title: Intracellular Mycobacterium avium subspecies paratuberculosis-THP-1 infection

description: 4 Technical (spot) replicates. Mycobacterium avium subspecies paratuberculosis, Intracellular bacteria-THP-1 infection

label_protocol: Forty µg samples of amplified RNA (aRNA) were labelled with either Alexa Fluor dye 647 or 555  purchased from Invitrogen, USA, following manufacturer's protocol. Purification of coupled aRNA was performed by RNeasy purification system (Qiagen) and incorporation of dye was evaluated using the Nanodrop spectrophotometer. Before hybridization, coupled aRNA was fragmented using the RNA fragmentation reagents (Ambion, Inc) following the manufacturer's protocol.

growth_protocol: MAP1515 (ATCC 43015) was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with 0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA), 2 mg/L of Mycobactin J (MicJ, Allied Monitors, Fayette, MO, USA) were also added. Cells were grown in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C before infection experiments.

extract_protocol: tot-RNA extracted with the RiboPure-Bacteria Kit (Ambion, Inc). Mycobacterial cells were re-suspended in 350µl of RNAwiz solution and transferred to a 0.5ml RNAse-free skirted screw-cap microcentrifuge tube containing 250µl of 0.1mm ice-cold Zirconia Beads. Tubes were immediately processed in the RiboLyser RNA Lysing Machine (RiboLyser FP120-HY-230, Hybaid) for 3 cycles (30s at speed 6.5 with 1 min of cooling interval between each bead beating step). Remaining steps were performed according to the manufacturer’s instructions. All RNA samples were treated with Dnase I (Ambion, Inc)  and  purified by RNeasy column (Qiagen). RNA yield and purity was evaluated with the Nanodrop spectrophotometer (NanoDrop1000, Thermo Scientific) and RNA quality was examined by Denaturing Gel Electrophoresis. We carried out ten independent experiments on ten different flasks. Good quality RNA samples obtained from each pellet were then pooled together and used for microarray experiments to get an average of ten separate experiments. mRNA was obtained by using the MICROBExpress Bacterial mRNA Purification Kit (Ambion) and was lineary amplified bu using the MessageAmp II Bacterial Kit (Ambion, Inc)

treatment_protocol: THP-1 infection was performed in T75 vented flasks containing monolayers with a confluence of approximately 1x105 cells /cm2 already differentiated in macrophages with the addiction of Phorbol 12-myristate 13-acetate (PMA) (Sigma) (50 ng/ml) in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (Sigma). Monolayers were washed 3 times with sterile PBS and 25 ml of fresh medium were added to each monolayer before infection. Inocula for infection were prepared by centrifugation (5000 x g, 15 min) of 10 ml of Map culture with a density of 8x108 bacteria/ml. Bacterial pellet was resuspended in 10 ml of pre-warmed RPMI medium at 37°C and cells were declumped by 10 passages through a 21 gauge needle. Monolayers were infected by Map with a multiplicity of infection (MOI) of 10:1 for 24 h at 37°C at 5% CO2. The next day, extracellular bacteria were killed by amikacin (Sigma) treatment (200 μg/ml) for 2h at 37°C. Supernatant was removed and monolayer was washed with 3 x PBS rounds. Infected cells were selectively lysed by addiction of 10 ml of lysis buffer per monolayer (4M guanidine thiocyanate, 0.5% Na N-lauryl sarcosine, 25 mM sodium citrate, and 0.1M β-mercaptoethanol) without killing intracellular bacteria as previosly described (Rohde et al., 2007; Mangan et al., 2002; Butcher et al., 1998). Flasks were shaked at 100 rpm for 15 minutes at room temperature and recovered lysate was thorougly vortexed for 2 minutes before being passed five times through a 21 gauge needle to shear infected cells and reduce viscosity. One hundred milliliters of lysate belonging to ten T75 flasks were centrifuged at 5000 x g for 30 min at 14°C and pellet was resuspended in 1 ml of fresh lysis buffer. A final centrifugation at 10000 x g for 2 min was performed to harvest bacterial cells and pellet was then stored at -80°C until RNA extraction.

source_name: Mycobacterium avium subspecies paratuberculosis bacteria grown in host medium

treatment_protocol: Bacterial cells were prepared by centrifugation (5000 x g, 15 min) of 10 ml of Map culture with a density of 8x108 bacteria/ml. Bacterial pellet was resuspended in 10 ml of pre-warmed RPMI medium at 37°C and cells were grown for 24 h. Cells were harvested by centrifugation at 5800 x g for 15min at 4°C and stored at -80°C until RNA extraction.


title: ABI3_ChIP 2/2, membrane B [070427ABI3]

status: Public on Jun 01 2012

type: genomic

city: Gatersleben

first: Gudrun

last: Moenke

address: Corrensstr. 3

country: Germany

institute: IPK

description:
070427ABI3
Raw data file: 070427_B_ABI3.txt
ChIP technical replicate of biol. replicate 2
Hybridization on membrane B

hyb_protocol: Arrays were prehybridized for 1h at 65°C in Church buffer (0,5M sodium phosphate, pH7,2, 7% SDS, 1% BSA, 1mM EDTA, 10µg/ml sheared salmon sperm DNA) per cm2 of membrane in a rotating thermal oven. Labelled probes were added and hybridization continued for 4 days. Membranes were washed twice in 0,2x SSC, 0,1% SDS for 20 min at 65°C and then placed on a moist Whatman paper, wrapped in Saran wrap and exposed to a Fuji image plate for 10 days in a lead chamber.

scan_protocol: Signals were detected using a FLA 3000 phosphoimager at 50µm resolution and 16 bit grey scale (Fuji). Spot intensities were obtained by aligning the pre-defined spotting pattern using ArrayVision software (GE Healthcare).

data_processing: Five ABI3 ChIP-chip experiments (three biological and two technical replicates) were performed, each consisting of a pair of hybridisations with amplified input chromatin and immuno-precipitated chromatin. For normalization, the median of log2 transformed signal intensities of each hybridisation was centred at zero. Quantile normalization (Bolstad et al. 2003) was applied separately to datasets of input and immuno-precipitated chromatin. Duplicated spotting of each amplicon on the arrays provided an internal quality control, which was used to exclude all signals with a difference of normalized log2 intensities larger than one between the two spots (1.56% of all signals). Missing values were again substituted by the mean of normalized log2 intensities from other hybridisations of the same kind, chromatin or immuno-precipitated chromatin, if the signal was excluded in no more than two hybridisations. Finally, the mean of normalized log2 intensities from both spots of each amplicon was calculated and the mean values of hybridisations with input chromatin were subtracted from the mean values of hybridizations with immuno-precipitated chromatin, resulting in log2 enrichment factors for most (> 99.85%) of the spotted amplicons in all five experiments.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Chromatin fragments precipitated with anti-ABI3 antibody, seeds

label_protocol: Labelled probes were obtained by combining three parallel random priming reactions using the Megaprime Kit (GE Healthcare, Uppsala, Sweden), 1ng amplified chromatin, and 50µCi [α-33P]dCTP per reaction.

growth_protocol: Arabidopsis plants were grown on soil, with a 16 h light/ 8 h dark cycle

extract_protocol: Chromatin was isolated from unripe seeds of Arabidopsis thaliana Col-0, harvested 11-13 days after pollination. Cross-linking was done with 1% formaldehyde  for 20 min under vacuum, terminated by addition of glycine with a final concentration of 125 mM. Seeds were Potter-homogenized, filtered and the nuclei collected by centrifugation. Nuclear membranes were dissolved with detergents and  the chromatin was collected by high speed centrifugation. Chromatin was fragmented to an average size of 500 bp by ultra sonic treatment.   10 µg chromatin were combined with 2 µg anti-ABI3 antibody. The antibody-chromatin complex was captured by protein A coated magnetic beads (Invitrogen). After different washings the TF-DNA complex was eluted from the beads at 65°C for 15 min using 1% SDS. Eluates were incubated overnight at 65°C to reverse the cross-links. DNA  fragments were purified using a QIAquick PCR Purification Kit (Qiagen) and their concentration was determined with a NanoDrop 3300 (Thermo Fisher Scientific) fluorescence spectrophotometer. An aliquot (0.5 µg) of non-immunoprecipitated chromatin served as input control.   DNA fragments were blunted and ligated  with the  adapters oJW102  and oJW103 (Young lab:jura.wi.mit.edu/young_public/hESregulation/ChIP.html).  Adapter-ligated fragments were amplified using oJW102 as sole primer.

tag: ecotype

tag: tissue

value: seed

tag: developmental stage according to boyes et al. (2004)

tag: chip antibody

value: anti-ABI3 Antibody


title: dnLEF-1 inducible cell line, treated with water control for 23 hr, biological replicate #2

type: RNA

city: Irvine

first: Marian

middle: L.

last: Waterman

state: CA

address: 19182 Jamboree Blvd.

department: Microbiology and Molecular Genetics

country: USA

institute: University of California, Irvine

description: Expression data from T20 cells cells induced with water control for 23hr

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix human HG-U133 Plus 2.0 arrays. GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: Affymetrix GeneChip measurements were obtained using the robust multi-array average (RMA) method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: T20 cells, treated with water control for 23 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

extract_protocol: Three plates per condition were pooled for RNA isolation, and three independent RNA isolations were performed, bringing the total number of independent cultures to 9 plates per condition.  Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell type

value: colon cancer cell, T-REx-regulated clonal stable cell

tag: mutated tumor suppressor

value: APC (Adenomatous polyposis coli) and p53

tag: constitutive signaling pathway

value: Wnt signaling pathway

value: No


title: mock cell, treated with water control for 23h, biological rep3

description: Expression data from DLD TR7 cells induced with water for 23hr. Control T-Rex cell line does not have any transgene

source_name: DLD TR7 cells, treated with water control for 23hr


title: mock cell, treated with 1ug/ml doxycycline for 23h, biological rep2

description: Expression data from DLD TR7 cells treated with 1ug/ml doxycycline for 23hr-control, but this T-Rex cell line does not express any transgene

source_name: DLD TR7 cells, treated with 1ug/ml doxycycline for 23hr


title: dnLEF-1 inducible cell line, treated with water control for 23 hr, biological replicate #3


title: mock cell, treated with water control for 23h, biological rep2


title: mock cell, treated with 1ug/ml doxycycline for 23h, biological rep3


title: mock cell, treated with 1ug/ml doxycycline for 23h, biological rep1


title: dnLEF-1 inducible cell line, treated with 1 ug/ml doxycycline for 23 hr, biological replicate #3

description: Expression data from T20 cells cells induced with 1 ug/ml doxycycline for 23 hr to induce expression of dnLEF-1 transgene

source_name: T20 cells, treated with 1 ug/ml for 23 hr


title: dnLEF-1 inducible cell line, treated with water control for 23 hr, biological replicate #1


title: dnLEF-1 inducible cell line, treated with 1 ug/ml doxycycline for 23 hr, biological replicate #1


title: mock cell, treated with water control for 23h, biological rep1


title: mutant dnTCF-1Emut inducible cell line, treated with 1ug/ml doxycycline for 23hr, biological replicate #3

description: Expression data from MT45 cells induced with 1 ug/ml doxycycline to express the mutant dnTCF-1E transgene for 23hr

source_name: MT45 cells, treated with 1 ug/ml doxycycline for 23 hr

value: mutant TCF-1E


title: wild-type dnTCF-1E inducible cell line, treated with water control for 23hr, biological replicate #2

description: Expression data from D7p11 cells induced with water control for 23 hr

source_name: D7p11 cells, treated with water control for 23hr


title: mutant dnTCF-1Emut inducible cell line, treated with water control for 23hr, biological replicate #2

description: Expression data from MT45 cells induced with water control for 23 hr

source_name: MT45 cells, treated with water control for 23 hr


title: mutant dnTCF-1Emut inducible cell line, treated with 1ug/ml doxycycline for 23hr, biological replicate #2


title: wild-type dnTCF-1E inducible cell line, treated with 6x10E-4ug/ml doxycycline for 23hr, biological replicate #3

description: Expression data from D7p11 cells induced with 6x10E-4ug/ml doxycycline to express wild-type dnTCF-1E for 23 hr

source_name: D7p11 cells, treated with 6x10E-4ug/ml doxycycline for 23hr


title: mutant dnTCF-1Emut inducible cell line, treated with 1ug/ml doxycycline for 23hr, biological replicate #1


title: mutant dnTCF-1Emut inducible cell line, treated with water control for 23hr, biological replicate #3


title: wild-type dnTCF-1E inducible cell line, treated with water control for 23hr, biological replicate #4


title: mutant dnTCF-1Emut inducible cell line, treated with water control for 8hr, biological replicate #3

description: Expression data from MT45 cells induced with water for 8hr, NO expression of the mutant dnTCF-1E transgene

source_name: MT45 cells, treated with water control for 8hr


title: wild-type dnTCF-1E inducible cell line, treated with water control for 23hr, biological replicate #3


title: dnLEF-1 inducible cell line, treated with 1 ug/ml doxycycline for 23 hr, biological replicate #2


title: wild-type dnTCF-1E inducible cell line, treated with water control for 23hr, biological replicate #1


title: wild-type dnTCF-1E inducible cell line, treated with 6x10E-4ug/ml doxycycline for 23hr, biological replicate #2


title: wild-type dnTCF-1E inducible cell line, treated with 6x10E-4ug/ml doxycycline for 23hr, biological replicate #1


title: wild-type dnTCF-1E inducible cell line, treated with 1 ug/ml doxycycline for 23hr, biological replicate #3

description: Expression data from D7p11 cells induced with 1ug/ml doxycycline to express maximum wild-type dnTCF-1E for 23 hr

source_name: D7p11 cells, treated with 1ug/ml doxycycline for 23hr


title: mutant dnTCF-1Emut inducible cell line, treated with water control for 23hr, biological replicate #1


title: wild-type dnTCF-1E inducible cell line, treated with 1 ug/ml doxycycline for 23hr, biological replicate #1


title: wild-type dnTCF-1E inducible cell line, treated with 1 ug/ml doxycycline for 23hr, biological replicate #2


title: mutant dnTCF-1Emut inducible cell line, treated with water control for 8hr, biological replicate #2


title: mutant dnTCF-1Emut inducible cell line, treated with 1ug/ml doxycycline for 8hr, biological replicate #3

description: Expression data from MT45 cells induced with 1ug/ml doxycycline for 8hr to express mutant dnTCF-1E

source_name: MT45 cells, treated with 1ug/ml doxycycline for 8hr

value: mutant dnTCF-1E


title: mutant dnTCF-1Emut inducible cell line, treated with water control for 8hr, biological replicate #1


title: mutant dnTCF-1Emut inducible cell line, treated with 1ug/ml doxycycline for 8hr, biological replicate #1


title: wild-type dnTCF-1E inducible cell line, treated with water control for 8hr, biological replicate #3

description: Expression data from D7p11 cells induced with water for 8hr, NO expression of the wildtype dnTCF-1E transgene

source_name: D7p11 cells, treated with water control for 8hr


title: wild-type dnTCF-1E inducible cell line, treated with water control for 8hr, biological replicate #1


title: wild-type dnTCF-1E inducible cell line, treated with 6x10E-4ug/ml doxycycline for 8hr, biological replicate #3

description: Expression data from D7p11 cells induced with 6x10E-4ug/ml doxycycline to express wild-type dnTCF-1E for 8hr

source_name: D7p11 cells, treated with 6x10E-4ug/ml doxycycline for 8hr


title: wild-type dnTCF-1E inducible cell line, treated with water control for 8hr, biological replicate #4


title: wild-type dnTCF-1E inducible cell line, treated with 6x10E-4ug/ml doxycycline for 8hr, biological replicate #2


title: mutant dnTCF-1Emut inducible cell line, treated with 1ug/ml doxycycline for 8hr, biological replicate #2


title: wild-type dnTCF-1E inducible cell line, treated with water control for 8hr, biological replicate #2


title: Induced pluripotent cells  [KMOS3_1]

city: Stanford

first: Leng

last: Han

address: 265 Campus Dr

institute: Stanford University

description: Gene expression data from iPSC

hyb_protocol: Hybridization were followed standard Affymetrix protocol in Affymetrix GeneChip Hybridization Oven 640

scan_protocol: GeneChips were scanned using theAffymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and RMA as normalization method.

source_name: iPSC generated with KMOS3

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

growth_protocol: Matrigel coated culture dishes and mTeSR

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions.

value: iPS cells

tag: genotype

value: Normal


title: wild-type dnTCF-1E inducible cell line, treated with 1 ug/ml doxycycline for 8hr, biological replicate #1

description: Expression data from D7p11 cells induced with 1ug/ml doxycycline to express maximum wild-type dnTCF-1E for 8 hr

source_name: D7p11 cells, treated with 1 ug/ml doxycycline for 8hr


title: Induced pluripotent cells  [KMOS_1]

description: Gene expression data from iPSC

source_name: iPSC generated with KMOS


title: human embryonic stem cells [hESC_2]

description: Gene expression data from hESC

source_name: human embryonic stem cells

value: Stem cells


title: wild-type dnTCF-1E inducible cell line, treated with 1 ug/ml doxycycline for 8hr, biological replicate #2


title: Induced pluripotent cells  [KMOS3_2]

description: Gene expression data from iPSC


title: wild-type dnTCF-1E inducible cell line, treated with 6x10E-4ug/ml doxycycline for 8hr, biological replicate #1


title: human adipose stem cells [hASC_1]

description: Gene expression data from hASC

source_name: human adipose stem cells

value: Adipose stem cells


title: human adipose stem cells [hASC_2]

description: Gene expression data from hASC


title: human embryonic stem cells [hESC_1]

description: Gene expression data from hESC


title: LC028, day 2, control

city: Chicago

first: Zarema

middle: H

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

institute: UIC

description: Gene expression data from PBMC controls, day two

hyb_protocol: Affymetrix standard wash protocol (FS450_0004)

scan_protocol: Affymetrix standard scanning protocol

data_processing: RMA processing using Partek Genomics Suite

source_name: day 2, control

label_protocol: Affymetrix standard eukariotic 3' labeling protocol

growth_protocol: 1 x e6 cells/ml PBMCs were grown in complete RPMI medium

extract_protocol: Qiagen RNeasy protocol

treatment_protocol: Cells were treated with 10 mkg/ml lead acetate for one day, washed and cultured for the second day in RPMI only

value: peripheral blood mononuclear cell (PBMC)


title: Induced pluripotent cells  [KMOS_2]

description: Gene expression data from iPSC


title: LPS, biological rep2

city: Beijing

first: Xiaofeng

last: Hu

address: No.8 South Gongti Road

department: Eye

country: China

institute: Beijing Chaoyang Hospital

description: monocytes stimulated by LPS

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3700.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) 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: monocytes stimulated with LPS

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

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

value: monocyte

tag: treatment

value: stimulated by LPS


title: Normal, biological rep3

description: Normal monocytes

source_name: monocytes


title: LC10, day 2 post-challenge

description: Gene expression data from PBMC challenged to 10 mkM lead acetate for day one and then cultured without Pb for day two

source_name: day 2 post-challenge


title: LPS, biological rep3

description: monocytes stimulated by LPS


title: LC010, day 2, control


title: LPS, biological rep1

description: monocytes stimulated by LPS


title: LC011, day 2, control


title: LC027, day 2 post-challenge


title: LC027, day 2, control


title: Normal, biological rep2

description: Normal monocytes


title: LC09, day 2 post-challenge


title: Normal, biological rep1

description: Normal monocytes


title: LC028, day 2 post-challenge


title: LC11, day 2 post-challenge


title: LC08, day 2 post-challenge


title: LC026, day 2, control


title: LC008, day 2, control


title: LC009, day 2, control


title: LC026, day 2 post-challenge


title: LC058, day 2 post-challenge


title: phyR deletion strain_rep2

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

hyb_protocol: Labeled cDNA was hybridized to GeneChip CauloHi1 according to GeneChip Expression analysis technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: After hybridization for 16 hours at 50°C, arrays were washed using protocol PRO-GE-W52-V3 and stained on a GeneChipFluidics Station (Affymetrix)  according to the Genechip Expression analysis technical manual.

data_processing: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL intensity files were generated by GCOS (Gene Chip Operating Software ) v. 1.4.

organism: Caulobacter vibrioides

source_name: Caulobacter phyR null strain harvested at OD=0.3

label_protocol: cDNA was column purified, fragmented using DNAseI (GE Life Sciences, Piscataway, NJ), and end labeled using GeneChip labeling reagent (Affymetrix, P/N 900542).

growth_protocol: Each strain was cultured in M2 xylose defined medium at 30 degrees C and grown to OD660=0.3.

extract_protocol: Trizol RNA extraction, followed by DNAseI treatment.  RNA was re-extracted using acid phenol, alcohol precipitated, and resuspended in deionized water.

treatment_protocol: Experiment is measuring steady-state differences in the transcriptomes of a phyR in-frame deletion strain versus a xylose-inducible phyR overexpression strain

tag: protocol

value: phyR deletion


title: LC056, day 2, control


title: phyR overexpress_rep2

source_name: Caulobacter xylX::phyR overexpression strain harvested at OD=0.3

value: phyR overexpression


title: LC057, day 2 post-challenge


title: LC058, day 2, control


title: LC056, day 2 post-challenge


title: phyR overexpress_rep1


title: phyR deletion strain_rep1


title: lovK-lovR overexpress 1

source_name: Caulobacter lovK-lovR overexpression strain (FC438)

growth_protocol: Each strain was cultured in M2 xylose defined medium supplemented with 500 micromolar vanillic acid and grown to OD660=0.3.  In this strain, lovK is induced from a plasmid integrated at the vanX locus, and lovR is induced from a plasmid integrated at the xylX locus.

treatment_protocol: Experiment is measuring steady-state differences in the transcriptomes of empty vector control (FC423) versus an inducible lovK-lovR overexpression strain (FC438)

value: lovK-lovR overexpression


title: lovK-lovR overexpress 2


title: LC007, day 2, control


title: LC055, day 2 post-challenge


title: LC055, day 2, control


title: LC057, day 2, control


title: LC051, day 2 post-challenge


title: LC053,day 2, control


title: empty vector control 1

source_name: Caulobacter control strain (FC423)

value: control (vector)


title: LC049, day 2 post-challenge


title: empty vector control 2


title: LC049, day 2, control


title: LC051, day 2, control


title: LC047, day 2 post-challenge


title: LC053, day 2 post-challenge


title: LC046, day 2 post-challenge


title: M031, day 2, control


title: LC042,day 2, control


title: LC041, day 2 post-challenge


title: LC040, day 2, control


title: 314136_Control-3_2009-05-08_532

city: Madison

first: Ravi

middle: C

last: Balijepalli

state: WI

address: 1300 University Ave, B370 SMI

department: Medicine

institute: University of Wisconsin School of medicine and Public Health

description: This sample is of wild-type mus musculus. It is the third of three wild-type biological replicates used in this experiment.

hyb_protocol: Hybridization was performed using standard operating protocols by Nimblegen Inc., Madison, WI, USA. See www.nimblegen.com

scan_protocol: Scanning was performed using standard operating protocols by Nimblegen Inc., Madison, WI, USA. See www.nimblegen.com

data_processing: The RMA_norm.pair data files were subjected to ArrayStar 3.0.1 Analysis: http://www.dnastar.com/products/arraystar.php. ArrayStar calculates a set of genes that can be considered differentially expresses at the levels of 2- or more, 4- or more and 8 fold or more. The fold change is calculated from the difference in expression between 2 samples for each gene.

organism: Mus musculus

label_protocol: 250 ng of cDNA from each sample was labelsed following standarrd operating protocols by Nimblegen Inc., Madison, WI, USA, with Cy3 dye using a NimbleGen One-Color DNA Labeling Kit (Cat# 05 223 555 001).See www.nimblegen.com

growth_protocol: All animals were 6 weeks of age.

extract_protocol: The procedure for RNA isolation, purification and cDNA synthesis was according to manufacturer's protocols.RNA was isolated from LV tissue of LMNA N195K mutant mice or WT littermate control mouse using Trizol reagent.  The isolated RNA was further purified using the RNAeasy cleanup kit from Qiagen. Purified RNA (70-100 ug) had a concentration of (5-15 ug/ul) between different samples. 10 ug of RNA was used to synthesize double stranded cDNA using the Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit (Cat#11917-010).  The cDNA had A260/A280 = 2.1 and A260/A230 = 2.

tag: genotype/variation

value: WT

tag: gender

value: male

tag: strain

value: Cardiac

tag: age

value: 6 weeks


title: Spleen_non-infected_rep3

first: Ning

last: Yang

address: 2nd Yuanmingyuan West Road

department: Animal Science

institute: China Agricultural University

description:
NS3
gene expression of non-infected spleens from controls

hyb_protocol: Arrays were incubated at 65℃ for 17h in Agilent’s microarray hybridization chambers and subsequently washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US) and Stabilization and Drying Solution (Agilent Technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) with default settings, Scan resolution=5μm, PMT 100%, 10%

data_processing: Raw data were normalized by Quantile algorithm by Gene Spring Software 11.0. The quality of features was also determined by Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, US). Features were deemed absent when not positive and significant or not above background. Features were deemed marginal when not uniform or if saturated or a population outlier. Features that were not absent or marginal were deemed present. P value and fold change in each comparison was calculated for each gene. False discovery rate (FDR) was controlled at 5%, and q values was calculated by the R program according to Storey and Tibshirani 's method

organism: Gallus gallus

source_name: non-infected spleens from controls, replicate3

label_protocol: Two ug total RNA were reverse transcribed into cDNA. The synthesized cDNA was transcribed into cRNA labelled with cyanine 3-labelled nucleotide. Labelled cRNA was purified with QIAGEN RNeasy® Mini Kit (Qiagen, Valecia, CA), and the same amount (875 ng) of Cy3 labeled cRNA probes were hybridized on 44K chicken Agilent arrays

extract_protocol: Total RNA was isolated using TRIZOL Reagent according to manufacturer’s instruction (Life Technologies, Carlsbad, CA, US). The RNA quantity and purity were determined by NanoDrop ND-1000 spectrophotometer at 260/280 nm. The integrity of total RNA was assessed with an Agilent Bioanalyzer 2100. The RNA Integrity Numbers (RINs) for the samples were obtained. All the RNA samples showed 8.7 or higher RIN values and 28S/18S > 1.3, indicating sufficient quality to be used for microarray.

treatment_protocol: Specific pathogen free White Leghorn (BWEL) were infected with MDV-GA (passage 9). Briefly, 150 one-day-old chicks were divided into two groups. One hundred chicks were infected intraperitoneally with 2000 plaque-forming units (PFU) of the MDV-GA and 50 were injected with the same volume of diluent (0.2 ml) as non-infected controls at one day of age. The two groups were housed in different isolation facilities.

tag: infection

value: non-infected

tag: mdv-infection susceptibility

value: control

value: spleen

tag: time


title: Spleen_non-infected_rep2

description:
NS2
gene expression of non-infected spleens from controls

source_name: non-infected spleens from controls, replicate2


title: Spleen_non-infected_rep4

description:
NS4
gene expression of non-infected spleens from controls

source_name: non-infected spleens from controls, replicate4


title: LC040, day 2 post-challenge


title: 313837_N195K-1_2009-05-08_532

description: This sample is of mus musculus N195K.It is the first of three mutant strain biological replicates used in this experiment.


title: 314189_N195K-3_2009-05-08_532

description: This sample is of mus musculus N195K.It is the third of three mutant strain biological replicates used in this experiment.


title: M031, day 2 post-challenge


title: LC047, day 2, control


title: 314143_Control-1_2009-05-08_532

description: This sample is of wild-type mus musculus. It is the first of three wild-type biological replicates used in this experiment.


title: LC041, day 2, control


title: LC046, day 2, control


title: LC042, day 2 post-challenge


title: LC038, day 2 post-challenge


title: Spleen_non-infected_rep1

description:
NS1
gene expression of non-infected spleens from controls

source_name: non-infected spleens from controls, replicate1


title: LC038, day 2, control


title: 314204_N195K-2_2009-05-08_532

description: This sample is of mus musculus N195K.It is the second of three mutant strain biological replicates used in this experiment.


title: LC-045, day 2 post-challenge


title: 314198_Control-2_2009-05-08_532

description: This sample is of wild-type mus musculus. It is the second of three wild-type biological replicates used in this experiment.


title: LC037, day 2, post-challenge


title: Spleen_MDV-resistant_rep3

description:
RS3
gene expression of resistant spleens from MDV-infected chickens

source_name: resistant spleens from MDV-infected chickens, replicate3

value: Marek's disease virus (MDV)

value: resistant


title: Spleen_MDV-resistant_rep4

description:
RS4
gene expression of resistant spleens from MDV-infected chickens

source_name: resistant spleens from MDV-infected chickens, replicate4


title: ABI3_ChIP 3/2, membrane A [070420ABI3]

description:
070420ABI3
Raw data file: 070420_A_ABI3.txt
ChIP technical replicate of biol. replicate 3
Hybridization on membrane A

source_name: Chromatin fragments precipitated with anti-ABI3 antibody, seeds

tag: ecotype

value: seed

value: anti-ABI3 Antibody


title: LC037, day 2, control

value: peripheral blood mononuclear cell (PBMC)


title: Input 3/2, membrane A [070420Chr]

description:
070420Chr
Raw data file: 070420_A_CHR.txt
control technical replicate of biol. replicate 3
Hybridization on membrane A

source_name: Control (input) non-immunoprecipitated chromatin fragments, seeds

tag: tissue

value: no


title: LC-033, day 2 post-challenge


title: LC-045, day 2, control


title: wild-type dnTCF-1E inducible cell line, treated with 1 ug/ml doxycycline for 8hr, biological replicate #3

description: Expression data from D7p11 cells induced with 1ug/ml doxycycline to express maximum wild-type dnTCF-1E for 8 hr

source_name: D7p11 cells, treated with 1 ug/ml doxycycline for 8hr

value: colon cancer cell, T-REx-regulated clonal stable cell

value: APC (Adenomatous polyposis coli) and p53

value: Wnt signaling pathway


title: Input 3/1, membrane A [070223Chr]

description:
070223Chr
Raw data file: 070223_A_CHR.txt
control biol.replicate 3
Hybridization on membrane A

tag: developmental stage according to boyes et al. (2004)


title: Spleen_MDV-resistant_rep1

description:
RS1
gene expression of resistant spleens from MDV-infected chickens

source_name: resistant spleens from MDV-infected chickens, replicate1


title: cell line_FS_rep1

city: Heidelberg

first: Thomas

last: Wolf

address: Im Neuenheimer Feld 580

institute: DKFZ

hyb_protocol: Standard Illuster hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation  in R

source_name: Cell line

label_protocol: 200 ng of RNA was labelled and hybridized to each array using standard Illumina protocols

extract_protocol: MiRNAs for microarray hybridization and quantitative RT-PCR (qRT-PCR) were purified from frozen tissue samples and sarcoma cell lines using miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: The sarcoma samples were collected at the Institute of Pathology, University of Heidelberg, snap-frozen in liquid nitrogen after surgical removal and stored at -80 °C

value: Cell line

tag: age (years)

tag: Sex

tag: grade

tag: molecuar confirmation

tag: reference source

value: american type culture collection

tag: culture condition

value: DMEM, 10% FCS, 1% PS


title: normal fat_Fat_2

source_name: Normal fat

value: Normal fat


title: normal fat_Fat_1


title: cell line_MLS_rep2

value: FUS-CHOP

value: Aman P et al., 1993

value: RPMI, 10% FCS, 1% PS


title: ABI3_ChIP 2/2, membrane A [070427ABI3]

description:
070427ABI3
Raw data file: 070427_A_ABI3.txt
ChIP technical replicate of biol. replicate 2
Hybridization on membrane A

tag: chip antibody


title: Spleen_MDV-susceptible_rep1

description:
SS1
gene expression of susceptible spleens from MDV-infected chickens

source_name: susceptible spleens from MDV-infected chickens, replicate1

value: male

value: susceptible

value: spleen


title: LC-029, day 2 post-challenge

description: Gene expression data from PBMC challenged to 10 mkM lead acetate for day one and then cultured without Pb for day two

source_name: day 2 post-challenge

tag: cell type


title: cell line_MLS_rep1


title: Spleen_MDV-susceptible_rep3

description:
SS3
gene expression of susceptible spleens from MDV-infected chickens

source_name: susceptible spleens from MDV-infected chickens, replicate3

tag: gender

value: Marek's disease virus (MDV)


title: LC-032, day 2, control

description: Gene expression data from PBMC controls, day two

source_name: day 2, control


title: cell line_DDLS_rep1

value: Nishio J et al., 2004


title: cell line_LS_rep1


title: LC-032, day 2 post-challenge

value: peripheral blood mononuclear cell (PBMC)


title: LC-029, day 2, control


title: Spleen_MDV-susceptible_rep2

description:
SS2
gene expression of susceptible spleens from MDV-infected chickens

source_name: susceptible spleens from MDV-infected chickens, replicate2


title: ABI3_ChIP 2/1, membrane A [070222ABI3]

description:
070222ABI3
Raw data file: 070222_A_ABI3.txt
ChIP biol. replicate 2
Hybridization on membrane A

value: seed

value: anti-ABI3 Antibody


title: Input 2/2, membrane A [070427Chr]

description:
070427Chr
Raw data file: 070427_A_CHR.txt
control technical replicate of biol. replicate 2
Hybridization on membrane A

value: no


title: LC-033, day 2, control


title: Spleen_MDV-susceptible_rep4

description:
SS4
gene expression of susceptible spleens from MDV-infected chickens

source_name: susceptible spleens from MDV-infected chickens, replicate4


title: ABI3_ChIP 1, membrane A [061220ABI3]

description:
061220ABI3
Raw data file: 061220_A_ABI3.txt
ChIP biol. replicate 1
Hybridization on membrane A


title: Input 2/1, membrane A [070222Chr]

description:
070222Chr
Raw data file: 070222_A_CHR.txt
control biol. replicate 2
Hybridization on membrane A


title: Spleen_MDV-resistant_rep2

description:
RS2
gene expression of resistant spleens from MDV-infected chickens

source_name: resistant spleens from MDV-infected chickens, replicate2

value: resistant


title: LC-024, day 2 post-challenge


title: Input 1, membrane A [061220Chr]

description:
061220Chr
Raw data file: 061220_A_CHR.txt
control biol. replicate 1
Hybridization on membrane A


title: cell line_WDLS_rep2

value: Cell line

value: Pedeutour F et al., 1999


title: LC-023, day 2, control


title: cell line_WDLS_rep1


title: LC-025, day 2, control


title: cell line_MPNST_rep3

value: Badache A & De Vries GH, 1998


title: LC-023, day 2 post-challenge


title: LX2_coculture_rep1

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

country: France

institute: INSERM

description: Cell line described in Gut. 2005 Jan;54(1):142-51. PMID: 15591520.

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 028004_D_F_20100430).

source_name: LX2 cocultured with HepaRG, Replicate 1

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions. Starting from 150 ng total RNA, amplification yield was 9.7±0.6 μg cRNA and specific activity was 20.3±1.3 pmol Cy3 per μg cRNA.

growth_protocol: HepaRG and LX2 cells were grown in serum- and DMSO-free William's E medium using 6-well plates. For coculture experiments, 1 µm pore size transwell inserts which allow diffusion of media components but prevent cell migration (BD Biosciences, San Jose, CA) were used.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: cell line


title: cell line_MPNST_rep2

value: Huynh DP & Pulst SM, 1996

value: DMEM, 10% FCS, 1% PS


title: LC-025, day 2 post-challenge


title: LX2_culture_rep1

source_name: LX2 cultured alone, Replicate 1


title: LX2_culture_rep3

source_name: LX2 cultured alone, Replicate 3


title: HepaRG_coculture_rep3

description: Cell line described in Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15655-60. PMID: 12432097.

source_name: HepaRG cocultured with LX2, Replicate 3

value: HepaRG


title: LX2_culture_rep2

source_name: LX2 cultured alone, Replicate 2


title: LX2_coculture_rep3

source_name: LX2 cocultured with HepaRG, Replicate 3


title: LC-024, day 2, control


title: cell line_SS_rep5

description: HS-SY-II

value: SS18/SSX 1

value: Sonobe H et al., 1992


title: LC-022, day 2 post-challenge


title: LX2_coculture_rep2

source_name: LX2 cocultured with HepaRG, Replicate 2


title: HepaRG_coculture_rep2

source_name: HepaRG cocultured with LX2, Replicate 2


title: HepaRG_culture_rep3

source_name: HepaRG cultured alone, Replicate 3


title: LC-021, day 2 post-challenge


title: HepaRG_culture_rep2

source_name: HepaRG cultured alone, Replicate 2


title: HepaRG_coculture_rep1

source_name: HepaRG cocultured with LX2, Replicate 1


title: cell line_MPNST_rep1

source_name: Cell line

value: DeClue JE et al., 1992


title: cell line_SS_rep3

value: SS18/SSX 2

value: Kawai A et al., 2004


title: cell line_SS_rep4

description: Fuji

value: Watanabe T et al., 2006

value: RPMI, 10% FCS, 1% PS


title: Space vs. Earth

city: Merritt Island

first: Wayne

middle: L

last: Nicholson

state: FL

address: 505 Odyssey Way, Rm. 201-B

department: Microbiology and Cell Science

institute: University of Florida

hyb_protocol: Identical quantities of cDNAs were used to probe 15,000-feature custom microarrays (Agilent) prepared from the B. subtilis strain 168 genomic sequence (Kunst et al., 1997).

scan_protocol: Scanning performed at UF-ICBR.

data_processing: Raw and normalized intensities were extracted from scanned images, background subtraction, quantile and Loess normalization were performed by UF-ICBR. The microarray contained 15,209 data points equivalent to 4,103 genes with an average number of 3.7 measurements per gene; the oligos were designed such that each Open Reading Frame (ORF) was sampled at multiple locations (n = 3 or 4). Log-transformed data sets for each ORF from simulated Mars-exposed spores were compared to the same ORF from the ground control spores using one-way Analysis of Variance (ANOVA).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Space-exposed spores, 60-min germination

label_protocol: Total RNA samples (20 μg) were sent to the University of Florida Interdisciplinary Center for Biotechnology Research (UF-ICBR). Samples were converted into Cy3- or Cy5-labelled cDNAs at UF-ICBR.

growth_protocol: To synchronize germination, spores in water (~1 x 10^9) were heat activated at 70˚C for 30 min, then harvested by centrifugation. To initiate germination, spores were resuspended in 100 ml of 2x LB medium containing the germinant L-alanine (10 mM final concentration) in a 250-ml Klett flask and agitated vigorously in a rotary water bath shaker at 37˚C. Germination was monitored by loss of optical density as measured in a Klett-Summerson photometer fitted with the No. 66 (660 nm; red) filter.

extract_protocol: Total RNA was isolated from germinated spores using the Ribo-Pure Bacteria Kit followed by treatment with RNase-free DNase, using the protocols supplied by the manufacturer (Ambion-Life Technologies, Grand Island, NY, USA).

treatment_protocol: After 60 min of germination, spores were harvested by centrifugation and the pellets stored frozen at   -20˚C until further analysis.

value: germinating spores

source_name: Earth control spores, 60-min germination


title: LC-020, day 2 post-challenge

source_name: day 2 post-challenge

value: peripheral blood mononuclear cell (PBMC)


title: cell line_SS_rep1

description: CME

value: Renwick PJ et al., 1995


title: LC-022, day 2, control

source_name: day 2, control


title: Mars vs. Earth

source_name: Simulated Mars-exposed spores, 60-min germination


title: LC-020, day 2, control


title: Human lymphocytes, sample 4

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description: Gene expression profile of human lymphocytes.

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to Affymetrix Human Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by the interPLIER algorithm with Affymetrix Expression Console.

label: Biotin

source_name: lymphocytes total RNA, non-diabetic

label_protocol: Standard Affymetrix Protocol, as described in the GeneChip Whole Transcript Sense Target Labeling Assay Manual, Version 4 (available at http://www.affymetrix.com/support/technical/product_updates/wt_1_1_assay.affx).

growth_protocol: Peripheral blood lymphocytes were freshly isolated from normal subjects.

extract_protocol: Total RNAs were prepared using Qiagen RNeasy mini kits.

treatment_protocol: None.

value: peripheral blood lymphocytes

tag: disease status

value: healthy, non-diabetic


title: LC-021, day 2, control


title: LC-019, day 2 post-challenge


title: LC-019, day 2, control


title: tumor_MLS_rep9

source_name: Right upper limb

value: Right upper limb

value: Female

value: III

value: FUS-CHOP I


title: tumor_MLS_rep7

source_name: Left upper limb

value: Left upper limb

value: Male

value: I


title: tumor_MLS_rep8

value: FUS-CHOP II


title: HepaRG_culture_rep1

source_name: HepaRG cultured alone, Replicate 1

value: HepaRG


title: Human lymphocytes, sample 3


title: tumor_MLS_rep6

source_name: Leg

value: Leg


title: Human lymphocytes, sample 1


title: LC-018, day 2, control


title: LC-018, day 2 post-challenge


title: Ind280_BEFORE 12 weeks of exercise

city: Miami

first: Evadnie

last: Rampersaud

address: 1501 NW 10th Ave. BRB

department: John P. Hussman Institute for Human Genomics

institute: University of Miami, Miller School of Medicine

description:
SAMPLE 118
Gene expression data for Ind280_BEFORE 12 weeks of exercise

hyb_protocol: Samples were hybridized with the Affymetrix GeneChip Human Gene 1.0 ST microarray for 17 hours at 65C according to the manufacturing recommendation.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Image analysis was performed using the Affymetrix Command Console Software (AGCC). Resulting CEL files were imported into Partek software (Partek, Inc., St. Louis, MO, USA) using median polish probe set summarization, GCRMA background correction, and quantile normalization. To identify differentially expressed genes, normalized log2 datafiles exported from Partek were analyzed with the Significance Analysis of Microarray (SAM v2.0) statistical package in R (http://www-stat.standford.edu/~tibs/SAM/)

source_name: whole blood

label_protocol: Samples were amplified and labeled using Ovation RNA Amplification kit (NuGEN). After sense-strand cDNA synthesis with WT-Ovation Exon Module (NuGEN) samples were fragmented and labeled using Encore Biotin Module (NuGEN)

extract_protocol: RNA isolation was performed using a PAXgene Blood RNA Kit (Qiagen) according to manufacturer instructions.

treatment_protocol: Subjects followed a supervised 12 week exercise program consisting of both cardiovascular and progressive resistance training. Twice per week, subjects performed combined exercise sessions (both cardiovascular and resistance training) while on the third day they performed cardiovascular exercise only.  The cardiovascular exercise protocol progressed systematically from 50% estimated relative VO2max (rVO2max) for 20 minutes during the first week to 75% estimated rVO2max for 45 minutes during the 12th week. During the combined sessions, subjects also completed a 10 exercise resistance training circuit. Initial loads were set at approximately 60% of one-rep max (1-RM).  Subjects were instructed to perform one set of 8-12 repetitions on each exercise. Once 12 repetitions could be performed in a slow-controlled manner, the load was increased by 5% for the next workout.  If muscular failure occurred prior to the 12th repetition, then the load was maintained for the next workout. This exercise training protocol is in accordance with recommendations set forth by the American College of Sports Medicine (ACSM, 2011).

tag: individuum

value: female

tag: race

value: WH

tag: ethnicity

value: Hispanic (HI)

value: Before 12 weeks of exercise

tag: relative vo2

value: Low responder

tag: heart rate

value: High responders

tag: composite score

value: Low responders


title: Ind288_BEFORE 12 weeks of exercise

description:
SAMPLE 120
Gene expression data for Ind288_BEFORE 12 weeks of exercise

value: Non-Hispanic (NH)

tag: time

value: High responder


title: tumor_MLS_rep5

tag: tissue

tag: age (years)

tag: Sex

value: Female

value: III

value: EWS-CHOP


title: ABI3_ChIP 3/1, membrane A [070223ABI3]

description:
070223ABI3
Raw data file: 070223_A_ABI3.txt
ChIP biol.replicate 3
Hybridization on membrane A

source_name: Chromatin fragments precipitated with anti-ABI3 antibody, seeds

tag: ecotype

value: seed

tag: developmental stage according to boyes et al. (2004)

value: anti-ABI3 Antibody


title: Ind280_AFTER 12 weeks of exercise

description:
SAMPLE 117
Gene expression data for Ind280_AFTER 12 weeks of exercise

value: After 12 weeks of exercise


title: Ind288_AFTER 12 weeks of exercise

description:
SAMPLE 119
Gene expression data for Ind288_AFTER 12 weeks of exercise


title: tumor_MLS_rep4

source_name: Lymph nodule groin + left upper limb

value: Lymph nodule groin + left upper limb

value: Male

tag: grade

value: I-II

tag: molecuar confirmation

tag: reference source

tag: culture condition


title: LC-017, day 2 post-challenge

description: Gene expression data from PBMC challenged to 10 mkM lead acetate for day one and then cultured without Pb for day two

tag: cell type

value: peripheral blood mononuclear cell (PBMC)


title: Ind271_BEFORE 12 weeks of exercise

description:
SAMPLE 116
Gene expression data for Ind271_BEFORE 12 weeks of exercise

tag: individuum

tag: gender

value: female

value: WH

value: Hispanic (HI)


title: LC-017, day 2, control

description: Gene expression data from PBMC controls, day two


title: Ind260_AFTER 12 weeks of exercise

description:
SAMPLE 111
Gene expression data for Ind260_AFTER 12 weeks of exercise

tag: race

tag: ethnicity


title: Ind267_BEFORE 12 weeks of exercise

description:
SAMPLE 114
Gene expression data for Ind267_BEFORE 12 weeks of exercise

value: Before 12 weeks of exercise

tag: relative vo2

tag: heart rate


title: Ind271_AFTER 12 weeks of exercise

description:
SAMPLE 115
Gene expression data for Ind271_AFTER 12 weeks of exercise

tag: time

value: Low responder

value: High responders

tag: composite score

value: Low responders


title: Ind260_BEFORE 12 weeks of exercise

description:
SAMPLE 112
Gene expression data for Ind260_BEFORE 12 weeks of exercise

value: High responder


title: tumor_MLS_rep3

tag: tissue

value: Left upper limb

tag: age (years)

value: Female

value: II

value: FUS-CHOP I


title: Ind259_AFTER 12 weeks of exercise

description:
SAMPLE 109
Gene expression data for Ind259_AFTER 12 weeks of exercise

value: Non-Hispanic (NH)

value: After 12 weeks of exercise


title: Ind267_AFTER 12 weeks of exercise

description:
SAMPLE 113
Gene expression data for Ind267_AFTER 12 weeks of exercise


title: LC-014, day 2 post-challenge


title: Ind259_BEFORE 12 weeks of exercise

description:
SAMPLE 110
Gene expression data for Ind259_BEFORE 12 weeks of exercise


title: Ind254_BEFORE 12 weeks of exercise

description:
SAMPLE 108
Gene expression data for Ind254_BEFORE 12 weeks of exercise


title: tumor_MLS_rep2

tag: Sex

value: Male

value: FUS-CHOP III


title: LC-014, day 2, control

value: peripheral blood mononuclear cell (PBMC)


title: Ind252_AFTER 12 weeks of exercise

description:
SAMPLE 105
Gene expression data for Ind252_AFTER 12 weeks of exercise

value: female


title: LC-013, day 2 post-challenge


title: Ind254_AFTER 12 weeks of exercise

description:
SAMPLE 107
Gene expression data for Ind254_AFTER 12 weeks of exercise

value: WH


title: Ind252_BEFORE 12 weeks of exercise

description:
SAMPLE 106
Gene expression data for Ind252_BEFORE 12 weeks of exercise


title: Ind248_BEFORE 12 weeks of exercise

description:
SAMPLE 104
Gene expression data for Ind248_BEFORE 12 weeks of exercise


title: Ind248_AFTER 12 weeks of exercise

description:
SAMPLE 103
Gene expression data for Ind248_AFTER 12 weeks of exercise


title: LC-013, day 2, control


title: tumor_DDLS_rep7

source_name: Retroperitoneum

value: Retroperitoneum

value: III


title: Ind247_BEFORE 12 weeks of exercise

description:
SAMPLE 102
Gene expression data for Ind247_BEFORE 12 weeks of exercise

value: Before 12 weeks of exercise

value: Low responder


title: Ind247_AFTER 12 weeks of exercise

description:
SAMPLE 101
Gene expression data for Ind247_AFTER 12 weeks of exercise

value: Low responders


title: LC-012, day 2 post-challenge

description: Gene expression data from PBMC challenged to 10 mkM lead acetate for day one and then cultured without Pb for day two


title: tumor_DDLS_rep8


title: Ind240_BEFORE 12 weeks of exercise

description:
SAMPLE 98
Gene expression data for Ind240_BEFORE 12 weeks of exercise

value: Hispanic (HI)

value: High responder


title: Ind243_AFTER 12 weeks of exercise

description:
SAMPLE 99
Gene expression data for Ind243_AFTER 12 weeks of exercise


title: LC-012, day 2, control

description: Gene expression data from PBMC controls, day two


title: tumor_DDLS_rep6

source_name: Duodenum

value: Duodenum


title: tumor_DDLS_rep5


title: tumor_DDLS_rep4

source_name: Abdomen

value: Abdomen

value: Female


title: tumor_DDLS_rep3


title: Ind240_AFTER 12 weeks of exercise

description:
SAMPLE 97
Gene expression data for Ind240_AFTER 12 weeks of exercise


title: Ind235_BEFORE 12 weeks of exercise

description:
SAMPLE 92
Gene expression data for Ind235_BEFORE 12 weeks of exercise

value: BL

value: Non-Hispanic (NH)

value: High responders


title: LC016, day 2 post-challenge


title: Ind238_BEFORE 12 weeks of exercise

description:
SAMPLE 96
Gene expression data for Ind238_BEFORE 12 weeks of exercise


title: Ind243_BEFORE 12 weeks of exercise

description:
SAMPLE 100
Gene expression data for Ind243_BEFORE 12 weeks of exercise


title: Ind235_AFTER 12 weeks of exercise

description:
SAMPLE 91
Gene expression data for Ind235_AFTER 12 weeks of exercise

value: After 12 weeks of exercise


title: LC015, day 2, control

value: peripheral blood mononuclear cell (PBMC)


title: Human lymphocytes, sample 2

description: Gene expression profile of human lymphocytes.

value: peripheral blood lymphocytes

tag: disease status

value: healthy, non-diabetic


title: LC015, day 2 post-challenge


title: Ind224_BEFORE 12 weeks of exercise

description:
SAMPLE 90
Gene expression data for Ind224_BEFORE 12 weeks of exercise

value: female

value: WH


title: tumor_DDLS_rep1

value: Male

tag: grade

value: II


title: Ind224_AFTER 12 weeks of exercise

description:
SAMPLE 89
Gene expression data for Ind224_AFTER 12 weeks of exercise

value: Low responders


title: Ind236_AFTER 12 weeks of exercise

description:
SAMPLE 93
Gene expression data for Ind236_AFTER 12 weeks of exercise

value: Low responder


title: Ind238_AFTER 12 weeks of exercise

description:
SAMPLE 95
Gene expression data for Ind238_AFTER 12 weeks of exercise

value: Hispanic (HI)


title: tumor_PLS_rep8

value: Left upper limb

value: III

tag: molecuar confirmation


title: Ind236_BEFORE 12 weeks of exercise

description:
SAMPLE 94
Gene expression data for Ind236_BEFORE 12 weeks of exercise

value: Before 12 weeks of exercise


title: LC016, day 2, control


title: M030, day 2, control


title: cell line_SS_rep2

source_name: Cell line

value: Cell line

value: SS18/SSX 2

tag: reference source

value: Xie Y et al., 2006

value: Ham´s F12, 10% FCS, 1% PS


title: Ind218_AFTER 12 weeks of exercise

description:
SAMPLE 87
Gene expression data for Ind218_AFTER 12 weeks of exercise

value: After 12 weeks of exercise


title: Ind218_BEFORE 12 weeks of exercise

description:
SAMPLE 88
Gene expression data for Ind218_BEFORE 12 weeks of exercise


title: tumor_DDLS_rep2

value: Abdomen

tag: culture condition


title: Ind217_BEFORE 12 weeks of exercise

description:
SAMPLE 86
Gene expression data for Ind217_BEFORE 12 weeks of exercise

value: Non-Hispanic (NH)

value: High responders


title: Ind217_AFTER 12 weeks of exercise

description:
SAMPLE 85
Gene expression data for Ind217_AFTER 12 weeks of exercise

value: female

value: WH


title: LC004, day 2 post-challenge

description: Gene expression data from PBMC challenged to 10 mkM lead acetate for day one and then cultured without Pb for day two

tag: cell type

value: peripheral blood mononuclear cell (PBMC)


title: LC007, day 2 post-challenge


title: Ind211_BEFORE 12 weeks of exercise

description:
SAMPLE 84
Gene expression data for Ind211_BEFORE 12 weeks of exercise

tag: individuum

value: High responder

value: Low responders


title: Ind211_AFTER 12 weeks of exercise

description:
SAMPLE 83
Gene expression data for Ind211_AFTER 12 weeks of exercise

tag: gender

value: Hispanic (HI)


title: tumor_PLS_rep7

source_name: Buttock

value: Buttock

value: Female


title: tumor_PLS_rep6

value: Right upper limb

value: Male

value: III


title: Ind210_BEFORE 12 weeks of exercise

description:
SAMPLE 82
Gene expression data for Ind210_BEFORE 12 weeks of exercise

tag: race

value: Before 12 weeks of exercise

value: Low responder


title: Ind210_AFTER 12 weeks of exercise

description:
SAMPLE 81
Gene expression data for Ind210_AFTER 12 weeks of exercise

tag: ethnicity

value: After 12 weeks of exercise


title: tumor_PLS_rep5


title: tumor_PLS_rep4

value: Left upper limb


title: LC004, day 2, control

description: Gene expression data from PBMC controls, day two


title: tumor_PLS_rep3

source_name: Left forearm

value: Left forearm


title: LC028, day 1, 10 mkM lead acetate

description: Gene expression data from PBMC challenged to 10 mkM lead acetate for one day

source_name: day 1, 10 mkM lead acetate


title: Ind195_BEFORE 12 weeks of exercise

description:
SAMPLE 76
Gene expression data for Ind195_BEFORE 12 weeks of exercise

value: BL

value: Non-Hispanic (NH)

tag: relative vo2


title: M030, day 2 post-challenge

source_name: day 2 post-challenge


title: Ind195_AFTER 12 weeks of exercise

description:
SAMPLE 75
Gene expression data for Ind195_AFTER 12 weeks of exercise

value: female

tag: heart rate


title: Ind192_AFTER 12 weeks of exercise

description:
SAMPLE 73
Gene expression data for Ind192_AFTER 12 weeks of exercise

value: WH

tag: time

value: High responders


title: Ind200_AFTER 12 weeks of exercise

description:
SAMPLE 77
Gene expression data for Ind200_AFTER 12 weeks of exercise

value: High responder

tag: composite score

value: Low responders


title: LC028, day 1, control

description: Gene expression data from PBMC controls, day one

source_name: day 1, control

value: peripheral blood mononuclear cell (PBMC)


title: Ind209_AFTER 12 weeks of exercise

description:
SAMPLE 79
Gene expression data for Ind209_AFTER 12 weeks of exercise

value: Hispanic (HI)


title: LC002, day 2 post-challenge


title: Ind192_BEFORE 12 weeks of exercise

description:
SAMPLE 74
Gene expression data for Ind192_BEFORE 12 weeks of exercise


title: tumor_PLS_rep1

tag: tissue


title: LC002, day 2, control

source_name: day 2, control


title: tumor_MFS_rep8

source_name: Left lower limb

value: Left lower limb

tag: age (years)

value: II


title: tumor_PLS_rep2

tag: Sex

value: Female

value: III


title: LC027, day 1, 10 mkM lead acetate


title: LC027, day 1, control


title: Ind190_BEFORE 12 weeks of exercise

description:
SAMPLE 72
Gene expression data for Ind190_BEFORE 12 weeks of exercise

value: Before 12 weeks of exercise

value: Low responder


title: Ind178_AFTER 12 weeks of exercise

description:
SAMPLE 69
Gene expression data for Ind178_AFTER 12 weeks of exercise

value: After 12 weeks of exercise


title: Ind200_BEFORE 12 weeks of exercise

description:
SAMPLE 78
Gene expression data for Ind200_BEFORE 12 weeks of exercise


title: Ind157_BEFORE 12 weeks of exercise

description:
SAMPLE 68
Gene expression data for Ind157_BEFORE 12 weeks of exercise


title: LC026, day 1, control


title: Ind157_AFTER 12 weeks of exercise

description:
SAMPLE 67
Gene expression data for Ind157_AFTER 12 weeks of exercise


title: LC11, day 1, 10 mkM lead acetate


title: tumor_MLS_rep1

source_name: Left upper limb

value: Left upper limb

value: FUS-CHOP II


title: tumor_MFS_rep6

source_name: Left tigh

value: Left tigh

value: Male


title: tumor_MFS_rep5

source_name: Thigh

value: Thigh

value: II-III


title: tumor_MFS_rep3


title: Ind209_BEFORE 12 weeks of exercise

description:
SAMPLE 80
Gene expression data for Ind209_BEFORE 12 weeks of exercise

source_name: whole blood

value: female

value: WH

value: High responder


title: Ind152_BEFORE 12 weeks of exercise

description:
SAMPLE 64
Gene expression data for Ind152_BEFORE 12 weeks of exercise

value: BL

value: Non-Hispanic (NH)

value: High responders

value: Low responders


title: LC09, day 1, 10 mkM lead acetate

value: peripheral blood mononuclear cell (PBMC)


title: tumor_MFS_rep4

source_name: Left shoulder

value: Left shoulder

value: Female

value: III


title: Ind152_AFTER 12 weeks of exercise

description:
SAMPLE 63
Gene expression data for Ind152_AFTER 12 weeks of exercise

value: After 12 weeks of exercise


title: Ind150_BEFORE 12 weeks of exercise

description:
SAMPLE 62
Gene expression data for Ind150_BEFORE 12 weeks of exercise

value: Hispanic (HI)

value: Before 12 weeks of exercise

value: Low responder


title: tumor_MFS_rep2

source_name: Left hip

value: Left hip


title: LC08, day 1, 10 mkM lead acetate

description: Gene expression data from PBMC challenged to 10 mkM lead acetate for one day


title: Ind178_BEFORE 12 weeks of exercise

description:
SAMPLE 70
Gene expression data for Ind178_BEFORE 12 weeks of exercise


title: LC10, day 1, 10 mkM lead acetate


title: Ind190_AFTER 12 weeks of exercise

description:
SAMPLE 71
Gene expression data for Ind190_AFTER 12 weeks of exercise


title: LC011, day 1, control


title: Ind153_BEFORE 12 weeks of exercise

description:
SAMPLE 65
Gene expression data for Ind153_BEFORE 12 weeks of exercise


title: Ind147_AFTER 12 weeks of exercise

description:
SAMPLE 59
Gene expression data for Ind147_AFTER 12 weeks of exercise


title: LC010, day 1, control

description: Gene expression data from PBMC controls, day one


title: tumor_MFH_rep11

source_name: Right lower limb

value: Right lower limb


title: tumor_MFS_rep1

value: Left upper limb


title: LC026, day 1, 10 mkM lead acetate


title: Ind145_BEFORE 12 weeks of exercise

description:
SAMPLE 58
Gene expression data for Ind145_BEFORE 12 weeks of exercise

value: female


title: Ind150_AFTER 12 weeks of exercise

description:
SAMPLE 61
Gene expression data for Ind150_AFTER 12 weeks of exercise

value: WH


title: Ind147_BEFORE 12 weeks of exercise

description:
SAMPLE 60
Gene expression data for Ind147_BEFORE 12 weeks of exercise

value: High responder


title: Ind144_BEFORE 12 weeks of exercise

description:
SAMPLE 56
Gene expression data for Ind144_BEFORE 12 weeks of exercise


title: Ind142_BEFORE 12 weeks of exercise

description:
SAMPLE 54
Gene expression data for Ind142_BEFORE 12 weeks of exercise


title: Ind144_AFTER 12 weeks of exercise

description:
SAMPLE 55
Gene expression data for Ind144_AFTER 12 weeks of exercise


title: Ind145_AFTER 12 weeks of exercise

description:
SAMPLE 57
Gene expression data for Ind145_AFTER 12 weeks of exercise

value: BL

value: Non-Hispanic (NH)


title: Ind153_AFTER 12 weeks of exercise

description:
SAMPLE 66
Gene expression data for Ind153_AFTER 12 weeks of exercise

value: Low responders


title: tumor_MFH_rep10_a

source_name: Right upper limb

value: Right upper limb


title: tumor_MFH_rep10_b


title: tumor_MFH_rep9

source_name: Groin + Right upper limb

value: Groin + Right upper limb

value: Male


title: LC009, day 1, control

value: peripheral blood mononuclear cell (PBMC)


title: tumor_MFH_rep7

value: Female

value: III


title: tumor_MFH_rep8


title: Ind138_BEFORE 12 weeks of exercise

description:
SAMPLE 52
Gene expression data for Ind138_BEFORE 12 weeks of exercise

value: Hispanic (HI)

value: Before 12 weeks of exercise


title: Ind142_AFTER 12 weeks of exercise

description:
SAMPLE 53
Gene expression data for Ind142_AFTER 12 weeks of exercise

value: After 12 weeks of exercise

value: Low responder

value: High responders


title: Ind138_AFTER 12 weeks of exercise

description:
SAMPLE 51
Gene expression data for Ind138_AFTER 12 weeks of exercise

value: female


title: tumor_MFH_rep6

value: Left upper limb


title: Ind136_BEFORE 12 weeks of exercise

description:
SAMPLE 50
Gene expression data for Ind136_BEFORE 12 weeks of exercise

value: WH


title: Ind124_BEFORE 12 weeks of exercise

description:
SAMPLE 46
Gene expression data for Ind124_BEFORE 12 weeks of exercise


title: Ind127_BEFORE 12 weeks of exercise

description:
SAMPLE 47
Gene expression data for Ind127_BEFORE 12 weeks of exercise

value: BL


title: Ind136_AFTER 12 weeks of exercise

description:
SAMPLE 49
Gene expression data for Ind136_AFTER 12 weeks of exercise


title: tumor_MFH_rep5


title: RPE1 cell, M129 oligo transfect, 72h

city: New York

first: Jingli

last: Cao

state: NY

department: Cell & Developmental Biology

institute: Weill Cornell Medical College

description:
RPE1-M129.CEL
Gene expression data from hTERT-RPE1 cell

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃  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 Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, and RMA normalization was done using Affy Suit in Bioconductor Package.

source_name: RPE1 cell transfeted with M129 oligo for 72h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: hTERT-RPE1 cell lines were cultured with DMEM/F-12 containing 10% FBS and 0.01mg/ml hygromycin B at 37°C, 5% CO2.

extract_protocol: Total RNA  was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: hTERT-RPE1 cells were transfected with control (Ctrl) or miR-129-3p (M129) oligos for 72 h using Lipofectimine RNAiMAX (Invitrogen)

tag: cell line

tag: genotype/variation

value: miR-129-3p overexpression


title: Ind124_AFTER 12 weeks of exercise

description:
SAMPLE 45
Gene expression data for Ind124_AFTER 12 weeks of exercise

value: Low responders


title: LC008, day 1, control

description: Gene expression data from PBMC controls, day one


title: Ind127_AFTER 12 weeks of exercise

description:
SAMPLE 48
Gene expression data for Ind127_AFTER 12 weeks of exercise

value: Non-Hispanic (NH)


title: Ind121_BEFORE 12 weeks of exercise

description:
SAMPLE 44
Gene expression data for Ind121_BEFORE 12 weeks of exercise

value: High responder


title: Ind114_AFTER 12 weeks of exercise

description:
SAMPLE 41
Gene expression data for Ind114_AFTER 12 weeks of exercise


title: Ind121_AFTER 12 weeks of exercise

description:
SAMPLE 43
Gene expression data for Ind121_AFTER 12 weeks of exercise


title: RPE1 cell, control oligo transfect, 72h

description:
RPE1-Ctrl.CEL
Gene expression data from hTERT-RPE1 cell

source_name: RPE1 cell transfeted with control oligo for 72h

value: control


title: Ind114_BEFORE 12 weeks of exercise

description:
SAMPLE 42
Gene expression data for Ind114_BEFORE 12 weeks of exercise


title: tumor_MFH_rep4

source_name: Right hip

value: Right hip

tag: grade

tag: molecuar confirmation


title: U87_miR-control_72h, biological rep 3

city: Singapore

first: Yukti

last: Choudhury

address: 31 Biopolis Way

country: Singapore

institute: Institute of Bioengineering and Nanotechnology, A*STAR

hyb_protocol: Hybridization cocktail was prepared with 20 µg labeled fragmented aRNA, Kreatech's Kreablock (75 µl), 5 µl oligoB2 and 15 µl 20X eukaryotic hyb control, 1X Affymetrix hybridization mix and nuclease-free water to 300 µl . Hyb cocktail was heated for 5 mins to 99°C, transferred to 45°C heatblock for 5 mins and centrifuged at 20,000xg for 5 mins. Arrays were pre-hybridized with 200 µl of pre-hybridization mix (Affymetrix) for 10 mins at 45°C with rotation at 60 rpm in GeneChip Hybridization Oven 640 (Affymetrix). Following pre-hyb, 200µl of clarified of hyb cocktail (15 µg of labeled RNA) was hybridized onto arrays for 16 h at 45 °C.  Arrays were washed and stained in Affymetrix GeneChip Fluidics Station 450 using FS-450-0004 protocol using recommended reagents from Affymetrix Hybridization, Wash and Stain kit

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with GCOS v 1.4.0.036, scaling and normalization factors were set to user-defined values of 1. The statistical expression algorithm was used for analysis.

label: biotin-ULS

source_name: U87 transfected with control miRNA (72 h)

label_protocol: For each sample, total RNA (1 µg) was labeled using Biotin-ULS following Kreatech ULS labeling protocol for Affymetrix (GEA-004). Affymetrix's Eukaryotic Poly-A RNA control (1 µl of stock diluted 1:10000) was spiked in to the initial oligo(dT) priming reaction. Amplified RNA (aRNA) was fragmented using 10X Fragmentation Buffer (Ambion).

growth_protocol: U87 cells cultured in supplemented DMEM before transfection. Transfections were done in PS-free DMEM

extract_protocol: Total RNA extracted using Trizol following manufacturer's protocol and purified once using Qiagen Rneasy Mini column.

treatment_protocol: Cells transfected with 50 nM miRNA duplexes using Lipofectamine RNAiMAX. Cells further incubated for 72 hours

value: U87 glioma cells

tag: transfected

value: control miRNA (72 h)


title: Ind113_AFTER 12 weeks of exercise

description:
SAMPLE 39
Gene expression data for Ind113_AFTER 12 weeks of exercise


title: Ind113_BEFORE 12 weeks of exercise

description:
SAMPLE 40
Gene expression data for Ind113_BEFORE 12 weeks of exercise


title: tumor_MFH_rep3

value: Right upper limb

value: Male

value: III

tag: reference source

tag: culture condition


title: Ind110_BEFORE 12 weeks of exercise

description:
SAMPLE 38
Gene expression data for Ind110_BEFORE 12 weeks of exercise

tag: individuum

tag: gender

value: Before 12 weeks of exercise

value: Low responder


title: Ind104_BEFORE 12 weeks of exercise

description:
SAMPLE 36
Gene expression data for Ind104_BEFORE 12 weeks of exercise

value: female

tag: race

tag: ethnicity


title: Ind110_AFTER 12 weeks of exercise

description:
SAMPLE 37
Gene expression data for Ind110_AFTER 12 weeks of exercise

value: After 12 weeks of exercise

tag: relative vo2

tag: heart rate


title: Ind104_AFTER 12 weeks of exercise

description:
SAMPLE 35
Gene expression data for Ind104_AFTER 12 weeks of exercise

tag: time

tag: composite score


title: U87_miR-control_72h, biological rep 1


title: U87_miR-control_72h, biological rep 2


title: tumor_MFH_rep2

tag: tissue

value: Left upper limb

tag: age (years)


title: U87_miR-376a*G_72h, biological rep 3

source_name: U87 transfected with miR-376a*G (72 h)

tag: cell line


title: tumor_MFS_rep7

tag: Sex

value: Female


title: tumor_MFH_rep1

tag: grade


title: Ind101_BEFORE 12 weeks of exercise

description:
SAMPLE 34
Gene expression data for Ind101_BEFORE 12 weeks of exercise

value: BL

value: High responders


title: Ind98_BEFORE 12 weeks of exercise

description:
SAMPLE 32
Gene expression data for Ind98_BEFORE 12 weeks of exercise

value: WH

value: Hispanic (HI)

value: Low responders


title: Ind98_AFTER 12 weeks of exercise

description:
SAMPLE 31
Gene expression data for Ind98_AFTER 12 weeks of exercise


title: tumor_MPNST_rep7

source_name: Soft tissue

value: Soft tissue

tag: molecuar confirmation

value: SS18/SSX neg


title: Ind101_AFTER 12 weeks of exercise

description:
SAMPLE 33
Gene expression data for Ind101_AFTER 12 weeks of exercise

value: Non-Hispanic (NH)

value: High responder


title: U87_miR-376a*G_72h, biological rep 2

value: U87 glioma cells

tag: transfected


title: U87_miR-376a*G_72h, biological rep 1


title: tumor_MPNST_rep6

source_name: Abdomen

value: Abdomen

value: III

tag: reference source


title: U87_miR-376a*A_72h, biological rep 2

source_name: U87 transfected with miR-376a*A (72 h)


title: Ind93_BEFORE 12 weeks of exercise

description:
SAMPLE 30
Gene expression data for Ind93_BEFORE 12 weeks of exercise

value: Before 12 weeks of exercise

value: Low responder


title: Ind93_AFTER 12 weeks of exercise

description:
SAMPLE 29
Gene expression data for Ind93_AFTER 12 weeks of exercise

value: female

value: After 12 weeks of exercise


title: U87_miR-376a*A_72h, biological rep 3


title: Ind92_BEFORE 12 weeks of exercise

description:
SAMPLE 28
Gene expression data for Ind92_BEFORE 12 weeks of exercise


title: tumor_MPNST_rep5

value: Right upper limb

value: Male

tag: culture condition


title: Ind85_AFTER 12 weeks of exercise

description:
SAMPLE 25
Gene expression data for Ind85_AFTER 12 weeks of exercise

tag: individuum


title: tumor_MPNST_rep8

source_name: muscle compartiment

value: muscle compartiment


title: Ind85_BEFORE 12 weeks of exercise

description:
SAMPLE 26
Gene expression data for Ind85_BEFORE 12 weeks of exercise

tag: gender

value: WH


title: U87_miR-376a*A_72h, biological rep 1


title: tumor_MPNST_rep4


title: U87_miR-control_24h, biological rep 3

description: Samples used for hybridization consisted of three biological replicates for each of miR-376a*A, miR-376a*G or control miRNA transfection of U87 cells. A total of nine hybridizations were performed. Expression data from control miRNA-transfected cells was used as  reference for determining genes differentially expressed upon miR-376a*A or miR-376a*G overexpression.

source_name: U87 transfected with control miRNA (24 h)

treatment_protocol: Cells transfected with 50 nM miRNA duplexes using Lipofectamine RNAiMAX. Cells further incubated for 24 hours

value: control miRNA (24 h)


title: Ind92_AFTER 12 weeks of exercise

description:
SAMPLE 27
Gene expression data for Ind92_AFTER 12 weeks of exercise

tag: race

value: Hispanic (HI)

value: Low responders


title: Ind81_BEFORE 12 weeks of exercise

description:
SAMPLE 24
Gene expression data for Ind81_BEFORE 12 weeks of exercise

tag: ethnicity


title: Ind81_AFTER 12 weeks of exercise

description:
SAMPLE 23
Gene expression data for Ind81_AFTER 12 weeks of exercise

tag: relative vo2


title: Ind79_BEFORE 12 weeks of exercise

description:
SAMPLE 22
Gene expression data for Ind79_BEFORE 12 weeks of exercise

tag: heart rate


title: Ind75_BEFORE 12 weeks of exercise

description:
SAMPLE 20
Gene expression data for Ind75_BEFORE 12 weeks of exercise

tag: time


title: U87_miR-control_24h, biological rep 2


title: U87_miR-376a*G_24h, biological rep 3

source_name: U87 transfected with miR-376a*G (24 h)


title: U87_miR-control_24h, biological rep 1


title: tumor_MPNST_rep3

value: SS18/SSX neg


title: tumor_MPNST_rep2

value: Female


title: tumor_MPNST_rep1

source_name: Left upper limb

value: Left upper limb


title: Ind75_AFTER 12 weeks of exercise

description:
SAMPLE 19
Gene expression data for Ind75_AFTER 12 weeks of exercise

source_name: whole blood

value: Non-Hispanic (NH)

value: High responder

tag: composite score


title: Ind63_BEFORE 12 weeks of exercise

description:
SAMPLE 18
Gene expression data for Ind63_BEFORE 12 weeks of exercise

value: High responders


title: tumor_SS_rep10

source_name: Lower limb

tag: tissue

value: Lower limb

value: II

value: SS18/SSX 1


title: tumor_SS_rep9

tag: age (years)

value: III


title: Ind79_AFTER 12 weeks of exercise

description:
SAMPLE 21
Gene expression data for Ind79_AFTER 12 weeks of exercise

value: female

value: After 12 weeks of exercise


title: Ind60_BEFORE 12 weeks of exercise

description:
SAMPLE 16
Gene expression data for Ind60_BEFORE 12 weeks of exercise

value: Before 12 weeks of exercise


title: Ind51_BEFORE 12 weeks of exercise

description:
SAMPLE 14
Gene expression data for Ind51_BEFORE 12 weeks of exercise

value: WH

value: Low responder


title: U87_miR-376a*G_24h, biological rep 1

tag: cell line

value: U87 glioma cells


title: U87_miR-376a*G_24h, biological rep 2


title: Ind60_AFTER 12 weeks of exercise

description:
SAMPLE 15
Gene expression data for Ind60_AFTER 12 weeks of exercise

value: Hispanic (HI)


title: Ind63_AFTER 12 weeks of exercise

description:
SAMPLE 17
Gene expression data for Ind63_AFTER 12 weeks of exercise

value: Low responders


title: U87_miR-376a*A_24h, biological rep 2

source_name: U87 transfected with miR-376a*A (24 h)


title: tumor_SS_rep8

tag: Sex

value: Male


title: Ind41_BEFORE 12 weeks of exercise

description:
SAMPLE 12
Gene expression data for Ind41_BEFORE 12 weeks of exercise

value: BL


title: U87_miR-376a*A_24h, biological rep 3


title: U87_miR-376a*A_24h, biological rep 1


title: SW1783_miR-control_24h, biological rep 3

description: Samples used for hybridization consisted of three biological replicates for each of miR-376a*A, miR-376a*G or control miRNA transfection of SW1783 cells. A total of nine hybridizations were performed. Expression data from control miRNA-transfected cells was used as  reference for determining genes differentially expressed upon miR-376a*A or miR-376a*G overexpression.

source_name: SW1783 transfected with control miRNA (24 h)

growth_protocol: SW1783 cells cultured in supplemented DMEM before transfection. Transfections were done in PS-free DMEM

treatment_protocol: Cells transfected with 50 nM miRNA duplexes using Lipofectamine RNAiMAX. Cells further incubated for 24 hours.

value: SW1783 human glioma cells

value: control miRNA (24 h)


title: Ind51_AFTER 12 weeks of exercise

description:
SAMPLE 13
Gene expression data for Ind51_AFTER 12 weeks of exercise


title: Ind33_AFTER 12 weeks of exercise

description:
SAMPLE 9
Gene expression data for Ind33_AFTER 12 weeks of exercise


title: tumor_SS_rep6

value: Left upper limb

tag: grade

value: SS18/SSX 2


title: Ind41_AFTER 12 weeks of exercise

description:
SAMPLE 11
Gene expression data for Ind41_AFTER 12 weeks of exercise

value: Non-Hispanic (NH)

value: High responders


title: tumor_SS_rep5

source_name: Left thumb

value: Left thumb

value: III

tag: molecuar confirmation

value: SS18/SSX 1


title: tumor_SS_rep7

source_name: Right lower limb

value: Right lower limb

value: II


title: tumor_SS_rep4

source_name: Right upper limb

value: Right upper limb

value: Female


title: Ind22_BEFORE 12 weeks of exercise

description:
SAMPLE 8
Gene expression data for Ind22_BEFORE 12 weeks of exercise

value: female

value: Before 12 weeks of exercise

value: Low responder


title: Ind33_BEFORE 12 weeks of exercise

description:
SAMPLE 10
Gene expression data for Ind33_BEFORE 12 weeks of exercise

value: WH

value: Hispanic (HI)

value: Low responders


title: Ind14_AFTER 12 weeks of exercise

description:
SAMPLE 4
Gene expression data for Ind14_AFTER 12 weeks of exercise

value: After 12 weeks of exercise


title: tumor_SS_rep3

value: SS18/SSX 2


title: Ind21_AFTER 12 weeks of exercise

description:
SAMPLE 5
Gene expression data for Ind21_AFTER 12 weeks of exercise


title: Ind22_AFTER 12 weeks of exercise

description:
SAMPLE 7
Gene expression data for Ind22_AFTER 12 weeks of exercise

value: BL

value: Non-Hispanic (NH)


title: SW1783_miR-control_24h, biological rep 2

value: SW1783 human glioma cells

tag: transfected

value: control miRNA (24 h)


title: Ind21_BEFORE 12 weeks of exercise

description:
SAMPLE 6
Gene expression data for Ind21_BEFORE 12 weeks of exercise


title: tumor_SS_rep2

source_name: Left lower limb

value: Left lower limb

value: II-III

value: SS18/SSX 1

tag: reference source


title: SW1783_miR-control_24h, biological rep 1


title: Ind14_BEFORE 12 weeks of exercise

description:
SAMPLE 3
Gene expression data for Ind14_BEFORE 12 weeks of exercise


title: Omental Metastases 11M

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

description: Gene expression data

hyb_protocol: Following fragmentation,  of about 2.3 ug cRNA were hybridized for 17 hr at 45C on each GeneST 1.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fluidics script FS450_007

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner equipped with an autoloader.

data_processing: The data were analyzed with RMA from Affymetrix Power Tools using HuGene-1_0-st-v1.r3.bgp, HuGene-1_0-st-v1.r3.pgf, and HuGene-1_0-st-v1.r3.clf files from Affymetrix. Some probe sets excluded due to the fact that the quantile normalization performed included only RefSeq genes.

source_name: Omental Metastases

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, Affymetrix).

extract_protocol: Qiazol and Qiagen RNAsy was performed following the manufacturer's instructions.

treatment_protocol: Tumors were fresh frozen immediately upon removal.

tag: tissue type

value: Omental Metastases


title: Omental Metastases 12M

description: Gene expression data


title: SW1783_miR-376a*G_24h, biological rep 3

source_name: SW1783 transfected with miR-376a*G (24 h)


title: Ind11_AFTER 12 weeks of exercise

description:
SAMPLE 1
Gene expression data for Ind11_AFTER 12 weeks of exercise

tag: individuum

value: High responders


title: Ind11_BEFORE 12 weeks of exercise

description:
SAMPLE 2
Gene expression data for Ind11_BEFORE 12 weeks of exercise

tag: gender

value: female


title: SW1783_miR-376a*G_24h, biological rep 2


title: Primary Tumor 11P

description: Gene expression data

source_name: Primary Tumor

value: Primary Tumor


title: Omental Metastases 10M

description: Gene expression data


title: tumor_SS_rep1

source_name: Right chest

value: Right chest

value: Female

value: III

tag: culture condition


title: SW1783_miR-376a*G_24h, biological rep 1


title: SW1783_miR-376a*A_24h, biological rep 3

source_name: SW1783 transfected with miR-376a*A (24 h)


title: tumor_LMS_rep13

source_name: Soft tissue

value: Soft tissue

value: I


title: Primary Tumor 10P

description: Gene expression data


title: Omental Metastases 9M

description: Gene expression data


title: Primary Tumor 12P

description: Gene expression data


title: SW1783_miR-376a*A_24h, biological rep 2


title: tumor_LMS_rep11

source_name: Large vessels

value: Large vessels

value: Male


title: Primary Tumor 8P

description: Gene expression data


title: tumor_LMS_rep9

source_name: Retroperitoneum

value: Retroperitoneum


title: tumor_LMS_rep8

value: II


title: tumor_LMS_rep12


title: SW1783_miR-376a*A_24h, biological rep 1

value: SW1783 human glioma cells


title: Primary Tumor 9P

description: Gene expression data


title: tumor_LMS_rep7

source_name: Abdomen

value: Abdomen


title: Omental Metastases 6M

description: Gene expression data


title: tumor_LMS_rep10


title: Primary Tumor 6P

description: Gene expression data


title: DKAT SCGM day14 rep2

city: Durham

first: Nicholas

last: D'Amato

state: NC

address: MSRB Room 217, Research Dr.

department: Pharmacology and Cancer Biology

institute: Duke University

description:
DKAT cells cultured in SCGM (Lonza) for 14 days
HGU133(+2.0)_14_E2.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized in an Affymetrix Hybridization Oven 640 for 16 hr at 45°C on HG-U133 Plus2.0 GeneChips. GeneChips were washed and stained on an Affymetrix Fluidics Station 450, using the manufacture’s recommended protocol.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with RMA using the affy package implemented in BRB array tools (Simon and Lam, ver. 3.7.0; R ver. 2.6.0)

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

growth_protocol: DKAT cells (passage 10) in MEGM were split and grown for 14 days either in MEGM (Lonza) or SCGM (Lonza) in adherent culture.

extract_protocol: Extraction of total RNA was performed using the Qiagen RNeasy kit according to the manufacturer's instructions with option DNAse step.

value: Human breast cancer-derived cell line DKAT

tag: culture medium

value: SCGM


title: DKAT SCGM day14 rep3

description:
DKAT cells cultured in SCGM (Lonza) for 14 days
HGU133(+2.0)_23_E3.CEL

treatment_protocol: DKAT cells (passage 10) in MEGM were split and grown for 14 days either in MEGM (Lonza) or SCGM (Lonza) in adherent culture.


title: Omental Metastases 4M

description: Gene expression data

value: Omental Metastases


title: Omental Metastases 8M

description: Gene expression data


title: Omental Metastases 5M

description: Gene expression data


title: Primary Tumor 5P

description: Gene expression data


title: DKAT MEGM rep3

description:
DKAT cells cultured in MEGM (Lonza)
HGU133(+2.0)_22_D3.CEL

source_name: DKAT cells cultured in MEGM (Lonza)

value: MEGM


title: tumor_LMS_rep6

source_name: Peritoneium

value: Peritoneium


title: Primary Tumor 7P

description: Gene expression data

value: Primary Tumor


title: DKAT SCGM day14 rep1

description:
DKAT cells cultured in SCGM (Lonza) for 14 days
HGU133(+2.0)_05_E1.CEL


title: DKAT MEGM rep2

description:
DKAT cells cultured in MEGM (Lonza)
HGU133(+2.0)_13_D2.CEL


title: Omental Metastases 7M

description: Gene expression data


title: tumor_LMS_rep5

value: Right upper limb


title: MDA-MB-231 rep3

description:
MDA-MB-231 cells cultured in MEGM (Lonza)
HGU133(+2.0)_16_6C.CEL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: DKAT, HMEC, or MDA-MB-231 cells were cultured in MEGM (Lonza).

value: Human breast cancer-derived cell line MDA-MB-231


title: Primary Tumor 4P

description: Gene expression data


title: MDA-MB-231 rep2

description:
MDA-MB-231 cells cultured in MEGM (Lonza)
HGU133(+2.0)_10_6B.CEL

treatment_protocol: DKAT, HMEC, or MDA-MB-231 cells were cultured in MEGM (Lonza).


title: L428-FOXO1(3A)ER_4OHT_rep1

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

description: L428-FOXO1(3A)ER cells incubated with 4OHT for 24 hours

hyb_protocol: Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were scanned with a Affymetrix GeneChip Scanner 3000 according to the Affimetrix protocol.

data_processing: The microarray data were processed using GeneSifter software (http://www.geospiza.com) using RMA normalization protocol.

label_protocol: The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

growth_protocol: KM-H2-FOXO1(3A)ER and L428-FOXO1(3A)ER cHL cells stably expressing FOXO1(3A)ER were grown in  RPMI1640 medium with addition of 10% FCS, glutamine and antibiotics at 37C, 5% CO2

extract_protocol: Total RNA was isolated with RNeasy mini kit (QIAGEN) according to the manufacturers instruction.

treatment_protocol: KM-H2-KLF4ER and L428-KLF4ER cells were incubated with 200 µM 4-OHT or with relevant amount of the vehicle (ethanol).  The experiment was done twice. After 24 h of incubation total RNA was isolated with RNeasy mini kit (QIAGEN).

value: classical Hodgkin lymphoma (cHL)


title: tumor_LMS_rep4

value: Female


title: tumor_LMS_rep3

source_name: Right ellbow

value: Right ellbow


title: L428-FOXO1(3A)ER_CON_rep2

description: L428-FOXO1(3A)ER cells incubated with vehicle for 24 hours

source_name: L428-FOXO1(3A)ER, vehicle, 24 h


title: tumor_LMS_rep2


title: tumor_LMS_rep1

value: III


title: MDA-MB-231 rep1

description:
MDA-MB-231 cells cultured in MEGM (Lonza)
HGU133(+2.0)_04_6A.CEL


title: DKAT rep2

description:
DKAT cells cultured in MEGM (Lonza)
HGU133(+2.0)_09_5B.CEL


title: DKAT rep3

description:
DKAT cells cultured in MEGM (Lonza)
HGU133(+2.0)_15_5C.CEL


title: KM-H2-FOXO1(3A)ER_4OHT_rep1

description: KM-H2-FOXO1(3A)ER cells incubated with 4OHT for 24 hours

source_name: KM-H2-FOXO1(3A)ER, 4OHT, 24 h


title: LM482

city: Houston

first: Pierre

last: Saintigny

address: 1515 Holcombe

department: Thoracic / Head and Neck Medical Oncology

institute: The University of Texas M.D. Anderson Cancer Center

description:
LM001_525_AGE_1_LM482_03_31_10
Inclusion number in the clinical trial : 334

hyb_protocol: Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol.

scan_protocol: Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

data_processing: Raw data of microarrays were processed using quantile normalization and RMA algorithm (RMAExpress); expression values were log2 transformed

source_name: BATTLE_trial_core biopsy_chemorefractory non-small cell lung cancer

label_protocol: WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols.

growth_protocol: Core biopsies from patients included in the Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE)

extract_protocol: RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol.

treatment_protocol: Samples were OCT-embedded and frozen before RNA extraction

tag: egfr mutation

value: WT

tag: kras mutation

value: Mutant

tag: egfr index

tag: histology-iw revised

value: Adenocarcinoma

tag: egfr-iw type

value: No

tag: kras-iw mutation  (yes/no)

value: Yes

tag: codon kras mut

tag: type of kras mut

tag: base change

value: G to T

tag: transition/transversion

value: Transversion

tag: type kras aa change

value: CYS

tag: glyc replaced by c, d, v and a

value: C

tag: aa change cys vs. other

value: Male

tag: race

value: White

value: IV

value: Former

tag: biopsy site (grouped)

tag: treatment

value: sorafenib

tag: markergroup

tag: 8-week disease control (1=yes, 0=no)

tag: pfsc (1=progressed; 0=not progressed)

tag: pfsm (month)


title: DKAT MEGM rep1

description:
DKAT cells cultured in MEGM (Lonza)
HGU133(+2.0)_04_D1.CEL

tag: cell line

value: Human breast cancer-derived cell line DKAT

tag: culture medium

value: MEGM


title: LM454

description: RNA was extracted and purified from OCT-embedded core biopsies using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol. RNA amplifications were performed using the WT-Amplification™ Pico (NuGEN) kit. For all experiments, the manufacturers' protocols were strictly followed. WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols. The quantity and quality of the amplified cRNA or cDNA were assessed by a ND-1000 spectrophotometer (Nanodrop Technologies), and Agilent Bioanalyzer (Agilent Technologies), respectively. Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol. Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

tag: egfr mutation

tag: kras mutation

tag: egfr index

tag: disease

value: non small cell lung cancer

value: VAL

value: V

value: Other


title: KM-H2-FOXO1(3A)ER_con_rep1

description: KM-H2-FOXO1(3A)ER cells incubated with vehicle for 24 hours

source_name: KM-H2-FOXO1(3A)ER, vehicle, 24 h

value: classical Hodgkin lymphoma (cHL)


title: L428-FOXO1(3A)ER_con_rep1


title: KM-H2-FOXO1(3A)ER_4OHT_rep2


title: DKAT rep1

description:
DKAT cells cultured in MEGM (Lonza)
HGU133(+2.0)_03_5A.CEL


title: L428-FOXO1(3A)ER_4OHT_rep2


title: KM-H2-FOXO1(3A)ER_con_rep2


title: HMEC rep2

description:
HMEC cells cultured in MEGM (Lonza)
HGU133(+2.0)_07_3B.CEL

source_name: HMEC cells cultured in MEGM (Lonza)

value: Human breast cancer-derived cell line HMEC


title: LM457

description:
LM001_525_AGE_1_LM457_08_05_09
Inclusion number in the clinical trial : 297

value: WT

value: Mutant

tag: histology-iw revised

value: Adenocarcinoma

tag: egfr-iw type

value: No

tag: kras-iw mutation  (yes/no)

value: Yes

tag: codon kras mut

tag: type of kras mut

tag: base change

value: G to A

tag: transition/transversion

value: Transition

value: SER

tag: gender

value: Female


title: LM456

description:
LM001_525_AGE_1_LM456_08_05_09
Inclusion number in the clinical trial : 295

value: G to T

value: Transversion

tag: type kras aa change

tag: glyc replaced by c, d, v and a

tag: aa change cys vs. other

value: Male

tag: race

value: White

value: IV

value: Former

tag: biopsy site (grouped)

tag: treatment

value: sorafenib

tag: markergroup

tag: 8-week disease control (1=yes, 0=no)


title: HMEC rep3

description:
HMEC cells cultured in MEGM (Lonza)
HGU133(+2.0)_13_3C.CEL

tag: cell line

value: Human breast cancer-derived cell line HMEC

tag: culture medium

value: MEGM


title: LM450

description:
LM001_525_AGE_1_LM450_08_19_09
Inclusion number in the clinical trial : 287

tag: egfr mutation

value: WT

tag: kras mutation

value: Mutant

tag: egfr index

tag: histology-iw revised

tag: egfr-iw type

value: CYS

value: C

tag: pfsc (1=progressed; 0=not progressed)

tag: pfsm (month)


title: LM429

tag: disease

value: non small cell lung cancer

value: Yes

value: G to C

value: ARG

value: Other


title: LM420

value: Transversion

value: ALA

value: A


title: LM480

description:
LM001_525_AGE_1_LM480_03_31_10
Inclusion number in the clinical trial : 330

value: Adenocarcinoma

value: No

tag: kras-iw mutation  (yes/no)

tag: codon kras mut

tag: type of kras mut

tag: base change

value: G to A

tag: transition/transversion

value: Transition

tag: type kras aa change

value: ASP

tag: glyc replaced by c, d, v and a

value: D

tag: gender

value: Female

value: White

value: IV

value: 8:Deep lymph nodes


title: LM431

value: WT

value: Mutant

value: non small cell lung cancer

value: Yes


title: LM309

value: G to T, G to T

value: Transversion

value: VAL/CYS

value: V/C

value: Other/CYS


title: 3636

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: sham-operated rats (S), 6h after MCAO

hyb_protocol: Purified and labeled cRNA (28 pmol of Cy3 labeled cRNA) was hybridised on the Agilent followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 9.1.1.1).

data_processing: Data as processed by the Agilent’s Feature Extraction software (version 9.1.1.1 - feature gProcessedSignal).

organism: Rattus norvegicus

source_name: brain cortex_sham_6h_rep1

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Total RNA was extracted with Trizol followed by silica column purification (Trizol Plus RNA purification kit, cat. N 12183-555, Life Technologies, Carlsbad, CA)

tag: strain

value: male

tag: weight

tag: tissue

value: brain cortex

tag: time

value: 6h after MCAO

tag: treatment


title: LM239

tag: egfr mutation

tag: kras mutation

tag: egfr index

value: erlotinib

tag: randomization date

tag: date of progression

tag: progression-free survival status

tag: progression-free survival time (months)

value: G to C

value: ALA

value: A

value: Other


title: 3351

description: ischemic rats undergoing MCAO with EPO treatment (IE), 6h after MCAO

source_name: brain cortex_ischemia_EPO_6h_rep3

value: erythropoietin


title: 3635

description: ischemic rats undergoing MCAO with EPO treatment (IE), 2h after MCAO

source_name: brain cortex_ischemia_EPO_2h_rep1

value: 2h after MCAO


title: LM231

value: WT

value: Mutant

tag: disease

value: non small cell lung cancer

value: A to C

value: HIS


title: LM421

tag: egfr activating mutation

value: unknown

tag: egfr mutation exon

value: Exon 21

tag: egfr mutation pattern

value: Yes

value: G to A

value: Transition

value: STOP


title: LM233

value: ASP

value: D