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00675_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_365_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_361_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00499-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00495-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00486-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00181-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00484-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_352_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_348_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_357_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_351_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_353_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_350_300609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_71_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_65_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_59_180609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_48_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_34_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_58_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_56_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_57_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_32_300609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_61_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_54_300609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_27_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_25_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_359_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_18_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_26_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_19_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_15_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_14_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_21_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_17_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_72_180609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_10_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_11_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_6_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_3_180609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_12_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_5_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_29_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00513-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays

source_name: squamous cell lung cancer

value: squamous cell lung cancer


title: CBE_ROM5-P1-2_S01071-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S01223-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S01189-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00512-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00511-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00508-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00441-T-sec_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00222-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00344-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00289-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S01068-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: 15-LOX2 transgenic (fl26) vs wild type (wt)_VP_R1


title: CBE_ROM5-P1-1_S00506-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00281-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00478-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00503-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00280-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S01225-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00115-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00223-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00242-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00258-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S01188-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00088-T-FF_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-1_S00276-T-FF_180310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00461_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00456-T-sec_170310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00444_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00450_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00434_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00429_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00426_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00422_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00404_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00414_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00458_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00409_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00424_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00249_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00374_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00271_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00227_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00239_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00247_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00119_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00185_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00210_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00081_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00086_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00457_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-2_S00093_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00446_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00455_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00448_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00440_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00443_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00463_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00420_200110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00437_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00412_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00408_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00401_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00417_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00399_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00392_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00373_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00396_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00428_290110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM5-P1-2_S00325-T-FF_160310_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00293_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00277_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00237_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00285_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00234_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00230_200110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00454_270110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00187_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00038_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_504_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_481_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00112_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_502_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00092_200110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_480_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_476_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_475_031209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_477_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_346_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_474_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_287_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_473_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_257_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00327_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_252_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_254_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P3-1_S00283_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_246_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_244_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_243_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_248_031209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_233_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_236_031209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_238_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_228_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_232_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_253_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_199_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_224_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_226_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_212_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_216_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_200_031209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_186_031209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_209_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_184_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_204_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_177_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_179_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_175_031209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_173_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_198_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_189_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_157_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-2_182_081209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM3-P1-1_117_041209_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_364_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_363_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_360_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_354_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_355_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_358_180609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_349_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4-P4-1_S00347_020210_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_70_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_73_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_69_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: HF-20889-(1)_Nsp

hyb_protocol: Mapping 500K arrays were hybridized according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using an Affymetrix model 640 hybridization oven.

scan_protocol: Mapping 500K arrays were scanned according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using a GS3000 scanner.

data_processing: Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time.  One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array.   The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  For Chromosome X, the average of the 20 normal female samples was used.   Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site.  The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.  GLAD segments composed of < 8 probesets were merged with the neighboring segment with the most similar copy number.

label_protocol: Following restriction enzyme digestion, biotin labeled DNA was prepared according to the Affymetrix protocol from 500ng of starting DNA (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005). The fluidics station model FS450 was used.


title: CBE_ROM2_62_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: HF-20931-(1)_Nsp


title: HF-21298-(1)_Nsp


title: CBE_ROM2_68_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM4_S00231_260110_GWS6

description: hybridized to 6.0 SNP arrays


title: HF-21648-(1)_Nsp


title: mir204_inhibition1_versus_Ctl_inhibition1

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

description: Experiment number 1 comparing the effect of inhibiting miR-204 in PASMC cells

hyb_protocol: Protocol from Agilent (G2545A Hybridization Oven User Manual version 2.0 + Agilent Microarray Hybridization Chamber User Guide version 1.0)

scan_protocol: Protocol from Agilent (Agilent G2565AA and G2565BA Microarray Scanner System User Manual Version 7.0)

data_processing: Data were extracted from scanned images using Feature extraction version 10.5.Text files were loaded into R (http://www.r-project.org/) using the limma package in BioConductor (http://www.bioconductor.org/). The background was subtracted prior to a normalization within array using loess normalization.

source_name: miR-204 inhibition 1 PASMC cells

label_protocol: Protocol from Agilent (Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) with Tecan HS Pro Hybridization version 5.7)

extract_protocol: Total RNA extraction was performed using mirVana Isolation Kit (catalog number AM1560)

value: pulmonary artery smooth muscle cells

source_name: Control inhibition 1 PASMC cells


title: HF-21664-(1)_Nsp


title: HF-21662-(1)_Nsp


title: CBE_ROM2_64_300609_GWS6

description: hybridized to 6.0 SNP arrays


title: HF-20996-(1)_Nsp


title: CBE_ROM2_60_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: PAH2_versus_Healthy2

description: Experiment number 2 comparing the second PAH patient to the second healthy one (Dye-swap)

source_name: pulmonary artery smooth muscle cells from person with pulmonary arterial hypertension

source_name: pulmonary artery smooth muscle cells from healthy person


title: HF-20757-(1)_Nsp


title: HF-20925-(1)_Nsp


title: HF-21666-(1)_Nsp


title: HF-21300-(1)_Nsp


title: mir204_inhibition1_versus_Ctl_inhibition2

description: Experiment number 2 comparing the effect of inhibiting miR-204 in PASMC cells

source_name: miR-204 inhibition 2 PASMC cells

source_name: Control inhibition 2 PASMC cells


title: HF-21652-(1)_Nsp

source_name: Ovarian tumor


title: HF-20917-(1)_Nsp


title: 2716GM

city: lleida

first: angela

last: canovas

state: lleida

address: 191, rovira roure

country: Spain

institute: irta

description: Duroc commercial line

hyb_protocol: Hybridisation protocol as recommented by Affymetrix using the Porcine Genome Array from Affymetrix.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A, as recommended by Affymetrix

data_processing: Data pre-processing, normalisation and class comparison analysis were carried out with the BRB-ArrayTools software version 3.7.1, which is available online at http://linus.nci.nih.gov/BRB-ArrayTools.html, as follows: microarray data normalisation was performed using the gcRMA algorithm, which corrects the intensity of each probe by its GC content; genes showing minimal variation across the set of arrays were excluded from the analysis, that is, only genes whose expression differed above 1.5 fold from the median in at least 20% of the arrays were retained. From the total 23937 spots of the array, 4299 spots passed these filtering conditions. For each probe, expression fold-change was calculated as the ratio between median values in both groups.

source_name: gluteus medius muscle from 190-days-old pigs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Duroc pigs were grown in standart commercial condictions, fed a commercial pellet diet and slaughtered at 190 days of age. Tissue samples were collected at slaughter, snap froxen in LN2 and stored at -80ºC until analysis

extract_protocol: total RNA was extracted from longissimus thoracis et lumborum muscle using Ribopure kit (AMBION) following the manufacturer's protocol

treatment_protocol: After slaughter, controled animals (n=350) were ranked based in 13 carcass, plasma and muscle fat deposition and fat composition traits. The top and bottom extreme of this distribution were selected to form the HIGH (n=10) and LOW (n=9) groups for longissimus thoracis et lumborum muscle microarrays experiment

tag: breed

value: Duroc commercial line

tag: group

value: gluteus medius muscle

value: 190 days-old


title: HF-20901-(1)_Nsp

value: primary ovarian tumor


title: HF-20923-(1)_Nsp


title: CBE_ROM2_45_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_44_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_49_180609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_31_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_41_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_42_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: HF-20921-(1)_Nsp


title: CBE_ROM2_23_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_30_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_20_300609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_24_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_13_070709_GWS6

description: hybridized to 6.0 SNP arrays


title: 1553GM

description: Duroc commercial line


title: CBE_ROM2_9_030709_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_8_300609_GWS6

description: hybridized to 6.0 SNP arrays


title: CBE_ROM2_4_020709_GWS6

description: hybridized to 6.0 SNP arrays


title: 2557GM

description: Duroc commercial line


title: 1917GM

description: Duroc commercial line


title: 1906GM

description: Duroc commercial line


title: 1497GM

description: Duroc commercial line


title: 1545GM

description: Duroc commercial line


title: 1450GM

description: Duroc commercial line


title: 2731GM

description: Duroc commercial line


title: Patient #7 second transplantation_Nsp

city: Belmont

first: Frederik

last: van Delft

address: 15 Cotswold Road

department: Haemato-oncology

institute: ICR

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labelled and hybridised to each array according the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing:
CEL and CHP (generated using Affymetrix Genotyping Console 4.0 using the BRLMM algorithm) files were visualised using CNAG version 3.0.
primary data description: The CHP files contain (1) SNP ID, (2) Chromosomal location, (3) Physical position, (4) dbSNP RS ID, (5) Genotype Call (SNP call): AA, AB, BB, NoCall, (6) Confidence.

label: Biotin

source_name: Patient #7 second transplantation

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukaemic blasts obtained from peripheral blood or bone marrow at diagnosis or after second transplantation using the Gentra Puregene DNA kit. DNA quantity and quality was assessed by using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: Stage

value: Second transplant


title: 1513GM

description: Duroc commercial line


title: 1503GM

description: Duroc commercial line


title: 2542GM

description: Duroc commercial line


title: 1901GM

description: Duroc commercial line


title: PAH1_versus_Healthy1

description: Experiment number 1 comparing the first PAH patient to the first healthy one

tag: cell type


title: 1488GM

description: Duroc commercial line


title: Stage 2 BV12_st2

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

country: France

institute: INRA

description: Syntax of the sample names:  arraySlide_embryoName_embryonicStage  Where the embryonic stage is either stage2, stage3, stage4 or stage5+

hyb_protocol: Prehybridisation in ExpressHybTM Hybridization Solution (Clontech) at 68°C during 1h (14ml). Hybridisation using new ExpressHybTM Hybridization Solution (Clontech) at 68°C overnight (10ml). Arrays were washed four times in 2X SSC, 1% SDS and once in 0.1X SSC, 0.5% SDS at 68°C for 30 min each. They were then exposed to phosphor-screens (Amersham) for 5 days.

scan_protocol: Scanner: STORM 760 from Molecular Dynamics. Raw data set : Feature extraction with Imagene 5.1 software from BioDiscovery (Proteigene)

data_processing: Intensity = Signal Mean Normalization = Signal mean were log2 transformed and normalized by the mean of the all intensities on the array  For the statistical analyses, described in the paper, the data was standardized  by gene.

organism: Bos taurus

source_name: Extra-embryonic tissues were immediately snap-frozen. Total RNA extracted with trizolTM (invitrogen). RNA quality  verified by intact A260/280 absorbance ratios.

label_protocol: aRNA was retro-transcribed and directly labelled with [alpha-33P]dATP as described  (Degrelle et al., 2008). 500ng of aRNA was mixed with 500ng of random hexamers in a volume of 25microl. The mixture was incubated at 70°C for 10 min and chilled on ice. cDNA was synthesised by the addition of 5microl 10X PCR buffer, 5microl 25mM MgCl2, 5 microl 0,1 mM DTT, 2,5microl 10mM mix dGTP, dCTP and dTTP, 2,5microl water, 50 microCi [alpha-33P]dATP and 200U Superscript II (Invitrogen) at 42°C for 50min. The RNA template was removed by the addition of 1microl RNAse H- and incubation at 37°C for 20 min. Labelled targets were then purified on Sephadex columns (G-50).

extract_protocol: IVT amplified RNA from each sample was synthesized with the MessageAmpTM aRNA Kit (Ambion) according to Degrelle et al., 2008 (RT on 1microg total RNA, IVT during 10h). aRNA was purified on Mini Quick Spin RNA columns (Roche Diagnostic).

treatment_protocol: Tissues were collected and immediately snap-frozen. Total RNA from stage2 (n=5), stage3 (n=5), stage4 (n=5) and stage5+ (n=5) embryos were extracted with TrizolTM (Invitrogen). RNA quality was first verified by A260/280 absorbance ratios.

tag: somatic tissue

value: no

tag: embryo

value: yes

tag: reproduction mode

value: AI

tag: embryonic stage


title: 2723GM

description: Duroc commercial line


title: 1446GM

description: Duroc commercial line


title: Patient #3_Nsp

description: Hybridized to 250K_Nsp

source_name: Patient #3

value: Diagnosis


title: Patient #7_Nsp

description: Hybridized to 250K_Nsp

source_name: Patient #7


title: Stage 4 BV108_st4


title: 2734GM

description: Duroc commercial line


title: Patient #3 second transplantation_Nsp

description: Hybridized to 250K_Nsp

source_name: Patient #3 second transplantation


title: 1567GM

description: Duroc commercial line


title: 1528GM

description: Duroc commercial line


title: 2195GM

description: Duroc commercial line


title: 2179GM

description: Duroc commercial line


title: Stage 5 BV145_st5


title: Stage 5 BV16_st5


title: Stage 5 BV130_st5


title: HF-21666-(1)_Sty


title: HF-21662-(1)_Sty


title: 2142GM

description: Duroc commercial line


title: 1502GM

description: Duroc commercial line


title: Stage 4 BV13_st4


title: Stage 2 BV193_st2


title: HF-21664-(1)_Sty


title: 1431GM

description: Duroc commercial line


title: 1412GM

description: Duroc commercial line


title: 1498GM

description: Duroc commercial line


title: HF-21648-(1)_Sty


title: Stage 3 BV174_st3


title: Stage 5 BV132_st5


title: 2701GM

description: Duroc commercial line


title: Stage 3 BV173_st3


title: HF-21298-(1)_Sty


title: HF-21652-(1)_Sty


title: Stage 4 BV196_st4


title: miRNA_quantification_PAH2

description: miRNA expression for PAH patient 2

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Data was processed using SDS 2.3 software (Applied Biosystems, Foster City, CA). Text files were imported using a custom script within R (http://www.r-project.org/). Data were normalized using the mean U6 Ct. Statistical signficance was assesed using limma.

label_protocol: Total RNA from primary culture cells was extracted using mirVana miRNA isolation kit (Ambion) and 500 ng of total RNAs was reverse transcribed using Megaplex RT primers and TaqMan miRNA Reverse transcription kit (Applied Biosystems). Newly synthesized cDNA followed by quantitative PCR using the TaqMan Low Density Array or TLDA technology (Plate A version 1, Applied Biosystems).

extract_protocol: Small RNA extraction was performed using mirVana Isolation Kit (Ambion catalog number AM1560)

value: pulmonary artery smooth muscle


title: 2178GM

description: Duroc commercial line


title: HF-20901-(1)_Sty


title: HF-21300-(1)_Sty


title: Stage 3 BV199_st3


title: 2556GM

description: Duroc commercial line


title: HF-20996-(1)_Sty


title: 2152GM

description: Duroc commercial line


title: HF-20889-(1)_Sty


title: 2550GM

description: Duroc commercial line


title: 1903GM

description: Duroc commercial line


title: Stage 4 BV64_st4


title: 2149GM

description: Duroc commercial line


title: Stage 2 BV201_st2


title: Stage 2 BV198_st2


title: Stage 3 BV48_st3


title: miRNA_quantification_Healthy2

description: miRNA expression for Healthy patient 2


title: HF-20931-(1)_Sty


title: HF-20925-(1)_Sty


title: Stage 2 BV200_st2


title: 1592GM

description: Duroc commercial line


title: Stage 5 BVT34_st5


title: miRNA_quantification_Healthy1

description: miRNA expression for Healthy patient 1


title: HF-20917-(1)_Sty


title: HF-20757-(1)_Sty


title: 1487GM

description: Duroc commercial line


title: Stage 3 BVT37_st3

description: Syntax of the sample names: arraySlide_embryoName_embryonicStage  Where the embryonic stage is either stage2, stage3, stage4 or stage5+


title: HF-20921-(1)_Sty


title: HF-20923-(1)_Sty


title: CLDN4 Replicate 2

status: Public on Dec 15 2010

first: Zhijian

last: Gao

address: Longwood 221

institute: BWH, Harvard Medical School

hyb_protocol: In all, 1.5μg of dye-labeled aRNA of each RNA preparation was fragmented and combined with hybridization controls using in situ Hybridization Kit Plus (Agilent Technologies, Santa Clara, CA). The GeneChips were hybridized overnight at 45℃ in a GeneMachine Hyb4 slide hybridization machine (Genomic Solutions, Ann Arbor, MI) and subsequently washed as recommended by the manufacturer.

scan_protocol: Scanning was performed on a ScanArray 4000XL Microarray Analysis System, and quantified using ScanArray Express (Perkin Elmer, Downers Grove, IL).

data_processing: Normalized sample to control ratios were used for analysis.  Dye swap comparisons were performed to assure that no bias was introduced by the hybridization process.

source_name: SKOV-3-IP-Luc ovarian cancer cell line

label_protocol: Dye-labeled aRNA was prepared as described in the Amino Allyl MessageAmp II aRNA Amplification kit Manual (Ambion Inc., Austin, TX). Briefly, 1 μg of purified total RNA was reverse transcribed to generate double-stranded cDNA using T7 Oligo primer and reverse transcriptase. Following second-strand cDNA synthesis and purification, biotin-labeled antisense RNA (aRNA) was modified with amino allyl UTP (aaUTP) by in vitro transcription and coupled with Cy3 and Cy5.

growth_protocol: SKOV-3 cells were were maintained in RPMI-1640 medium (Sigma-Aldrich) supplemented with 10%FBS

extract_protocol: Total RNAs were extracted and purified from the confluent cultures using the RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: CLDN4 gene was knocked down by CLDN4 siRNA lentivirus, and the knockdown effect was tested by Westen blot, q-RT-PCR and GFP luciference.

tag: cell line

tag: protocol

value: CLDN4 overexpression (control)

value: CLDN4 knockdown


title: 1483GM

description: Duroc commercial line


title: CLDN4 Replicate 3


title: MCCw324

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

description: Merkel cell carcinoma primary tumor RNA (macrodissected, includes stroma) from a 78 year old

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

source_name: Merkel cell carcinoma

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: 78 year old

value: Merkel cell carcinoma primary tumor

tag: sample type


title: Stage 4 BVU42-1_st4


title: SUM-149shNS_rep3

city: Detroit

first: Andrea

last: Baillo

address: 4100 John R

institute: Wayne State University

description:
replicate 3
SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: SUM-149 cells were cultured in Ham's F-12 medium supplemented with fungizone (0.5 µg/mL), gentamicin (5 µg/mL), hydrocortisone (1 µg/mL), insulin (5 µg/mL, and 5% fetal bovine serum. Sh4, shPld, and shNS were cultured in the same media, but with the addition of puromycin (1mg/ml).

extract_protocol: RNA was extracted with the QIAGEN Rneasy Plus kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanylizer and the Agilent RNA 6000 Nano Kit.

value: breast cancer SUM-149

tag: disease state

value: triple negative inflammatory breast carcinoma

tag: genotype/variation

value: non-silencing vector (shNS)


title: MCCw224

description: Merkel cell carcinoma skin metastasis tumor RNA (macrodissected, includes stroma) from a74 year old

tag: age

value: 74 year old


title: CLDN4 Replicate 1


title: SUM-149shPld_rep3

description:
replicate 3
SAMPLE 11

value: three AREG shRNA viruses (shPld)


title: Patient #7_Sty

description: Hybridized to 250K_Sty


title: MCCw225

description: Merkel cell carcinoma skin metastasis tumor RNA (macrodissected, includes stroma) from a 75 year old

value: 75 year old


title: MCCw251

description: Merkel cell carcinoma primary tumor RNA (macrodissected, includes stroma) from a 73 year old

value: 73 year old


title: SUM-149sh4_rep3

description:
replicate 3
SAMPLE 10

value: single AREG shRNA virus (sh4)


title: Patient #3_Sty

description: Hybridized to 250K_Sty


title: Patient #7 second transplantation_Sty

description: Hybridized to 250K_Sty

value: Second transplant


title: SUM-149_rep3

description:
replicate 3
SAMPLE 9

value: control


title: MCCw436

description: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 85+ year old

value: 85+ year old

value: Merkel cell carcinoma tumor


title: MCCw433

description: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 67 year old

value: 67 year old


title: 63972_MCCw168

description: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a male patient with poor prognosis (progression to distant met)

value: unknown


title: SUM-149shNS_rep2

description:
replicate 2
SAMPLE 8


title: MCCw432

description: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 44 year old

value: 44 year old


title: MCCw323

description: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 64 year old

value: 64 year old


title: SUM-149shPld_rep2

description:
replicate 2
SAMPLE 7


title: MCCw435

value: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 85+ year old


title: MCCw313

description: Merkel cell carcinoma primary tumor RNA (macrodissected, includes stroma) from a 77 year old

value: 77 year old

value: Merkel cell carcinoma primary tumor


title: Patient #3 second transplantation_Sty

description: Hybridized to 250K_Sty


title: MCCw307

description: Merkel cell carcinoma primary tumor RNA (macrodissected, includes stroma) from a 60 year old

value: 60 year old


title: MCCw434

description: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 74 year old

value: 74 year old


title: SUM-149_rep2

description:
replicate 2
SAMPLE 5

value: breast cancer SUM-149

value: triple negative inflammatory breast carcinoma


title: SUM-149sh4_rep2

description:
replicate 2
SAMPLE 6


title: SUM-149shNS_rep1

description:
replicate 1
SAMPLE 4

value: non-silencing vector (shNS)


title: MCCw284

description: Merkel cell carcinoma skin metastasis tumor RNA (macrodissected, includes stroma) from a 54 year old

value: 54 year old


title: MCCw281

description: Merkel cell carcinoma primary tumor RNA (macrodissected, includes stroma) from a 74 year old


title: MCCw264

description: Merkel cell carcinoma primary tumor RNA (macrodissected, includes stroma) from a 70 year old

value: 70 year old


title: 63968_MCCw155

description: Merkel cell carcinoma nodal metastasis tumor RNA (macrodissected, includes stroma) from a 66 year old

value: 66 year old


title: SUM-149shPld_rep1

description:
replicate 1
SAMPLE 3

value: three AREG shRNA viruses (shPld)


title: MCCw265

value: Merkel cell carcinoma tumor

value: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 67 year old


title: 63967_MCCw145

description: Merkel cell carcinoma recurrence tumor RNA (macrodissected, includes stroma) from a 66 year old

value: Merkel cell carcinoma recurrence tumor


title: miRNA_quantification_PAH1

description: miRNA expression for PAH patient 1

value: pulmonary artery smooth muscle


title: SUM-149_rep1

description:
replicate 1
SAMPLE 1

value: control


title: 63956_MCCL6

description: Merkel cell carcinoma nodal metastasis tumor RNA (macrodissected, includes stroma) from a 70 year old


title: SUM-149sh4_rep1

description:
replicate 1
SAMPLE 2

value: single AREG shRNA virus (sh4)


title: RER-Horse-4-Pool-Controls-Longissimus-replicate-2

city: EVRY

first: ERIC

last: BARREY

address: 3bis Christophe Colomb

institute: INSERM-INRA

description: Biological replicate RER longissimus lumborum muscle horse against the pool of control longissimus lumborum muscles of sound horses

hyb_protocol: The 5µg of aaRNA were completely vacuum-dried and resuspended in 9µL of coupling buffer and 11µL of dye, the tubes were mixed by vortexing and incubated for 30 minutes in the dark. The reaction was quenched by addition of 0.73 M Hydroxylamine and incubation for 15 minutes in the dark. Excess dye was removed from the labeled aaRNA by purification on a column. Purified labeled aaRNA were subsequently mixed with 10 µg poly (A) RNA, 10 µg yeast tRNA, 10 µg Cot 1 mouse RNA, then precipitated with 0.5 volumes of 7.5 M ammonium acetate and 2.5 volumes of absolute ethanol. After centrifugation at 16,000 x g for 45 minutes to 1 hour at 4°C, the supernatant was removed and the pellet was washed once with 700 µL of 70% ethanol. The samples were centrifuged at 16000 g for 15 minutes at 4°C. The aaRNA pellet was vacuum-dried for 1 minute and then dissolved in 50 µL of the hybridization mix preheated at 50°C: 2 x SSC, 0.1% SDS and 0.1% Salmon sperm DNA. It was mixed by vortexing and incubated in a water bath at 50°C to dissolve the mRNA pellet. Each slide was rehydrated in a humidified chamber for 1 hour at room temperature then dried in a dessicator for 1 hour. The slides were prehybridized in 0.3% Ethanolamine and 0.05 M Na Borate pH9. The slides were plunged 1 minute in water and dried by centrifugation for 7 minutes at 100 x g. The probe was heated for 2 minutes at 100°C and placed between the slide and a cover slip. The arrays were incubated overnight in a water bath at 50°C in a humidified slide chamber and washed in a first solution of 0.1x SSC with 0.1% SDS for 5 minutes followed by two washing steps in 0.1x SSC for 5 minutes each at room temperature, under agitation and safe from the light. The arrays were dried by centrifugation at 100 x g for 7 minutes. The image of fluorescence intensities of Cy3 (532 nm) and Cy5 (635 nm) were scanned separately with the laser scanner (GenePix® 4000B).

scan_protocol: The tiff images (10 µm/pixel) were analyzed using a specific software for microarray image analysis (GenePix® Pro 6.0 software) which allowed locating the spots automatically with manual control and quantifying the fluorescence intensity of each spot. For each microarray, the data output were the fluorescence intensities of all the spots corresponding to each gene. These data were imported in a genomic data analysis software (Gene Spring® software) to normalize the data before filtering and statistical analysis. For each sample (horse), a duplicate analysis (dye-swap) was made and the average fluorescence results were used.

data_processing: Then, all the results were normalized per spot and per microarray by the Lowess regression method in order to remove systematic variations. Finally, for each sample and each gene an expression ratio was obtained.    Ratio = Expression of each PSSM muscle / expression in the reference control muscle   For statistical analysis, a log transformation ratio was used to normalize the distribution.

organism: Equus caballus

source_name: Longissimus-muscle-RER-horse

label_protocol: After purification of the amino-modified RNA, monofunctional forms of the Cyanine 3 (Cy3) or Cyanine 5 (Cy5) fluorochrome were coupled to 5 µg of the studied sample and control sample by an indirect method: the ester groups linked to the fluorochromes were bound on the amino-allyl groups incorporated on the RNA during the in vitro transcription. The marked targets were then mixed and hybridized on the same chip for immediate comparison of the two nucleic acid populations. For each sample, a dye-swap (duplicate measurement) was performed to avoid asymmetry of marker affinity (Cy3 and Cy5). The two results were averaged before statistical results.

extract_protocol: Total RNA was extracted from tissues by a phenol-chloroform method (TRIZOL reagent).

tag: muscle type

value: Longissimus-muscle-RER

source_name: Longissimus-muscle-Pool-Control-horses

tag: reference

value: Longissimus-muscle-Pool-Control-horses


title: RER-Horse-4-Pool-Controls-Longissimus-replicate-1


title: RER-Horse-3-Pool-Controls-Longissimus-replicate-2


title: 63978_MCCw219

description: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 55 year old

value: 55 year old

tag: tissue


title: 63962_MCCL13

description: Merkel cell carcinoma nodal metastasis tumor RNA (macrodissected, includes stroma) from a 65 year old

value: 65 year old


title: 63964_MCCL17

description: Merkel cell carcinoma tumor RNA (recurrence, macrodissected, includes stroma) from a 73 year old

value: 73 year old


title: 63963_MCCL14

description: Merkel cell carcinoma nodal metastasis tumor RNA (macrodissected, includes stroma) from a  male patient with poor prognosis (progression to distant met)

value: unknown


title: RER-Horse-2-Pool-Controls-Longissimus-replicate-1


title: RER-Horse-5-Pool-Controls-Longissimus-replicate-2


title: RER-Horse-1-Pool-Controls-Longissimus-replicate-2


title: RER-Horse-5-Pool-Controls-Longissimus-replicate-1


title: 63969_MCCw156

description: Merkel cell carcinoma primary tumor RNA (macrodissected, from wide local excision, includes stroma) from a 65 year old

value: Merkel cell carcinoma primary tumor


title: RER-Horse-3-Pool-Controls-Longissimus-replicate-1


title: 63977_MCCw214

description: Merkel cell carcinoma recurrence tumor RNA (macrodissected, includes stroma) from a 47 year old

value: 47 year old


title: RER-Horse-2-Pool-Controls-Longissimus-replicate-2


title: 63975_MCCw200M

description: SAME PATIENT AS 63975_w200p: Merkel cell carcinoma nodal metastasis tumor RNA (macrodissected, includes stroma) from a 60 year old

value: 60 year old

value: SAME PATIENT AS 63975_w200p:Merkel cell carcinoma nodal metastasis tumor RNA (macrodissected, includes stroma) from a 60 year old


title: 63976_MCCw205

description: Merkel cell carcinoma metastasis tumor RNA (macrodissected, includes stroma) from a 45 year old

value: 45 year old

value: Merkel cell carcinoma metastasis tumor


title: 63975_MCCw200P

description: Merkel cell carcinoma primary tumor RNA (macrodissected, includes stroma) from a 60 year old


title: 63971_MCCw162

description: Merkel cell carcinoma metastasis tumor RNA (macrodissected, includes stroma) from a 58 year old

value: 58 year old


title: RER-Horse-1-Pool-Controls-Longissimus-replicate-1


title: RER-Horse-4-Pool-Controls-Gluteus-replicate-2

description: Biological replicate RER gluteus medius muscle horse against the pool of control gluteus medius muscles of sound horses

source_name: Gluteus-muscle-RER-horse

value: Gluteus-muscle-RER

source_name: Gluteus-muscle-Pool-Control-horses

value: Gluteus-muscle-Pool-Control-horses


title: RER-Horse-5-Pool-Controls-Gluteus-replicate-1


title: RER-Horse-4-Pool-Controls-Gluteus-replicate-1


title: RER-Horse-3-Pool-Controls-Gluteus-replicate-2


title: RER-Horse-5-Pool-Controls-Gluteus-replicate-2


title: wky_ctrl_3

city: Indianapolis

first: Joseph

last: Unthank

state: IN

address: 1001 West Tenth St

institute: Indiana University

description: Gene expression data from rat

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RG*34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Affymetrix Gene Chip Operating Software (GCOS) using the MAS 5.0 algorithm using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

organism: Rattus norvegicus

source_name: Rat mesentaric arteries

label_protocol: Biotinylated cRNA were prepared from <1ug of total RNA,  see McClintick, J. N., R. E. Jerome, et al. (2003). "Reproducibility of oligonucleotide arrays using small samples." BMC Genomics 4(1): 4.

extract_protocol: total RNA was purified by using an RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Collateral artery model created by adjacent arterial occlusion, see Unthank JL, Fath SW, et al. (1996). "Wall remodeling during luminal expansion of mesenteric arterial collaterals in the rat." Circulation Research 79: 1015.

tag: vessel type

value: control

tag: strain

value: wky


title: RER-Horse-3-Pool-Controls-Gluteus-replicate-1


title: wky_collat_2

description: Gene expression data from rat

value: collateral


title: 63955_MCCL4

description: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 77 year old

value: 77 year old

value: Merkel cell carcinoma tumor


title: RER-Horse-2-Pool-Controls-Gluteus-replicate-1


title: 63970_MCCw160

description: Merkel cell carcinoma nodal metastasis tumor RNA (macrodissected, includes stroma) from a 63 year old

value: 63 year old


title: wky_ctrl_2

description: Gene expression data from rat


title: RER-Horse-2-Pool-Controls-Gluteus-replicate-2


title: wky_collat_1

description: Gene expression data from rat


title: 63974_MCCw197

description: Merkel cell carcinoma primary tumor RNA (macrodissected, includes stroma) from an 85+ year old

value: 85+ year old


title: wky_collat_3

description: Gene expression data from rat


title: 63953_MCCL1

description: Merkel cell carcinoma tumor RNA (macrodissected, includes stroma) from a 63 year old


title: MCCw282

description: Merkel cell carcinoma skin metastasis (regional) tumor RNA (macrodissected, includes stroma) from a 80 year old

value: 80 year old


title: dig1ste12-mChLacI_LacOFUS1_3

city: San Francisco

first: Hiten

last: Madhani

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: No further information

hyb_protocol: arrays blocked with Agilent aCGH blocking buffer and each probe was hybridized 1:1 using Agilent hybridization buffer.  Hybes were allowed to proceed for 40hrs at 65 degrees.

scan_protocol: Scanned with GenePix 4000B at 5uM

data_processing: Median background subtracted first, then normalized using a loess algorithm

source_name: cells grown in YPAD

label_protocol: DNA was amplified using strand displacement amplification.  Random 9-mers were used to prime followed by amplification with dNTPs and exo- Klenow.  During the last amplification step, a mix of aadUTP:dTTP was used to generate amino-allyl-DNA probe that could be labeled with Cy3 or Cy5 dye.

growth_protocol: Cells were diluted from saturated cultures into -Ura media for 4hrs.  Cells were again diluted into YPAD, grown for another 4hrs and collected.  All growth done at 30 degrees.

extract_protocol: Culture was crosslinked with 1.5mM EGS for 30min followed by 1% formaldehyde for 30min.  Crosslinking was quenched with 0.125M glycine for 5min.  DNA was extracted by bead beating 6x1min followed by light sonication (2x5min on low setting).  mCherry-LacI was immunoprecipitated using an anti-DsRed polyclonal antibody (1:100 dilution).

value: ste12::NATMX, LacOarray-HISMX-pFUS1-FUS1 at FUS1 locus, mCherry-LacI, dig1::KANMX

value: IP for mCherry-LacI bound DNA

value: input


title: RER-Horse-1-Pool-Controls-Gluteus-replicate-1


title: shr_collat_2

description: Gene expression data from rat

value: shr


title: shr_ctrl_1

description: Gene expression data from rat


title: wky_collat_4

description: Gene expression data from rat


title: shr_collat_1

description: Gene expression data from rat


title: shr_ctrl_2

description: Gene expression data from rat


title: RER-Horse-1-Pool-Controls-Gluteus-replicate-2


title: dig1ste12-mChLacI_LacOFUS1_4

description: No further information

extract_protocol: Culture was crosslinked with 1.5mM EGS for 30min followed by 1% formaldehyde for 30min.  Crosslinking was quenched with 0.125M glycine for 5min.  DNA was extracted by bead beating 6x1min followed by light sonication (2x5min on low setting).


title: shr_collat_4

description: Gene expression data from rat


title: shr_ctrl_3

description: Gene expression data from rat


title: dig1-mChLacI_LacOFUS1_3

description: No further information

value: Ste12-eGFP-HYGMX, LacOarray-HISMX-pFUS1-FUS1 at FUS1 locus, mCherry-LacI, dig1::KANMX


title: shr_collat_3

description: Gene expression data from rat


title: dig1-mChLacI_LacOFUS1_4

description: No further information


title: WT-mChLacI_LacOFUS1_4

description: No further information

value: Ste12-eGFP-HYGMX, LacOarray-HISMX-pFUS1-FUS1 at FUS1 locus, mCherry-LacI


title: shr_ctrl_4

description: Gene expression data from rat


title: WT-mChLacI_LacOFUS1_3

description: No further information


title: dig1-mChLacI_LacOFUS1_2

description: No further information

value: Ste12-eGFP-HYGMX, lacoarray-hismx-pfus1-fus1 at fus1 locus, mcherry-laci, dig1::KANMX

value: IP


title: dig1ste12-mChLacI_LacOFUS1_1

description: No further information


title: dig1_LacOFUS1_1

description: No further information

value: Ste12-eGFP-HYGMX, lacoarray-hismx-pfus1-fus1 at fus1 locus, dig1::KANMX


title: WT-mChLacI_LacOFUS1_xF_1

description: No further information

growth_protocol: Cells were diluted from saturated cultures into -Ura media for 4hrs.  Cells were again diluted into YPAD, grown for another 4hrs and collected after treatment with 5uM alpha factor for 1hr.  All growth done at 30 degrees.


title: dig1ste12-mChLacI_LacOFUS1_2

description: No further information


title: WT_LacOFUS1_1

description: No further information

value: Ste12-eGFP-HYGMX, LacOarray-HISMX-pFUS1-FUS1 at FUS1 locus


title: WT-mChLacI_LacOFUS1_2

description: No further information


title: dig1-mChLacI_LacOFUS1_1

description: No further information


title: Total epidermal cells, all layers Sample 1

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS 5.0

source_name: Human epidermis from brest reduction

label_protocol: Standard Affymetrix protocol

extract_protocol: Standard Affymetrix protocol

value: Total epidermal cells

tag: donor


title: Suprabasal epidermal cells, Sample 1

tag: cell type

value: Suprabasal epidermal cells


title: wky_ctrl_1

description: Gene expression data from rat

value: control

value: wky


title: Suprabasal epidermal cells, Sample 2  replicate


title: PCT SHBG_testosterone_rep1

city: Vancouver

first: Geoffrey

middle: L

last: Hammond

state: British Columbia

address: 950 West 28th Ave

department: OB/Gyn

country: Canada

institute: University of British Columbia

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with the BeadStudio Program from Illumina.

source_name: PCT cells constitutively expressing wild-type human SHBG, 24h testosterone

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

growth_protocol: To generate PCT cells that constitutively express wild-type human SHBG or the human SHBG mutant deficient in steroid-binding, we transfected PKSV-PCT cells with cDNA constructs within pRC/CMV. Cell lines expressing human SHBG (PCT-SHBG) or a human SHBG mutant (PCT-SHBG S42L) with no detectable steroid-binding activity were obtained by limiting dilution cloning and screening the culture medium for secreted SHBG using an ultra-sensitive time-resolved fluorescence immunoassay. Cells were cultured in DMEM/F12 medium supplemented with 2% fetal bovine serum, insulin (5 μg/ml), dexamethasone (5 x 10-8M), selenium (60nM), transferrin (5 μg/ml), triiodothyronine (5 x 10-8M), EGF (10 ng/ml), D-glucose (20 mM), penicillin (100 U/mol), and streptomycin (100 μg/ml).

extract_protocol: RNA was extracted with the QIAGEN RNeasy mini kit with DNaseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol: 100 nM Testosterone or 100 nM 5a-dihydrotestosterone treatment of cells for 24 hours followed by 3 days in steroid-free medium.

value: PKSV-PCT

tag: shbg expression

value: wild-type SHBG

tag: treatment

value: testosterone


title: D.rerio_GFP+ cells vs GFP- cells from 48hpf embryos tails_2 Replicate 2

city: Bethesda

first: Viviana

last: Gallardo

address: 50 South Dr. Bldg 50. Room 5535

institute: NHGRI/NIH

hyb_protocol: 200 picomoles of Cy3 and 100 picomoles of Cy5 labeled cRNAs are put in a total volume of 24 ul (qsp with DEPC H20) and 6 microliter of 5x fragmentation buffer from Affymetrix. the mixture is incubated at 94 ¡C for 15 minutes. Then, 25 ul of 2X hybridization buffer (250 _l Formamide, 250 _l 20xSSC and 20 _l 10%SDS). The mixture is then denatured for 2 minutes and applied on the Maui (BioMicro Systems, Inc) hybridization chamber/ array slide sandwich. The hybridization is performed at 45 degre for 20 hours.

scan_protocol: Microarray slides were scanned with a confocal laser (Agilent Technologies, Palo Alto, CA)

data_processing: PLab/DeArray. Data points with quality values below 0.7 were eliminated and the datasets were Lowess normalized. Normalized data were log-transformed and GFP+ and GFP- values were separately averaged over the eight experiments. Fold differences were calculated from log averages and Student’s t-test with Benjamini and Hochberg correction to generate p-values that were used to determined statistical significance. FileMaker Pro 9 (FileMaker, Inc.) and GeneSifter (http://www.genesifter.net/) softwares were used.

organism: Danio rerio

source_name: D.rerio_GFP-cells from 36hpf embryo tails_2 rep2

label_protocol: Approximately 500 ng to 800 ng RNA was linearly amplified by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) with yields ranging from 12 to 30 µg of aRNA. aRNA samples were split and labeled, half with Cy3 mono NHS ester and half with Cy5 mono NHS ester (CyDyes from GE Healthcare; post-labeling reagents from the MessageAmp II kit).

growth_protocol: Embryos were grown at 28.5°C in E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, and 0.1% Methylene Blue)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: We used the tails of the Cldnb:gfp transgenic embryos in order to avoid recovering GFP-expressing cells in tissues other than the lateral line. Fish were anaesthetized and the tail was transected with a sharp scalpel adjacent to the end of the yolk extension. Tails of embryos were recovered from 36 hpf (for isolating primordium cells) or from 48 hpf (for neuromast cells) embryos, then transferred to Hank's medium containing 0.25% trypsin and 1mM EDTA and incubated for 15 to 30 min at room temperature during which they were dissociated mechanically by pipetting them up and down every 5 minutes. The digestion was stopped by adding fetal bovine serum to 10% and cell suspensions were then filtered through 40 µm nylon mesh, washed twice with PBS, pelleted by centrifugation at 600Xg for 2 minutes and resuspended in L-15 medium supplemented with 10% fetal bovine serum. FACS of single cell suspensions (GFP+ cell fraction and GFP- cell fraction) was performed at room temperature using a FACSAria.

tag: developmental stage

value: 48 hpf zebrafish embryo

value: GFP- cell from embryonic tails

tag: genotype

value: Cldnb:gfp transgenic

source_name: D.rerio_GFP+cells from 36hpf embryo tails_2 rep2

value: GFP+ cell from embryonic tails


title: PCT SHBG_testosterone_rep2

tag: cell line


title: PCT SHBG_testosterone_rep3


title: Total epidermal cells, all layers Sample 2


title: Suprabasal epidermal cells, Sample 2


title: PCT SHBG S42L_testosterone_rep3

source_name: PCT cells constitutively expressing the human SHBG S42L mutant, 24h testosterone

value: SHBG S42L mutant


title: D.rerio_GFP+ cells vs GFP- cells from 48hpf embryos tails_2 Replicate 3

source_name: D.rerio_GFP-cells from 36hpf embryo tails_2 rep3

source_name: D.rerio_GFP+cells from 36hpf embryo tails_2 rep3


title: WT-mChLacI_LacOFUS1_1

description: No further information

value: Ste12-eGFP-HYGMX, LacOarray-HISMX-pFUS1-FUS1 at FUS1 locus, mCherry-LacI

value: input


title: D.rerio_GFP+ cells vs GFP- cells from 48hpf embryos tails_1 Replicate 4

source_name: D.rerio_GFP-cells from 48hpf embryo tails_1 rep4

source_name: D.rerio_GFP+cells from 48hpf embryo tails_1 rep4


title: PCT SHBG S42L_testosterone_rep2


title: D.rerio_GFP+ cells vs GFP- cells from 48hpf embryos tails_2 Replicate 1

source_name: D.rerio_GFP-cells from 36hpf embryo tails_2 rep1

source_name: D.rerio_GFP+cells from 36hpf embryo tails_2 rep1


title: D.rerio_GFP+ cells vs GFP- cells from 48hpf embryos tails_2 Replicate 4

source_name: D.rerio_GFP-cells from 36hpf embryo tails_2 rep4

source_name: D.rerio_GFP+cells from 36hpf embryo tails_2 rep4


title: 55C_REP2

city: Quebec

first: Eve-Lyne

last: Sylvestre

state: Quebec

address: 2440 Boul Hochelaga

institute: Université Laval

description:
Library was constructed with RNA extracted from 14 GV oocytes (CREATOR SMART, Clontech)
13724628_55°C_647

hyb_protocol: Sample probe was hybridized in technical replicate (2 replicates single-channel, on two slides) in SlideHyb™ Glass Array Hybridization Buffer #1 (Ambion, Streetville, Canada) for 18 hours at 45, 50, and 55°C respectively. Glass slides were then washed respectably at either 45, 50, or 55°C twice with 2X SCC/0.5% SDS for 15 min, twice with 0.5X SSC/0.5% SDS for 15 min, and rapidly washed in 1X SSC and H2O.

scan_protocol: Slides were scanned using the VersArray ChipReader System (Bio-Rad) at 5 microns resolution and analyzed using the ChipReader and ArrayPro Analyzer software (Media Cybernetics, San Diego, CA).

data_processing: Data processed/normalized with ChipReader and ArrayPro Analyzer software (Media Cybernetics, San Diego, CA).  Data were first normalized by Loess (by replicate within a same T°C), and signal was defined as present if intensity was above the threshold, calculated as negative and exogen DNA control cells mean  intensity plus 1x standard deviation (GFP, plant and Alien DNA (Stratagene), SSC) for each array.

source_name: human oocyte cDNA library 55°C

label_protocol: 2µg  of cDNAs  Purified PCR were then labelled using ULS Labeling Kit Alexafluor 547 and 647 dye pack (Kreatech, Amsterdam, The Netherlands); Diagnostics) according to manufacturer's instructions and unincorporated dyes were removed with Qiaquick PCR purification kit.

extract_protocol: Total RNA was isolated from 14 GV using PicoPure RNA isolation kit (Molecular Devices, Sunnyvale, CA) following manufacturer's instruction. DNase treatment was performed with Rnase-free DNase I (Qiagen, Missisauga, On, Canada). RNA quantification and integrity were assessed with a 2100 BioAnalyzer apparatus (Agilent, Mississauga, On, Canada) using the RNA 6000 Picochip a Bioanalyzer (Agilent). The full-length human oocyte cDNA library was generated using the Creator SMART cDNA Library Construction Kit (Clontech, Mountain View, CA). a unique human probe was generated from plasmid library by PCR amplification using 50X Advantage 2 polymerase Mix (Clontech), and primers corresponding to pDNR-LIB sequence (Up : 5’- AGTCGACGGTACCGGACATA-3’, Low : 5’-GCCAAACGAATGGTCTAGAAA-3’) for 17 thermal cycles.

tag: library

value: Human GV full-length oocyte cDNA library

tag: hybridization temperature


title: 55C_REP1

description:
Library was constructed with RNA extracted from 14 GV oocytes (CREATOR SMART, Clontech)
13724581_55°C_547


title: T1C3 vs IC8 melanoma cell line swap2

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

institute: Université Lyon I

description: RNA from T1C3 and IC8 cells cultured to 70% confluency, hybridization T1C3 vs IC8

hyb_protocol: Direct hybridization sample (Cy5 vs Cy3)

scan_protocol: Axon 4000B Genepix software

data_processing: Loess normalization

source_name: IC8 melanoma cell line

label_protocol: Ambion / Amino Allyl MessageAmp II aRNA kit

extract_protocol: Tripure extraction Reagent

value: IC8 melanoma cells

source_name: T1C3 malanoma cell line

value: T1C3 melanoma cells


title: T1C3 vs IC8 melanoma cell line 2

source_name: T1C3 melanoma cell line


title: D.rerio_GFP+ cells vs GFP- cells from 48hpf embryos tails_1 Replicate 2

source_name: D.rerio_GFP-cells from 48hpf embryo tails_1 rep2

source_name: D.rerio_GFP+cells from 48hpf embryo tails_1 rep2


title: PCT SHBG_DHT_rep2

source_name: PCT cells constitutively expressing wild-type human SHBG, 24h DHT

value: 5a-dihydrotestosterone (DHT)


title: PCT SHBG_DHT_rep3


title: 50C_REP2

description:
Library was constructed with RNA extracted from 14 GV oocytes (CREATOR SMART, Clontech)
13724580_50°C_547

source_name: human oocyte cDNA library 50°C


title: 50C_REP1

description:
Library was constructed with RNA extracted from 14 GV oocytes (CREATOR SMART, Clontech)
13724626_50°C_647