title: Pig-control-7day-rep3

city: wuhan

first: yongtao

last: Li

state: Hubei

address: shizisan street,number 1

institute: Unit of Animal Infectious Diseases, National Key Laboratory of Agricultural

description: We only selected 3 pieces of lung tissues of 3 different pigs from each pool of control 3 day, infected 3 day, control 7 day and infected 7 day respectively.

hyb_protocol: 0.875 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 4x44K Porcine Oligo Microarrays） for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: Agilent Feature Extraction was used for reading the data, Scan resolution 5μm, PMT 100%, 10% and LOWESS normalization

organism: Sus scrofa

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer(Shanghaibio, China).

growth_protocol: A total of 30 piglets of high-health status were obtained from a commercial herd and were raised in isolated facilities.Prior to challenge, all pigs'sera  were confirmed negative for the antibodies against H1 and H3 swine influenza viruses by HI (Hemagglutination Inhibition) Test and ELISA.

extract_protocol: RNA extraction from pig lungs prepared from the same lesion, areas of localized infection (with viral mRNA present) was performed using TRIzol following standard instructions (Invitrogen, Carlsbad, CA) and a clean-up was carried out using RNeasy columns (Qiagen, Beijing, China). RNA integrity and concentration were evaluated by Agilent 2100 Bioanalyzer followed by manufacturer's instructions (Agilent Technologies, Palo Alto, CA).

treatment_protocol: The animals were sacrificed to collect lung tissues, which were immediately preserved in liquid nitrogen and subsequently stored in a -80℃ freezer.

value: Lung

tag: disease state


title: Pig-infected-7day-rep2

status: Public on Apr 27 2011

type: RNA

country: China

molecule: total RNA

tag: tissue

value: H1N1 infected


title: Pig-infected-7day-rep3


title: Pig-control-7day-rep2


title: Gastric cancer cell, MPS-1 knockdown, rep1

city: Shanghai

first: Zhongyin

last: Yang

address: NO.197 Ruijin er road

department: Department of Surgery

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: Gene expression in MPS-1 knockdown gastric cancer cells

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction software 9.1(Agilent technologies, Santa Clara, CA, US) with default settings, scan resolution=5μm, PMT 100%, 10%.

organism: Homo sapiens

source_name: Gastric cancer cell, MPS-1 knockdown, replicate 1

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: cell line

value: gastric cancer cell line

tag: genotype/variation

value: MPS-1 knockdown


title: N2_mixed_replica1 [ChIP03]

type: genomic

city: Worcester

first: Kirsten

last: Hagstrom

state: MA

address: 377 Plantation street

department: Molecular Medicine

country: USA

institute: University of Massachusetts, Medical School

description: LIN-54 ChIP-chip on wild type worms (biological replica 1)

hyb_protocol: Samples were then hybridized on the Nimblegen C. elegans ChIP-chip 385K Whole-Genome Tiling - 3 Array Set (GPL7482, GPL7483, GPL7484) using standard Nimblegen protocols.

scan_protocol: Arrays were scanned on Nimblegen's 2-μm, high-resolution MS 200 Microarray Scanner. Data was extracted from the images at Roche NimbleGen, according to the protocol described NimbleScan v2.5 Software User's Guide, Version 2.5, October 2008.

data_processing: Raw ChIP-chip data were retrieved from Nimblegen and analyzed using MA2C (Song et al., Genome Biol, 2007). MA2C analysis was performed with the following settings: # MA2C Score Method (median), Band Width (300), p-value cut off (-6), and other parameters were set as default. WS180 was used to annotate gene names. MA2C-defined LIN-54 ChIP peaks are listed in the file 'GSE28852_MA2C_processed_LIN-54_ChIP_peaks.txt'.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: LIN-54 ChIP DNA

label_protocol: For each experiment, a control sample as well as an experimental sample were prepared with a concentration of ~250 ng/ul. At least 4 ug of each of these samples was then sent to Nimblegen where the samples were labeled with respectively Cy-3 and Cy-5 dyes using standard Nimblegen protocols.

extract_protocol: ChIP was performed as described (Mukhopadhyay et al., Nat. Protocol., 2008). Briefly, mixed stage wild-type worms were cultured in S-basal at 20oC. Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with anti-LIN-54 antibody or pre-bleed antibody control. ChIP samples including the input were subjected to two rounds of linear amplification, using the genomePlex complete whole genome amplification kit (Sigma), and minimum difference between original precipitates and amplified precipitate confirmed by qPCR.

treatment_protocol: Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with anti-LIN-54 antibody.

tag: strain

value: N2 (Bristol)

tag: antibody

value: LIN-54 antibody; non-commercial antibody raised in guinea pig, see Harrison et al. PNAS 2006

tag: developmental stage

value: mixed staged worm culture

source_name: input DNA from pre-bleed antibody control.

treatment_protocol: Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with  pre-bleed antibody control.


title: Gastric cancer cells_negative control_1_rep2

description: Gene expression in negative control gastric cancer cells

source_name: Gastric cancer cell, negative control, replicate 2

value: control


title: Gastric cancer cell, MPS-1 knockdown, rep2

source_name: Gastric cancer cell, MPS-1 knockdown, replicate 2


title: Cancer sample 21 vs. paired normal control

first: Wenzhang

last: Wang

address: Handan Road 220#

institute: Fudan University

description: paired normal tissue

hyb_protocol: The samples are hybridized on the miRCURY™ LNA Array (v.11.0)

scan_protocol: Scanned on an Axon GenePix 4000B. Images were quantified using GenePix pro V6.0.

data_processing: LOWESS and VSN normalized

source_name: pancreatic cancer tissue

label_protocol: The samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit

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

value: pancreatic cancer tissue

source_name: paired normal tissue

value: paired normal tissue


title: Cancer sample 38 vs. paired normal control

description: paired normal tissue


title: Pig-infected-3day-rep3

description: We only selected 3 pieces of lung tissues of 3 different pigs from each pool of control 3 day, infected 3 day, control 7 day and infected 7 day respectively.Gene expression of the infected pig lung at 3 day (replicate 3)


title: Gastric cancer cell, MPS-1 knockdown, rep3

source_name: Gastric cancer cell, MPS-1 knockdown, replicate 3


title: Cancer sample 35 vs. paired normal control

description: paired normal tissue


title: mENT1-KO Heart_b

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

country: Canada

institute: University of Alberta

description: gene expression in knockout vs wild type mice

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4648A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  The data was them imported into GeneSpring 10 and default normalization (75th percentile) procedures were used. The kidney samples were normalized as a group and the heart samples normalized seperately as another group.

organism: Mus musculus

source_name: heart, mENT1 knockout

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: A polytron was used to disrupt tissue in the pressence of Trizol (SigmaAldrich). The sample was then phenol/chloroform extracted, the aquaous layer was adjusted to 30% ethanol and applied to an RNeasy column (Qiagen) according to the manufacturer's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genotype

value: mENT1 knockout

tag: genetic background

value: FVB/N

value: heart


title: Gastric cancer cells_negative control_1_rep3

source_name: Gastric cancer cell, negative control, replicate 3


title: Pig-infected-7day-rep1


title: Pig-infected-3day-rep1


title: Pig-control-3day-rep3


title: Pig-control-7day-rep1


title: Pig-control-3day-rep2


title: Pig-control-3day-rep1


title: Gastric cancer cells_negative control_1_rep1

source_name: Gastric cancer cell, negative control, replicate 1


title: PBL, 8 wpi, pool 2

status: Public on Apr 26 2011

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description:
PBL8WP2
Time-point 4 of 6, biological replicate 2 of 2.

hyb_protocol: Hybridized according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays.

scan_protocol: Arrays were scanned using a GenePix 4100A at a resolution of 5 microns.

data_processing: GenePix Pro 6.0 was used for spot to grid alignment, feature extraction and quantification. After removal of flagged spots, lowess normalization was performed.

organism: Salmo salar

source_name: PBL of infected salmon, 8 wpi

label_protocol: Amplified and labeled according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol using the Agilent Quick Amp Labelling Kit.

growth_protocol: Salmon (average weight 50g) were kept in tanks with sea water.

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with PureLink RNA mini kits.

treatment_protocol: Injection of PMCV was performed after sedation (benzocaine, 30-40 mg L-1). Infected groups received an intraperitoneal (i.p.) injection dose (0.2 ml) of a supernatant from a GF-1 cell line (derived from the fin tissue of orange-spotted grouper, Epinephelus coioides) infected with PMCV.

value: peripheral blood leukocytes

value: post-smolt

tag: infection

value: piscine myocarditis virus (PMCV)

tag: time (wpi)

source_name: PBL of control salmon, 8 wpi

value: post-smelt


title: ES ToR G1 phase vs. S phase DNA rep1

city: Jerusalem

first: Itamar

last: Simon

address: Ein Karem Campus

department: Molecular Biology

country: Israel

institute: The Hebrew university

description: G1/S ES rep1 LogRatio

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent  scanner. Images were quantified using Agilent Feature Extraction Software

data_processing: Data obtained from log2 of processed Red signal/processed Green signal.

source_name: ES cells, G1 phase DNA, replicate 1

label_protocol: 250-1000 ng DNA was labeled with either dUTP-cy3 or dUTP-cy5 by direct labeling using Agilent labeling kit

extract_protocol: DNA was extracted using a strandard protocol - incubation with lysis buffer that included ProteinaseK, that was followed by phenol-chlorophorm extraction, sonication of the DNA to smaller fragments (300-1000bp) and Ethanol precipitationand purification using QIAGEN PCR purification kit.

value: mES (mouse embryonic stem cells)

source_name: ES cells, S phase DNA, replicate 1


title: Spleen, 8 wpi, pool 2

description:
S8WP2
Time-point 4 of 6, biological replicate 2 of 2.

source_name: Spleen of infected salmon, 8 wpi

value: spleen

source_name: Spleen of control salmon, 8 wpi


title: Kidney, 8 wpi, pool 1

description:
K8WP1
Time-point 4 of 6, biological replicate 1 of 2.

source_name: Kidney of infected salmon, 8 wpi

value: mid-kidney

source_name: Kidney of control salmon, 8 wpi


title: NPC ToR S phase vs. G1 phase DNA rep2

description: G1/S NPC rep2 LogRatio

source_name: NPC cells, S phase DNA, replicate 2

value: NPC (neuronal progenitor cells derived from the same ES line)

source_name: NPC cells, G1 phase DNA, replicate 2


title: NPC ToR G1 phase vs. S phase DNA rep1

description: G1/S NPC rep1 LogRatio

source_name: NPC cells, G1 phase DNA, replicate 1

source_name: NPC cells, S phase DNA, replicate 1


title: RBC, 8 wpi, pool 1

description:
RBC8WP1
Time-point 4 of 6, biological replicate 1 of 2.

source_name: RBC of infected salmon, 8 wpi

value: red blood cells

source_name: RBC of control salmon, 8 wpi


title: Kidney, 8 wpi, pool 2

description:
K8WP2
Time-point 4 of 6, biological replicate 2 of 2.


title: ES ToR G1 phase vs. S phase DNA rep2

description: G1/S ES rep2 LogRatio

source_name: ES cells, G1 phase DNA, replicate 2

source_name: ES cells,S phase DNA, replicate 2


title: PBL, 8 wpi, pool 1

description:
PBL8WP1
Time-point 4 of 6, biological replicate 1 of 2.


title: Spleen, 8 wpi, pool 1

description:
S8WP1
Time-point 4 of 6, biological replicate 1 of 2.


title: small intestine, distal part, 45E% fat, replicate 10

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA in Bioconductor, applying the emperical Bayes (EB) model for background estimation. Arrays were normalized per intestinal part.

label: biotin

source_name: distal small intestine, scraped off epithelial (mucosal) cells, 45E%

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix, as per the manufacturer's instructions.

growth_protocol: Male C57BL/6J mice were obtained from Charles River at three weeks of age and were maintained on normal lab chow. Mice were housed in pairs.

extract_protocol: For RNA isolation, small intestine was excised, divided in three equal parts, cut open longitudinally, and washed with PBS. The mucosa was scraped and snap frozen in liquid nitrogen. Total RNA was extracted from intestinal scrapings with TRIzol reagent (Invitrogen, Carlsbad, CA), treated with DNAse and purified on columns using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.

treatment_protocol: At twelve weeks of age, all mice received a control, low-fat diet as a run-in diet for four weeks. After the run-in period, mice were divided in four groups that received diets containing 45, 30, 20, or 10 energy % (10E%) of dietary fat (n=10 per group). The 10E% diet served as reference (control) diet. Palm oil was the main fat source in the diets. The only other variable in the diets was the amount of corn starch.

tag: background strain

tag: gender

value: male

tag: age

value: 20 weeks

value: distal small intestine

tag: cell type

value: mucosal

tag: dietary fat


title: Liver, 8 wpi, pool 2

description:
L8WP2
Time-point 4 of 6, biological replicate 2 of 2.

source_name: Liver of infected salmon, 8 wpi

value: liver

source_name: Liver of control salmon, 8 wpi


title: Liver, 8 wpi, pool 1

description:
L8WP1
Time-point 4 of 6, biological replicate 1 of 2.


title: Pig-infected-3day-rep2

value: Lung

value: H1N1 infected


title: Heart, 8 wpi, pool 3

description:
H8WP3
Time-point 4 of 6, biological replicate 3 of 4.

source_name: Heart of infected salmon, 8 wpi

value: heart

source_name: Heart of control salmon, 8 wpi


title: Heart, 8 wpi, pool 4

description:
H8WP4
Time-point 4 of 6, biological replicate 4 of 4.


title: small intestine, distal part, 45E% fat, replicate 4


title: small intestine, distal part, 45E% fat, replicate 1


title: small intestine, distal part, 45E% fat, replicate 9


title: small intestine, distal part, 45E% fat, replicate 6


title: small intestine, distal part, 45E% fat, replicate 5


title: small intestine, distal part, 45E% fat, replicate 2


title: small intestine, distal part, 45E% fat, replicate 8


title: RBC, 8 wpi, pool 2

description:
RBC8WP2
Time-point 4 of 6, biological replicate 2 of 2.


title: small intestine, distal part, 45E% fat, replicate 7


title: small intestine, distal part, 30E% fat, replicate 7

source_name: distal small intestine, scraped off epithelial (mucosal) cells, 30E%


title: Control bone marrow - Biological Replicate 2 - Technical Replicate 2

city: Roma

first: Federica

last: Moschella

address: Viale Regina Elena 299

department: Cell Biology and Neurosciences

country: Italy

institute: Istituto Superiore di Sanità

description: Biological replicate 2 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated

hyb_protocol: Labeled samples, diluted in Hybridization buffer (5X SSC; 50% Formamide; salmon sperm-DNA 100 ng/ul; 0.1% SDS), were applied to microarrays enclosed in Corning hybridization chambers - 42°C over night.

scan_protocol: Slides were scanned on GenePix® 4200A instrument (Axon Instruments) Images were quantified using GenePix Pro 6.0

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. BRBArrayTools software was used.

source_name: bone marrow cells

label_protocol: aRNA were obtained using the Ambion Amino Allyl MessageAmp™ II aRNA Amplification Kit, according to the manufacturer's instructions. 12 µg of aRNA were labeled with Amersham Cy5 (RNA samples) or Cy3 (Reference RNA)

extract_protocol: Total RNA was extracted using Qiagen RNeasy Midi Kit following manufacturer's instructions

treatment_protocol: Untreated mice

value: bone marrow cells

treatment_protocol: Mice were treated with 83 mg/Kg cyclophosphamide

value: pool of untreated bone marrow cells

tag: sample type

value: reference


title: small intestine, distal part, 45E% fat, replicate 3


title: small intestine, distal part, 20E% fat, replicate 9

source_name: distal small intestine, scraped off epithelial (mucosal) cells, 20E%


title: small intestine, distal part, 30E% fat, replicate 9


title: small intestine, distal part, 30E% fat, replicate 6


title: small intestine, distal part, 30E% fat, replicate 4


title: small intestine, distal part, 30E% fat, replicate 5


title: small intestine, distal part, 30E% fat, replicate 10


title: small intestine, distal part, 30E% fat, replicate 1


title: small intestine, distal part, 20E% fat, replicate 10


title: small intestine, distal part, 30E% fat, replicate 2


title: small intestine, distal part, 20E% fat, replicate 4


title: WT Heart_b

source_name: heart, wildtype (FVB/N)

value: wildtype

value: FVB/N


title: small intestine, distal part, 20E% fat, replicate 7


title: small intestine, distal part, 20E% fat, replicate 3


title: small intestine, distal part, 20E% fat, replicate 5


title: small intestine, distal part, 10E% fat, replicate 10

source_name: distal small intestine, scraped off epithelial (mucosal) cells, 10E%


title: small intestine, distal part, 10E% fat, replicate 6


title: small intestine, distal part, 30E% fat, replicate 8


title: small intestine, distal part, 10E% fat, replicate 5


title: small intestine, distal part, 20E% fat, replicate 1


title: small intestine, distal part, 10E% fat, replicate 4


title: small intestine, distal part, 20E% fat, replicate 2


title: small intestine, distal part, 10E% fat, replicate 9


title: small intestine, distal part, 10E% fat, replicate 8


title: small intestine, distal part, 20E% fat, replicate 8


title: small intestine, distal part, 10E% fat, replicate 3


title: small intestine, middle part, 45E% fat, replicate 6

source_name: middle small intestine, scraped off epithelial (mucosal) cells, 45E%

value: middle small intestine


title: small intestine, distal part, 20E% fat, replicate 6


title: small intestine, distal part, 10E% fat, replicate 1


title: small intestine, middle part, 45E% fat, replicate 4


title: small intestine, middle part, 45E% fat, replicate 3


title: small intestine, distal part, 10E% fat, replicate 7


title: small intestine, middle part, 45E% fat, replicate 5


title: small intestine, middle part, 30E% fat, replicate 9

source_name: middle small intestine, scraped off epithelial (mucosal) cells, 30E%


title: small intestine, distal part, 10E% fat, replicate 2


title: small intestine, middle part, 45E% fat, replicate 10


title: small intestine, middle part, 45E% fat, replicate 9


title: small intestine, middle part, 30E% fat, replicate 10


title: small intestine, distal part, 30E% fat, replicate 3


title: small intestine, middle part, 45E% fat, replicate 1


title: small intestine, middle part, 45E% fat, replicate 8


title: small intestine, middle part, 45E% fat, replicate 2


title: small intestine, middle part, 45E% fat, replicate 7


title: small intestine, middle part, 30E% fat, replicate 8


title: small intestine, middle part, 30E% fat, replicate 7


title: small intestine, middle part, 30E% fat, replicate 5


title: small intestine, middle part, 30E% fat, replicate 6


title: small intestine, middle part, 30E% fat, replicate 3


title: small intestine, middle part, 30E% fat, replicate 2


title: small intestine, middle part, 20E% fat, replicate 10

source_name: middle small intestine, scraped off epithelial (mucosal) cells, 20E%


title: small intestine, middle part, 30E% fat, replicate 1


title: small intestine, middle part, 20E% fat, replicate 9


title: small intestine, middle part, 30E% fat, replicate 4


title: small intestine, middle part, 20E% fat, replicate 8


title: small intestine, middle part, 20E% fat, replicate 6


title: small intestine, middle part, 20E% fat, replicate 7


title: small intestine, middle part, 20E% fat, replicate 1


title: small intestine, middle part, 20E% fat, replicate 3


title: small intestine, middle part, 20E% fat, replicate 4


title: small intestine, middle part, 10E% fat, replicate 9

source_name: middle small intestine, scraped off epithelial (mucosal) cells, 10E%


title: small intestine, middle part, 10E% fat, replicate 10


title: small intestine, middle part, 10E% fat, replicate 8


title: small intestine, middle part, 20E% fat, replicate 5


title: small intestine, middle part, 20E% fat, replicate 2


title: small intestine, middle part, 10E% fat, replicate 3


title: small intestine, middle part, 10E% fat, replicate 1


title: small intestine, middle part, 10E% fat, replicate 5


title: small intestine, proximal part, 45E% fat, replicate 8

source_name: proximal small intestine, scraped off epithelial (mucosal) cells, 45E%

value: proximal small intestine


title: small intestine, proximal part, 45E% fat, replicate 9


title: small intestine, proximal part, 45E% fat, replicate 6


title: small intestine, middle part, 10E% fat, replicate 4


title: small intestine, middle part, 10E% fat, replicate 2


title: small intestine, proximal part, 45E% fat, replicate 7


title: small intestine, proximal part, 45E% fat, replicate 3


title: small intestine, proximal part, 45E% fat, replicate 5


title: small intestine, proximal part, 45E% fat, replicate 10


title: small intestine, proximal part, 45E% fat, replicate 1


title: small intestine, proximal part, 30E% fat, replicate 9

source_name: proximal small intestine, scraped off epithelial (mucosal) cells, 30E%


title: small intestine, proximal part, 45E% fat, replicate 4


title: small intestine, proximal part, 30E% fat, replicate 8


title: small intestine, middle part, 10E% fat, replicate 7


title: small intestine, proximal part, 30E% fat, replicate 7


title: small intestine, proximal part, 30E% fat, replicate 10


title: small intestine, proximal part, 30E% fat, replicate 6


title: small intestine, proximal part, 45E% fat, replicate 2


title: small intestine, middle part, 10E% fat, replicate 6


title: small intestine, proximal part, 30E% fat, replicate 4


title: sod-/- 7MONTH @ edl 2

city: Winter Park

first: Hui

last: Xie

state: FL

address: 2566 Lee Rd.

department: TRI

institute: Florida Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Genes were considered to be presented if their detection p-value <0.05. The data were normalised using quantile normalisation with SAS(V9.1)

source_name: mouse muscle

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

extract_protocol: RNA was isolated/purified using Qiagen RNeasy Fibrous Tissue Mini Kit (Cat# 74704).

value: muscle

value: sod-/-

value: 7 MONTHS


title: wild-type 7MONTH @ edl 2

value: wild type


title: sod-/- 7MONTH @ edl 4


title: wild-type 7MONTH @ edl 4


title: small intestine, proximal part, 30E% fat, replicate 5

value: male

value: 20 weeks


title: small intestine, proximal part, 30E% fat, replicate 1

value: mucosal


title: sod-/- 7MONTH @ edl 1


title: small intestine, proximal part, 20E% fat, replicate 9

source_name: proximal small intestine, scraped off epithelial (mucosal) cells, 20E%


title: small intestine, proximal part, 20E% fat, replicate 7


title: wild-type 7MONTH @ edl 3


title: small intestine, proximal part, 20E% fat, replicate 5


title: small intestine, proximal part, 20E% fat, replicate 10


title: small intestine, proximal part, 20E% fat, replicate 6


title: wild-type 7MONTH @ edl 1


title: heart_treatment_rep4

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

description: replicate 4

data_processing: The data were normalized with the rank invariant normalization in the Illumina BeadStudio 1.5.1.3 software

source_name: heart, treatment

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: Mice were given a normal diet for six weeks

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit, followed by quantification using the NanoDrop spectrophotometer and qualitation using the Agilent Bioanalyzer

treatment_protocol: Control group was given distilled water while treatment group was given OPP (1500 ppm GAE) as drinks ad libitum

tag: diet supplement

value: oil palm phenolics (OPP)

value: BALB/c

value: 12 weeks

tag: group

value: treatment


title: sod-/- 7MONTH @ edl 3

tag: tissue


title: heart_treatment_rep3

description: replicate 3

value: heart


title: spleen_treatment_rep3

description: replicate 3

source_name: spleen, treatment

value: spleen


title: spleen_treatment_rep4

description: replicate 4


title: heart_treatment_rep2

description: replicate 2


title: small intestine, proximal part, 30E% fat, replicate 2


title: small intestine, proximal part, 30E% fat, replicate 3


title: Spleen, 4 wpi, pool 2

description:
S4WP2
Time-point 2 of 6, biological replicate 2 of 2.

source_name: Spleen of infected salmon, 4 wpi

value: post-smolt

value: piscine myocarditis virus (PMCV)

source_name: Spleen of control salmon, 4 wpi

value: post-smelt


title: spleen_treatment_rep2

description: replicate 2


title: heart_treatment_rep1

description: replicate 1


title: small intestine, proximal part, 20E% fat, replicate 4

value: proximal small intestine


title: small intestine, proximal part, 20E% fat, replicate 8


title: PBL, 4 wpi, pool 1

description:
PBL4WP1
Time-point 2 of 6, biological replicate 1 of 2.

source_name: PBL of infected salmon, 4 wpi

value: peripheral blood leukocytes

source_name: PBL of control salmon, 4 wpi


title: small intestine, proximal part, 20E% fat, replicate 1


title: Kidney, 4 wpi, pool 2

description:
K4WP2
Time-point 2 of 6, biological replicate 2 of 2.

source_name: Kidney of infected salmon, 4 wpi

value: mid-kidney

source_name: Kidney of control salmon, 4 wpi


title: RBC, 4 wpi, pool 1

description:
RBC4WP1
Time-point 2 of 6, biological replicate 1 of 2.

source_name: RBC of infected salmon, 4 wpi

value: red blood cells

source_name: RBC of control salmon, 4 wpi


title: small intestine, proximal part, 20E% fat, replicate 2


title: small intestine, proximal part, 10E% fat, replicate 10

source_name: proximal small intestine, scraped off epithelial (mucosal) cells, 10E%


title: PBL, 4 wpi, pool 2

description:
PBL4WP2
Time-point 2 of 6, biological replicate 2 of 2.


title: RBC, 4 wpi, pool 2

description:
RBC4WP2
Time-point 2 of 6, biological replicate 2 of 2.


title: spleen_treatment_rep1

description: replicate 1


title: Kidney, 4 wpi, pool 1

description:
K4WP1
Time-point 2 of 6, biological replicate 1 of 2.


title: liver_treatment_rep3

description: replicate 3

source_name: liver, treatment

value: liver


title: Spleen, 4 wpi, pool 1

description:
S4WP1
Time-point 2 of 6, biological replicate 1 of 2.


title: Liver, 4 wpi, pool 1

description:
L4WP1
Time-point 2 of 6, biological replicate 1 of 2.

source_name: Liver of infected salmon, 4 wpi

source_name: Liver of control salmon, 4 wpi


title: small intestine, proximal part, 20E% fat, replicate 3

value: male


title: Heart, 10 wpi, pool 2

description:
H10WP2
Time-point 6 of 6, biological replicate 2 of 2.

source_name: Heart of infected salmon, 10 wpi

source_name: Heart of control salmon, 10 wpi


title: small intestine, proximal part, 10E% fat, replicate 9

value: 20 weeks


title: Heart, 10 wpi, pool 1

description:
H10WP1
Time-point 6 of 6, biological replicate 1 of 2.


title: Liver, 4 wpi, pool 2

description:
L4WP2
Time-point 2 of 6, biological replicate 2 of 2.


title: liver_treatment_rep1

description: replicate 1


title: Heart, 9 wpi, pool 2

description:
H9WP2
Time-point 5 of 6, biological replicate 2 of 2.

source_name: Heart of infected salmon, 9 wpi

source_name: Heart of control salmon, 9 wpi


title: Heart, 8 wpi, pool 2

description:
H8WP2
Time-point 4 of 6, biological replicate 2 of 4.

source_name: Heart of infected salmon, 8 wpi

source_name: Heart of control salmon, 8 wpi


title: liver_treatment_rep2

description: replicate 2


title: Heart, 9 wpi, pool 1

description:
H9WP1
Time-point 5 of 6, biological replicate 1 of 2.


title: small intestine, proximal part, 10E% fat, replicate 6

value: mucosal


title: small intestine, proximal part, 10E% fat, replicate 5


title: Heart, 8 wpi, pool 1

description:
H8WP1
Time-point 4 of 6, biological replicate 1 of 4.


title: Heart, 6 wpi, pool 2

description:
H6WP2
Time-point 3 of 6, biological replicate 2 of 2.

source_name: Heart of infected salmon, 6 wpi

source_name: Heart of control salmon, 6 wpi


title: Heart, 4 wpi, pool 3

description:
H4WP3
Time-point 2 of 6, biological replicate 3 of 4.

source_name: Heart of infected salmon, 4 wpi

source_name: Heart of control salmon, 4 wpi


title: small intestine, proximal part, 10E% fat, replicate 4


title: Heart, 4 wpi, pool 4

description:
H4WP4
Time-point 2 of 6, biological replicate 4 of 4.


title: small intestine, proximal part, 10E% fat, replicate 8


title: small intestine, proximal part, 10E% fat, replicate 3


title: E. coliO157: H7_Parental_FlhC mutant 2

city: Fargo

first: Birgit

middle: Magdalene

last: Pruess

state: North Dakota

address: 1523 Centennial Blvd.

department: Veterinary and Microbiological Sciences

institute: North Dakota State University

description: Biological sample 2/3

hyb_protocol: Hybridized as per the recommendation of manufacturer(Ocimum Biosoultions). Sample loaded onto Hyb4 (Genomic Solutions)

scan_protocol: Slides were scanned in GenePix Scanner 4000B (Molecular devices)

data_processing: Processing was done using GenePix 6.0.

label: Alex Fluor 555

organism: Escherichia coli O157:H7

source_name: Wild type

label_protocol: RNA was reverse transcribed using amino-allyl labeled dUTP followed by labelling with Alexa fluor 555(WT) and alexa fluor 647(FlhC mutant)

growth_protocol: Bacteria grown on surface of meat for 10 days at 10°C. uninnoculated control kept.

extract_protocol: Total RNA was extracted using hot phenol chloroform

value: Wild type

label: Alexa Fluor 647

source_name: FlhC mutant

value: FlhC mutant


title: E. coliO157: H7_Parental_FlhC mutant 3

description: Biological sample 2/3


title: Heart, 4 wpi, pool 1

description:
H4WP1
Time-point 2 of 6, biological replicate 1 of 4.


title: Heart, 4 wpi, pool 2

description:
H4WP2
Time-point 2 of 6, biological replicate 2 of 4.


title: E. coliO157: H7_Parental_FlhC mutant 5

description: Biological sample 3/3


title: Heart, 6 wpi, pool 1

description:
H6WP1
Time-point 3 of 6, biological replicate 1 of 2.


title: small intestine, proximal part, 10E% fat, replicate 7


title: E. coliO157: H7_Parental_FlhC mutant 4

description: Biological sample 3/3


title: Heart, 2 wpi, pool 2

description:
H2WP2
Time-point 1 of 6, biological replicate 2 of 2.

source_name: Heart of infected salmon, 2 wpi

source_name: Heart of control salmon, 2 wpi


title: small intestine, proximal part, 10E% fat, replicate 2

source_name: proximal small intestine, scraped off epithelial (mucosal) cells, 10E%


title: E. coliO157: H7_Parental_FlhC mutant 1

description: Biological sample 1/3


title: Ebf2-lacZ-expressing osteoblastic cells from Ebf2-/- mice

city: Freiburg

first: Rudolf

last: Grosschedl

address: Stübeweg 51

country: Germany

institute: Max-Planck Institute of Immunobiology

description: osteoblastic cells from tibia and femur of Ebf2 knockout mice (n=3 each) were loaded with FDG, FACS sorted and total RNA was isolated. cDNA was synthesised using the One-Cycle cDNA Synthesis Kit (Affymetrix), and labeled cRNA was synthesized by transcription in vitro, using the IVT labelling kit (Affymetrix). The labeled RNA was fragmented and hybridized to GeneChip® Mouse genome 430 2.0 arrays (GPL1261), according to the manufacturer’s instructions.

scan_protocol: performed according to the GeneChip® Expression Analysis Technical Manual (GeneChip Scanner  3000)

data_processing: Data analysis was done with the GeneChip Operating Software using the MAS5 algorithm

source_name: Osteoblastic cell preparation, sorted for lacZ Marker (Ebf2-lacZ; Kieslinger et al., 2006), expanded in culture without passaging.

label_protocol: IVT Labeling Kit (Affymetrix, P/N 900449)

growth_protocol: alpha MEM supplemented with 10% FCS, Penicillin/Streptomycin and L-Glutamine

extract_protocol: total RNA was prepared with Trizol reagent (Invitrogen) according to the manufacturer’s instructions

value: E18.5 embryo

tag: genotype/variation

value: osteoblast preparation expanded in culture without passaging

value: tibia, femur


title: small intestine, proximal part, 10E% fat, replicate 1


title: Heart, 2 wpi, pool 1

description:
H2WP1
Time-point 1 of 6, biological replicate 1 of 2.

value: heart


title: colon carcinoma_MS163

status: Public on Apr 25 2011

city: West Point

first: Michael

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

description: human colorectal tumor RNA

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybrid

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction s

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the

source_name: pool of individual tumors

label_protocol: Custom automated version of the aminoallyl MessageAmp II kit from Ambion

extract_protocol: Total RNA was isolated from the adipose samples  by Qiagen RNeasy spin columns with DNAse treatment. 2 µg of each sample was precipitated in ethanol and re-suspended in 14 µl of water. Globin mitigation performed using Ambion's GLOBINclear kit (cat# AM1

value: reference

source_name: colon carcinoma_MS163

tag: Stage

tag: overall survival (years)

tag: overall survival censor (1-censored,0-non-censored)

tag: metastasis (1-yes, 0-no)

tag: time to metastasis (years)

tag: time to recurrence (years)

tag: age at diagnosis

tag: tumor location

value: rectum

tag: duke's stage

value: B


title: colon carcinoma_MS146

description: human colorectal tumor RNA

source_name: colon carcinoma_MS146

value: sigmoid

value: C


title: colon carcinoma_MS161

description: human colorectal tumor RNA

source_name: colon carcinoma_MS161


title: colon carcinoma_MS159

description: human colorectal tumor RNA

source_name: colon carcinoma_MS159


title: Ebf2-lacZ-expressing osteoblastic cells from Ebf2+/- mice

description: osteoblastic cells from tibia and femur of Ebf2 heterozygous mice (n=3 each) were loaded with FDG, FACS sorted and total RNA was isolated. cDNA was synthesised using the One-Cycle cDNA Synthesis Kit (Affymetrix), and labeled cRNA was synthesized by transcription in vitro, using the IVT labelling kit (Affymetrix). The labeled RNA was fragmented and hybridized to GeneChip® Mouse genome 430 2.0 arrays (GPL1261), according to the manufacturer’s instructions.

hyb_protocol: performed according to the GeneChip® Expression Analysis Technical Manual

extract_protocol: total RNA was preparedwith Trizol reagent (Invitrogen) according to the manufacturer’s instructions

tag: strain

tag: developmental stage


title: colon carcinoma_MS152

description: human colorectal tumor RNA

source_name: colon carcinoma_MS152


title: colon carcinoma_MS147

description: human colorectal tumor RNA

source_name: colon carcinoma_MS147


title: colon carcinoma_MS134

description: human colorectal tumor RNA

source_name: colon carcinoma_MS134


title: colon carcinoma_MS84-3

description: human colorectal tumor RNA

source_name: colon carcinoma_MS84-3

value: rectosigm


title: colon carcinoma_MS127

description: human colorectal tumor RNA

source_name: colon carcinoma_MS127

value: transvers


title: colon carcinoma_MS143

description: human colorectal tumor RNA

source_name: colon carcinoma_MS143


title: colon carcinoma_MS168

description: human colorectal tumor RNA

source_name: colon carcinoma_MS168


title: colon carcinoma_MS71-2

description: human colorectal tumor RNA

source_name: colon carcinoma_MS71-2

value: coecum


title: colon carcinoma_MS158

description: human colorectal tumor RNA

source_name: colon carcinoma_MS158


title: colon carcinoma_MS155

description: human colorectal tumor RNA

source_name: colon carcinoma_MS155


title: colon carcinoma_MS150

description: human colorectal tumor RNA

source_name: colon carcinoma_MS150


title: colon carcinoma_MS129

description: human colorectal tumor RNA

source_name: colon carcinoma_MS129

value: ascend


title: colon carcinoma_MS151

description: human colorectal tumor RNA

source_name: pool of individual tumors

source_name: colon carcinoma_MS151


title: colon carcinoma_MS128

description: human colorectal tumor RNA

source_name: colon carcinoma_MS128


title: colon carcinoma_MS154-2

description: human colorectal tumor RNA

source_name: colon carcinoma_MS154-2


title: colon carcinoma_MS136

description: human colorectal tumor RNA

source_name: colon carcinoma_MS136


title: colon carcinoma_MS126

description: human colorectal tumor RNA

source_name: colon carcinoma_MS126

value: A


title: colon carcinoma_MS167

description: human colorectal tumor RNA

source_name: colon carcinoma_MS167


title: colon carcinoma_MS131

description: human colorectal tumor RNA

source_name: colon carcinoma_MS131


title: colon carcinoma_MS132

description: human colorectal tumor RNA

source_name: colon carcinoma_MS132

value: appendix


title: colon carcinoma_MS123

description: human colorectal tumor RNA

source_name: colon carcinoma_MS123


title: colon carcinoma_MS122

description: human colorectal tumor RNA

source_name: colon carcinoma_MS122


title: colon carcinoma_MS124

description: human colorectal tumor RNA

source_name: colon carcinoma_MS124


title: colon carcinoma_MS120

description: human colorectal tumor RNA

source_name: colon carcinoma_MS120


title: colon carcinoma_MS116

description: human colorectal tumor RNA

source_name: colon carcinoma_MS116


title: colon carcinoma_MS114

description: human colorectal tumor RNA

source_name: colon carcinoma_MS114


title: colon carcinoma_MS113

description: human colorectal tumor RNA

source_name: colon carcinoma_MS113


title: colon carcinoma_MS118

description: human colorectal tumor RNA

source_name: colon carcinoma_MS118


title: colon carcinoma_MS112

description: human colorectal tumor RNA

source_name: pool of individual tumors

source_name: colon carcinoma_MS112


title: colon carcinoma_MS107

description: human colorectal tumor RNA

source_name: colon carcinoma_MS107


title: colon carcinoma_MS103

description: human colorectal tumor RNA

source_name: colon carcinoma_MS103


title: colon carcinoma_MS102

description: human colorectal tumor RNA

source_name: colon carcinoma_MS102


title: colon carcinoma_MS105

description: human colorectal tumor RNA

source_name: colon carcinoma_MS105


title: colon carcinoma_MS109

description: human colorectal tumor RNA

source_name: colon carcinoma_MS109


title: colon carcinoma_MS88

description: human colorectal tumor RNA

source_name: colon carcinoma_MS88


title: colon carcinoma_MS96

description: human colorectal tumor RNA

source_name: colon carcinoma_MS96


title: colon carcinoma_MS98

description: human colorectal tumor RNA

source_name: colon carcinoma_MS98


title: colon carcinoma_MS108

description: human colorectal tumor RNA

source_name: colon carcinoma_MS108


title: colon carcinoma_MS99

description: human colorectal tumor RNA

source_name: colon carcinoma_MS99


title: colon carcinoma_MS117

description: human colorectal tumor RNA

source_name: colon carcinoma_MS117


title: colon carcinoma_MS104

description: human colorectal tumor RNA

source_name: colon carcinoma_MS104


title: colon carcinoma_MS93

description: human colorectal tumor RNA

source_name: colon carcinoma_MS93


title: colon carcinoma_MS110

description: human colorectal tumor RNA

source_name: colon carcinoma_MS110


title: colon carcinoma_MS106

description: human colorectal tumor RNA

source_name: colon carcinoma_MS106


title: colon carcinoma_MS97

description: human colorectal tumor RNA

source_name: pool of individual tumors

source_name: colon carcinoma_MS97


title: colon carcinoma_MS119

description: human colorectal tumor RNA

source_name: colon carcinoma_MS119


title: colon carcinoma_MS95

description: human colorectal tumor RNA

source_name: colon carcinoma_MS95


title: colon carcinoma_MS101

description: human colorectal tumor RNA

source_name: colon carcinoma_MS101


title: colon carcinoma_MS89

description: human colorectal tumor RNA

source_name: colon carcinoma_MS89


title: colon carcinoma_MS94

description: human colorectal tumor RNA

source_name: colon carcinoma_MS94


title: colon carcinoma_MS90

description: human colorectal tumor RNA

source_name: colon carcinoma_MS90


title: colon carcinoma_MS87

description: human colorectal tumor RNA

source_name: colon carcinoma_MS87

value: D


title: colon carcinoma_3194

description: human colorectal tumor RNA

source_name: colon carcinoma_3194


title: colon carcinoma_MS29

description: human colorectal tumor RNA

source_name: colon carcinoma_MS29


title: colon carcinoma_MS25

description: human colorectal tumor RNA

source_name: colon carcinoma_MS25


title: colon carcinoma_MS52

description: human colorectal tumor RNA

source_name: colon carcinoma_MS52


title: colon carcinoma_MS80

description: human colorectal tumor RNA

source_name: colon carcinoma_MS80


title: colon carcinoma_3189

description: human colorectal tumor RNA

source_name: colon carcinoma_3189


title: colon carcinoma_MS47

description: human colorectal tumor RNA

source_name: colon carcinoma_MS47


title: colon carcinoma_MS86

description: human colorectal tumor RNA

source_name: colon carcinoma_MS86


title: colon carcinoma_MS26

description: human colorectal tumor RNA

source_name: pool of individual tumors

source_name: colon carcinoma_MS26


title: colon carcinoma_MS78

description: human colorectal tumor RNA

source_name: colon carcinoma_MS78


title: colon carcinoma_MS34

description: human colorectal tumor RNA

source_name: colon carcinoma_MS34


title: colon carcinoma_3190

description: human colorectal tumor RNA

source_name: colon carcinoma_3190


title: colon carcinoma_3197

description: human colorectal tumor RNA

source_name: colon carcinoma_3197


title: colon carcinoma_MS02

description: human colorectal tumor RNA

source_name: colon carcinoma_MS02


title: colon carcinoma_MS51

description: human colorectal tumor RNA

source_name: colon carcinoma_MS51


title: colon carcinoma_MS82

description: human colorectal tumor RNA

source_name: colon carcinoma_MS82


title: colon carcinoma_MS79

description: human colorectal tumor RNA

source_name: colon carcinoma_MS79


title: colon carcinoma_MS21

description: human colorectal tumor RNA

source_name: colon carcinoma_MS21


title: colon carcinoma_3209

description: human colorectal tumor RNA

source_name: colon carcinoma_3209


title: colon carcinoma_MS11

description: human colorectal tumor RNA

source_name: colon carcinoma_MS11


title: colon carcinoma_3244

description: human colorectal tumor RNA

source_name: colon carcinoma_3244


title: colon carcinoma_3191

description: human colorectal tumor RNA

source_name: colon carcinoma_3191


title: colon carcinoma_MS69

description: human colorectal tumor RNA

source_name: colon carcinoma_MS69


title: colon carcinoma_MS48

description: human colorectal tumor RNA

source_name: colon carcinoma_MS48


title: colon carcinoma_MS57

description: human colorectal tumor RNA

source_name: pool of individual tumors

source_name: colon carcinoma_MS57


title: colon carcinoma_3193

description: human colorectal tumor RNA

source_name: colon carcinoma_3193


title: colon carcinoma_3210

description: human colorectal tumor RNA

source_name: colon carcinoma_3210


title: colon carcinoma_MS38

description: human colorectal tumor RNA

source_name: colon carcinoma_MS38


title: colon carcinoma_3188

description: human colorectal tumor RNA

source_name: colon carcinoma_3188


title: colon carcinoma_3153

description: human colorectal tumor RNA

source_name: colon carcinoma_3153


title: colon carcinoma_3151

description: human colorectal tumor RNA

source_name: colon carcinoma_3151


title: colon carcinoma_3148

description: human colorectal tumor RNA

source_name: colon carcinoma_3148


title: colon carcinoma_3113

description: human colorectal tumor RNA

source_name: colon carcinoma_3113


title: colon carcinoma_3223

description: human colorectal tumor RNA

source_name: colon carcinoma_3223


title: colon carcinoma_3152

description: human colorectal tumor RNA

source_name: colon carcinoma_3152


title: colon carcinoma_3146

description: human colorectal tumor RNA

source_name: colon carcinoma_3146


title: colon carcinoma_3207

description: human colorectal tumor RNA

source_name: colon carcinoma_3207


title: colon carcinoma_3219

description: human colorectal tumor RNA

source_name: colon carcinoma_3219


title: colon carcinoma_3206

description: human colorectal tumor RNA

source_name: colon carcinoma_3206


title: colon carcinoma_3183

description: human colorectal tumor RNA

source_name: colon carcinoma_3183


title: colon carcinoma_3154

description: human colorectal tumor RNA

source_name: pool of individual tumors

source_name: colon carcinoma_3154


title: colon carcinoma_3145

description: human colorectal tumor RNA

source_name: colon carcinoma_3145


title: colon carcinoma_3216

description: human colorectal tumor RNA

source_name: colon carcinoma_3216


title: colon carcinoma_3187

description: human colorectal tumor RNA

source_name: colon carcinoma_3187


title: colon carcinoma_3205

description: human colorectal tumor RNA

source_name: colon carcinoma_3205


title: colon carcinoma_3184

description: human colorectal tumor RNA

source_name: colon carcinoma_3184


title: colon carcinoma_3247

description: human colorectal tumor RNA

source_name: colon carcinoma_3247


title: colon carcinoma_3240

description: human colorectal tumor RNA

source_name: colon carcinoma_3240


title: colon carcinoma_3105

description: human colorectal tumor RNA

source_name: colon carcinoma_3105


title: colon carcinoma_3203

description: human colorectal tumor RNA

source_name: colon carcinoma_3203


title: colon carcinoma_3103

description: human colorectal tumor RNA

source_name: colon carcinoma_3103


title: colon carcinoma_3251

description: human colorectal tumor RNA

source_name: colon carcinoma_3251


title: colon carcinoma_3202

description: human colorectal tumor RNA

source_name: colon carcinoma_3202


title: colon carcinoma_3248

description: human colorectal tumor RNA

source_name: colon carcinoma_3248


title: early atherosclerotic plaque13

city: Maastricht

first: Marco

last: Manca

state: Limburg

address: P. Debyelaan 25

department: CARIM

institute: University of Maastricht

description: Early atherosclerotic plaque from human carotid (autopsy)

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

scan_protocol: GeneChip Scanner 3000 (Affymetrix, Santa Clara, USA, CA)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label: Biotin

source_name: postmortem plaque

label_protocol: GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, USA, CA)

extract_protocol: Guanidine isothiocyanate/CsCl method followed by further purification and concentration using RNease mini columns (Qiagenm Hilden, Germany)

value: carotid artery

tag: phenotype

value: early atherosclerotic plaque


title: colon carcinoma_3218

description: human colorectal tumor RNA

tag: sample type

source_name: colon carcinoma_3218


title: colon carcinoma_3111

description: human colorectal tumor RNA

source_name: pool of individual tumors

source_name: colon carcinoma_3111


title: early atherosclerotic plaque10


title: early atherosclerotic plaque12


title: colon carcinoma_3179

description: human colorectal tumor RNA

source_name: colon carcinoma_3179


title: early atherosclerotic plaque5


title: early atherosclerotic plaque3


title: colon carcinoma_3177

description: human colorectal tumor RNA

source_name: colon carcinoma_3177


title: colon carcinoma_3102

description: human colorectal tumor RNA

source_name: colon carcinoma_3102


title: early atherosclerotic plaque11


title: early atherosclerotic plaque6


title: early atherosclerotic plaque9


title: colon carcinoma_3181

description: human colorectal tumor RNA

source_name: colon carcinoma_3181


title: colon carcinoma_3214

description: human colorectal tumor RNA

source_name: colon carcinoma_3214


title: early atherosclerotic plaque7


title: colon carcinoma_3201

description: human colorectal tumor RNA

source_name: colon carcinoma_3201


title: early atherosclerotic plaque4


title: colon carcinoma_3198

description: human colorectal tumor RNA

source_name: colon carcinoma_3198


title: colon carcinoma_3174

description: human colorectal tumor RNA

source_name: colon carcinoma_3174


title: early atherosclerotic plaque8


title: early atherosclerotic plaque1


title: early atherosclerotic plaque2


title: colon carcinoma_3186

description: human colorectal tumor RNA

source_name: colon carcinoma_3186


title: advanced atherosclerotic plaque16

description: Advanced atherosclerotic plaque from human carotid (autopsy)

value: advanced atherosclerotic plaque


title: colon carcinoma_3239

description: human colorectal tumor RNA

source_name: colon carcinoma_3239


title: colon carcinoma_3176

description: human colorectal tumor RNA

source_name: colon carcinoma_3176


title: colon carcinoma_3173

description: human colorectal tumor RNA

source_name: colon carcinoma_3173


title: THP-1 ATRA+RAD001

city: Kyoto

first: Toshihiko

last: Imamura

address: 465 Kajiichou Hirokouji Kawaramachi Sakyo-ku

department: Pediatrics

country: Japan

institute: Kyoto Prefectural University of Medicine

description: ATRA (1mM) and RAD001 (2.5nM)

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented and hybridized to Whole Human Genome 4 X 44K Microarrays (G4112F) using Gene Expression Hybridization Kit according to manufacture's prptocol.

scan_protocol: Arrays were scanned using a laser confocal scanner (Agilent Technologies, Inc.).

data_processing: The image processing and expression analysis were performed using the Agilent Feature Extraction Software v10.5.1.1 (Protocol GE1_105_Dec08 and Grid 014850_D_F_20100115) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: THP-1treated with ATRA+RAD001

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: THP-1 cells were cultured in suspension in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/mL), and streptomycin (10 mg/mL) at 37ºC in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Samples were quantified using the NanoDrop ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies), and the quality of RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: The working concentrations used for the experiments were 1.0 mM ATRA and 2.5 nM RAD001. The cell line was seeded at 1 ×105 cells/ml and then treated with ATRA alone, RAD001 alone, or the combination (or an equivalent volume of the vehicle controls) for 5 days.

tag: cell

tag: agent

value: ATRA (1mM) and RAD001 (2.5nM)


title: advanced atherosclerotic plaque13

source_name: postmortem plaque

tag: tissue


title: advanced atherosclerotic plaque15


title: advanced atherosclerotic plaque8


title: Immature oocyte In vitro rep4

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: Gene expression from immature in vitro derived bovine oocyte

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix).

data_processing: The data was analysed using the R library farms (Factor Analysis for Robust Microarray Summarization).

organism: Bos taurus

source_name: Immature in vitro oocyte

label_protocol: 100 ng of total RNA was subjected to two rounds of linear amplification using the GeneChip® Expression 3’-Amplification Two-Cycle cDNA Synthesis kit (Affymetrix Inc., Santa Clara, CA) according to the manufacturer’s instructions. cDNA was synthesized during the first cycle and biotin-labeled nucleotides were incorporated during the second in vitro transcription reaction.

growth_protocol: Immature bovine oocytes were collected immediately (T0) while in vitro matured oocytes were collected after 24 h of submission to maturation medium.

extract_protocol: Total RNA extraction was carried out using PicoPure RNA Isolation kit (Arcturus Bioscience, Mountain View, CA, USA), by incorporating a DNase treatment step using RNase-free DNase set (Qiagen, West Sussex, UK), according to the manufacturer’s instructions.

treatment_protocol: Immature cumulus oocyte complexes (COCs) were obtained by aspirating 3 to 8 mm follicles on the ovaries collected from cows slaughtered at a local abattoir. Good quality COCs, judged morphologically with multiple cumulus layers and homogenous cytoplasm, were selected under the stereo microscope and washed repeatedly in phosphate-buffered saline (PBS). Following washing, half of the COCs were immediately denuded by repeated pippeting in PBS. Intact oocytes with no cumulus traces were pooled in groups of 10 oocytes per tube and immediately snap frozen in liquid nitrogen. The remaining intact COCs were incubated in maturation medium [TCM-199 supplemented with 10% (v/v) fetal calf serum and 10 ng/ml epidermal growth factor] in 4-well dishes (Nunc, Roskilde, Denmark) at 39°C for 24 h under an atmosphere of 5% CO2 in air with maximum humidity. At 24 h, in vitro matured (IVM) COCs were denuded and snap frozen as described above.

tag: cell type

value: immature oocytes


title: advanced atherosclerotic plaque11


title: advanced atherosclerotic plaque12


title: advanced atherosclerotic plaque10


title: advanced atherosclerotic plaque6


title: THP-1 untreated

description: untreated

source_name: THP-1 untreated


title: advanced atherosclerotic plaque3


title: advanced atherosclerotic plaque5


title: Immature oocyte In vitro rep2


title: Mature oocyte in vitro rep3

description: Gene expression from mature in vitro derived bovine oocyte

source_name: Mature in vitro oocyte

value: matured oocytes


title: Mature oocyte in vitro rep1


title: Mature oocyte in vitro rep2


title: advanced atherosclerotic plaque9


title: Mature oocyte in vitro rep5


title: colon carcinoma_3199

description: human colorectal tumor RNA

source_name: pool of individual tumors

value: reference

source_name: colon carcinoma_3199

tag: Stage


title: Immature oocyte In vitro rep1


title: advanced atherosclerotic plaque7


title: Immature oocyte In vitro rep5


title: Mature oocyte in vitro rep4


title: Immature oocyte In vitro rep3


title: advanced atherosclerotic plaque2


title: advanced atherosclerotic plaque4


title: UMC-11

description: lung cancer cell line

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 45oC 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: Standard RefRMA pipleline as implemented in APT (Affymetrix Power Tools software) using default settings

source_name: ATCC

label_protocol: Standard 1xAffy amplification protocol

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.

tag: cell line


title: breast surgical IMC 84

city: Nashville

first: Melinda

middle: E

last: Sanders

state: TN

address: 23rd Ave. S. at Pierce Ave.

department: Pathology

institute: Vanderbilt University

description:
IMC 125 (583MS171)
Gene expression data from sugical breast cancer specimens.

hyb_protocol: See Vanderbilt Microarray Shared Resource, Affymetrix.

data_processing: The data was RMA summarized, quantile normalized and baseline transformed to the median of all samples using GeneSpring GX Software (Agilent).

source_name: breast tumor surgical specimen

growth_protocol: All samples are from frozen primary breast surgical specimens.

extract_protocol: Frozen specimens were sectioned and laser capture microdissected for invasive tumor cells, and total RNA was isolated according to the manufacturer's instructions.

treatment_protocol: All samples are surgical specimens obtained prior to treatment.

value: primary breast tumor

tag: disease state

value: invasive mammary carcinoma


title: advanced atherosclerotic plaque14


title: breast surgical IMC 89

description:
IMC 130 (583MS234)
Gene expression data from sugical breast cancer specimens.

scan_protocol: See Vanderbilt Microarray Shared Resource, Affymetrix.


title: SW1573

description: lung cancer cell line


title: MSTO-211H

description: lung cancer cell line


title: breast surgical IMC 87

description:
IMC 128 (583MS232)
Gene expression data from sugical breast cancer specimens.

label_protocol: See Vanderbilt Microarray Shared Resource, Affymetrix.


title: advanced atherosclerotic plaque1


title: SKMES1

description: lung cancer cell line


title: RERF_LC_MS

description: lung cancer cell line


title: breast surgical IMC 88

description:
IMC 129 (583MS233)
Gene expression data from sugical breast cancer specimens.


title: RERF_LC_ad2

description: lung cancer cell line


title: breast surgical IMC 85

description:
IMC 126 (583MS179)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 82

description:
IMC 123 (583MS153)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 83

description:
IMC 124 (583MS160)
Gene expression data from sugical breast cancer specimens.


title: PC7

description: lung cancer cell line


title: LXF289

description: lung cancer cell line


title: SKLU1

description: lung cancer cell line


title: LUDLU1

description: lung cancer cell line


title: breast surgical IMC 80

description:
IMC 118 (583MS130)
Gene expression data from sugical breast cancer specimens.


title: LCLC103H

description: lung cancer cell line


title: KNS62

description: lung cancer cell line


title: Hs573.T

description: lung cancer cell line


title: LK2

description: lung cancer cell line


title: LU99A

description: lung cancer cell line


title: breast surgical IMC 86

description:
IMC 127 (583MS231)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 81

description:
IMC 120 (583MS132)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 79

description:
IMC 117 (583MS129)
Gene expression data from sugical breast cancer specimens.


title: HCC827

description: lung cancer cell line


title: breast surgical IMC 76

description:
IMC 114 (583MS126)
Gene expression data from sugical breast cancer specimens.


title: HLFa

description: lung cancer cell line

value: HLFa


title: breast surgical IMC 69

description:
IMC 105 (583MS117)
Gene expression data from sugical breast cancer specimens.


title: HCC4006

description: lung cancer cell line


title: breast surgical IMC 75

description:
IMC 113 (583MS125)
Gene expression data from sugical breast cancer specimens.


title: HARA

description: lung cancer cell line

value: HARA


title: HCC15

description: lung cancer cell line


title: HCC44

description: lung cancer cell line


title: HCC78

description: lung cancer cell line


title: breast surgical IMC 78

description:
IMC 116 (583MS128)
Gene expression data from sugical breast cancer specimens.


title: HARA_B

description: lung cancer cell line


title: breast surgical IMC 72

description:
IMC 110 (583MS199)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 77

description:
IMC 115 (583MS127)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 73

description:
IMC 111 (583MS123)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 71

description:
IMC 108 (583MS120)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 70

description:
IMC 107 (583MS119)
Gene expression data from sugical breast cancer specimens.


title: H727

description: lung cancer cell line


title: HCC 366

description: lung cancer cell line

value: HCC 366


title: breast surgical IMC 74

description:
IMC 112 (583MS124)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 67

description:
IMC 103 (583MS115)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 68

description:
IMC 104 (583MS116)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 66

description:
IMC 102 (583MS114)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 65

description:
IMC 101 (583MS113)
Gene expression data from sugical breast cancer specimens.


title: H661

description: lung cancer cell line


title: H647

description: lung cancer cell line


title: H460

description: lung cancer cell line


title: H596

description: lung cancer cell line


title: breast surgical IMC 62

description:
IMC 98 (583MS110)
Gene expression data from sugical breast cancer specimens.


title: H522

description: lung cancer cell line


title: breast surgical IMC 64

description:
IMC 100 (583MS112)
Gene expression data from sugical breast cancer specimens.


title: H520

description: lung cancer cell line


title: breast surgical IMC 61

description:
IMC 97 (583MS109)
Gene expression data from sugical breast cancer specimens.


title: H292

description: lung cancer cell line


title: H441

description: lung cancer cell line


title: breast surgical IMC 59

description:
IMC 93 (583MS105)
Gene expression data from sugical breast cancer specimens.


title: H358

description: lung cancer cell line


title: H2452

description: lung cancer cell line


title: breast surgical IMC 58

description:
IMC 87 (583MS101)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 60

description:
IMC 95 (583MS108)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 56

description:
IMC 84 (583MS99)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 57

description:
IMC 85 (583MS100)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 63

description:
IMC 99 (583MS111)
Gene expression data from sugical breast cancer specimens.


title: H2347

description: lung cancer cell line


title: SW403

description: colon cancer cell line

label_protocol: Nugen amplification protocol


title: breast surgical IMC 55

description:
IMC 83 (583MS98)
Gene expression data from sugical breast cancer specimens.


title: SNUC2B

description: colon cancer cell line


title: H2444

description: lung cancer cell line


title: breast surgical IMC 54

description:
IMC 82 (583MS97)
Gene expression data from sugical breast cancer specimens.


title: H28

description: lung cancer cell line


title: SW626

description: colon cancer cell line


title: SW948

description: colon cancer cell line


title: NCIH716

description: colon cancer cell line


title: H2342

description: lung cancer cell line


title: NCIH508

description: colon cancer cell line


title: SW480

description: colon cancer cell line


title: RKO

description: colon cancer cell line

value: RKO


title: NCIH747

description: colon cancer cell line


title: LS1034

description: colon cancer cell line


title: HCT116TSP531026

description: colon cancer cell line


title: CL11

description: colon cancer cell line


title: LS513

description: colon cancer cell line


title: SW837

description: colon cancer cell line


title: NCIH630

description: colon cancer cell line


title: H226

description: lung cancer cell line


title: breast surgical IMC 53

description:
IMC 81 (583MS96)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 51

description:
IMC 79 (583MS94)
Gene expression data from sugical breast cancer specimens.


title: T84

description: colon cancer cell line


title: H2228

description: lung cancer cell line


title: H23

description: lung cancer cell line


title: H2172

description: lung cancer cell line


title: LS174T

description: colon cancer cell line


title: breast surgical IMC 52

description:
IMC 80 (583MS95)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 49

description:
IMC 77 (583MS92)
Gene expression data from sugical breast cancer specimens.


title: H2126

description: lung cancer cell line


title: DLD1

description: colon cancer cell line


title: SKCO1

description: colon cancer cell line


title: breast surgical IMC 50

description:
IMC 78 (583MS93)
Gene expression data from sugical breast cancer specimens.


title: MDST8

description: colon cancer cell line


title: GEO

description: colon cancer cell line

value: GEO


title: HCT8

description: colon cancer cell line


title: H2170

description: lung cancer cell line


title: H2122

description: lung cancer cell line


title: RKOAS451

description: colon cancer cell line


title: breast surgical IMC 47

description:
IMC 75 (583MS90)
Gene expression data from sugical breast cancer specimens.


title: HCC56

description: colon cancer cell line


title: CX1

description: colon cancer cell line


title: SW1116

description: colon cancer cell line


title: H2085

description: lung cancer cell line


title: CL14

description: colon cancer cell line


title: H2073

description: lung cancer cell line


title: breast surgical IMC 45

description:
IMC 72 (583MS87)
Gene expression data from sugical breast cancer specimens.


title: OUMS23

description: colon cancer cell line


title: breast surgical IMC 44

description:
IMC 71 (583MS63)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 46

description:
IMC 73 (583MS88)
Gene expression data from sugical breast cancer specimens.


title: H2052

description: lung cancer cell line


title: breast surgical IMC 43

description:
IMC 70 (583MS62)
Gene expression data from sugical breast cancer specimens.


title: DLDDKO3

description: colon cancer cell line


title: GP2D

description: colon cancer cell line


title: COLO201

description: colon cancer cell line


title: breast surgical IMC 41

description:
IMC 68 (583MS85)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 42

description:
IMC 69 (583MS200)
Gene expression data from sugical breast cancer specimens.


title: H2030

description: lung cancer cell line


title: CL40

description: colon cancer cell line


title: H2009

description: lung cancer cell line


title: KM20

description: colon cancer cell line


title: COLO206F

description: colon cancer cell line


title: SW1463

description: colon cancer cell line


title: breast surgical IMC 40

description:
IMC 67 (583MS60)
Gene expression data from sugical breast cancer specimens.


title: H2023

description: lung cancer cell line


title: COLO320DM

description: colon cancer cell line


title: COLO678

description: colon cancer cell line


title: breast surgical IMC 39

description:
IMC 66 (583MS59)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 38

description:
IMC 65 (583MS83)
Gene expression data from sugical breast cancer specimens.


title: SNUC2A

description: colon cancer cell line


title: H1975

description: lung cancer cell line


title: RKOE6

description: colon cancer cell line


title: H1944

description: lung cancer cell line


title: SW48

description: colon cancer cell line


title: LS411N

description: colon cancer cell line


title: HT29GLUCC1

description: colon cancer cell line


title: H1993

description: lung cancer cell line


title: LS123

description: colon cancer cell line


title: H1915

description: lung cancer cell line


title: breast surgical IMC 37

description:
IMC 64 (583MS57)
Gene expression data from sugical breast cancer specimens.


title: COLO205

description: colon cancer cell line


title: H2106

description: lung cancer cell line


title: DLDDKO4

description: colon cancer cell line


title: SW1417

description: colon cancer cell line


title: CL34

description: colon cancer cell line


title: breast surgical IMC 36

description:
IMC 63 (583MS56)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 35

description:
IMC 61 (583MS53)
Gene expression data from sugical breast cancer specimens.


title: COCM1

description: colon cancer cell line


title: SNUC1

description: colon cancer cell line


title: H1838

description: lung cancer cell line


title: breast surgical IMC 34

description:
IMC 59 (583MS51)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 33

description:
IMC 57 (583MS80)
Gene expression data from sugical breast cancer specimens.


title: HCT116

description: colon cancer cell line


title: LS180

description: colon cancer cell line


title: H1793

description: lung cancer cell line


title: COLO741

description: colon cancer cell line


title: LOVO

description: colon cancer cell line

value: LOVO


title: HT29

description: colon cancer cell line


title: breast surgical IMC 32

description:
IMC 56 (583MS79)
Gene expression data from sugical breast cancer specimens.


title: HT55

description: colon cancer cell line


title: H1755

description: lung cancer cell line


title: H1792

description: lung cancer cell line


title: H1703

description: lung cancer cell line


title: breast surgical IMC 30

description:
IMC 51(583MS14)
Gene expression data from sugical breast cancer specimens.


title: H1734

description: lung cancer cell line


title: GP5D

description: colon cancer cell line


title: breast surgical IMC 48

description:
IMC 76 (583MS91)
Gene expression data from sugical breast cancer specimens.


title: C2BBE1

description: colon cancer cell line


title: breast surgical IMC 29

description:
IMC 50 (583MS41)
Gene expression data from sugical breast cancer specimens.


title: CCK81

description: colon cancer cell line


title: COLO320HSR

description: colon cancer cell line


title: H1693

description: lung cancer cell line


title: breast surgical IMC 31

description:
IMC 52 (583MS201)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 28

description:
IMC 48 (583MS40)
Gene expression data from sugical breast cancer specimens.


title: RCM1

description: colon cancer cell line


title: SW620

description: colon cancer cell line


title: WIDR

description: colon cancer cell line

value: WIDR


title: H1666

description: lung cancer cell line


title: breast surgical IMC 27

description:
IMC 47 (583MS39)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 26

description:
IMC 46 (583MS38)
Gene expression data from sugical breast cancer specimens.


title: CAR1

description: colon cancer cell line


title: HCT116HKH2

description: colon cancer cell line


title: HCT15

description: colon cancer cell line


title: G20RatTestis_DBP50_Rep4

city: Wilmington

first: Kamin

middle: J

last: Johnson

state: DE

address: 1600 Rockland Road

department: Nemours Biomedical Research

institute: Alfred I. duPont Hospital for Children

description: Dam was exposed daily via oral gavage from GD12 to 20 with 50 mg/kg (body weight) dibutyl phthalate (DBP).  DBP mixed with corn oil vehicle, and a volume of 1 ml mixture/kg body weight was administered.  Six hours after the final exposure, tissue was harvested.

hyb_protocol: Following fragmentation, 15 ug of labeled cRNA was hybridized for 16 hours at 45C on a GeneChip Rat Genome 230 2.0 Array.  GeneChips were washed and stained in a Affymetrix Fluidics Station 400.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip Scanner 3000 7

data_processing: Summarized probeset data were generated using Robust MultiChip Average (RMA) method.

organism: Rattus norvegicus

source_name: GD20RatTestis_50 mg/kg DBP_GD12to20

label_protocol: Biotinylated cRNA were prepared from 1 ug total RNA using an Affymetrix One Cycle Target Labeling and Control Reagents kit according to the manufacturer's protocol.

extract_protocol: Testes were extracted with TRIzol reagent (Invitrogen) and total RNA purifed using an RNeasy Micro kit (Qiagen).

treatment_protocol: Beginning on gestational day (GD) 12 and ending on GD20, dams were exposed once per day via oral gavage.  Testes were harvested six hours after the final exposure and snap frozen.

tag: gender

value: Male

value: Fischer 344

tag: age

value: gestational day 20

tag: exposure

value: dibutyl phthalate

tag: dibutyl phthalate dose level

value: 50 mg/kg (body weight)

tag: bioanalyzer rna integrity number

value: testis


title: H1651

description: lung cancer cell line


title: HT115

description: colon cancer cell line


title: H1573

description: lung cancer cell line


title: G20RatTestis_DBP50_Rep3


title: H1648

description: lung cancer cell line


title: breast surgical IMC 24

description:
IMC 44 (583MS09)
Gene expression data from sugical breast cancer specimens.


title: H1650

description: lung cancer cell line


title: G20RatTestis_Oil_Rep3

description: Dam was exposed daily via oral gavage from GD12 to 20 to 1 ml corn oil/kg body weight.  Six hours after the final exposure, tissue was harvested.

value: corn oil


title: H1568

description: lung cancer cell line


title: H1869

description: lung cancer cell line


title: G20RatTestis_DBP50_Rep2


title: G20RatTestis_Oil_Rep4


title: G20RatTestis_DBP50_Rep1


title: G20RatTestis_Oil_Rep2


title: breast surgical IMC 22

description:
IMC 39 (583MS71)
Gene expression data from sugical breast cancer specimens.


title: G20RatTestis_Oil_Rep1


title: H1563

description: lung cancer cell line


title: D2 green/C2 red

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

description: biological duplicate in dye-swap

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 825 ng of Cyanine 3-labelled and 825 ng of Cyanine5-labelled cRNA per hybridization. The hybridization reaction were performed at  65°C for 17 hours using Agilent’s Genen Expression Hybridization Kit into the single genome human chip.After hybridization, slides were washed with Agilent Gene Expression Wash Buffer 1, Gene Expression Wash Buffer 2 and Acetonitril for one minute at room temperature

scan_protocol: Chips were scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1) and the GE2-v4_91 extraction protocol.

data_processing: The signal values used for the subsequent analysis (for both channels)  are median feature signals, non background substracted, and corrected using multiple detrending.  Microsoft Excel software was used to filter out unreliable features (essentially features with expression values smaller than background + 3 Standard deviations of the background) and to perform the dye swap normalization. Agilent GeneSpring GX Software (v 7.3) was used for the LOWESS normalization. To select differentially expressed genes, up- and down-regulated features were selected both from the dye-swap normalized data and from the LOWESS normalized data, then these two sets were intersected.

source_name: Human intestinal Caco-2 cells

label_protocol: 500ng of Poly A+RNA were labelled, using Cyanine 3-CTP or Cyanine 5-CTP (Perkin Elmer) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns

growth_protocol:
Caco-2 cells were mantained in high glucose DMEM supplemented with 10% HIFBS (Hyclone),  1% Non Essential Amino Acid, 4mM Glutamine and antibiotics in incubator with 10% CO2. Cells were subcultured for at least 10 passages when cell reach 50% of confluence before applying the differetiation protocol.
For differentiation procedure Caco-2 cells were seeded with a cells density of 3E05 cell x cm2 on PET inserts (Falcon 3090) and let to differenentiate for 21 days. Medium was changed three times a week.

extract_protocol: Total RNA was extracted using TRIzol following manufacturer's instructions

tag: cells

value: cycling

value: intestine

tag: passage

value: 21-days differentiated


title: DLDDKO1

description: colon cancer cell line


title: breast surgical IMC 21

description:
IMC 38 (583MS35)
Gene expression data from sugical breast cancer specimens.

value: primary breast tumor

value: invasive mammary carcinoma


title: breast surgical IMC 25

description:
IMC 46 (583MS07)
Gene expression data from sugical breast cancer specimens.


title: D1 red/C1 green

description: biological duplicate in dye-swap


title: D2 red/C2 green

description: biological duplicate in dye-swap


title: Male E13 cell_biological rep3

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
Male E13-3
Gene expression data from E13 testis cells sub-culture incubated for 6 days.

hyb_protocol: Following fragmentation, ssDNA were hybridized on the Affymetrix Rat Gene 1.0 ST Array according to the standard Affymetrix protocol. Chips were washed and stained in the  Affymetrix Fluidics Station 4500.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data (all 18 CEL files together) were analyzed with Partek Genomic Suite 6.5 beta software (Partek Inc., St. Louis, MO) using RMA, GC-content adjusted pre-processing algorithm for background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.  Hybridization date batch effect was removed.

source_name: E13 male testis cell sub-culture, no treatment, 6 days

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Male or female E13 embryos (14 to 18 tail somite-stage) were collected from timed-pregnant females.  Gonads from E13 animals were dissected and each pair of gonads from individual animals was placed into one well of a 24-well plate with 500 µl Ham F-12 medium until embryos could be sexed.  The gonads were then pooled and digested with trypsin (2.5%) and collagenase (1mg/ml type I) plus DNase (3mg/ml) to disassociate the cells.  All the cells from the digested testes or ovaries were then cultured on 100 mm plates in Ham’s F-12 with 10% bovine calf serum (Sigma).  Cells initially multiplied well in culture and were split two times (1:2) as they reached confluence, at which point cell division slowed considerably.  Cells were maintained in culture, changing medium every three days, until growth plaques were observed at approximately one month. These growth plaques were then collected for further propagation and frozen stocks were prepared for subsequent cell splitting such that cells could be maintained at fewer than 12 subcultures.

extract_protocol: RNA was isolated from each of 3 well/plate separately after scraping cells from well bottom in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to the manufacturer’s instructions.

treatment_protocol: Cells between sub 8 and 12 were transfected using Lipofectamine 2000 (Invitrogen, Carlsbad, CA). Four µg expression plasmid was mixed with 10 µl Lipofectamine 2000 in 500 µl Opti-MEM medium (Invitrogen) for each well of a 6-well plate.  This 500 µl mix was added to each well containing ~90% confluent cultured E13 testis cells in 2 ml Ham’s F-12 medium without antibiotics and incubated at 32oC for 24 hours.  After 24 hours, medium was aspirated from cells and replaced with 1ml Ham’s F-12 with 10% serum.  Cells were incubated 6-7 days. In the end, 1 ml of Trizol was added and cells were collected for RNA extraction for microarray analysis.

tag: strain

value: Sprague-Dawley

value: male

tag: developmental stage

value: embryonic

tag: sub-cultured

value: less than 12 times

tag: treatment

tag: treatment time

value: 6 days

tag: hybridization date


title: H1299

description: lung cancer cell line


title: breast surgical IMC 18

description:
IMC 25 (583MS32)
Gene expression data from sugical breast cancer specimens.

tag: tissue


title: H1437

description: lung cancer cell line


title: D1 green/C1 red

description: biological duplicate in dye-swap


title: breast surgical IMC 20

description:
IMC 27 (583MS70)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 17

description:
IMC 23 (583MS30)
Gene expression data from sugical breast cancer specimens.


title: H1395

description: lung cancer cell line


title: Male E13 cell_biological rep1

description:
Male E13-1
Gene expression data from E13 testis cells sub-culture incubated for 6 days.


title: H1155

description: lung cancer cell line


title: myotube_Dex_24h_rep4

city: Berkeley

first: Jen-Chywan

last: Wang

state: CA

address: 315 Morgan Hall, UC Berkeley

department: Nutritional Sciences & Toxicology

institute: UC Berkeley

description:
Dex.24h.4
replicate 4

data_processing: The data were pre-processed using lumi package in R with bgAdjust.affy for background correction, quantile normalization, and slide effect removed using linear model.

source_name: C2C12 myotubes

label_protocol: Biotin-labeled cRNA samples were prepared with 750 ng of total RNA template.  Following synthesis and purification, the biotin-labeled samples were evaluated by both 260/280 absorbance spectrophotometry and capillary electrophoresis.

extract_protocol: Total cellular RNA was isolated utilizing the NucleoSpin RNA II kit (Macherey-Nagel) per manufacturers’ directions.  RNA isolates were first quantified by standard spectrophotometry, and then qualitatively evaluated by capillary electrophoresis employing the Bio-Rad Experion system following the manufacturers’ instruction.

value: myotube

tag: agent

value: Dex

tag: time


title: breast surgical IMC 23

description:
IMC 41 (583MS37)
Gene expression data from sugical breast cancer specimens.

tag: disease state


title: Male E13 cell_biological rep2

description:
Male E13-2
Gene expression data from E13 testis cells sub-culture incubated for 6 days.

tag: gender


title: myotube_Dex_24h_rep3

description:
Dex.24h.3
replicate 3


title: myotube_Dex_24h_rep2

description:
Dex.24h.2
replicate 2


title: EPLC_272H

description: lung cancer cell line

tag: cell line


title: Fem-E13_Tcf21+Tcf12_biological rep1

description:
F-E13_Tcf21+Tcf12-1
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing both rat Tcf21 and Tcf12 (Reb-alfa) genes.

source_name: E13 ovarian cell sub-culture, expression plasmid pCMV-myc over-expressing both Tcf21 and Tcf12 (Reb-alfa) genes, 6 days

value: female

value: ovary

tag: age

value: Tcf21 and Tcf12 (Reb-alfa) overexpression


title: myotube_Dex_24h_rep1

description:
Dex.24h.1
replicate 1


title: Fem-E13_Tcf21+Tcf12_biological rep2

description:
F-E13_Tcf21+Tcf12-2
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing both rat Tcf21 and Tcf12 (Reb-alfa) genes.


title: breast surgical IMC 19

description:
IMC 26 (583MS33)
Gene expression data from sugical breast cancer specimens.


title: myotube_Dex_24h_rep5

description:
Dex.24h.5
replicate 5


title: breast surgical IMC 16

description:
IMC 20 (583MS69)
Gene expression data from sugical breast cancer specimens.


title: Fem-E13_Tcf21+Tcf12_biological rep3

description:
F-E13_Tcf21+Tcf12-3
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing both rat Tcf21 and Tcf12 (Reb-alfa) genes.


title: breast surgical IMC 15

description:
IMC 19 (583MS68)
Gene expression data from sugical breast cancer specimens.


title: DV90

description: lung cancer cell line


title: EBC1

description: lung cancer cell line


title: myotube_ETOH_24h_rep5

description:
ETOH.24h.5
replicate 5

value: ETOH


title: CORL23/R23-

description: lung cancer cell line


title: myotube_ETOH_24h_rep4

description:
ETOH.24h.4
replicate 4


title: breast surgical IMC 14

description:
IMC 18 (583MS25)
Gene expression data from sugical breast cancer specimens.


title: CORL23/R

description: lung cancer cell line


title: myotube_ETOH_24h_rep3

description:
ETOH.24h.3
replicate 3


title: myotube_ETOH_24h_rep2

description:
ETOH.24h.2
replicate 2


title: breast surgical IMC 13

description:
IMC 17 (583MS67)
Gene expression data from sugical breast cancer specimens.


title: myotube_Dex_6h_rep3

description:
Dex.6h.3
replicate 3


title: breast surgical IMC 8

description:
IMC 9 (583MS23)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 10

description:
IMC 13 (583MS45)
Gene expression data from sugical breast cancer specimens.


title: myotube_ETOH_24h_rep1

description:
ETOH.24h.1
replicate 1


title: breast surgical IMC 12

description:
IMC 16 (583MS03)
Gene expression data from sugical breast cancer specimens.


title: Fem-E13_Tcf12_biological rep3

description:
F-E13_Tcf12-3
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing rat Tcf12 (Reb-alfa) gene.

source_name: E13 ovarian cell sub-culture, expression plasmid pCMV-myc over-expressing Tcf12 (Reb-alfa) gene, 6 days

value: Tcf12 (Reb-alfa) overexpression


title: breast surgical IMC 11

description:
IMC 15 (583MS47)
Gene expression data from sugical breast cancer specimens.


title: Fem-E13_Tcf21_biological rep3

description:
F-E13_Tcf21-3
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing rat Tcf21 gene.

source_name: E13 ovarian cell sub-culture, expression plasmid pCMV-myc over-expressing Tcf21 gene, 6 days

value: Tcf21 overexpression


title: Fem-E13_Tcf21_biological rep2

description:
F-E13_Tcf21-2
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing rat Tcf21 gene.


title: Fem-E13_Tcf21_biological rep1

description:
F-E13_Tcf21-1
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing rat Tcf21 gene.


title: Fem-E13_Tcf12_biological rep2

description:
F-E13_Tcf12-2
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing rat Tcf12 (Reb-alfa) gene.


title: myotube_Dex_6h_rep4

description:
Dex.6h.4
replicate 4


title: CORL23

description: lung cancer cell line


title: COLO_668

description: lung cancer cell line


title: CORL_105

description: lung cancer cell line


title: Fem-E13_Tcf12_biological rep1

description:
F-E13_Tcf12-1
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing rat Tcf12 (Reb-alfa) gene.


title: Fem-E13_SRY_biological rep3

description:
F-E13_SRY-4
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing rat Sry gene.

source_name: E13 ovarian cell sub-culture, expression plasmid pCMV-myc over-expressing Sry gene, 6 days

value: Sry overexpression


title: COLO-699N

description: lung cancer cell line


title: CORL-23/CPR

description: lung cancer cell line


title: myotube_Dex_6h_rep2

description:
Dex.6h.2
replicate 2


title: breast surgical IMC 9

description:
IMC 12 (583MS44)
Gene expression data from sugical breast cancer specimens.


title: breast surgical IMC 7

description:
IMC 8 (583MS02)
Gene expression data from sugical breast cancer specimens.


title: COLO699

description: lung cancer cell line


title: myotube_Dex_6h_rep1

description:
Dex.6h.1
replicate 1


title: breast surgical IMC 6

description:
IMC 7 (583MS66)
Gene expression data from sugical breast cancer specimens.


title: Fem-E13_SRY_biological rep2

description:
F-E13_SRY-3
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing rat Sry gene.


title: CHAGO-K-1

description: lung cancer cell line


title: CAL12T

description: lung cancer cell line


title: myotube_ETOH_6h_rep4

description:
ETOH.6h.4
replicate 4


title: breast surgical IMC 5

description:
IMC 6 (583MS65)
Gene expression data from sugical breast cancer specimens.


title: Fem-E13_Control_biological rep3

description:
F-E13_Con-3
Gene expression data from E13 ovarian cell sub-culture incubated in the presence of 2 ug empty expression plasmid pCMV-myc for 6 days.

source_name: E13 ovarian cell sub-culture, empty expression plasmid pCMV-myc, 6 days

value: control


title: breast surgical IMC 2

description:
IMC 3 (583MS18)
Gene expression data from sugical breast cancer specimens.

value: primary breast tumor


title: A427

description: lung cancer cell line


title: Fem-E13_SRY_biological rep1

description:
F-E13_SRY-2
Gene expression data from E13 ovarian cell sub-culture incubated for 6 days in the presence of 2 ug expression plasmid pCMV-myc over-expressing rat Sry gene.


title: Fem-E13_Control_biological rep1

description:
F-E13_Con-1
Gene expression data from E13 ovarian cell sub-culture incubated in the presence of 2 ug empty expression plasmid pCMV-myc for 6 days.


title: Fem-E13_Control_biological rep2

description:
F-E13_Con-2
Gene expression data from E13 ovarian cell sub-culture incubated in the presence of 2 ug empty expression plasmid pCMV-myc for 6 days.


title: breast surgical IMC 3

description:
IMC 4 (583MS19)
Gene expression data from sugical breast cancer specimens.

value: invasive mammary carcinoma


title: breast surgical IMC 1

description:
IMC 2 (583MS17)
Gene expression data from sugical breast cancer specimens.