title: 14286649 - Rap78 vs col

hyb_protocol: col Cy5 / Rap78 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286640 - Rap22 vs Rap22-NaCl

status: Public on Jul 01 2013

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Characterization to raptor mutants (partner of the kinase TOR) and of their answer to the salt stress.

hyb_protocol: Rap22-NaCl Cy5 / Rap22 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media=MS/2 hygrometry=in vitro, Room 70% Temperature=22°C Light=Light

extract_protocol: Rap22-NaCl:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:NaCl - abiotic stress - abiotic stress,nacl 200 mm:quantity 200mM time 3hour . Sowing on metal grids on MS/2 medium with continuous light (90 μE/m2/s 22°C). Transfer after 12 days of culture for 3h to liquid MS/2 medium containing or not 200 mM NaCl.

tag: ecotype

value: columbia

tag: genotype/variation

value: raptor mutants (rap22)

tag: dev.stage (boyes et al. plant cell 2001)

value: boyes 1.04

extract_protocol: Rap22:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment


title: 14286653 - col-NaCl vs Rap78-NaCl

hyb_protocol: Rap78-NaCl Cy5 / col-NaCl Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Rap78-NaCl:5ug. (Qiagen_RNeasy.pdf)

source_name: col-NaCl

extract_protocol: col-NaCl:5ug. (Qiagen_RNeasy.pdf)

value: wild type


title: 0hr_Unstim_Rep3

status: Public on Jul 02 2013

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

country: Australia

institute: Monash University

description: Gene expression in unstimulated bone marrow macrophages

hyb_protocol: The resulting cRNA was fragmented, hybridized to Agilent 4x44k Whole Mouse Genome Expression Microarrays and the slides washed according to manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing using an Agilent DNA Microarray Scanner (G2505B) according to manufacters instructions

data_processing: Feature extraction was performed with Agilent Feature Extraction Software 9.5 using default parameters excluding non-uniform flagged outliers

organism: Mus musculus

source_name: Bone marrow derived macrophages

label_protocol: 200 ng of RNA was Cy3 labeled with the one colour low RNA input Quick Amplification kit (Agilent) according to manufacters instructions

growth_protocol: For the generation of murine bone marrow-derived macrophages (BMDMs) bone marrow from female 6-10 weeks old C57BL/6 mice was flushed out from the femur and tibia and washed in PBS. The cells were re-suspended in RPMI 1640 medium (Gibco, VIC, Australia) containing 10 % (v/v) heat-inactivated fetal calf serum (Thermo Electron, VIC, Australia) supplemented with 1% penicillin/streptomycin (Gibco), 1% Glutamax (Gibco), and 20% of growth supernatant of L929 cells

extract_protocol: The BMDMs were harvested and RNA was extracted using Qiagen RNeasy mini column with on-column DNAse digestion according to manufacturers instructions

treatment_protocol: Overnight cultures of L. acidophilus and H. pylori were harvested by centrifugation at 1250 x g for 10 min at 4º C and washed twice in sterile phosphate-buffered saline (PBS).  Bacteria were re-suspended in RPMI 1640 medium (without FCS and antibiotics) and, unless stated otherwise, added (100 µl/well) to the BMDMs at a MOI of 1:1 (or medium for a final volume of 600 µl/well). The cell cultures were incubated at 37 ºC in 5 % CO2. In the inhibitor experiments, BMDMs were pre-incubated for 30 min with the endosomal acidification blockers Chloroquine (final concentration 10 μM) and Bafilomycin A1 (final concentration 25 μM) prior to stimulation with L. acidophilus

tag: strain

tag: Sex

value: female

tag: age

value: 6-10 weeks old

tag: treatment

value: Untreated

tag: cell type

value: Bone marrow derived macrophages


title: 14286647 - Rap22 vs col

hyb_protocol: col Cy5 / Rap22 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col

extract_protocol: col:5ug. (Qiagen_RNeasy.pdf)


title: 14286632 - Ctrl-1h_BR1 vs Benzene-1h_BR1

description: Improving the knowledge of the metabolic pathways of benzene in higher plants.

hyb_protocol: Benzene-1h_BR1 Cy5 / Ctrl-1h_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

organism: Brassica oleracea

growth_protocol: caulin leaf - Media=Compost hygrometry Temperature=20°C Light

extract_protocol: Benzene-1h_BR1:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Benzene 1h - environmental treatment - abiotic stress,benzene:time 1hour . 2 months old cabbages are exposed to 3ppm of atmospheric benzene in a 300 liters hermetic chamber. Exposures were conducted over periods of 1h, 3h and 24h. We made biological replicates of exposures of 1h and 3h. As controls, non-exposed plants are located next the exposure chamber for each experiment. At the end of the exposure, pieces of leaves from 3 different plants were pooled and immediatly flash-frozen with liquid nitrogen and stored at -80°C until RNA extraction.

tag: variety

value: Var. Prover

tag: harvest date

extract_protocol: Ctrl-1h_BR1:5ug. (Qiagen_RNeasy.pdf)


title: 14286645 - Rap78-NaCl vs Rap78

hyb_protocol: Rap78 Cy5 / Rap78-NaCl Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Rap78:5ug. (Qiagen_RNeasy.pdf)


title: 14286641 - Rap22-NaCl vs Rap22

hyb_protocol: Rap22 Cy5 / Rap22-NaCl Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286642 - Rap78 vs Rap78-NaCl

hyb_protocol: Rap78-NaCl Cy5 / Rap78 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286634 - Ctrl-1h_BR2 vs Benzene-1h_BR2

hyb_protocol: Benzene-1h_BR2 Cy5 / Ctrl-1h_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Benzene-1h_BR2:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: Ctrl-1h_BR2:5ug. (Qiagen_RNeasy.pdf)


title: 14286646 - col vs Rap22

hyb_protocol: Rap22 Cy5 / col Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Control_non-affected liver tissue_M778

type: genomic

city: Graz

first: Vendula

last: Svendova

address: Auenbruggerplatz 2

country: Austria

institute: Medical University Graz

description: non-affected liver tissue from 18 month-old mouse

hyb_protocol: samples were hybridized on a 8x60k CGH Array according to the Agilents protocol; hybridization buffer (Agilent in situ Hybridization kit plus) were added, samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers

scan_protocol: The slides were scanned with Agilent´s DNA Microarray Scanner (Scan Control Software version 3.0)

data_processing: The datasets were extracted with FeatureExtraction software 10.0.1.1 and subsequently analyzed by AGW 6.5

molecule: genomic DNA

source_name: liver tissue, aged 18 month, untreated

label_protocol: 500 ng gDNA were primed with BioPrimeLabeling Kit according to the manufacturer`s protocol; samples were incubated at 37°C, 2 h for amplifing and labeling

extract_protocol: gDNA was isolated using the Qiagen DNeasy Blood and Tissue kit following manufacturer's instructions; instead of washing buffer 2, 80% EtOH was used

tag: tissue

value: liver tissue

value: 18 month old

value: liver


title: Logarithmic young-Sir3 rep2

city: MIAOLI COUNTY

first: GUNN-GUANG

last: LIOU

state: TAIWAN

address: 35 KEYAN ROAD, JHUNAN TOWN

department: INSTITUTE OF MOLECULAR AND GENOMIC MEDICINE

country: Taiwan

institute: NATIONAL HEALTH RESEARCH INSTITUTES

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

scan_protocol: The protocol for scanning one-color NimbleGen arrays with a GenePix 4000B Scanner and associated software Genepix6.0. (NimbleGen_ChIP_Users_Guide_v3p1)

data_processing: Images were aligned and quantified using NimbleScan software  (V2.4) (Roche NimbleGen) which produced .pair reports of raw data and converted to ratio of Cy5 vs Cy3

organism: Saccharomyces cerevisiae

source_name: Sir 3

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

extract_protocol: Myc-antibody coupling resin was incubated with cell lysate at 4°C overnight. Beads were then washed once with cell lysis buffer (50 mM Hepes-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 0.5% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and protease inhibitors), twice with 50 mM Hepes-KOH pH 7.5, 250 mM NaCl, 1 mM EDTA, 0.25% Triton X-100, 0.1% sodium deoxycholate, 0.05% SDS, and protease inhibitors, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 0.5% NP40, 0.5% sodium deoxycholate, and 1 mM EDTA, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl and 1 mM EDTA, and once with TE (10 mM Tris-HCl pH 8.0 and 1 mM EDTA pH 8.0) at room temperature. Beads were eluted by incubating with 100 ul of 50 mM Tris-HCl pH 8.0, 10 mM EDTA, and 1% SDS at 65°C for 15 minutes. Elute was transferred to a fresh tube and pooled with a final bead wash of 150 ul TE with 0.67% SDS. For input DNA, 200 ul TE with 1% SDS was added to 50 ul cell lysate extract. To reverse the cross-links, all samples were incubated at 65°C overnight, combined with 250 ul TE, 5 ug glycogen, and 100 mg proteinase K, and incubated at 37°C for 2 h. After adding 55 ul of 4 M LiCl, samples were extracted once with phenol/chloroform and once with chloroform. The remaining associated DNA was precipitated by the addition of 400 mM LiCl, and 2 volumes of ethanol, washed with 75% ethanol, air dried, and resuspended in 50 ul TE with RNase A (20 mg/ml for input DNA and 2 mg/ml for affinity-precipitated DNA) and incubated at 37°C for 1 hour

tag: growth phase

value: Logarithmic phase

tag: chip antibody

value: Myc

tag: construct

source_name: input DNA

value: input DNA


title: Logarithmic young-Sir3 rep1


title: DBD11B

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Liver sample DBD11B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using robust spline normalisation with Bioconductor (v:2.5) Lumi package

label: biotin

organism: Homo sapiens

source_name: Liver Tissue

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: The tissue was cut after extraction into 2 mm2 pieces and immediately stored in diethyl pyrocarbonate (DEPC) solution, a nuclease inhibitor. In less than 24 hours the tissue was frozen and stored at -80º C. RNA extraction: Total RNAs were prepared from the lysates of liver with Trizol reagent (Invitrogen) according to the instructions provided by the manufacturer. RNA was treated with TURBO DNA-free Kit to remove DNA contamination according to the instructions provided by the manufacturer (Ambion, Austin, TX).

tag: trasplant donor origin

value: Donors after brain death without early allograft dysfunction (DBD)


title: DBD8A

description: Liver sample DBD8A

tag: time

value: A


title: EAD11B

description: Liver sample EAD11B

value: Donors after brain death with early allograft dysfunction (EAD)

value: B


title: DBD10B

description: Liver sample DBD10B


title: DBD4B

description: Liver sample DBD4B


title: CONT2

description: Liver sample CONT2

value: Control


title: DBD5A

description: Liver sample DBD5A


title: CONT3

description: Liver sample CONT3


title: DBD7B

description: Liver sample DBD7B


title: DBD6B

description: Liver sample DBD6B


title: EAD7B

description: Liver sample EAD7B


title: DBD5B

description: Liver sample DBD5B


title: Stationary old-Sir3

value: Stationary phase


title: DBD10A

description: Liver sample DBD10A


title: DBD3A

description: Liver sample DBD3A


title: DBD7A

description: Liver sample DBD7A


title: DBD11A

description: Liver sample DBD11A


title: sample.24 6.25 mg/kg DB[a,h]A

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned at a resolution of 5 mm using an Agilent G2505B scanner.

data_processing: The log2 of median signal intensites were cyclic lowess normalized and the technical replicates were averaged using the median.

label: Cyanine 3-pCp

source_name: liver

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit (Agilent Tech, Mississauga, ON, Canada).

extract_protocol: Total RNA containing the small fraction was isolated from each sample using the miRVana miRNA Isolation Kit (Ambion), Streetsville, ON, Canada). Quality was confirmed using the Agilent 2100 Bioanalyzer and RNA Nano 6000 chips.

treatment_protocol: 10-week old male Muta™Mouse (i.e., transgenic mouse strain 40.6) were dosed daily via oral gavage for 28-days with DB[a,h]A dissolved in olive oil (6.25, 12.50 and 25 mg/kg body weight/day).  Each dose group contained 5 animals; 5 animals were also dosed with a vehicle (olive oil) control. Following a 3 day expression period after the last treatment, mice were euthanized with isofluorane followed by cervical dislocation. Liver was then excised, flash-frozen in liquid nitrogen, and stored at -80ºC until use.

tag: dose

value: 6.25 mg/kg DB[a,h]A

value: part of liver

tag: gender

value: male

value: 10 weeks

value: MutaMouse (transgenic mouse strain 40.6)

tag: date of exposure

value: January 24- February 22

tag: time post exposure

value: 3 days


title: CONT1

description: Liver sample CONT1

value: liver


title: DBD3B

description: Liver sample DBD3B


title: EAD11A

description: Liver sample EAD11A


title: DBD6A

description: Liver sample DBD6A


title: DBD8B

description: Liver sample DBD8B


title: DBD4A

description: Liver sample DBD4A


title: EAD9B

description: Liver sample EAD9B


title: EAD9A

description: Liver sample EAD9A


title: DCD1B

description: Liver sample DCD1B

value: Donor after cardiac death (DCD)


title: EAD1A

description: Liver sample EAD1A


title: EAD6A

description: Liver sample EAD6A


title: EAD2B

description: Liver sample EAD2B


title: EAD6B

description: Liver sample EAD6B


title: DCD7B

description: Liver sample DCD7B


title: LD11B

description: Liver sample LD11B

value: Living Donor (LD)


title: DCD5A

description: Liver sample DCD5A


title: DCD3B

description: Liver sample DCD3B


title: DCD9A

description: Liver sample DCD9A


title: DCD6B

description: Liver sample DCD6B


title: EAD4A

description: Liver sample EAD4A


title: DCD6A

description: Liver sample DCD6A


title: DCD4A

description: Liver sample DCD4A


title: DCD8B

description: Liver sample DCD8B


title: EAD3A

description: Liver sample EAD3A


title: EAD1B

description: Liver sample EAD1B


title: DCD8A

description: Liver sample DCD8A


title: DCD5B

description: Liver sample DCD5B


title: DCD9B

description: Liver sample DCD9B


title: EAD7A

description: Liver sample EAD7A


title: EAD3B

description: Liver sample EAD3B


title: DCD4B

description: Liver sample DCD4B


title: DCD3A

description: Liver sample DCD3A


title: EAD4B

description: Liver sample EAD4B


title: DCD1A

description: Liver sample DCD1A


title: EAD2A

description: Liver sample EAD2A


title: DCD7A

description: Liver sample DCD7A


title: LD11A

description: Liver sample LD11A


title: LD10A

description: Liver sample LD10A


title: LD8A

description: Liver sample LD8A


title: LD4B

description: Liver sample LD4B


title: LD6B

description: Liver sample LD6B


title: LD5A

description: Liver sample LD5A


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 6 of 10

city: New Delhi

first: Pankaj

last: Kumar

state: Delhi

address: Mall Road,

department: G N R Knowledge Center for Genome Informatics

country: India

institute: Institiue of Genomics and Integrative Biology

hyb_protocol: ChIP-DNA samples were labeled and hybridized to NimbleGen HD microarrays (NimbleGen Systems). DNA was labeled according to NimbleGen Systems’ protocol. Samples were hybridized at 42°C for 16 hours on a MAUI 12-bay hybridization station (BioMicro Systems).

scan_protocol: Arrays were scanned on a the Axon Genepix 4000B scanner at 5 microns for both 532nm and 635nm channels

data_processing: Scanned images were processed using NimbleScan

source_name: H4K16ac ChIP DNA from HEK293 cells

extract_protocol: DMEM high glucose with 10% FBS, culture at 37C in 5% CO2

tag: cell line

tag: antibody

source_name: Input DNA from HEK293 cells

tag: sample type

value: input


title: LD10B

description: Liver sample LD10B


title: LD4A

description: Liver sample LD4A


title: LD3B

description: Liver sample LD3B


title: LD3A

description: Liver sample LD3A


title: LD9A

description: Liver sample LD9A


title: LD8B

description: Liver sample LD8B


title: LD1A

description: Liver sample LD1A


title: LD9B

description: Liver sample LD9B


title: LD5B

description: Liver sample LD5B


title: H4 Cy3 vs. N2 Cy5

city: Valencia

first: Rut

last: Lucas

address: Autopista Saler 16,

institute: Centro Investigación Príncipe Felipe

description: 72h hypoxic incubation vs normoxia

hyb_protocol: hybridized with Human Genome CGH Microarray 44K (Agilent p/n G4426B-014950; http://www.genomics.agilent.com) containing 43,000+ coding and non-coding human sequences.

scan_protocol: scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol;

data_processing: data were extracted by Agilent Feature Extraction Software 10.7.1, following the Agilent protocol CGH_107_Sep09,grid template 014950_D_F_20090929 and the QC Metric Set CGH_QCMT_Sep09

label_protocol: Cyanine 3-dUTP and cyanine 5-dUTP were used for fluorescent labeling of digested gDNAs using the ‘Genomic DNA Enzymatic Labeling Kit’ Agilent p/n 5190-0449

growth_protocol: Human dental pulp stem cells (DPSC) were cultured in low glucose-glucose Dulbecco´s modified Eagle´s medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

extract_protocol: Cell line genomic DNA was purified by the ‘WizardR Genomic DNA Purification Kit’ (Promega)

treatment_protocol: The hypoxic condition was generated by culturing cells in a chamber (In vivo2 400, Ruskinn Life Sciences, Pencoed, Bridgend, U.K., http://www.ruskinn.com) flushed with pre-mixed gas consisting of 1% O2, 5% CO2 and 94% N2 at 37ºC.

value: 72 hours

value: DPSC

tag: stress

value: hypoxia

value: normoxia


title: N1 Cy3 vs. H3 Cy5

description: 48h hypoxic incubation vs normoxia dye swap

value: 48 hours

tag: cell type


title: genomic DNA from Normal Bone Marrow 1

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

description:
Normal Bone Marrow
Sample name: NB1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software v2010.3 with the Methylation module.
The signal_intensities matrix reporting unmethylated and methylated signal intensities is linked as a supplementary file on the Series record.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted aaccording to standard protocaols and DNA purity and concentration determined by spechtrophotometry.

tag: disease state

value: Normal Bone Marrow (control)

tag: tumor/control

value: Control

tag: cpg island methylator phenotype (cimp) subgroup

value: CIMP-


title: genomic DNA from Normal Bone Marrow 2

description:
Normal Bone Marrow
Sample name: NB2


title: LD6A

description: Liver sample LD6A

tag: tissue

value: A


title: genomic DNA from Normal Bone Marrow 3

description:
Normal Bone Marrow
Sample name: NB3


title: H3 Cy3 vs. N1 Cy5

description: 48h hypoxic incubation vs normoxia


title: genomic DNA from stimulated Tcell P7/R2

description:
Stimulated T cells
Sample name: P7_R2

value: Stimulated T cells (control)


title: N2 Cy3 vs. H4 Cy5

description: 72 hypoxic incubation vs normoxia dye swap


title: genomic DNA from T-ALL sample 42

description:
BM T-ALL sample
Sample name: 42

source_name: T-ALL Sample 42

value: BM T-ALL sample

value: Tumor


title: genomic DNA from stimulated Tcell S1/PHA

description:
Stimulated T cells
Sample name: L2


title: HEK293 H4K16ac NimbleGen Human Whole-Genome Tiling Array Set 4 of 10

label_protocol: ChIP-DNA samples were labeled and hybridized to NimbleGen HD microarrays (NimbleGen Systems). DNA was labeled according to NimbleGen Systems’ protocol. Samples were hybridized at 42°C for 16 hours on a MAUI 12-bay hybridization station (BioMicro Systems).


title: genomic DNA from T-ALL sample 43

description:
BM T-ALL sample
Sample name: 43

source_name: T-ALL Sample 43


title: genomic DNA from T-ALL sample 39

description:
BM T-ALL sample
Sample name: 39

source_name: T-ALL Sample 39

value: CIMP+


title: genomic DNA from T-ALL sample 37

description:
BM T-ALL sample
Sample name: 37

source_name: T-ALL Sample 37


title: genomic DNA from T-ALL sample 41

description:
BM T-ALL sample
Sample name: 41

source_name: T-ALL Sample 41


title: genomic DNA from T-ALL sample 36

description:
BM T-ALL sample
Sample name: 36

source_name: T-ALL Sample 36


title: genomic DNA from T-ALL sample 40

description:
BM T-ALL sample
Sample name: 40

source_name: T-ALL Sample 40


title: Control IWAT Gettys06_CON_IWAT4

city: Baton Rouge

first: Kirsten

middle: P

last: Stone

address: 6400 Perkins Rd

country: USA

institute: Pennington Biomedical Research Center

hyb_protocol: 10 ug of fragmented DIG-labeled cRNA used for array hybridization according to Applied Biosystems protocol

scan_protocol: Chemiluminescence detection, imaging, and image analysis performed according to Applied Biosystems protocols and using the 1700 Chemiluminescent Microarray Analyzer Software v 1.0.3

label: DIG-UTP

organism: Rattus norvegicus

source_name: IWAT, CON diet

label_protocol: 1 ug of total RNA was transcribed to DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT kit v2.0

extract_protocol: RNA extracted using TriReagent (Molecular Research Center, Inc. Cincinnati, OH), with added purification of the aqueous layer using Qiagen Rneasy MiniKit. Concentration and quality of RNA assessed using Agilent Bioanalyzer.

treatment_protocol: IWAT tissue flash frozen in liquid nitrogen immediately after dissection; stored at -80C

tag: strain

value: Fischer 344

value: Male

value: inguinal white adipose

tag: treatment

value: control diet


title: genomic DNA from T-ALL sample 38

description:
BM T-ALL sample
Sample name: 38

source_name: T-ALL Sample 38


title: Methionine restriction Gettys06_MR_IWAT2

source_name: IWAT, MR diet

value: methionine restricted diet


title: Methionine restriction Gettys06_MR_IWAT3


title: Methionine restriction Gettys06_MR_IWAT1


title: Control IWAT Gettys06_CON_IWAT2


title: Control IWAT Gettys06_CON_IWAT1


title: genomic DNA from T-ALL sample 35

description:
BM T-ALL sample
Sample name: 35

source_name: T-ALL Sample 35


title: genomic DNA from T-ALL sample 34

description:
BM T-ALL sample
Sample name: 34

source_name: T-ALL Sample 34


title: genomic DNA from T-ALL sample 30

description:
BM T-ALL sample
Sample name: 30

source_name: T-ALL Sample 30


title: genomic DNA from T-ALL sample 32

description:
BM T-ALL sample
Sample name: 32

source_name: T-ALL Sample 32


title: genomic DNA from T-ALL sample 31

description:
BM T-ALL sample
Sample name: 31

source_name: T-ALL Sample 31


title: Control IWAT Gettys06_CON_IWAT3


title: Methionine restriction Gettys06_MR_IWAT4


title: genomic DNA from T-ALL sample 28

description:
BM T-ALL sample
Sample name: 28

source_name: T-ALL Sample 28


title: B9P10_C with array type Medicago from Affymetrix

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description:
medicago truncatula (cv jemalong)  - age: 4week
-In natural ecosystems most terrestrial plants form arbuscular mycorrhiza (AM), mutualistic symbioses with soil fungi belonging to the order Glomeromycota. This symbiosis takes place when phosphate is limiting and enables the plant to acquire nutrients (in particular phosphate) in exchange of carbon provided to the fungus A hypermycorrhizal mutant B9 was identified (Morandi et al. Mycorrhiza (2009) 19: 435) which displayed higher root colonization by Glomus intraradices. This phenotype could be linked to a defect in phosphate sensing or transport. We have undertaken the analysis of the root transcriptome of both WT and mutant plants grown on limiting or non-limiting phosphate to determine which processes are affected in the hypermycorrhizal mutant.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Medicago truncatula

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: roots - -Plants were grown in chamber under long days: 22°C light (380 µE m-2 s-1) for 16 h, 19°C dark for 8h, on a mixture of gamma irradiated clay loam soil containing 20% sand and watered 3 times per week with a modified Long Ashton solution.

treatment_protocol: Name:MUT - environmental treatment - abiotic stress,phosphate:quantity 130uM . Sample_Treated name (name of the treatment to apply at this sample): B9 P/10 A (130 µM phosphate) Reference protocol or description Sample treatment protocol : - Plants were grown in chamber under long days: 22°C light (380 µE m-2 s-1) for 16 h, 19°C dark for 8h, on a mixture of gamma irradiated clay loam soil containing 20% sand and watered 3 times per week with a modified Long Ashton solution (P/10) containing 130 µM phosphate.

tag: genotype/variation


title: B9P10_B with array type Medicago from Affymetrix


title: genomic DNA from T-ALL sample 33

description:
BM T-ALL sample
Sample name: 33

source_name: T-ALL Sample 33


title: B9P10_A with array type Medicago from Affymetrix


title: B9P2_B with array type Medicago from Affymetrix


title: genomic DNA from T-ALL sample 29

description:
BM T-ALL sample
Sample name: 29

source_name: T-ALL Sample 29


title: WTP2_C with array type Medicago from Affymetrix

treatment_protocol: Name:WT - environmental treatment - abiotic stress,phosphate:quantity 130uM . Reference protocol or description Sample treatment protocol : - Plants were grown in chamber under long days: 22°C light (380 µE m-2 s-1) for 16 h, 19°C dark for 8h, on a mixture of gamma irradiated clay loam soil containing 20% sand and watered 3 times per week with a modified Long Ashton solution (P/10) containing 130 µM phosphate. Treatment date (month/day/year) : plants were cultivated for 4 weeks with 130 µM phosphate

value: WT


title: WTP10_A with array type Medicago from Affymetrix


title: prostate_cancer_primary_541

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using fRMA package (v.1.4.0) and Bioconductor (v.2.8). The data matrix (available on Series records) contains quantile normalized PSR (probe selection regions) level expression values from fRMA.
probe group file: HuEx-1_0-st-v1.r2.pgf

source_name: primary prostate cancer FFPE tissue sample

label_protocol: RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 2.0 (NuGEN)

growth_protocol: not applicable

extract_protocol: RNA was extracted from four 10 um FFPE sections. The highest Gleason grade was macrodissected from surrounding non-neoplastic cells, guided by an H&E stained slide for tumor identification. RNA was extracted and purified using the Roche HighPure FFPE kit.

treatment_protocol: not applicable

tag: gleason score

tag: metastatic event


title: prostate_cancer_primary_537


title: prostate_cancer_primary_542


title: prostate_cancer_primary_538


title: genomic DNA from T-ALL sample 27

description:
BM T-ALL sample
Sample name: 27

source_name: T-ALL Sample 27


title: prostate_cancer_primary_539


title: prostate_cancer_primary_544


title: prostate_cancer_primary_540


title: B9P2_A with array type Medicago from Affymetrix


title: prostate_cancer_primary_545


title: B9P2_C with array type Medicago from Affymetrix


title: WTP10_C with array type Medicago from Affymetrix


title: genomic DNA from T-ALL sample 24

description:
BM T-ALL sample
Sample name: 24

source_name: T-ALL Sample 24


title: genomic DNA from T-ALL sample 23

description:
BM T-ALL sample
Sample name: 23

source_name: T-ALL Sample 23


title: genomic DNA from T-ALL sample 18

description:
BM T-ALL sample
Sample name: 18

source_name: T-ALL Sample 18


title: genomic DNA from T-ALL sample 25

description:
BM T-ALL sample
Sample name: 25

source_name: T-ALL Sample 25


title: LD1B

description: Liver sample LD1B

source_name: Liver Tissue

value: liver

tag: trasplant donor origin

value: Living Donor (LD)

tag: time

value: B


title: genomic DNA from T-ALL sample 26

description:
BM T-ALL sample
Sample name: 26

source_name: T-ALL Sample 26


title: genomic DNA from T-ALL sample 22

description:
BM T-ALL sample
Sample name: 22

source_name: T-ALL Sample 22


title: genomic DNA from T-ALL sample 19

description:
BM T-ALL sample
Sample name: 19

source_name: T-ALL Sample 19


title: genomic DNA from T-ALL sample 17

description:
BM T-ALL sample
Sample name: 17

source_name: T-ALL Sample 17


title: genomic DNA from T-ALL sample 21

description:
BM T-ALL sample
Sample name: 21

source_name: T-ALL Sample 21


title: WTP2_B with array type Medicago from Affymetrix

growth_protocol: roots -  -Plants were grown in chamber under long days: 22°C light (380 µE m-2 s-1) for 16 h, 19°C dark for 8h, on a mixture of gamma irradiated clay loam soil containing 20% sand and watered 3 times per week with a modified Long Ashton solution.


title: genomic DNA from T-ALL sample 14

description:
BM T-ALL sample
Sample name: 14

source_name: T-ALL Sample 14


title: genomic DNA from T-ALL sample 16

description:
BM T-ALL sample
Sample name: 16

source_name: T-ALL Sample 16


title: prostate_cancer_primary_543


title: WTP10_B with array type Medicago from Affymetrix


title: prostate_cancer_primary_536


title: genomic DNA from T-ALL sample 20

description:
BM T-ALL sample
Sample name: 20

source_name: T-ALL Sample 20


title: prostate_cancer_primary_535


title: prostate_cancer_primary_533


title: prostate_cancer_primary_534


title: genomic DNA from T-ALL sample 15

description:
BM T-ALL sample
Sample name: 15

source_name: T-ALL Sample 15


title: prostate_cancer_primary_532


title: WTP2_A with array type Medicago from Affymetrix


title: prostate_cancer_primary_531


title: prostate_cancer_primary_529


title: prostate_cancer_primary_530


title: prostate_cancer_primary_528


title: prostate_cancer_primary_526


title: prostate_cancer_primary_525


title: prostate_cancer_primary_527


title: prostate_cancer_primary_524


title: prostate_cancer_primary_523


title: prostate_cancer_primary_522


title: prostate_cancer_primary_520


title: genomic DNA from T-ALL sample 11

description:
BM T-ALL sample
Sample name: 11

source_name: T-ALL Sample 11


title: genomic DNA from T-ALL sample 13

description:
BM T-ALL sample
Sample name: 13

source_name: T-ALL Sample 13


title: genomic DNA from T-ALL sample 12

description:
BM T-ALL sample
Sample name: 12

source_name: T-ALL Sample 12


title: prostate_cancer_primary_521

source_name: primary prostate cancer FFPE tissue sample


title: genomic DNA from T-ALL sample 8

description:
BM T-ALL sample
Sample name: 8

source_name: T-ALL Sample 8


title: genomic DNA from T-ALL sample 10

description:
BM T-ALL sample
Sample name: 10

source_name: T-ALL Sample 10


title: genomic DNA from T-ALL sample 7

description:
BM T-ALL sample
Sample name: 7

source_name: T-ALL Sample 7


title: genomic DNA from T-ALL sample 2

description:
BM T-ALL sample
Sample name: 2

source_name: T-ALL Sample 2


title: prostate_cancer_primary_519


title: prostate_cancer_primary_518


title: genomic DNA from T-ALL sample 9

description:
BM T-ALL sample
Sample name: 9

source_name: T-ALL Sample 9


title: genomic DNA from T-ALL sample 4

description:
BM T-ALL sample
Sample name: 4

source_name: T-ALL Sample 4


title: prostate_cancer_primary_517


title: genomic DNA from T-ALL sample 6

description:
BM T-ALL sample
Sample name: 6

source_name: T-ALL Sample 6


title: genomic DNA from T-ALL sample 1

description:
BM T-ALL sample
Sample name: 1

source_name: T-ALL Sample 1


title: prostate_cancer_primary_515


title: prostate_cancer_primary_514


title: prostate_cancer_primary_513


title: prostate_cancer_primary_516


title: genomic DNA from T-ALL sample 5

description:
BM T-ALL sample
Sample name: 5

source_name: T-ALL Sample 5


title: prostate_cancer_primary_512


title: OC3 cell_Gα12 siRNA

city: Zhunan, Miaoli County

first: Shiou-Ling

last: Jian

address: 35 Keyan Road

department: Institute of Molecular and Genomic Medicine

institute: National Health Research Institutes

hyb_protocol: Samples were hybridized with GeneChip Human Gene 1.0 ST Arrays (Affymetrix).

scan_protocol: Arrays were scanned at the NHRI Microarray Core Facility according to the manufacturer's instructions (Affymetrix).

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.2.0.20) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options. Core exons were included in the analysis. Transcript assignments are based on genome build hg18.

source_name: OC-3 transfected with Gα12 siRNA for 48h

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the Applause WT Amp ST System (Nugen) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: HSC-3 and OC-3 cells were cultured in MEM and DMEM/KSFM supplemented with 10% fetal bovine serum and maintained in a 37°C incubator with 5% CO2/humidified air atmosphere.

extract_protocol: Total RNA samples were extracted from cells using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with 50nM control or Gα12 siRNA using DharmaFECT transfection reagents (Dharmacon) for 48 hours.

value: oral squamous cell carcinoma (OSCC) cells

tag: Sex

value: male

tag: sirna


title: prostate_cancer_primary_510


title: prostate_cancer_primary_509


title: prostate_cancer_primary_508


title: prostate_cancer_primary_507


title: genomic DNA from T-ALL sample 3

description:
BM T-ALL sample
Sample name: 3

source_name: T-ALL Sample 3


title: OC3 cell_control siRNA

source_name: OC-3 transfected with control siRNA for 48h

tag: cell line

value: control


title: prostate_cancer_primary_511


title: prostate_cancer_primary_505


title: prostate_cancer_primary_506


title: HSC3 cell_Gα12 siRNA

source_name: HSC-3 transfected with Gα12 siRNA for 48h


title: prostate_cancer_primary_504


title: prostate_cancer_primary_503


title: prostate_cancer_primary_502


title: P3C t=4 donor4

city: Nijmegen

first: Marloes

last: Vissers

address: Geert Grooteplein Zuid 10

department: Department of Pediatrics

country: Netherlands

institute: Radboud university medical center

hyb_protocol: standard Affymetrix hybridization and wash protocol

scan_protocol: standard Affymetrix scan protocol

data_processing:
Affymetrix expression console core RMA sketch
HuEX-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: monocyte derived macrophages

label_protocol: standard Affymetrix terminal labeling protocol

extract_protocol: qiagen Rneasy total RNA isolation

tag: individual

value: donor 4

value: monocyte derived macrophages


title: LPS t=4 donor3

value: donor 3

value: LPS


title: prostate_cancer_primary_501


title: LPS t=4 donor4


title: prostate_cancer_primary_500


title: P3C t=4 donor2

value: donor 2


title: HSC3 cell_control siRNA

source_name: HSC-3 transfected with control siRNA for 48h


title: Cd-2

city: Taipei

first: Ming Yi

last: Chou

state: Taiwan

address: 128 Sec. 2 Acdemia Rd.

department: Cellular and Organismic Biology

country: Japan

institute: Acdemia Sinica

description: The commercial zebrafish 14K oligonucleotide set (MWG Biotech AG, Ebersbach, Germany) was obtained and printed on UltraGAPS-coated slides (Corning, New York, NY) with an OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI) according to the manufacturer’s instructions. The 14,067 oligonucleotides represented 9666 genes (7009 singlet genes and 2657 redundant genes), and the redundancy of the chip was 31%. A detailed description of the oligonucleotide information can be obtained on the Ocimun Biosolution website (http://www.ocimumbio.com/web/default.asp).

hyb_protocol: The zebrafish 14K OciChip array chip was pretreated with 1% bovine serum albumin (BSA) (fraction V), 4x saline-sodium citrate (SSC), and 1% sodium dodecylsulfate (SDS) at 42 °C for 45 min, and then hybridized overnight in a cocktail containing 5x Denhardt's solution, 6x SSC, 0.5% SDS, 50% formamide, 50 mM sodium phosphate, and 2 µg/µl yeast tRNA. Slides were washed with 2x SSC and 0.1% SDS (for 5 min), 1x SSC and 0.1% SDS (for 5 min), 0.5x SSC (for 5 min), and twice with 0.1x SSC (for 2 min each).

scan_protocol: Scanning was performed with a Genepix scanner (Molecular Devices, Sunnyvale, CA). The acquired images were analyzed using Genepix and Genespring software (Aglient Technologies, Foster City, CA). The measurements of spots were filtered by flags, and Lowess normalization was performed after subtracting the median background.

data_processing: The experiment contained 3 biological replicates with different samples. Differentially expressed genes were selected from those with at least 2 of 3 significant signals (with a ratio > 2 or < 0.5), and then the Significant Analysis of Microarray method (SAM 3.02) was used to determine statistical significance.

label: Alexa Flour 647

organism: Danio rerio

source_name: Cd treatment embryos

label_protocol: cDNA probes were synthesized by reverse transcription of 10 μg total RNA using a SuperScript indirect cDNA labeling system (Invitrogen) and were labeled with Alexa Flour 647 (cold-treatment groups) and Alexa Flour 555 (control groups) (Invitrogen).

extract_protocol: Total RNA was extracted using an RNA Trizol B kit (Teltest, Paisley, Scotland). Forty-five embryos or larvae were homogenized with 4.5 mL RNA Trizol B reagent. The homogenate was mixed with 200 μL chloroform, shaken gently for 15 s, and kept on ice for 5 min before centrifugation at 11,000 rpm for 10 min at 4 °C. An aliquot of 600 μL of supernatant was mixed well with 600 μL isopropanol and 3 M acetic acid, and stored at 15 °C for 10 min before further centrifugation at 11,000 rpm for 10 min at 4 °C. The supernatant was removed, and the precipitate was washed with 75% ethanol. The precipitate was allowed to dry for 30 min and was dissolved again in an adequate amount of diethylpyrocarbonate (DEPC, Sigma) to obtain total RNA. The RNA extract was dried at 37 °C for 5~10 min before measuring its total RNA content in a spectrophotometer (Hitachi U-2000, Japan) at OD 260/280 nm.

tag: agent

value: Cd

value: whole embryo

label: Alexa Flour 555

source_name: Control embryos

value: Control


title: prostate_cancer_primary_498

source_name: primary prostate cancer FFPE tissue sample


title: prostate_cancer_primary_499


title: LPS t=4 donor2

tag: cell type


title: PolyI:C t=4 donor4


title: P3C t=4 donor3


title: mock t=4 donor3

value: mock


title: PolyI:C t=4 donor3


title: prostate_cancer_primary_496


title: Cd-1


title: mock t=4 donor4


title: P3C t=4 donor1

value: donor 1


title: PolyI:C t=4 donor1


title: PolyI:C t=4 donor2


title: mock t=4 donor2


title: prostate_cancer_primary_494


title: Cd-3


title: prostate_cancer_primary_492


title: mock t=4 donor1


title: prostate_cancer_primary_497


title: prostate_cancer_primary_490


title: prostate_cancer_primary_491


title: prostate_cancer_primary_495


title: LPS t=4 donor1


title: prostate_cancer_primary_488


title: prostate_cancer_primary_493


title: prostate_cancer_primary_487


title: prostate_cancer_primary_486


title: prostate_cancer_primary_485


title: Sole_rep1

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip® Expression Wash, Stain and Scan User Manual (www.affymetrix.com).

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Image analysis used the Affymetrix Command Console version 3 (AGCC v3.0) software, processed with the Expression Console PLIER algorithm and the manufacturer’s specifications.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.na31.hg19.probeset_extended.mps

source_name: Epidermis and dermis from punch biopsy

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter engineered random primers for cDNA synthesis, and Ambion® WT Expression Kit (www.affymetrix.com).

growth_protocol: After biopsy, samples were stored in RNAlater prior to RNA extraction. No growth.

extract_protocol: Qiangen Fibrous RNA kit

treatment_protocol: no treatments

tag: skin

value: Sole

tag: volar or non-volar

value: volar

tag: upper or lower extremity

value: lower


title: prostate_cancer_primary_484


title: Sole_rep3


title: prostate_cancer_primary_483


title: prostate_cancer_primary_482


title: prostate_cancer_primary_481


title: Hand_rep3

value: Hand

value: non-volar

value: upper


title: Palm_rep2

value: Palm


title: Sole_rep2


title: Palm_rep3


title: Palm_rep1


title: Hand_rep4


title: Hand_rep1


title: Foot_rep3

value: Foot


title: Sole_rep4


title: Palm_rep4


title: prostate_cancer_primary_480


title: Foot_rep4


title: Foot_rep2


title: prostate_cancer_primary_478


title: prostate_cancer_primary_479


title: Foot_rep1


title: Hand_rep2


title: prostate_cancer_primary_477


title: prostate_cancer_primary_475


title: prostate_cancer_primary_473


title: prostate_cancer_primary_472


title: prostate_cancer_primary_470


title: NK cell replicate 3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 12.5 micrograms of biotinylated cRNA were hybridized for 16 hr at 45C on an Affymetrix GeneChip Mouse 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Expression values were summarized using the MAS5 algorithm as implemented in the GCOS v1.4 software (Affymetrix). Signals were variance adjusted by log-transformation prior to statistical analysis.  Analysis of variance (ANOVA) was performed using Partek Genomics Suite v6.4. The false discovery rate was controlled at a level of 0.05 unless otherwise stated.

source_name: Human peripheral blood monor nuclear cells

label_protocol: Biotinylated cRNA were prepared according to the two-cycle eukaryote target Affymetrix protocol starting from 10-100 nanograms of total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini/Micro kit accroding to the manufacturer's instructions.

treatment_protocol: Lymphocyte subsets were sorted with FACSAriaII (BD Biosciences, San Jose, CA).

tag: immunophenotype

value: CD3-CD56+ NK cell


title: prostate_cancer_primary_471


title: prostate_cancer_primary_469


title: prostate_cancer_primary_476


title: prostate_cancer_primary_468


title: prostate_cancer_primary_467


title: iNKT cell replicate 2

value: CD3+TCRValpha+ iNKT-cell


title: KIR-CD56+ T cell replicate 3

value: KIR-CD3+CD56+ T-cell


title: KIR+CD56+ T cell replicate 3

value: KIR+CD3+CD56+ T-cell


title: iNKT cell replicate 3


title: KIR-CD56+ T cell replicate 2


title: CD56- T cell replicate 3

value: CD3+CD56- T-cell


title: CD56+ T cell replicate 3

value: CD3+CD56+ T-cell


title: prostate_cancer_primary_474


title: prostate_cancer_primary_465


title: CD56+ T cell replicate 2


title: prostate_cancer_primary_466


title: KIR+CD56+ T cell replicate 1


title: prostate_cancer_primary_463


title: CD56- T cell replicate 2


title: KIR-CD56+ T cell replicate 1


title: prostate_cancer_primary_462


title: NK cell replicate 1


title: prostate_cancer_primary_489


title: CD56+ T cell replicate 1


title: prostate_cancer_primary_464


title: KIR+CD56+ T cell replicate 2


title: NK cell replicate 2


title: prostate_cancer_primary_461


title: prostate_cancer_primary_459


title: prostate_cancer_primary_458


title: prostate_cancer_primary_457


title: iNKT cell replicate 1


title: CD56- T cell replicate 1


title: U2OS Nutlin-3 treated, Replicate 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: U2OS cells treated with 10 uM Nutlin-3 for 24 hr

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..

source_name: U2OS Nutlin-3 treated

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.

growth_protocol: U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.

extract_protocol: RNA from U2OS cells was extracted using the RNeasy Midi kit  with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.

treatment_protocol: for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs

value: osteosarcoma


title: U2OS DMSO treated, Replicate 2

description: U2OS cells treated with 0.1% DMSO for 24 hr, control for Nutlin-treated cells

source_name: U2OS DMSO treated

value: DMSO (control for Nutlin-treated cells)


title: U2OS Nutlin-3 treated, Replicate 1


title: prostate_cancer_primary_455


title: U2OS DMSO treated, Replicate 3


title: prostate_cancer_primary_454


title: U2OS DMSO treated, Replicate 1


title: U2OS Doxorubicin treated, Replicate 1

description: U2OS cells treated with 0.6 ug/ml Doxorubicin for 24 hr

source_name: U2OS Doxorubicin treated

value: Doxorubicin


title: U2OS Nutlin-3 treated, Replicate 2


title: U2OS Doxorubicin treated, Replicate 2


title: U2OS No Treatment, Replicate 3

description: U2OS No Treatment control 24 hr, control for Doxorubicin-treated cells

source_name: U2OS No Treatment

value: No Treatment (control for Doxorubicin-treated cells)


title: prostate_cancer_primary_453


title: prostate_cancer_primary_460


title: U2OS No Treatment, Replicate 2


title: prostate_cancer_primary_452


title: U2OS No Treatment, Replicate 1


title: prostate_cancer_primary_449


title: prostate_cancer_primary_450


title: prostate_cancer_primary_456


title: prostate_cancer_primary_451


title: prostate_cancer_primary_448


title: prostate_cancer_primary_446


title: U2OS Doxorubicin treated, Replicate 3


title: prostate_cancer_primary_447


title: prostate_cancer_primary_444


title: prostate_cancer_primary_445


title: prostate_cancer_primary_443


title: shFOXO1_noDox2

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

institute: CCRI, St.Anna Children Cancer Research Institute

description: A673sh transiently transfected with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt, replica 2

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm

source_name: A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)

label_protocol: Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).

growth_protocol: A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).

extract_protocol: Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.

treatment_protocol: transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations.

tag: transfection

value: A673sh transiently with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt


title: shFOXO1_Dox2

description: A673sh transiently transfected with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt + doxycycline for 48h post transfection, replica 2

treatment_protocol: transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations, EWS-FLI1 knockdown was induced by addition of 1µg/ml doxycycline for 48h

value: A673sh transiently with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt + doxycycline for 48h post transfection


title: shFOXO1_Dox1

description: A673sh transiently transfected with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt + doxycycline for 48h post transfection, replica 1


title: prostate_cancer_primary_442


title: prostate_cancer_primary_439


title: sh_scrm_noDox1

description: A673sh transiently transfected with the pRS-sh-scrambled plasmid, replica 1

value: A673sh transiently with the pRS-sh-scrambled plasmid


title: prostate_cancer_primary_441


title: shFOXO1_noDox1

description: A673sh transiently transfected with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt, replica 1


title: FLAG_FOXO1_double

description: A673sh transiently transfected with the pCDNA3-based FLAG-FOXO1-S249A/S298A plasmid (CDK2 phosphorylation resistant Flag-tagged FOXO1, S249A/S298A), replica 1

value: A673sh transiently with the pCDNA3-based FLAG-FOXO1-S249A/S298A plasmid


title: pCDNA3empty

description: A673sh transiently transfected with the empty vector control (pCDNA3), replica 1

value: with the empty vector control (pCDNA3)


title: prostate_cancer_primary_438


title: prostate_cancer_primary_437


title: prostate_cancer_primary_436


title: sh_scrm_Dox2

description: A673sh transiently transfected with the pRS-sh-scrambled plasmid + doxycycline for 48h post transfection, replica 2

value: A673sh transiently with the pRS-sh-scrambled plasmid + doxycycline for 48h post transfection


title: prostate_cancer_primary_440


title: prostate_cancer_primary_435


title: prostate_cancer_primary_434


title: sh_scrm_noDox2

description: A673sh transiently transfected with the pRS-sh-scrambled plasmid, replica 2


title: prostate_cancer_primary_433


title: prostate_cancer_primary_432


title: prostate_cancer_primary_431


title: H5N1-infected monocytes, set 2, biological rep1

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

country: Germany

institute: Hannover Medical School

description: Gene expression data from H5N1-infected monocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with (GCOS) version 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: H5N1-infected monocytes, biological rep1

label_protocol: cRNA were prepared and SAGE-labeld according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA from 5 ug total RNA.

extract_protocol: Rneasy

value: primary human monocytes

tag: infection


title: FPV-infected monocytes, set 2, biological rep3

description: Gene expression data from FPV-infected monocytes

source_name: FPV-infected monocytes, biological rep3

value: FPV-infected


title: H5N1-infected monocytes, set 2, biological rep3

source_name: H5N1-infected monocytes, biological rep3


title: PR8-infected monocytes, set 2, biological rep3

description: Gene expression data from PR8-infected monocytes

source_name: PR8-infected monocytes, biological rep3


title: FPV-infected monocytes, set 2, biological rep1

source_name: FPV-infected monocytes, biological rep1


title: prostate_cancer_primary_430


title: H5N1-infected monocytes, set 2, biological rep2

source_name: H5N1-infected monocytes, biological rep2


title: prostate_cancer_primary_429


title: FLAG_FOXO1_AAA

description: A673sh transiently transfected with the pCDNA3-based FLAG-FOXO1-AAA plasmid (AKT phosphorylation resistant Flag-tagged FOXO1, T24A S256A S319A), replica 1

value: A673sh transiently with the pCDNA3-based FLAG-FOXO1-AAA plasmid


title: FPV-infected monocytes, set 2, biological rep2

source_name: FPV-infected monocytes, biological rep2


title: PR8-infected monocytes, set 2, biological rep1

source_name: PR8-infected monocytes, biological rep1


title: sh_scrm_Dox1

description: A673sh transiently transfected with the pRS-sh-scrambled plasmid + doxycycline for 48h post transfection, replica 1


title: prostate_cancer_primary_428


title: control monocytes, set 2, biological rep2

description: Gene expression data from control monocytes

source_name: control monocytes, biological rep2

value: control


title: prostate_cancer_primary_427

source_name: primary prostate cancer FFPE tissue sample


title: PR8-infected monocytes, set 2, biological rep2

source_name: PR8-infected monocytes, biological rep2


title: prostate_cancer_primary_426


title: control monocytes, set 2, biological rep1

source_name: control monocytes, biological rep1


title: control monocytes, set 2, biological rep3

source_name: control monocytes, biological rep3


title: prostate_cancer_primary_425


title: prostate_cancer_primary_424


title: prostate_cancer_primary_420


title: prostate_cancer_primary_419


title: prostate_cancer_primary_418


title: prostate_cancer_primary_417


title: prostate_cancer_primary_423


title: prostate_cancer_primary_413


title: prostate_cancer_primary_416


title: prostate_cancer_primary_410


title: prostate_cancer_primary_412


title: prostate_cancer_primary_408


title: prostate_cancer_primary_409


title: prostate_cancer_primary_422


title: prostate_cancer_primary_421


title: Pt32_Post

city: Bethesda

first: Eric

middle: C

last: Polley

address: 9609 Medical Center Drive, Rm 5W118

department: Biometric Research Branch

institute: National Cancer Institute

hyb_protocol: Hybridization, staining, and scanning were performed in quadruplicate using the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix)

scan_protocol: Affymetrix GeneChip Scanner 3000 according to the manufacturer’s protocol

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.

source_name: Tumor

label_protocol: Affymetrix GeneChip 3’ IVT Express Labeling Kit, manufacturer's protocol

extract_protocol: standard Affymetrix protocol

tag: timepoint

value: Post-Cediranib treatment


title: Pt34_Post


title: Pt34_Pre

value: Pre-Cediranib treatment


title: Pt32_Pre


title: prostate_cancer_primary_407

tag: gleason score


title: Pt25_Pre


title: Pt24_Post


title: Pt25_Post


title: prostate_cancer_primary_415

tag: metastatic event


title: prostate_cancer_primary_406


title: prostate_cancer_primary_411


title: prostate_cancer_primary_403


title: prostate_cancer_primary_414


title: prostate_cancer_primary_404


title: prostate_cancer_primary_401


title: prostate_cancer_primary_402


title: prostate_cancer_primary_405


title: prostate_cancer_primary_400


title: prostate_cancer_primary_396


title: prostate_cancer_primary_395


title: Pt23_Post


title: prostate_cancer_primary_398


title: Pt24_Pre


title: Pt38_Post


title: prostate_cancer_primary_397


title: Parietal lobe of control

city: Beijing

first: chan

last: tian

address: Changbai Road, Changping district

country: China

institute: Chinese Center for Disease Control and Prevention, China CDC

description: Gene expression data from commercial normal human parietal cortex pooled from four male/female

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix scanners 3000 7G.

data_processing: The CEL image was processed using the Affymetrix GCOS 1.4 software. The generated documents were analyzed according to the “Affymetrix Statistical Algorithms Description Document”. The ontologies (GO) and molecular functions of the genes from the patient that showed 6-fold increased or decreased expression compared with that of normal control were further analyzed by CapitalBio® Molecule Annotation System V3.0 (MAS3.0)

source_name: Commercial normal human brain total RNA(clontech)

label_protocol: Label protocol: Biotinylated cRNA were prepared according to the Manual of MessageAmp Premier RNA Amplification Kit from 200ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Total RNA of control was purchased from Clontech. See manufacturer's instruction.

tag: tissue

value: Brain parietal lobe

tag: genotype

value: PRNP-Wild type

tag: age


title: prostate_cancer_primary_394


title: prostate_cancer_primary_393


title: Pt38_Pre


title: prostate_cancer_primary_392


title: prostate_cancer_primary_390


title: prostate_cancer_primary_391


title: prostate_cancer_primary_389


title: prostate_cancer_primary_388


title: Parietal lobe of G114V gCJD

description: Gene expression data from parietal cortex of G114V gCJD patient brain

source_name: Human brain from a G114V gCJD patient(postmortem)

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction. Total RNA of control was purchased from Clontech.

value: 47 year


title: Pt23_Pre


title: prostate_cancer_primary_399


title: prostate_cancer_primary_386


title: prostate_cancer_primary_385


title: prostate_cancer_primary_383


title: prostate_cancer_primary_384


title: prostate_cancer_primary_379


title: prostate_cancer_primary_377


title: prostate_cancer_primary_381


title: prostate_cancer_primary_380


title: prostate_cancer_primary_382


title: prostate_cancer_primary_375


title: prostate_cancer_primary_374


title: prostate_cancer_primary_376


title: prostate_cancer_primary_378


title: prostate_cancer_primary_372


title: prostate_cancer_primary_370


title: prostate_cancer_primary_371


title: prostate_cancer_primary_366


title: prostate_cancer_primary_367


title: prostate_cancer_primary_361


title: prostate_cancer_primary_362


title: prostate_cancer_primary_373


title: prostate_cancer_primary_360


title: prostate_cancer_primary_358


title: prostate_cancer_primary_359


title: prostate_cancer_primary_368


title: prostate_cancer_primary_364


title: prostate_cancer_primary_363


title: prostate_cancer_primary_356


title: prostate_cancer_primary_387


title: prostate_cancer_primary_365


title: prostate_cancer_primary_355


title: prostate_cancer_primary_357


title: prostate_cancer_primary_352


title: prostate_cancer_primary_349


title: prostate_cancer_primary_348


title: prostate_cancer_primary_354


title: prostate_cancer_primary_351


title: prostate_cancer_primary_345


title: prostate_cancer_primary_369


title: prostate_cancer_primary_344


title: prostate_cancer_primary_350


title: prostate_cancer_primary_347


title: prostate_cancer_primary_346


title: prostate_cancer_primary_353


title: prostate_cancer_primary_343


title: prostate_cancer_primary_342


title: prostate_cancer_primary_340


title: prostate_cancer_primary_338


title: prostate_cancer_primary_339


title: prostate_cancer_primary_337


title: prostate_cancer_primary_336


title: prostate_cancer_primary_334


title: prostate_cancer_primary_335


title: prostate_cancer_primary_332


title: prostate_cancer_primary_331


title: prostate_cancer_primary_330


title: prostate_cancer_primary_341


title: prostate_cancer_primary_329


title: FL cells, at 24 h after exposure to 1.0 µM MNNG, biological rep2

city: hangzhou

first: li

last: hongjuan

address: 353 yan'an road

institute: zhejiang university

description: Gene expression data from FL cells exposed to 1.0 µM MNNG

hyb_protocol: The biotinlyated cRNAs were fragmented and hybridized to the microarrays at 45°C for 16 h in the Hybridization Oven 640 rotating at 60 rpm. Following hybridization, the microarrays were washed and stained with streptavidin-phycoerythrin in the Fluidics Station 400,

scan_protocol: Based on the Affymetrix Microarray Suite 5.0 platform, GeneChips were scanned using the GeneChip Scanner 3000, and original Affymetrix .dat proprietary output files were generated.

data_processing: Microarray data analysis was conducted according to the Affymetrix Statistical Algorithms Description Document. Raw data were collected and analyzed using the Expression Console software. All transcripts spots were filtered based on spot quality, statistical test, and corrections before subsequent analyses. Data normalization with the RMA (robust multichip analysis) algorithm and differential expression analysis with ANOVA (analysis of variation) statistical method were performed by using Genomics Suite v6.5 software. Genes differentially expressed among the comparisons of the treatments and the controls were selected based upon both relative and statistical criteria (1.5-fold change cutoff; FDR (false discovery rate) <0.05; p-value<0.05 in pairwise contrasts between the treatment and the control).

source_name: human amnion epithelial FL cells exposed to 1.0 µM MNNG for 2 h, and subsequently recovered for additional 22 h

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

growth_protocol: Human amnion epithelial FL cells were grown as monolayers in minimal essential medium (MEM, Gibco-Invitrogen, Carlsbad, CA) supplemented with 10% newborn bovine serum (Gibco-Invitrogen), 100 U/mL penicillin, and 100 µg/mL streptomycin in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated with Trizol reagents (Invitrogen), and further purified using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturers’ protocols. Isolated total RNA was analyzed on an Agilent Bioanalyzer 2100 to verify that the starting material was of good quality.

treatment_protocol: At the logarithmic growth phase, the cultures were exposed to vehicle control (0.1%, V/V) and a low concentration (1.0 µM) MNNG for 2 h in a culture medium that did not contain 10% newborn bovine serum, followed by additional growth for 1, 10 and 22 h, respectively, in a fresh medium containing 10% newborn bovine serum. The cultures were rinsed twice with phosphate buffer solution before change of the medium.

value: human amnion epithelial FL cells

tag: gender

value: female


title: prostate_cancer_primary_327


title: prostate_cancer_primary_326


title: prostate_cancer_primary_333


title: FL cells, at 12 h after exposure to 1.0 µM MNNG, biological rep1

source_name: human amnion epithelial FL cells exposed to 1.0 µM MNNG for 2 h, and subsequently recovered for additional 10 h


title: FL cells, at 12 h after exposure to 1.0 µM MNNG, biological rep2


title: FL cells, at 12 h after exposure to DMSO vehicle control, biological rep2

description: Gene expression data from FL cells exposed to DMSO vehicle control

source_name: human amnion epithelial FL cells exposed to DMSO vehicle control for 2 h, and subsequently recovered for additional 10 h


title: FL cells, at 12 h after exposure to DMSO vehicle control, biological rep1


title: FL cells, at 24 h after exposure to DMSO vehicle control, biological rep2

source_name: human amnion epithelial FL cells exposed to DMSO vehicle control for 2 h, and subsequently recovered for additional 22 h


title: prostate_cancer_primary_325


title: FL cells, at 24 h after exposure to 1.0 µM MNNG, biological rep3


title: FL cells, at 24 h after exposure to 1.0 µM MNNG, biological rep1


title: FL cells, at 24 h after exposure to DMSO vehicle control, biological rep1


title: FL cells, at 24 h after exposure to DMSO vehicle control, biological rep3


title: FL cells, at 3 h after exposure to 1.0 µM MNNG, biological rep3

source_name: human amnion epithelial FL cells exposed to 1.0 µM MNNG for 2 h, and subsequently recovered for additional 1 h


title: FL cells, at 12 h after exposure to DMSO vehicle control, biological rep3


title: FL cells, at 12 h after exposure to 1.0 µM MNNG, biological rep3


title: FL cells, at 3 h after exposure to 1.0 µM MNNG, biological rep1


title: FL cells, at 3 h after exposure to 1.0 µM MNNG, biological rep2


title: FL cells, at 3 h after exposure to DMSO vehicle control, biological rep2

source_name: human amnion epithelial FL cells exposed to DMSO vehicle control for 2 h, and subsequently recovered for additional 1 h


title: prostate_cancer_primary_328


title: FL cells, at 3 h after exposure to DMSO vehicle control, biological rep1


title: FL cells, at 3 h after exposure to DMSO vehicle control, biological rep3


title: prostate_cancer_primary_322


title: prostate_cancer_primary_323


title: prostate_cancer_primary_321


title: prostate_cancer_primary_324


title: prostate_cancer_primary_320


title: prostate_cancer_primary_319


title: prostate_cancer_primary_317


title: prostate_cancer_primary_316


title: prostate_cancer_primary_315


title: prostate_cancer_primary_314


title: prostate_cancer_primary_313


title: prostate_cancer_primary_312


title: prostate_cancer_primary_318


title: prostate_cancer_primary_310


title: prostate_cancer_primary_309


title: PC-3_originating cell line_R2

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

address: Ft. Detrick

department: DTP

institute: NCI Frederick

description:
PC-3 P0 T2
Gene expression data from PC-3 originating cell line.

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

scan_protocol: Microarray images were captured using a GeneChip® 3000 Scanner.

data_processing: Affymetrix Expression Console v1.3.

source_name: PC-3, originating cell line

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

growth_protocol: All cell lines were obtained from the Division of Cancer Treatment and Diagnosis Tumor Repository (DTP, FNLCR, Frederick, MD) or American Type Culture Collection (ATCC) (Manassas, Va). In addition, the identities of all cell lines used in this study were confirmed using Identifiler® STR genotyping (Applied Biosystems). All mice used in the study were obtained from the Animal Production Program (FNLCR, Frederick, MD). Tumor cells for inoculation were derived from the 4th in vitro passage from cryopreserved cell stocks. Cells (1 x 10^7 cells/0.1 ml/inoculation) were inoculated subcutaneously into mice (n=10 or more mice depending on the tumor cell line). For comparative purposes, 2-3 samples of in vitro cultivated cells at passage 4 post-cryopreservation were also prepared for microarray analysis (P0). When tumors at P1, P4 and P10 reached approximately 500 mg (10x10 mm), 5 tumors were harvested, cut into small pieces and flash frozen in liquid nitrogen using pre-chilled tubes. Samples were transferred to a -70°C freezer for holding prior to processing. Serial tumor passage was achieved by harvesting donor tumor material (n=2 to 5 donors) at each passage, mincing the tumors (2x2 mm fragments), pooling the samples and inoculating the next recipients subcutaneously using tumor implant trocars. Athymic nude mice (nu/nu NCr) served as the primary host for most xenograft studies. In several instances (particularly with human leukemias and lymphomas) it was difficult to establish and passage tumors in nu/nu NCr mice. In these instances, SCID.NCr or NOD.SCID/NCr mice were assessed for suitability. In general, female mice were used as they are less aggressive, easily group-housed and routinely used in xenograft experiments. Male mice were used for prostate tumors (PC-3, PC-3/M). Finally, in those instances where hormone effects on tumor growth are important (e.g., estradiol-dependent breast), mice were supplemented with estradiol.

extract_protocol: Total RNA was isolated using RNeasy (Qiagen).

tag: originating cell line

tag: tumor type

value: adenocarcinoma prostate

tag: in vivo passage


title: OVCAR-5_Passage 10 xenograft_R3

description:
OVCAR-5 P10 T3
Gene expression data from OVCAR-5 Passage 10 xenograft.

source_name: OVCAR-5, passage 10 xenograft

value: adenocarcinoma ovarian


title: OVCAR-5_Passage 4 xenograft_R5

description:
OVCAR-5 P04 T5
Gene expression data from OVCAR-5 Passage 4 xenograft.

source_name: OVCAR-5, passage 4 xenograft


title: OVCAR-5_Passage 4 xenograft_R3

description:
OVCAR-5 P04 T3
Gene expression data from OVCAR-5 Passage 4 xenograft.


title: OVCAR-5_Passage 10 xenograft_R5

description:
OVCAR-5 P10 T5
Gene expression data from OVCAR-5 Passage 10 xenograft.


title: OVCAR-5_Passage 10 xenograft_R2

description:
OVCAR-5 P10 T2
Gene expression data from OVCAR-5 Passage 10 xenograft.


title: OVCAR-5_Passage 4 xenograft_R2

description:
OVCAR-5 P04 T2
Gene expression data from OVCAR-5 Passage 4 xenograft.


title: OVCAR-5_Passage 10 xenograft_R1

description:
OVCAR-5 P10 T1
Gene expression data from OVCAR-5 Passage 10 xenograft.


title: PC-3_originating cell line_R1

description:
PC-3 P0 T1
Gene expression data from PC-3 originating cell line.


title: OVCAR-5_Passage 1 xenograft_R5

description:
OVCAR-5 P01 T5
Gene expression data from OVCAR-5 Passage 1 xenograft.

source_name: OVCAR-5, passage 1 xenograft


title: prostate_cancer_primary_308

source_name: primary prostate cancer FFPE tissue sample


title: OVCAR-5_Passage 1 xenograft_R4

description:
OVCAR-5 P01 T4
Gene expression data from OVCAR-5 Passage 1 xenograft.


title: OVCAR-5_Passage 4 xenograft_R1

description:
OVCAR-5 P04 T1
Gene expression data from OVCAR-5 Passage 4 xenograft.


title: prostate_cancer_primary_307


title: prostate_cancer_primary_306


title: OVCAR-5_originating cell line_R1

description:
OVCAR-5 P0 T1
Gene expression data from OVCAR-5 originating cell line.

source_name: OVCAR-5, originating cell line


title: prostate_cancer_primary_305


title: OVCAR-5_originating cell line_R2

description:
OVCAR-5 P0 T2
Gene expression data from OVCAR-5 originating cell line.


title: OVCAR-5_Passage 1 xenograft_R3

description:
OVCAR-5 P01 T3
Gene expression data from OVCAR-5 Passage 1 xenograft.


title: OVCAR-5_Passage 1 xenograft_R1

description:
OVCAR-5 P01 T1
Gene expression data from OVCAR-5 Passage 1 xenograft.


title: prostate_cancer_primary_304


title: prostate_cancer_primary_303


title: OVCAR-5_Passage 1 xenograft_R2

description:
OVCAR-5 P01 T2
Gene expression data from OVCAR-5 Passage 1 xenograft.


title: OVCAR-5_Passage 10 xenograft_R4

description:
OVCAR-5 P10 T4
Gene expression data from OVCAR-5 Passage 10 xenograft.


title: OVCAR-5_Passage 4 xenograft_R4

description:
OVCAR-5 P04 T4
Gene expression data from OVCAR-5 Passage 4 xenograft.


title: OVCAR-3_Passage 10 xenograft_R4

description:
OVCAR-3 P10 T4
Gene expression data from OVCAR-3 Passage 10 xenograft.

source_name: OVCAR-3, passage 10 xenograft


title: prostate_cancer_primary_302


title: OVCAR-3_Passage 10 xenograft_R5

description:
OVCAR-3 P10 T5
Gene expression data from OVCAR-3 Passage 10 xenograft.


title: prostate_cancer_primary_301


title: prostate_cancer_primary_299


title: prostate_cancer_primary_300


title: prostate_cancer_primary_297


title: OVCAR-3_Passage 10 xenograft_R3

description:
OVCAR-3 P10 T3
Gene expression data from OVCAR-3 Passage 10 xenograft.


title: prostate_cancer_primary_298


title: OVCAR-3_Passage 10 xenograft_R2

description:
OVCAR-3 P10 T2
Gene expression data from OVCAR-3 Passage 10 xenograft.


title: OVCAR-3_Passage 10 xenograft_R1

description:
OVCAR-3 P10 T1
Gene expression data from OVCAR-3 Passage 10 xenograft.


title: OVCAR-3_Passage 4 xenograft_R4

description:
OVCAR-3 P04 T4
Gene expression data from OVCAR-3 Passage 4 xenograft.

source_name: OVCAR-3, passage 4 xenograft


title: prostate_cancer_primary_296


title: OVCAR-3_Passage 4 xenograft_R3

description:
OVCAR-3 P04 T3
Gene expression data from OVCAR-3 Passage 4 xenograft.


title: prostate_cancer_primary_293


title: prostate_cancer_primary_294


title: prostate_cancer_primary_292


title: prostate_cancer_primary_290


title: OVCAR-3_Passage 4 xenograft_R5

description:
OVCAR-3 P04 T5
Gene expression data from OVCAR-3 Passage 4 xenograft.


title: prostate_cancer_primary_289


title: prostate_cancer_primary_291


title: OVCAR-3_Passage 1 xenograft_R5

description:
OVCAR-3 P01 T5
Gene expression data from OVCAR-3 Passage 1 xenograft.

source_name: OVCAR-3, passage 1 xenograft


title: prostate_cancer_primary_295


title: prostate_cancer_primary_287


title: prostate_cancer_primary_288


title: OVCAR-3_Passage 1 xenograft_R4

description:
OVCAR-3 P01 T4
Gene expression data from OVCAR-3 Passage 1 xenograft.


title: prostate_cancer_primary_286


title: OVCAR-3_Passage 4 xenograft_R1

description:
OVCAR-3 P04 T1
Gene expression data from OVCAR-3 Passage 4 xenograft.


title: prostate_cancer_primary_285


title: OVCAR-3_Passage 1 xenograft_R1

description:
OVCAR-3 P01 T1
Gene expression data from OVCAR-3 Passage 1 xenograft.


title: prostate_cancer_primary_283


title: prostate_cancer_primary_284


title: prostate_cancer_primary_282


title: OVCAR-3_Passage 1 xenograft_R3

description:
OVCAR-3 P01 T3
Gene expression data from OVCAR-3 Passage 1 xenograft.


title: NCI-H522_Passage 10 xenograft_R5

description:
NCI-H522 P10 T5
Gene expression data from NCI-H522 Passage 10 xenograft.

source_name: NCI-H522, passage 10 xenograft

value: adenocarcinoma lung


title: OVCAR-3_originating cell line_R2

description:
OVCAR-3 P0 T2
Gene expression data from OVCAR-3 originating cell line.

source_name: OVCAR-3, originating cell line


title: prostate_cancer_primary_281


title: OVCAR-3_Passage 1 xenograft_R2

description:
OVCAR-3 P01 T2
Gene expression data from OVCAR-3 Passage 1 xenograft.


title: OVCAR-3_originating cell line_R1

description:
OVCAR-3 P0 T1
Gene expression data from OVCAR-3 originating cell line.


title: prostate_cancer_primary_279


title: NCI-H522_Passage 10 xenograft_R4

description:
NCI-H522 P10 T4
Gene expression data from NCI-H522 Passage 10 xenograft.


title: prostate_cancer_primary_280


title: prostate_cancer_primary_278


title: prostate_cancer_primary_311


title: prostate_cancer_primary_277


title: OVCAR-3_Passage 4 xenograft_R2

description:
OVCAR-3 P04 T2
Gene expression data from OVCAR-3 Passage 4 xenograft.


title: prostate_cancer_primary_276


title: prostate_cancer_primary_274


title: prostate_cancer_primary_272


title: prostate_cancer_primary_275


title: prostate_cancer_primary_273


title: prostate_cancer_primary_271


title: prostate_cancer_primary_270


title: NCI-H522_Passage 10 xenograft_R3

description:
NCI-H522 P10 T3
Gene expression data from NCI-H522 Passage 10 xenograft.


title: prostate_cancer_primary_269


title: NCI-H522_Passage 10 xenograft_R2

description:
NCI-H522 P10 T2
Gene expression data from NCI-H522 Passage 10 xenograft.


title: prostate_cancer_primary_266


title: NCI-H522_Passage 4 xenograft_R4

description:
NCI-H522 P04 T4
Gene expression data from NCI-H522 Passage 4 xenograft.

source_name: NCI-H522, passage 4 xenograft


title: prostate_cancer_primary_268


title: prostate_cancer_primary_265


title: prostate_cancer_primary_267


title: NCI-H522_Passage 4 xenograft_R5

description:
NCI-H522 P04 T5
Gene expression data from NCI-H522 Passage 4 xenograft.


title: NCI-H522_Passage 1 xenograft_R3

description:
NCI-H522 P01 T3
Gene expression data from NCI-H522 Passage 1 xenograft.

source_name: NCI-H522, passage 1 xenograft


title: NCI-H522_Passage 4 xenograft_R2

description:
NCI-H522 P04 T2
Gene expression data from NCI-H522 Passage 4 xenograft.


title: NCI-H460_Passage 10 xenograft_R3

description:
NCI-H460 P10 T3
Gene expression data from NCI-H460 Passage 10 xenograft.

source_name: NCI-H460, passage 10 xenograft

value: large cell carcinoma lung


title: NCI-H522_Passage 10 xenograft_R1

description:
NCI-H522 P10 T1
Gene expression data from NCI-H522 Passage 10 xenograft.


title: NCI-H522_Passage 1 xenograft_R1

description:
NCI-H522 P01 T1
Gene expression data from NCI-H522 Passage 1 xenograft.


title: NCI-H522_originating cell line_R2

description:
NCI-H522 P0 T2
Gene expression data from NCI-H522 originating cell line.

source_name: NCI-H522, originating cell line


title: NCI-H460_Passage 10 xenograft_R4

description:
NCI-H460 P10 T4
Gene expression data from NCI-H460 Passage 10 xenograft.


title: NCI-H522_Passage 1 xenograft_R5

description:
NCI-H522 P01 T5
Gene expression data from NCI-H522 Passage 1 xenograft.


title: NCI-H460_Passage 10 xenograft_R5

description:
NCI-H460 P10 T5
Gene expression data from NCI-H460 Passage 10 xenograft.


title: NCI-H522_Passage 1 xenograft_R4

description:
NCI-H522 P01 T4
Gene expression data from NCI-H522 Passage 1 xenograft.


title: NCI-H522_Passage 1 xenograft_R2

description:
NCI-H522 P01 T2
Gene expression data from NCI-H522 Passage 1 xenograft.


title: NCI-H522_Passage 4 xenograft_R3

description:
NCI-H522 P04 T3
Gene expression data from NCI-H522 Passage 4 xenograft.


title: NCI-H522_originating cell line_R1

description:
NCI-H522 P0 T1
Gene expression data from NCI-H522 originating cell line.


title: prostate_cancer_primary_264


title: prostate_cancer_primary_262


title: NCI-H460_Passage 10 xenograft_R2

description:
NCI-H460 P10 T2
Gene expression data from NCI-H460 Passage 10 xenograft.


title: prostate_cancer_primary_263


title: NCI-H460_Passage 10 xenograft_R1

description:
NCI-H460 P10 T1
Gene expression data from NCI-H460 Passage 10 xenograft.


title: NCI-H522_Passage 4 xenograft_R1

description:
NCI-H522 P04 T1
Gene expression data from NCI-H522 Passage 4 xenograft.


title: NCI-H460_Passage 4 xenograft_R4

description:
NCI-H460 P04 T4
Gene expression data from NCI-H460 Passage 4 xenograft.

source_name: NCI-H460, passage 4 xenograft


title: prostate_cancer_primary_260


title: NCI-H460_Passage 4 xenograft_R1

description:
NCI-H460 P04 T1
Gene expression data from NCI-H460 Passage 4 xenograft.


title: prostate_cancer_primary_259


title: prostate_cancer_primary_258


title: prostate_cancer_primary_257


title: prostate_cancer_primary_261


title: NCI-H460_Passage 1 xenograft_R5

description:
NCI-H460 P01 T5
Gene expression data from NCI-H460 Passage 1 xenograft.

source_name: NCI-H460, passage 1 xenograft


title: prostate_cancer_primary_255


title: NCI-H460_Passage 4 xenograft_R3

description:
NCI-H460 P04 T3
Gene expression data from NCI-H460 Passage 4 xenograft.


title: prostate_cancer_primary_252


title: prostate_cancer_primary_254


title: NCI-H460_Passage 1 xenograft_R4

description:
NCI-H460 P01 T4
Gene expression data from NCI-H460 Passage 1 xenograft.


title: prostate_cancer_primary_256


title: prostate_cancer_primary_251


title: NCI-H460_Passage 1 xenograft_R3

description:
NCI-H460 P01 T3
Gene expression data from NCI-H460 Passage 1 xenograft.


title: NCI-H460_Passage 1 xenograft_R2

description:
NCI-H460 P01 T2
Gene expression data from NCI-H460 Passage 1 xenograft.


title: prostate_cancer_primary_249


title: prostate_cancer_primary_248


title: NCI-H23_Passage 10 xenograft_R5

description:
NCI-H23 P10 T5
Gene expression data from NCI-H23 Passage 10 xenograft.

source_name: NCI-H23, passage 10 xenograft

value: adenocarcinoma NSCLC lung


title: NCI-H460_Passage 4 xenograft_R5

description:
NCI-H460 P04 T5
Gene expression data from NCI-H460 Passage 4 xenograft.


title: prostate_cancer_primary_247


title: NCI-H460_originating cell line_R3

description:
NCI-H460 P0 T3
Gene expression data from NCI-H460 originating cell line.

source_name: NCI-H460, originating cell line


title: NCI-H460_Passage 1 xenograft_R1

description:
NCI-H460 P01 T1
Gene expression data from NCI-H460 Passage 1 xenograft.


title: NCI-H460_originating cell line_R1

description:
NCI-H460 P0 T1
Gene expression data from NCI-H460 originating cell line.


title: prostate_cancer_primary_253


title: NCI-H460_Passage 4 xenograft_R2

description:
NCI-H460 P04 T2
Gene expression data from NCI-H460 Passage 4 xenograft.


title: prostate_cancer_primary_246


title: NCI-H23_Passage 10 xenograft_R3

description:
NCI-H23 P10 T3
Gene expression data from NCI-H23 Passage 10 xenograft.


title: NCI-H460_originating cell line_R2

description:
NCI-H460 P0 T2
Gene expression data from NCI-H460 originating cell line.


title: prostate_cancer_primary_245


title: prostate_cancer_primary_250


title: prostate_cancer_primary_244


title: NCI-H23_Passage 4 xenograft_R5

description:
NCI-H23 P04 T5
Gene expression data from NCI-H23 Passage 4 xenograft.

source_name: NCI-H23, passage 4 xenograft


title: NCI-H23_Passage 10 xenograft_R2

description:
NCI-H23 P10 T2
Gene expression data from NCI-H23 Passage 10 xenograft.


title: prostate_cancer_primary_243


title: prostate_cancer_primary_242


title: NCI-H23_Passage 10 xenograft_R4

description:
NCI-H23 P10 T4
Gene expression data from NCI-H23 Passage 10 xenograft.


title: NCI-H23_Passage 4 xenograft_R4

description:
NCI-H23 P04 T4
Gene expression data from NCI-H23 Passage 4 xenograft.


title: NCI-H23_Passage 4 xenograft_R2

description:
NCI-H23 P04 T2
Gene expression data from NCI-H23 Passage 4 xenograft.


title: NCI-H23_Passage 4 xenograft_R1

description:
NCI-H23 P04 T1
Gene expression data from NCI-H23 Passage 4 xenograft.


title: NCI-H23_Passage 4 xenograft_R3

description:
NCI-H23 P04 T3
Gene expression data from NCI-H23 Passage 4 xenograft.


title: NCI-H23_Passage 10 xenograft_R1

description:
NCI-H23 P10 T1
Gene expression data from NCI-H23 Passage 10 xenograft.


title: NCI-H23_Passage 1 xenograft_R5

description:
NCI-H23 P01 T5
Gene expression data from NCI-H23 Passage 1 xenograft.

source_name: NCI-H23, passage 1 xenograft


title: NCI-H23_Passage 1 xenograft_R4

description:
NCI-H23 P01 T4
Gene expression data from NCI-H23 Passage 1 xenograft.


title: prostate_cancer_primary_238

source_name: primary prostate cancer FFPE tissue sample


title: prostate_cancer_primary_237


title: prostate_cancer_primary_236


title: prostate_cancer_primary_241


title: prostate_cancer_primary_235


title: prostate_cancer_primary_233


title: prostate_cancer_primary_239


title: prostate_cancer_primary_234


title: prostate_cancer_primary_240


title: NCI-H23_originating cell line_R2

description:
NCI-H23 P0 T2
Gene expression data from NCI-H23 originating cell line.

source_name: NCI-H23, originating cell line


title: NCI-H23_originating cell line_R1

description:
NCI-H23 P0 T1
Gene expression data from NCI-H23 originating cell line.