title: EZH2 vs Dam

type: genomic

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: EZH2 samples compared to Dam controls

hyb_protocol: A mixture of fragmented biotinylated DNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Promoter 1.0 R Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing:
MAT (Model-based Analysis for Tiling Arrays) analysis algorithm used to detect regions enriched by immunoprecipitation on Affymetrix tiling array.
The MAT analysis generates two types of output files. Bar-files are binary files containing the MAT score for each probe. Bed-files are text files containing the enriched genomic regions.

molecule: genomic DNA

source_name: HeLa cells, integrated EZH2WT-Dam cassette

label_protocol: Samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Double-Stranded DNA Terminal Labeling Kit.

growth_protocol: Polyclonal stable HeLa cell lines with integrated EZH2-Dam transgenes were generated and grown following standard cell culture procedures, using G418 as selective agent (also: see Vogel et al. 2007 as cited below)

extract_protocol: Genomic DNA was extracted from cells (Sigma GeneElute Mammalian Genomic DNA Minprep kit) and processed according to the DamID protocol published in (Vogel, M.J., Peric-Hupkes, D., and van Steensel, B. 2007. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nature protocols 2(6): 1467-1478.)

treatment_protocol: No additional treatment.

tag: cell line

value: HeLa

tag: transgene

value: integrated EZH2WT-Dam cassette

source_name: HeLa cells, integrated Dam cassette

value: integrated Dam cassette


title: S6 - saline treated mouse, day7, bio rep3

status: Public on Nov 13 2012

type: RNA

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

country: USA

institute: Children's National Medical Center

description: Gene expression data from Balb/c mouse15, treated with saline on day7.

hyb_protocol: Following fragmentation, 15.1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MouseGenome430_2 Array. 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 Affymetric Expression Console program, using PLIER (Probe Logarithmic Intensity Error) algorithm.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: S6 - saline treated mouse, day7

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng mRNA, 2-cycle amplification protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Preparation of NTHi lysates. Bacteria were grown on chocolate agar at 37ºC in 5% CO2 overnight and inoculated in brain heart infusion (BHI) broth supplemented with 3.5 mg of nicotinamide adenine dinucleotide per ml. After overnight incubation, bacteria were subcultured into 5 ml of fresh brain heart infusion (BHI) and upon reaching log phase growth, NTHi were washed and suspended in phosphate-buffered saline (PBS) followed by sonication for lysis.

extract_protocol: Trizol extraction of total RNA, following by RNeasy Mini Kit (Qiagen) columns cleaning, was performed according to the manufacturer's instructions.

treatment_protocol: Three transtympanic inoculation of 6 Balb/c mice middle ears (3 animals, 6 ears) with 50 uL of 300 ug/ml of NTHi bacterial lysate and 6 Balb/c mice middle ears (3 animals, 6 ears) with 50 uL of 1X phosphate buffered saline (PBS) were carried out weekly over 4 weeks (injection on days 7, 14, and 21). On day 28, the mice were euthanized and their bullae harvested.

tag: tissue

value: middle ear epithelial cells

tag: strain

value: Balb/c

tag: age

value: adult


title: S5 - saline treated mouse, day7, bio rep2

description: Gene expression data from Balb/c mouse14, treated with saline on day7.

source_name: S5 - saline treated mouse, day7


title: WT3 - untreated mouse, bio rep 3

description: Gene expression data from Balb/c mouse12, untreated.

source_name: WT3 - untreated mouse


title: WT1 - untreated mouse, bio rep 1

description: Gene expression data from Balb/c mouse10, untreated.

source_name: WT1 - untreated mouse


title: WT2 - untreated mouse, bio rep 2

description: Gene expression data from Balb/c mouse11, untreated.

source_name: WT2 - untreated mouse


title: TP5 vs Dam

description: TP5 samples compared to Dam controls

organism: Homo sapiens

source_name: HeLa cells, integrated EZH2mTP5-Dam cassette

value: integrated EZH2mTP5-Dam cassette


title: N5 - NTHi treated mouse, day 7, bio rep2

description: Gene expression data from Balb/c mouse8, treated with NTHi on day7.

source_name: N5 - NTHi treated mouse, day 7


title: S4 - saline treated mouse, day7, bio rep1

description: Gene expression data from Balb/c mouse13, treated with saline on day7.

source_name: S4 - saline treated mouse, day7


title: Donor 5 p6

status: Public on Nov 14 2012

city: Enschede

first: Jeroen

last: Leijten

address: Drienerlolaan 5

country: Netherlands

institute: University of Twente

description:
Isolated RNA from human chondrocytes after 6 passages
Donor 5 p6

hyb_protocol: Hybridization was processed according to the standard Illumina protocol.

scan_protocol: Beadchips were scanned according to standard protocol using a Illumina iScan array scanner

data_processing:
The data were analyzed with Illumina's Genomestudio v. 2010,1 software with the default settings adviced by Illumina.
All sample probe profiles were exported from Genomestudio and imported into Genespring v11.

source_name: articular chondrocytes

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

growth_protocol: human chondrocytes were seeded at 25,000 cells/cm2 after isolation and splitting. Cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol: Total RNA was isolated using NucleoSpin RNA II kit (Macherey-Nagel).

treatment_protocol: Cells were split, reseeded at 25,000 cells/cm2 and continued to be cultured in identical fresh culture medium up until passage 8

tag: cell type

value: Dedifferentiating chondrocytes

tag: donor

tag: passage


title: Tp53-/- tumor tissue, rep3

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

description:
S1142_9287_p53_T2
Colon tumor tissue from mice treated with Azoxymethane and sacrificed after 16-20 weeks of tumor growth.

hyb_protocol: Affymetrix GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console 1.1 using Affymetrix default analysis settings andRMA as normalization method.

source_name: intestinal mouse tumor tissue, p53 knockout

label_protocol: GeneChip WT Terminal Labelling Kit.

growth_protocol: To delete exon 2-10 of Tp53 in IEC, we crossed floxed Tp53 obtained from the MMHC National Cancer Institute to villin-Cre or villin-CreERT2 mice.

extract_protocol: Total RNA was extracted from  tumor tissue using an RNeasy Mini Kit (Qiagen). For synthesis of cDNA, Superscript II Reverse Transcriptase was used (Invitrogen).

treatment_protocol: Azoxymethane was injected intraperitoneally (i.p.) once a week for 6 weeks at 10mg/kg.

tag: strain/background

value: FvB

value: colon tumor

tag: genotype


title: Tp53-/- tumor tissue, rep2

description:
S1141_9287_p53_T1
Colon tumor tissue from mice treated with Azoxymethane and sacrificed after 16-20 weeks of tumor growth.


title: TREx_Flp_FTO_siRNA_2

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description: Gene expression data from Flp-In™ 293 T-Rex cells after 48h of depletion from FTO

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in a GeneArray Scanner (Agilent).

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

label: Biotin

source_name: Flp-In™ 293 T-Rex

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% FCS, 1% penstrep and appropriate concentration of selective antibiotics

extract_protocol: RNA was extracted using the RNeasy mini kit (QIAGEN), treated with DNase I, followed by cleaning-up on spin columns (RNeasy mini kit. Qiagen)

treatment_protocol: Doxocycline was used to induce expression of integrated FTO copy. siRNA transfection was performed using Lipofectamine 2000 reagent following manufacture's instruction

tag: treatment

value: siRNA trasfected - 48h of depletion from FTO


title: Donor 4 p2

description:
Isolated RNA from human chondrocytes after 2 passages
Donor 4 p2


title: wt tumor tissue, rep 2

description:
S1138_9286_WT_T5
Colon tumor tissue from mice treated with Azoxymethane and sacrificed after 16-20 weeks of tumor growth.

source_name: intestinal mouse tumor tissue, wt

value: wild-type


title: EAS4 vs. Cholesteatoma 4

city: Bielefeld

first: Jörn

last: Kalinowski

address: Universitätsstr. 27

department: Centrum für Biotechnologie

institute: Universität Bielefeld

hyb_protocol: Hybridization to whole human genome microarray gene expression chips (Agilent) and dye swaps (Cy3 and Cy5) were performed for RNA amplified from each specimen.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization. The protocol used was GE2_107_Sep09.

molecule: polyA RNA

source_name: middle ear, auditory canal skin

label_protocol: 500ng of the purified total RNA was subjected to T7-based amplifications using Agilent Amp Labeling Kit to generate fluorescent cRNA. The method uses T7 RNA polymerase, which at the same time amplifies target material and incorporates cyanin 3- or cyanin 5-labeled CTP.

growth_protocol: Acquired cholesteatomas and external auditory canal skin specimens were obtained from patients undergoing middle ear surgery at Klinikum Bielefeld Mitte (Bielefeld, Germany).

extract_protocol: RNA was extracted from cholesteatoma and external auditory canal skin using RNasy Mini Kits (Qiagen, Mississauga, ON, Canada) according to manufacturer’s instructions.

treatment_protocol: All samples (skin and cholesteatoma) were directly placed into liquid nitrogen in the surgical theatre and stored at -80°Cprior to RNA extraction.

value: middle ear, auditory canal skin

tag: disease state

value: cholesteatoma

value: normal


title: N1 - NTHi treated mouse, day 1, bio rep1

description: Gene expression data from Balb/c mouse4, treated with NTHi on day1.

source_name: N1 - NTHi treated mouse, day 1


title: wt tumor tissue, rep 3

description:
S1139_31658_WT_T1
Colon tumor tissue from mice treated with Azoxymethane and sacrificed after 16-20 weeks of tumor growth.


title: N4 - NTHi treated mouse, day 7, bio rep1

description: Gene expression data from Balb/c mouse7, treated with NTHi on day7.

source_name: N4 - NTHi treated mouse, day 7


title: OA-treated, biological rep2

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

country: Canada

institute: University of Guelph

hyb_protocol: For each sample, 100 ng of total RNA was prepared for hybridization to Affymetrix Mouse Gene 1.1 ST array strips, according to the manufacturer’s instructions. Strips were then washed and stained on the Affymetrix GeneAtlas platform.

scan_protocol: Strips were scanned on the Affymetrix GeneAtlas platform.

data_processing: The data was imported into R (version 2.15.0)/Bioconductor (Biobase version 2.16.0) and normalized using the robust multichip average (RMA) implementation in the Affy package (version 1.34.0). Normalized data consists of transcript cluster IDs as identifiers.

source_name: 3T3-L1 preadipocytes_OA-treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA according to the manufacturer's instructions.

growth_protocol: 3T3-L1 preadipocytes were seeded at a density of 6.0x10^4 cells per well in six-well plates. Cells were cultured at 37°C in 5% CO2 in basic media consisting of DMEM supplemented with 5% heat-inactivated FBS and 1% penicillin-streptomycin. Differentiation was induced at 2 days post confluence (i.e. day 0) by adding a standard differentiation cocktail consisting of Dex (1 µM), IMBX (0.5 mM), and insulin (5 µg/ml) to basic media. After 2 days the differentiation media was replaced with maintenance media, which consisted of basic media supplemented with only insulin (5 µg/ml). Maintenance media was changed every 2 days for the reminder of the experiment. On day 7 FBS was removed from the media and the duration of the experiment was conducted in serum-free conditions.

extract_protocol: After the treatment period, total RNA was extracted from differentiated preadipocytes using the Qiagen RNeasy Mini Kit (Qiagen, Mississauga, Ontario, Canada) according to the manufacturer’s protocol. Extracted RNA was quantified using a Nanodrop (Fisher Scientific, Waltham, Massachusetts), and stored at -80oC for future analyses. RNA quality was verified using the Agilent 2100 BioAnalyzer (Agilent Technologies Inc., Santa Clara, CA, USA), and only samples with an RNA integrity number (RIN) greater than 9.0 were used for microarray analyses.

treatment_protocol: Stocks (25mM) of freshly prepared palmitic acid (PA, 16:0), palmitoleic acid (PMA, 16:1n7), stearic acid (SA, 18:0), and oleic acid (OA, 18:1n9) were dissolved in 100% ethanol (Sigma Aldrich, MO, USA). FA stock solutions were subsequently diluted 1:100 in serum-free maintenance media containing 2% (wt/vol) BSA for a final concentration of 250 µM. Differentiated preadipocytes were treated for 48 hrs with the various FA solutions starting on day 8. The control treatment consisted of cells treated with 2% (wt/vol) BSA and a 1:100 dilution of 100% EtOH for 48 hrs.

value: differentiated 3T3-L1 preadipocytes

tag: treated with

value: 250 μM Oleic Acid for 48 hrs

tag: sample group

value: MUFA


title: N3 - NTHi treated mouse, day 1, bio rep3

description: Gene expression data from Balb/c mouse6, treated with NTHi on day1.

source_name: N3 - NTHi treated mouse, day 1


title: Tp53-/- tumor tissue, rep1

description:
S1140_9285_p53_T2
Colon tumor tissue from mice treated with Azoxymethane and sacrificed after 16-20 weeks of tumor growth.


title: OA-treated, biological rep3


title: N2 - NTHi treated mouse, day 1, bio rep2

description: Gene expression data from Balb/c mouse5, treated with NTHi on day1.

source_name: N2 - NTHi treated mouse, day 1


title: N6 - NTHi treated mouse, day 7, bio rep3

description: Gene expression data from Balb/c mouse9, treated with NTHi on day7.

source_name: N6 - NTHi treated mouse, day 7


title: TREx_Flp_Scrambled_siRNA_1

description: Gene expression data from Flp-In™ 293 T-Rex cells treated with scrambled siRNA, after 48h

value: treated with scrambled siRNA, after 48h


title: TREx_Flp_FTO_siRNA_1


title: wt tumor tissue, rep 1

description:
S1137_9286_WT_T2
Colon tumor tissue from mice treated with Azoxymethane and sacrificed after 16-20 weeks of tumor growth.


title: TREx_Flp_Scrambled_siRNA_2


title: FTO2_D4_24h

description: Gene expression data from generated FTO2_D4 clone, 24h after induced espression of integrated copy of the FTO gene

value: FTO


title: FTO2_D4_48h

description: Gene expression data from generated FTO2_D4 clone, 48h after induced espression of integrated copy of the FTO gene


title: SA-treated, biological rep3

source_name: 3T3-L1 preadipocytes_SA-treated

value: 250 μM Stearic Acid for 48 hrs

value: SFA


title: OA-treated, biological rep1


title: SA-treated, biological rep2


title: S2 - saline treated mouse, day 1, bio rep2

description: Gene expression data from Balb/c mouse2, treated with saline on day1.

source_name: S2 - saline treated mouse, day 1

value: middle ear epithelial cells

value: Balb/c

value: adult


title: SA-treated, biological rep4


title: spore of evo39 rep4

city: Rehovot

first: Avihu

last: Yona

address: Hertzel 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institue of Science

data_processing: RMA algorithm in the Matlab bioinformatix toolbox

organism: Saccharomyces cerevisiae

source_name: spore of evo39 rep4

label_protocol: cDNA was prepared using poly(T) primers, labeled cRNA was prepared using the GeneChip system according to manufacture instructions.

growth_protocol: 18 generations of growth in stress-free conditions

extract_protocol: Total RNA using EPICENTER yeast RNA purification

treatment_protocol: before extraction samples were grown to mid log phase

tag: condition

value: spore of evo39

tag: replicate


title: SA-treated, biological rep1


title: FTO2_D4_ni

description: Gene expression data from generated FTO2_D4 clone, not induced

value: noninduced


title: S3 - saline treated mouse, day 1, bio rep3

description: Gene expression data from Balb/c mouse3, treated with saline on day1.

source_name: S3 - saline treated mouse, day 1


title: PMO-treated, biological rep2

source_name: 3T3-L1 preadipocytes_PMO-treated

value: 250 μM Palmitoleic Acid for 48 hrs


title: S1 - saline treated mouse, day1, bio rep1

description: Gene expression data from Balb/c mouse1, treated with saline on day1.

source_name: S1 - saline treated mouse, day1


title: PA-treated, biological rep4

source_name: 3T3-L1 preadipocytes_PA-treated

value: 250 μM Palmitic Acid for 48 hrs


title: control, biological rep3

source_name: 3T3-L1 preadipocytes_Control

value: 2% (wt/vol) BSA and a 1:100 dilution of 100% EtOH for 48 hrs

value: Control


title: PMO-treated, biological rep3


title: PMO-treated, biological rep1


title: control, biological rep4


title: PA-treated, biological rep1


title: PA-treated, biological rep2


title: control, biological rep2


title: PA-treated, biological rep3


title: Donor 5 p2

description:
Isolated RNA from human chondrocytes after 2 passages
Donor 5 p2

source_name: articular chondrocytes

value: Dedifferentiating chondrocytes


title: control, biological rep1

value: differentiated 3T3-L1 preadipocytes


title: FTO1_C1_48h

description: Gene expression data from generated FTO1_C1 clone, 48h after induced espression of integrated copy of the FTO gene

source_name: Flp-In™ 293 T-Rex


title: pulp_unripe3

city: SP

first: Joao

middle: P

last: Fabi

state: SP

address: Avenida Lineu Prestes, 580

department: Departamento de Alimentos e Nutrição Experimental

country: Brazil

institute: USP

description: UNRIPE 3

hyb_protocol: Genomic DNA was hybridized with ATH1-121501 for 16 hours at 45 °C using standard hybridization protocols (Affymetrix©) and analyzed by computed scanning. Using a perl script available at http://affymetrix.arabidopsis.info/xpecies and a range of user-defined threshold values (from 0 to 500), computer files (CDF) were created with papaya genomic DNA hybridization data (mask files). Probe-pairs were retained for analysis if their signal values were greater than the defined threshold. Probe-sets were retained if they contained more than one probe-pair. Purified cRNA (15 μg) were heat-fragmented and hybridized to ATH1-121501 for 16 hours at 45 °C. The complete protocol has already been published (Hammond et al., 2005) and it is available at http://www.plantmethods.com/content/1/1/10.

scan_protocol: GeneChip® arrays were scanned on an Affymetrix G2500A GeneArray scanner and cell intensity files (.cel file) were generated using Microarray Analysis Suite (MAS Version 5.0; Affymetrix).

data_processing:
CEL files were loaded into GeneSpring version 7.2 (Agilent Technologies) software using the Robust Multichip Average (RMA) pre-normalization algorithm. The computer files that were being loaded in GeneSpring were filtered using the CDF files generated using the genomic DNA hybridization. For each replicate array, each probe-set signal value from ripe samples was compared to the probe-set signal value of unripe samples to give gene expression ratios. Differentially expressed genes were identified using one-way ANOVA with a Benjamini and Hochberg false discovery rate multiple testing correction.
Signal calculated by GeneSpring using the normalized CDF file with a threshold value 75 (mask 75) generated after genomic DNA hybridization and differentially expressed genes were identified using one-way ANOVA with a Benjamini and Hochberg false discovery rate multiple testing correction (p<0.05).

organism: Carica papaya

source_name: pulp unripe

label_protocol: Genomic DNA was labelled with the Bioprime DNA labelling System kit (Invitrogen™). Total RNA (5 μg) from papaya pulp was reverse-transcribed to generate first strand cDNA containing a 5'-T7 RNA polymerase promoter sequence. Double stranded cDNA was synthesized using standard protocol, and the resulting samples were in-vitro transcribed by T7 DNA polymerase using biotinylated nucleotides to generate complementary RNAs (cRNAs).

growth_protocol: Papaya fruit (Carica papaya L. cv. ‘Golden’) were harvested at colour break to ¼ yellow (around 150 days after anthesis). One replicate of each unripe and ripe fruit samples for microarray assay was obtained from a previous study in 2007 (Fabi et al., 2007). The other two replicates of unripe and ripe samples for microarray and also for quantitative PCR analyses were obtained in 2010. Soon after harvest, the initial respiration and ethylene levels were determined (Fabi et al., 2007). Each experimental sample (unripe papaya and successive time points during the ripening process) comprised 12 individual fruits. After removal of the peel and seeds, the sliced pulp of each fruit was frozen in liquid N2 and stored at -80°C.

extract_protocol: Genomic DNA and total RNA extraction protocols were the same as previously described (Fabi et al., 2009b). Total RNA was purified using the “RNeasy® Kit” (Qiagen). Nucleic acids were quantified in the NanoDrop® ND-1000 (Nanodrop Technologies©) and gel analyzed to verify their integrity (Sambrook et al., 2000). Total RNA were also analyzed with Agilent 2100 Bioanalyser” (Agilent Technologies©) to confirm its integrity before each hybridization.

tag: cultivar

value: Golden

value: pulp

tag: Stage

value: unripe


title: Identification of miR-200c target genes in renal cell carcinoma, A498

status: Public on Nov 12 2012

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1 Inohana,Chuo-ku

department: School of Medicine

country: Japan

institute: Chiba University

description: Differentially expressed genes by miR-200c transfection.

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software version 9.5.3

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: control miRNA transfected cell line (A498)

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

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

treatment_protocol: microRNA transfection using Lipofectamine RNiMAX (Invitrogen).

tag: cell line

value: renal cell carcinoma

tag: transfected mirna or sirna

value: control

source_name: miR-200c transfected cell line (A498)


title: pulp_ripe3

description: RIPE 3

source_name: pulp ripe

tag: tissue

value: ripe


title: Identification of miR-429 target genes in renal cell carcinoma, A498

description: Differentially expressed genes by miR-429 transfection.

source_name: miR-429 transfected cell line (A498)


title: Identification of miR-206 target genes in renal cell carcinoma, A498

description: Differentially expressed genes by miR-206 transfection.

source_name: miR-206 transfected cell line (A498)


title: Identification of differentially expressed genes by knocking down of TAGLN2 in bladder cancer, BOY

description: Differentially expressed genes by si-TAGLN2 transfection.

source_name: control siRNA transfected cell line (BOY)

value: BOY

value: bladder cancer

source_name: si-TAGLN2 transfected cell line (BOY)


title: Identification of miR-1285 target genes in renal cell carcinoma, 786-O

description: Differentially expressed genes by miR-1285 transfection.

source_name: control miRNA transfected cell line (786-O)

source_name: miR-1285 transfected cell line (786-O)


title: Identification of differentially expressed genes by knocking down of TAGLN2 in bladder cancer, T24

source_name: control siRNA transfected cell line (T24)

source_name: si-TAGLN2 transfected cell line (T24)


title: FTO1_C1_24h

description: Gene expression data from generated FTO1_C1 clone, 24h after induced espression of integrated copy of the FTO gene

tag: transgene

value: FTO


title: Identification of miR-504 target genes in HNSCC, SAS

description: Differentially expressed genes by miR-504 transfection.

value: SAS

tag: cell type

value: head and neck squamous cell carcinoma

source_name: miR-504 transfected cell line (SAS)


title: Identification of miR-1291 target genes in renal cell carcinoma, 786-O

description: Differentially expressed genes by miR-1291 transfection.

source_name: miR-1291 transfected cell line (786-O)


title: FTO1_C1_ni

description: Gene expression data from generated FTO1_C1 clone, not induced

value: noninduced


title: Identification of miR-504 target genes in HNSCC, FaDu

value: FaDu

source_name: miR-504 transfected cell line (FaDu)


title: Identification of miR-1291 target genes in renal cell carcinoma, A498

source_name: miR-1291 transfected cell line (A498)


title: Identification of miR-141 target genes in renal cell carcinoma, caki-1

description: Differentially expressed genes by miR-141 transfection.

source_name: miR-141 transfected cell line (caki-1)


title: Identification of miR-200a target genes in renal cell carcinoma, A498

description: Differentially expressed genes by miR-200a transfection.

source_name: miR-200a transfected cell line (A498)


title: Identification of differentially expressed genes by knocking down of TAGLN2 in HNSCC, FaDu

source_name: control siRNA transfected cell line (FaDu)

source_name: si-TAGLN2 transfected cell line (FaDu)


title: Identification of miR-218 target genes in HNSCC, SAS

description: Differentially expressed genes by miR-218 transfection.

source_name: control miRNA transfected cell line (SAS)

source_name: miR-218 transfected cell line (SAS)


title: Identification of miR-874 target genes in HNSCC, FaDu

description: Differentially expressed genes by miR-874 transfection.

source_name: control miRNA transfected cell line (FaDu)

source_name: miR-874 transfected cell line (FaDu)


title: PMO-treated, biological rep4

source_name: 3T3-L1 preadipocytes_PMO-treated

value: 250 μM Palmitoleic Acid for 48 hrs

value: MUFA


title: Identification of differentially expressed genes by knocking down of TAGLN2 in HNSCC, HSC3

source_name: control siRNA transfected cell line (HSC3)

source_name: si-TAGLN2 transfected cell line (HSC3)


title: Identification of miR-874 target genes in HNSCC, SAS

source_name: miR-874 transfected cell line (SAS)


title: Identification of miR-218 target genes in renal cell carcinoma, A498

source_name: control miRNA transfected cell line (A498)

source_name: miR-218 transfected cell line (A498)


title: Identification of miR-200b target genes in renal cell carcinoma, A498

description: Differentially expressed genes by miR-200b transfection.

source_name: miR-200b transfected cell line (A498)


title: Identification of miR-138 target genes in renal cell carcinoma, A498

description: Differentially expressed genes by miR-138 transfection.

source_name: miR-138 transfected cell line (A498)


title: Identification of miR-375 target genes in esophageal squamous cell carcinoma, T.Tn

description: Differentially expressed genes by miR-375 transfection.

source_name: control miRNA transfected cell line (T.Tn)

value: esophageal squamous cell carcinoma

source_name: miR-375 transfected cell line (T.Tn)


title: Identification of differentially expressed genes by knocking down of FOXA1 in prostate cancer, LNCap [si-FOXA1_1]

description: Differentially expressed genes by si-FOXA1 transfection.

source_name: control siRNA transfected cell line (LNCaP)

value: LNCaP

value: prostate cancer

source_name: si-FOXA1_1 transfected cell line (LNCaP)


title: Identification of miR-141 target genes in renal cell carcinoma, A498

source_name: miR-141 transfected cell line (A498)


title: Identification of miR-429 target genes in renal cell carcinoma, caki-1

source_name: miR-429 transfected cell line (caki-1)


title: Identification of miR-200c target genes in renal cell carcinoma, caki-1

description: Differentially expressed genes by miR-200c transfection.

source_name: miR-200c transfected cell line (caki-1)


title: Identification of miR-145 target genes in HNSCC, IMC-3

description: Differentially expressed genes by miR-145 transfection.

source_name: control miRNA transfected cell line (IMC-3)

source_name: miR-145 transfected cell line (IMC-3)


title: Identification of miR-200a target genes in renal cell carcinoma, caki-1

source_name: miR-200a transfected cell line (caki-1)


title: Identification of miR-1285 target genes in renal cell carcinoma, A498

source_name: miR-1285 transfected cell line (A498)


title: Identification of miR-222 target genes in prostate cancer, PC3

description: Differentially expressed genes by miR-222 transfection.

source_name: control miRNA transfected cell line (PC3)

source_name: miR-222 transfected cell line (PC3)


title: Identification of miR-200b target genes in renal cell carcinoma, caki-1

source_name: control miRNA transfected cell line (A498)

source_name: miR-200b transfected cell line (caki-1)


title: Identification of miR-31 target genes in prostate cancer, PC3

description: Differentially expressed genes by miR-31 transfection.

source_name: miR-31 transfected cell line (PC3)


title: Identification of miR-375 target genes in esophageal squamous cell carcinoma, TE2

source_name: control miRNA transfected cell line (TE2)

source_name: miR-375 transfected cell line (TE2)


title: Identification of miR-218 target genes in HNSCC, FaDu

source_name: control miRNA transfected cell line (FaDu)

source_name: miR-218 transfected cell line (FaDu)


title: Salivary duct carcinoma (SDC) of parotid  gland No.5

extract_protocol: TriZol procedure

tag: tissue type

value: Non-tumorous tissue

value: Tumor tissue

tag: age (yrs)

tag: gender

value: male

tag: histlogical type

value: salivary duct carcinoma

value: IVA


title: colonic CD56-NKp46lowCD117brightCD127bright cells_ rep1

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

description:
Gene expression data from human healthy colonic RORgammat+ ILC cells
EVR_R9-D1_U133_2

hyb_protocol: cRNA were hybridized on Human Genome HG_U133 +2.0 Affymetrix chips according to manufacturer protocol.

scan_protocol: Chip images were generated using Affymetrix AGCC version 3.2 software.

data_processing: Expression data were obtained using Affymetrix Expression Console software (version 1.1).

source_name: healthy colonic RORgammat+ ILC cells

label_protocol: Biotinylated cRNA were prepared following the double amplification protocol of MessagaAmp II aRNA Amplification Kit (Ambion).

extract_protocol: Sorted cells were immediately lysed in RLT buffer supplemented with 10% beta-mercaptoethanol (Quiagen, France). Lysates of three distinct donors were pooled and RNA was isolated by using RNAeasy Microkit (Quiagen, France).

treatment_protocol: Colonic hematopoietic cells were isolated from human healthy colon fragment upon enzymatic digestion with Collagenase VIII (Sigma).

value: colon


title: Salivary duct carcinoma (SDC) of parotid  gland No.4

value: II


title: colonic CD56-NKp46lowCD117brightCD127bright cells_ rep2

description:
Gene expression data from human healthy colonic RORgammat+ ILC cells
EVR_R9-D2_U133_2


title: Identification of differentially expressed genes by knocking down of FOXA1 in prostate cancer, LNCap [si-FOXA1_3]

source_name: control siRNA transfected cell line (LNCaP)

value: control

source_name: si-FOXA1_3 transfected cell line (LNCaP)


title: Salivary duct carcinoma (SDC) of parotid  gland No.2

value: IVC


title: colonic CD56+NKp46+CD117-CD127- cells_rep2

description:
Gene expression data from human healthy colonic NK cells
EVR_R10-D2_U133_2

source_name: healthy colonic NK cells

value: CD56+NKp46+CD117-CD127- cells


title: Identification of miR-375 target genes in HNSCC, IMC-3

source_name: control miRNA transfected cell line (IMC-3)

value: head and neck squamous cell carcinoma

source_name: miR-375 transfected cell line (IMC-3)


title: Hypopharyngeal squamous cell carcinoma (HSCC) No.42

value: moderately differentiated squamous cell carcinoma


title: Hypopharyngeal squamous cell carcinoma (HSCC) No.41

value: III


title: colonic CD56+NKp46+CD117-CD127- cells_rep1

description:
Gene expression data from human healthy colonic NK cells
EVR_R10-D1_U133_2


title: Salivary duct carcinoma (SDC) of parotid  gland No.6


title: Hypopharyngeal squamous cell carcinoma (HSCC) No.37

value: basaloid squamous cell carcinoma


title: Hypopharyngeal squamous cell carcinoma (HSCC) No.3


title: Hypopharyngeal squamous cell carcinoma (HSCC) No.31

value: female


title: Testes

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University

description: Gene expression data of Human testes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were normalized with MAS5 and quantile normalization using R software.
MAS5 and quantile normalization signal intensity. Note that the intensities were converted to a logarithmic scale (base 2). The call in an absolute analysis by MAS5call that indicates if the transcript was present (P), marginal (M) or absent (A).

source_name: pooled Human testes total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).

extract_protocol: Samples of total RNA from Human tissues were purchased from several companies (Clontech, Ambion, Stratagene, Cell Applications). HeLa and SH-SY5Y cells were cultured in standard DMEM / 10% FBS medium. Total RNA was extracted from cells with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.

value: testes

tag: ethnicity

value: caucasian


title: HeLa

description: Gene expression data of Human HeLa cells

source_name: Human HeLa cells total RNA

value: HeLa cells


title: Thyroid

description: Gene expression data of Human thyroid

source_name: pooled Human thyroid total RNA

value: thyroid


title: Trachea

description: Gene expression data of Human trachea

source_name: pooled Human trachea total RNA

value: trachea


title: SHSY5Y

description: Gene expression data of Human SH-SY5Y cells

source_name: Human SH-SY5Y cells total RNA

value: SH-SY5Y cells


title: SpinalCord

description: Gene expression data of Human spinal cord

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: Hypopharyngeal squamous cell carcinoma (HSCC) No.23

value: Non-tumorous tissue

value: Tumor tissue

value: male

value: well differentiated squamous cell carcinoma

value: IVA


title: Hypopharyngeal squamous cell carcinoma (HSCC) No.26


title: Maxillary sinus squamous cell carcinoma (MSSCC) No.40

value: poorly differentiated squamous cell carcinoma

value: IVC


title: Maxillary sinus squamous cell carcinoma (MSSCC) No.78


title: Maxillary sinus squamous cell carcinoma (MSSCC) No.7

value: moderately differentiated squamous cell carcinoma


title: Hypopharyngeal squamous cell carcinoma (HSCC) No.32


title: SmallIntestine

description: Gene expression data of Human small intestine

source_name: pooled Human small intestine total RNA

value: small intestine


title: Hypopharyngeal squamous cell carcinoma (HSCC) No.51


title: Stomach

description: Gene expression data of Human stomach

source_name: pooled Human stomach total RNA

value: stomach


title: SalivaryGland

description: Gene expression data of Human salivary gland

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Lung

description: Gene expression data of Human lung

source_name: pooled Human lung total RNA

value: lung

value: caucasian


title: Maxillary sinus squamous cell carcinoma (MSSCC) No.9


title: Renal cell carcinoma (RCC) No.5

value: clear cell carcinoma


title: Maxillary sinus squamous cell carcinoma (MSSCC) No.6

value: female

value: IVB


title: Maxillary sinus squamous cell carcinoma (MSSCC) No.14


title: Maxillary sinus squamous cell carcinoma (MSSCC) No.1


title: Spleen

description: Gene expression data of Human spleen

source_name: pooled Human spleen total RNA

value: spleen


title: Thymus

description: Gene expression data of Human thymus

source_name: pooled Human thymus total RNA

value: thymus


title: Prostate

description: Gene expression data of Human prostate

source_name: pooled Human prostate total RNA

value: prostate


title: Renal cell carcinoma (RCC) No.4

value: Non-tumorous tissue

value: Tumor tissue

value: male


title: Heart

description: Gene expression data of Human heart

source_name: pooled Human heart total RNA

value: heart


title: Renal cell carcinoma (RCC) No.3


title: SkeletalMuscle

description: Gene expression data of Human skeletal muscle

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: Pancreas

description: Gene expression data of Human pancreas

source_name: pooled Human pancreas total RNA

value: pancreas


title: Renal cell carcinoma (RCC) No.1


title: Uterus

description: Gene expression data of Human uterus

source_name: pooled Human uterus total RNA

value: uterus


title: Colon

description: Gene expression data of Human colon

source_name: pooled Human colon total RNA

value: colon


title: NSPC Overexpressing Bmi1 rep2

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

description:
2DT
NSPC isolated from  neocortices  of Cre/LoxP-based conditional transgenic mouse

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: neural stem/progenitor  cells

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

growth_protocol: Cells were grown in mitogen rich medium (DMEM/F12 from Invitrogen, mouserecombinant EGF 20ng/ml, FGF2 20 ng/ml (both from Peprotech) and 1% B-27 from Invitrogen) in a humidified incubator in normoxic conditions (5% CO2, balance O2 at 37°C).

extract_protocol: Total RNA preparation from NS or NSC cultured in monolayer was performed using Trizol reagent from Invitrogen following the manufacturer’s protocol. RNA was immediately treated with DNaseI (invitrogen) to minimize genomic contamination. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were grown in suspension in proliferation medium. 5 days after plating, the resulting neurospheres were harvested, the pellet was washed with 0.01% DEPC in PBS 1x and immediately snap frozen.

tag: strain

tag: transgenic

value: Overexpressing Bmi1


title: FetalBrain

description: Gene expression data of Human fetal brain

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: Liver

description: Gene expression data of Human liver

source_name: pooled Human liver total RNA

value: liver

value: caucasian


title: Cerebellum

description: Gene expression data of Human cerebellum

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: Kidney

description: Gene expression data of Human kidney

source_name: pooled Human kidney total RNA

value: kidney


title: NSPC Overexpressing Bmi1 rep1

description:
1DT
NSPC isolated from  neocortices  of Cre/LoxP-based conditional transgenic mouse


title: nnrR mutant, SNP rep2

status: Public on Nov 11 2012

city: Bunkyo-ku

first: Hiroyuki

last: Arai

address: Yayoi 1-1-1

department: Department of Biotechnology

institute: The University of Tokyo

description: Gene expression data from R. sphaeroides nnrR mutant after exposure to SNP. It is the second of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Target hybridization, staining, and scanning were performed according to the instructions designed for the Pseudomonas aeruginosa genome array by Affymetrix

scan_protocol: Agilent GeneArray scanner under the control of the Affymetrix GCOS

data_processing: The Affymetrix GeneChip Operating Software was used for data acquisition and processing.

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides nnrR mutant treated with sodium nitroprusside (SNP) replicate 2

label_protocol: cDNA synthesized from total RNA was fragmented and labeled using the Enzo BioArray terminal labeling kit

growth_protocol: R. sphaeroides strains were grown semiaerobically in glass bottles in Sistom’s minimal medium A containing succinate as a carbon source at 30°C. The culture was continuously bubbled with a gas mixture of 97% N2, 2% O2, and 1% CO2.

extract_protocol: Total RNA was extracted by a modified hot-phenol method described in J. Biol. Chem. 279:9146-9155, 2004

treatment_protocol: Total RNA was extracted directly from the culture

tag: genotype

value: nnrR mutant

tag: agent

value: sodium nitroprusside


title: NSPC transgenic control rep1

description:
5CTR
NSPC isolated from  neocortices  of Cre/LoxP-based conditional transgenic mouse

source_name: neural stem/progenitor  cells NSPC

value: Transgenic control


title: BoneMarrow

description: Gene expression data of Human bone marrow

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: nnrR mutant, GSNO rep2

description: Gene expression data from R. sphaeroides nnrR mutant after exposure to GSNO. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides nnrR mutant treated with S-nitrosoglutathione (GSNO) replicate 2

value: S-nitrosoglutathione


title: Renal cell carcinoma (RCC) No.2

value: Non-tumorous tissue

value: Tumor tissue

value: female

value: clear cell carcinoma


title: Cortex

description: Gene expression data of Human cortex

source_name: pooled Human cortex total RNA

value: cortex


title: nnrR mutant, SNP rep1

description: Gene expression data from R. sphaeroides nnrR mutant after exposure to SNP. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides nnrR mutant treated with sodium nitroprusside (SNP) replicate 1


title: NSPC transgenic control rep2

description:
7CTR
NSPC isolated from  neocortices  of Cre/LoxP-based conditional transgenic mouse


title: nnrR mutant, GSNO rep1

description: Gene expression data from R. sphaeroides nnrR mutant after exposure to GSNO. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides nnrR mutant treated with S-nitrosoglutathione (GSNO) replicate 1


title: nnrR mutant, untreated rep2

description: Gene expression data from R. sphaeroides nnrR mutant before exposure to nitrosating reagents. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides nnrR mutant untreated replicate 2

value: untreated


title: blood from HIV resistant women_ML1622

city: winnipge

first: binhua

last: liang

address: 1015 Arlington Street

institute: National Microbiology Laboratory

description:
Gene expression data from whole blood of HIV resistant women
ML1622.CHP
ML1622.CEL

hyb_protocol: done in the Centre For Applied Genomics, Hospitals for Sick Children, Toronto.

data_processing: Background substraction and probe signal summarization was analyzed uing R Bioconductor software. And the data were analyzed by Affymetrix MAS5 package, followed by Array Assist software. The ratio of the genometic means of expression analysis of the relevant genes to estimate P values and a P value of 0.05 or less were considered significant.  Only genes with differences between the resistance and mormal controls > 1.3 fold and p value of 0.005  and called as present in at least 50% of the samples tested were considered as differentially expressed.

source_name: human blood in HIV resistant women

extract_protocol: Total RNA was extracted in Nairobi according to the manufacturer's protocol (Qiagen)

value: whole blood

tag: hiv status

value: HIV resistant


title: blood from HIV resistant women_ML1589

description:
Gene expression data from whole blood of HIV resistant women
ML1589.CHP
ML1589.CEL

scan_protocol: done in the Centre For Applied Genomics, Hospitals for Sick Children, Toronto.


title: blood from HIV resistant women_ML1643

description:
Gene expression data from whole blood of HIV resistant women
ML1643.CHP
ML1643.CEL

label_protocol: done in the Centre For Applied Genomics, Hospitals for Sick Children, Toronto.


title: blood from HIV resistant women_ML1764

description:
Gene expression data from whole blood of HIV resistant women
ML1764.CHP
ML1764.CEL


title: blood from HIV resistant women_ML1705

description:
Gene expression data from whole blood of HIV resistant women
ML1705.CHP
ML1705.CEL


title: blood from HIV resistant women_ML1356

description:
Gene expression data from whole blood of HIV resistant women
ML1356.CHP
ML1356.CEL


title: nnrR mutant, untreated rep1

description: Gene expression data from R. sphaeroides nnrR mutant before exposure to nitrosating reagents. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides nnrR mutant untreated replicate 1


title: blood from HIV resistant women_ML1362

description:
Gene expression data from whole blood of HIV resistant women
ML1362.CHP
ML1362.CEL


title: blood from HIV resistant women_ML1769

description:
Gene expression data from whole blood of HIV resistant women
ML1769.CHP
ML1769.CEL


title: blood from HIV resistant women_ML1732

description:
Gene expression data from whole blood of HIV resistant women
ML1732.CHP
ML1732.CEL


title: blood from HIV resistant women_ML1437

description:
Gene expression data from whole blood of HIV resistant women
ML1437.CHP
ML1437.CEL


title: blood from HIV resistant women_ML1515

description:
Gene expression data from whole blood of HIV resistant women
ML1515.CHP
ML1515.CEL


title: blood from HIV resistant women_ML1601

description:
Gene expression data from whole blood of HIV resistant women
ML1601.CHP
ML1601.CEL


title: blood from HIV resistant women_ML1766

description:
Gene expression data from whole blood of HIV resistant women
ML1766.CHP
ML1766.CEL


title: blood from HIV resistant women_ML1482

description:
Gene expression data from whole blood of HIV resistant women
ML1482.CHP
ML1482.CEL


title: blood from HIV resistant women_ML1573

description:
Gene expression data from whole blood of HIV resistant women
ML1573.CHP
ML1573.CEL


title: R. sphaeroides 2.4.1, SNP rep2

description: Gene expression data from R. sphaeroides 2.4.1 after exposure to SNP. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides 2.4.1 wild type treated with sodium nitroprusside (SNP) replicate 2

value: wild type


title: blood from HIV resistant women_ML1358

description:
Gene expression data from whole blood of HIV resistant women
ML1358.CHP
ML1358.CEL


title: blood from HIV resistant women_ML1327

description:
Gene expression data from whole blood of HIV resistant women
ML1327.CHP
ML1327.CEL


title: blood from HIV resistant women_ML1376

description:
Gene expression data from whole blood of HIV resistant women
ML1376.CHP
ML1376.CEL


title: blood from HIV resistant women_ML1286

description:
Gene expression data from whole blood of HIV resistant women
ML1286.CHP
ML1286.CEL


title: blood from HIV resistant women_ML1529

description:
Gene expression data from whole blood of HIV resistant women
ML1529.CHP
ML1529.CEL


title: R. sphaeroides 2.4.1, SNP rep1

description: Gene expression data from R. sphaeroides 2.4.1 after exposure to SNP. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides 2.4.1 wild type treated with sodium nitroprusside (SNP) replicate 1


title: blood from HIV resistant women_ML1266

description:
Gene expression data from whole blood of HIV resistant women
ML1266.CHP
ML1266.CEL


title: R. sphaeroides 2.4.1, untreated rep1

description: Gene expression data from R. sphaeroides 2.4.1 before exposure to nitrosating reagents. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides 2.4.1 wild type untreated replicate 1


title: R. sphaeroides 2.4.1, GSNO rep1

description: Gene expression data from R. sphaeroides 2.4.1 after exposure to GSNO. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides 2.4.1 wild type treated with S-nitrosoglutathione (GSNO) replicate 1


title: R. sphaeroides 2.4.1, untreated rep2

description: Gene expression data from R. sphaeroides 2.4.1 before exposure to nitrosating reagents. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides 2.4.1 wild type untreated replicate 2


title: blood from HIV resistant women_ML0767

description:
Gene expression data from whole blood of HIV resistant women
ML0767.CHP
ML0767.CEL


title: blood from HIV resistant women_ML0935

description:
Gene expression data from whole blood of HIV resistant women
ML0935.CHP
ML0935.CEL


title: blood from HIV resistant women_ML1025

description:
Gene expression data from whole blood of HIV resistant women
ML1025.CHP
ML1025.CEL


title: blood from HIV resistant women_ML0893

description:
Gene expression data from whole blood of HIV resistant women
ML0893.CHP
ML0893.CEL


title: blood from HIV resistant women_ML1260

description:
Gene expression data from whole blood of HIV resistant women
ML1260.CHP
ML1260.CEL


title: blood from HIV resistant women_ML1275

description:
Gene expression data from whole blood of HIV resistant women
ML1275.CHP
ML1275.CEL


title: blood from HIV resistant women_ML0887

description:
Gene expression data from whole blood of HIV resistant women
ML0887.CHP
ML0887.CEL


title: blood from HIV resistant women_ML0881

description:
Gene expression data from whole blood of HIV resistant women
ML0881.CHP
ML0881.CEL


title: Leaves of R2 drought plant #13

status: Public on Nov 10 2012

city: Yokohama

first: Dung

middle: Tien

last: Le

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Plant Science Center

institute: RIKEN Yokohama Institute

hyb_protocol: Each sample was hybridized to an Affymetrix Soybean Gene 1.0 ST array by standard procedures.

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Raw data from .CEL files were initially analyzed by Affymetrix Expression Console with library files supplied by Affymetrix. Analysis was done using the RMA method for gene levels without normalization. The log2 transformed data were exported individually for use in analysis in GeneSpring software. The data in text format were imported to GeneSping software and normalized using a 75 percentage threshhold.
T-test was used to analyze for statistical significance of the same gene in different conditions. To further increase the reliability, multivarate test, FDR, was used to calculate for the corrected p-values. All of these tests were performed with GeneSpring GX11 software.

organism: Glycine max

source_name: 3rd trifoliate counting from shoots, R2 reproductive stage, drought

label_protocol: Samples were fragmented and end-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit according to the manufacturer's instructions.

growth_protocol: Soybean plants (cv. Williams 82) were grown in pots (3 plants per 6-liter pot) containing supermix (Supermix A, Sakata, Japan). Water was given to the pots once a day until the plants reached the R1 stage (started flowering) under greenhouse conditions (continuous 30°C temperature, photoperiod of 12 h/12 h, 80 µmol m−2 s−1 photon flux density and 50% relative humidity).

extract_protocol: Soybean leaves were collected and quickly frozen in liquid nitrogen, and stored at -80oC. Total RNA was extracted using Trizol reagent, and DNase I treatment was performed prior to quality assessment using an Agilent 2100 Bioanalyzer. All samples were prepared using the Ambion WT expression kit for cDNA synthesis, cRNA amplification, and conversion to sense strand cDNA according to the manufacturer's instructions.

treatment_protocol: Soybean plants at the R1 stage (start flowering) were withheld from watering for 5 days in the drought-treated pot. In the control pot, water (well water) was given as usual.

tag: cultivar

value: Williams 82

value: 3rd trifoliate

tag: growth stage

value: R2 reproductive stage

tag: treatment

value: water withholding


title: Leaves of R2 drought plant #12


title: blood from HIV resistant women_ML0556

description:
Gene expression data from whole blood of HIV resistant women
ML0556.CHP
ML0556.CEL


title: blood from HIV resistant women_ML0466

description:
Gene expression data from whole blood of HIV resistant women
ML0466.CHP
ML0466.CEL


title: Leaves of R2 well water plant #4

source_name: 3rd trifoliate counting from shoots, R2 reproductive stage, well water

value: well water


title: R. sphaeroides 2.4.1, GSNO rep2

description: Gene expression data from R. sphaeroides 2.4.1 after exposure to GSNO. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: R. sphaeroides 2.4.1 wild type treated with S-nitrosoglutathione (GSNO) replicate 2


title: Leaves of R2 drought plant #11


title: Leaves of R2 well water plant #1


title: Leaves of R2 well water plant #3


title: HBL-1

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

description: Gene expression data from a DLBCL cell line.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.

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

data_processing: Data were normalized with Bioconductor software using the RMA algorithm.

source_name: Diffuse large B-cell lymphoma cell line HBL1

label_protocol: The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin at 37ºC and 5% CO2.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: No treatment was performed.

tag: cell line

value: diffuse large B-cell lymphoma (DLBCL) cells

tag: tumor subtype

value: activated B-cell like


title: SSK-41_R2

description: Gene expression data from an SMZL cell line.

source_name: Splenic marginal zone lymphoma cell line SSK41

value: splenic marginal zone lymphoma cells


title: OCI-Ly-10

source_name: Diffuse large B-cell lymphoma cell line OCI-Ly10

growth_protocol: Cells were grown in IMDM supplemented with 20% human serum, 55 mM b-mercaptoethanol, 200 units/mL of penicillin and 200 mg/mL of streptomycin at 37ºC and 5% CO2.


title: VL-51_R2

source_name: Splenic marginal zone lymphoma cell line VL51


title: OCI-Ly-3

source_name: Diffuse large B-cell lymphoma cell line OCI-Ly3


title: SSK-41_R1


title: OCI-Ly-1

source_name: Diffuse large B-cell lymphoma cell line OCI-Ly1

growth_protocol: Cells were grown in IMDM supplemented with 10% fetal bovine serum, 200 units/mL of penicillin and 200 mg/mL of streptomycin at 37ºC and 5% CO2.


title: U-2932

source_name: Diffuse large B-cell lymphoma cell line U2932


title: VL-51_R1


title: KARPAS-1718_R1

source_name: Splenic marginal zone lymphoma cell line KARPAS-1718


title: KARPAS-1718_R2


title: SU-DHL-7

source_name: Diffuse large B-cell lymphoma cell line SUDHL7

growth_protocol: Cells were grown in RPMI 1640 10 mM HEPES supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin at 37ºC and 5% CO2.

value: germinal center B-cell like


title: OCI-Ly-4

source_name: Diffuse large B-cell lymphoma cell line OCI-Ly4

growth_protocol: Cells were grown in IMDM supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin at 37ºC and 5% CO2.


title: PFEIFFER

source_name: Diffuse large B-cell lymphoma cell line PFEIFFER

value: PFEIFFER


title: HLY-1

source_name: Diffuse large B-cell lymphoma cell line HLY1


title: FARAGE

source_name: Diffuse large B-cell lymphoma cell line FARAGE

value: FARAGE


title: TOLEDO

source_name: Diffuse large B-cell lymphoma cell line TOLEDO

value: TOLEDO


title: NU-DHL-1

source_name: Diffuse large B-cell lymphoma cell line NUDHL1

growth_protocol: Cells were grown in RPMI 1640 supplemented with 20% heat-inactivated fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin  at 37ºC and 5% CO2.


title: OCI-Ly-7

source_name: Diffuse large B-cell lymphoma cell line OCI-Ly7


title: DOHH-2

source_name: Diffuse large B-cell lymphoma cell line DOHH2


title: pb treated mouse 3 liver 5mC profile (91d)

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: PB exposed mouse liver tissue

hyb_protocol: Labelled samples were applied commercially to a Nimblegen 2.1M Deluxe promoter array by Nimblegen, Iceland

scan_protocol: Arrays were scanned commercially by Nimblegen, Iceland

data_processing: Pair files normalised within arrays (loess), normalised between arrays (sclae normalisation), log2(IP/input)

source_name: 91 day PB exposed whole liver

label_protocol: Amplification of DNA samples was carried out commercially by NimbleGen, Iceland  (Cy5- (IP) or Cy3- (Input) labelled)

growth_protocol: PB exposed mouse liver tissue

extract_protocol: Genomic DNA (5mC-IP - 2.5 µg in 450 µl TE), sonicated to yield a fragment distribution of approximately 300-1000 bp, was denatured by incubation at 100°C for 10 min. Samples were rapidly chilled on wet-ice. At this point, 45 µl (10%) of denatured sample was removed and saved as input, and 45 µl of 10X IP buffer (100 mM Na-Phosphate pH 7.0  (mono and dibasic), 1.4 M NaCl, 0.5 % Triton X-100) and 1 µg of -5mC (ActiveMotif; #39769) antibody were added to the remaining sample. Samples were incubated at 4C with gentle agitation overnight. Then, 40 µl of magnetic beads (Dynabeads® Protein G, Invitrogen, UK) in 1X IP buffer were added to each sample to allow magnetic separation of the antibody from the unbound DNA using a magnetic tube rack. Samples were incubated at 4C for 1 hr with gentle agitation. Beads were collected with a magnetic rack and washed with 1000 µl of 1X IP buffer at RT for 10 min with gentle agitation; washing was repeated three times. Beads were collected with a magnetic rack and re-suspended in 250 µl of digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA , 0.5 % SDS) followed by addition of 10 µl of proteinase K  (20 mg/ml; Roche Applied Science, Mannheim, Germany) and incubation at 52C for 1.5 hr with constant shaking (≥800 rpm). Finally, beads were removed using a magnetic rack and DNA was purified from the remaining sample using a QIAquick PCR Purification Kit (QIAGEN,CA, USA), eluting in a final volume of 40 µl dH2O. Inputs were also purified using a QIAquick PCR Purification Kit and eluted in 40 µl dH2O. Subsequently, 10 ng of input and IP DNA was subjected to whole genome amplification (WGA) using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, UK) as per the manufacturer's instructions. Amplified DNA was run on a 1.2% agarose gel to confirm consistency of fragment size between samples.

treatment_protocol: genomic DNA extracted from mouse liver following 91 day exposed to Phenobarbital

value: M

tag: antibody

tag: antibody manufacturer

value: Eurogentec

value: phenobarbital

tag: tissue

value: liver

tag: time

source_name: PB exposed mouse liver tissue

value: none (Input)


title: PR-1

source_name: Diffuse large B-cell lymphoma cell line PR1

tag: cell type


title: pb treated mouse 3 liver 5mC profile (1d)

description: PB exposed mouse liver tissue

source_name: 1 day PB exposed whole liver

treatment_protocol: genomic DNA extracted from mouse liver following 1 day exposed to Phenobarbital

tag: gender


title: control mouse 3 liver 5mC profile (91d)

description: normal whole liver genomic DNA

source_name: normal whole liver

growth_protocol: normal mouse liver tissue

treatment_protocol: genomic DNA extracted from normal mouse liver

value: control


title: pb treated mouse 4 liver 5mC profile (1d)

description: PB exposed mouse liver tissue


title: OCI-Ly-19

source_name: Diffuse large B-cell lymphoma cell line OCI-Ly19


title: pb treated mouse 5 liver 5mC profile (91d)

description: PB exposed mouse liver tissue


title: control mouse 1 liver 5mC profile (91d)

description: normal whole liver genomic DNA


title: pb treated mouse 4 liver 5mC profile (91d)

description: PB exposed mouse liver tissue


title: pb treated mouse 2 liver 5mC profile (1d)

description: PB exposed mouse liver tissue


title: control mouse 2 liver 5mC profile (91d)

description: normal whole liver genomic DNA


title: control mouse 4 liver 5mC profile (91d)

description: normal whole liver genomic DNA


title: SC-1

source_name: Diffuse large B-cell lymphoma cell line SC1


title: ROS-50

source_name: Diffuse large B-cell lymphoma cell line ROS50


title: 380

source_name: Diffuse large B-cell lymphoma cell line 380


title: DB

source_name: Diffuse large B-cell lymphoma cell line DB

value: DB


title: SU-DHL-4

source_name: Diffuse large B-cell lymphoma cell line SUDHL4


title: pb treated mouse 5 liver 5mC profile (7d)

description: PB exposed mouse liver tissue

source_name: 7 day PB exposed whole liver

treatment_protocol: genomic DNA extracted from mouse liver following 7 day exposed to Phenobarbital


title: control mouse 1 liver 5mC profile (1d)

description: normal whole liver genomic DNA


title: pb treated mouse 4 liver 5mC profile (7d)

description: PB exposed mouse liver tissue


title: pb treated mouse 5 liver 5mC profile (1d)

description: PB exposed mouse liver tissue


title: control mouse 5 liver 5mC profile (7d)

description: normal whole liver genomic DNA


title: pb treated mouse 2 liver 5mC profile (7d)

description: PB exposed mouse liver tissue


title: OCI-Ly-8

source_name: Diffuse large B-cell lymphoma cell line OCI-Ly8


title: control mouse 5 liver 5mC profile (91d)

description: normal whole liver genomic DNA


title: pb treated mouse 1 liver 5mC profile (1d)

description: PB exposed mouse liver tissue


title: control mouse 3 liver 5mC profile (1d)

description: normal whole liver genomic DNA


title: SU-DHL-8

source_name: Diffuse large B-cell lymphoma cell line SUDHL8


title: RCK-8

source_name: Diffuse large B-cell lymphoma cell line RCK8


title: control mouse 5 liver 5mC profile (1d)

description: normal whole liver genomic DNA


title: SU-DHL-5

source_name: Diffuse large B-cell lymphoma cell line SUDHL5


title: control mouse 3 liver 5mC profile (7d)

description: normal whole liver genomic DNA


title: control mouse 2 liver 5mC profile (1d)

description: normal whole liver genomic DNA


title: KARPAS-422

source_name: Diffuse large B-cell lymphoma cell line KARPAS-422


title: NUDUL-1

source_name: Diffuse large B-cell lymphoma cell line NUDUL1


title: SU-DHL-6

source_name: Diffuse large B-cell lymphoma cell line SUDHL6


title: pb treated mouse 1 liver 5mC profile (91d)

description: PB exposed mouse liver tissue

source_name: 91 day PB exposed whole liver

source_name: PB exposed mouse liver tissue


title: SU-DHL-10

source_name: Diffuse large B-cell lymphoma cell line SUDHL10


title: KARPAS-231

source_name: Diffuse large B-cell lymphoma cell line KARPAS-231


title: SU-DHL-16

source_name: Diffuse large B-cell lymphoma cell line SUDHL16


title: 8µg/ml_T_rep3

city: Wuhan

first: Liu

last: yingyu

address: Hongshan district, No.1

country: China

institute: Huazhong agricultural university

description: Gene expression in H. parasuis SH0165 induced by 8µg/ml tilmicosin group 3.

hyb_protocol: 875 ng of Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 2.2 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 11 µl of 10x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the Agilent H. parasuis Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using twice scan Dye channel is set to Green PMT is set to 100% and 10% (4x44k array slides, Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) running Normalize. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data were normalized using the quantile method.

organism: Glaesserella parasuis SH0165

source_name: 8µg/ml tilmicosin group

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 4 ug cRNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: TRIzol (Invitrogen Life Technologies, USA) was used for RNA extraction and total RNA was extracted according to the QIAGEN RNeasy mini kit (QIAGEN, USA).

treatment_protocol: H. parasuis SH0165 was induced by 0.25µg/ml tilmicosin at OD600 >0.3 for 16 hours, or by 8µg/ml tilmicosin at OD600 >0.3 for 50 mins. The control group was normal culture with no tilmicosin at OD600 >0.3 for 12 hours. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: 8µg/ml tilmicosin


title: pb treated mouse 1 liver 5mC profile (7d)

description: PB exposed mouse liver tissue


title: 8µg/ml_T_rep2

description: Gene expression in H. parasuis SH0165 induced by 8µg/ml tilmicosin group 2.


title: 0.25µg/ml_T_rep3

description: Gene expression in H. parasuis SH0165 induced by 0.25µg/ml tilmicosin group 3.

source_name: 0.25µg/ml tilmicosin group

value: 0.25µg/ml tilmicosin


title: VAL

source_name: Diffuse large B-cell lymphoma cell line VAL

value: VAL


title: WSU-DLCL-2

source_name: Diffuse large B-cell lymphoma cell line WSU-DLCL2

value: diffuse large B-cell lymphoma (DLBCL) cells


title: control mouse 2 liver 5mC profile (7d)

description: normal whole liver genomic DNA

source_name: normal whole liver


title: 0.25µg/ml_T_rep2

description: Gene expression in H. parasuis SH0165 induced by 0.25µg/ml tilmicosin group 2.


title: 8µg/ml_T_rep1

description: Gene expression in H. parasuis SH0165 induced by 8µg/ml tilmicosin group 1.


title: WSU-NHL

source_name: Diffuse large B-cell lymphoma cell line WSU-NHL

value: WSU-NHL


title: 0.25µg/ml_T_rep1

description: Gene expression in H. parasuis SH0165 induced by 0.25µg/ml tilmicosin group 1.


title: pb treated mouse 3 liver 5mC profile (7d)

description: PB exposed mouse liver tissue

source_name: 7 day PB exposed whole liver


title: RIVA

source_name: Diffuse large B-cell lymphoma cell line RIVA

value: RIVA

value: activated B-cell like


title: MD-901

source_name: Diffuse large B-cell lymphoma cell line MD901


title: control group_rep2

description: Gene expression in H. parasuis SH0165 control group 2.

source_name: Control group


title: control mouse 4 liver 5mC profile (7d)

description: normal whole liver genomic DNA


title: control group_rep1

description: Gene expression in H. parasuis SH0165 control group 1.


title: RL

source_name: Diffuse large B-cell lymphoma cell line RL

value: RL

value: germinal center B-cell like


title: control group_rep3

description: Gene expression in H. parasuis SH0165 control group 3.


title: pb treated mouse 5 liver 5hmC profile (91d)

description: PB exposed mouse liver tissue

extract_protocol: Genomic DNA (5hmC-IP - 2.5 µg in 450 µl TE), sonicated to yield a fragment distribution of approximately 300-1000 bp, was denatured by incubation at 100°C for 10 min. Samples were rapidly chilled on wet-ice. At this point, 45 µl (10%) of denatured sample was removed and saved as input, and 45 µl of 10X IP buffer (100 mM Na-Phosphate pH 7.0  (mono and dibasic), 1.4 M NaCl, 0.5 % Triton X-100) and 1 µg of -5hmC (ActiveMotif; #39769) antibody were added to the remaining sample. Samples were incubated at 4C with gentle agitation overnight. Then, 40 µl of magnetic beads (Dynabeads® Protein G, Invitrogen, UK) in 1X IP buffer were added to each sample to allow magnetic separation of the antibody from the unbound DNA using a magnetic tube rack. Samples were incubated at 4C for 1 hr with gentle agitation. Beads were collected with a magnetic rack and washed with 1000 µl of 1X IP buffer at RT for 10 min with gentle agitation; washing was repeated three times. Beads were collected with a magnetic rack and re-suspended in 250 µl of digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA , 0.5 % SDS) followed by addition of 10 µl of proteinase K  (20 mg/ml; Roche Applied Science, Mannheim, Germany) and incubation at 52C for 1.5 hr with constant shaking (≥800 rpm). Finally, beads were removed using a magnetic rack and DNA was purified from the remaining sample using a QIAquick PCR Purification Kit (QIAGEN,CA, USA), eluting in a final volume of 40 µl dH2O. Inputs were also purified using a QIAquick PCR Purification Kit and eluted in 40 µl dH2O. Subsequently, 10 ng of input and IP DNA was subjected to whole genome amplification (WGA) using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, UK) as per the manufacturer's instructions. Amplified DNA was run on a 1.2% agarose gel to confirm consistency of fragment size between samples.

value: Active Motif


title: VAL, LITAF-specific siRNA, REP3

description:
VAL_siRNA_R3
Gene expression data from a DLBCL cell line.

source_name: DLBCL cell line VAL transfected with a LITAF-specific siRNA

growth_protocol: Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.

treatment_protocol: Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.

value: LITAF-specific siRNA


title: pb treated mouse 1 liver 5hmC profile (91d)

description: PB exposed mouse liver tissue

source_name: 91 day PB exposed whole liver

value: M


title: VAL, LITAF-specific siRNA, REP2

description:
VAL_siRNA_R2
Gene expression data from a DLBCL cell line.


title: VAL, non-targeting siRNA, REP3

description:
VAL_SC_R3
Gene expression data from a DLBCL cell line.

source_name: DLBCL cell line VAL transfected with a non-targeting siRNA

value: non-targeting siRNA


title: pb treated mouse 3 liver 5hmC profile (91d)

description: PB exposed mouse liver tissue

value: phenobarbital

value: liver

source_name: PB exposed mouse liver tissue


title: VAL, LITAF-specific siRNA, REP1

description:
VAL_siRNA_R1
Gene expression data from a DLBCL cell line.


title: HT

source_name: Diffuse large B-cell lymphoma cell line HT

value: HT


title: control mouse 5 liver 5hmC profile (91d)

description: normal whole liver genomic DNA

value: control

value: none (Input)


title: pb treated mouse 2 liver 5hmC profile (91d)

description: PB exposed mouse liver tissue


title: control mouse 4 liver 5hmC profile (91d)

description: normal whole liver genomic DNA


title: control mouse 4 liver 5mC profile (1d)

description: normal whole liver genomic DNA

value: Eurogentec


title: WT-2

city: La Jolla

first: Anton

last: Maximov

state: CA

address: 10550 North Torrey Pines DNC216

department: Cell Biology, Dorris Neuroscience Center

institute: The Scripps Research Institute

hyb_protocol: Hybridization was performed using standard procedures recommended by Affymetrix

scan_protocol: Scanning was performed using standard procedures recommended by Affymetrix

data_processing:
Data was normalized using RMA express 1.0 (http://rmaexpress.bmbolstad.com); The sample clustering was performed using BRB-Array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html); The ComBat function was used to adjust for batch effect (Johnson et al., 2007);
The Limma and Rank products methods were used to identify statistically significant differentially expressed transcripts.

source_name: Cortical neurons expressing WT HDAC4

label_protocol: Labeling was performed using standard procedures recommended by Affymetrix

growth_protocol: Neurons were isolated from the cortex of P0 mice, dissociated with Trypsin and seeded into Matrigel-coated plates. Cultures were maintained in MEM supplemented with B27, Glucose, Transferrin and AraC

extract_protocol: Total RNA was isolated with RNAeasy kit (Qiagen)

treatment_protocol: Neurons were infected at 5DIV and analyzed at 14DIV

value: mixed C57BL6/129SV

value: cultured cortical neurons

tag: age


title: control mouse 3 liver 5hmC profile (91d)

description: normal whole liver genomic DNA


title: WT-1

tag: strain


title: control mouse 2 liver 5hmC profile (91d)

description: normal whole liver genomic DNA


title: WT-3


title: 3SA-3

source_name: Cortical neurons expressing 3SA HDAC4


title: KARPAS-231, LITAF-specific siRNA, REP3

description:
KARPAS-231_siRNA_R3
Gene expression data from a DLBCL cell line.

source_name: DLBCL cell line KARPAS-231 transfected with a LITAF-specific siRNA

value: diffuse large B-cell lymphoma (DLBCL) cells


title: 3SA-2


title: OZ

source_name: Diffuse large B-cell lymphoma cell line OZ

value: OZ


title: pb treated mouse 4 liver 5hmC profile (1d)

description: PB exposed mouse liver tissue

source_name: 1 day PB exposed whole liver


title: KARPAS-231, LITAF-specific siRNA, REP2

description:
KARPAS-231_siRNA_R2
Gene expression data from a DLBCL cell line.


title: VAL, non-targeting siRNA, REP2

description:
VAL_SC_R2
Gene expression data from a DLBCL cell line.

value: VAL


title: 3SA-1


title: KARPAS-231, LITAF-specific siRNA, REP1

description:
KARPAS-231_siRNA_R1
Gene expression data from a DLBCL cell line.


title: LPS activated spleen with IFN-alpha pretreament (4-3)

type: protein

city: harbin

first: Huayang

last: Pan

state: heilongjiang

address: youzheng street

department: general  surgery

institute: The First Affiliated Hospital of Harbin Medical University

description: test

hyb_protocol: see linked Experimental Procedures PDF file see linked Experimental Procedures PDF file

scan_protocol: By comparing the signal intensities, relative expression levels of cytokines can be made. The intensities of signals can be quantified by densitometry. Positive control can be used to normalize the results from different membranes being compared.

data_processing:
The relative gray value of microarray has been recorded in the attached excel table, control group includes 1-1, 1-2 and1-3, IFN-α group includes 2-1, 2-2 and2-3, LPS group includes 3-1, 3-2 and3-3, IFN-α+ LPS group includes 4-1, 4-2 and4-3, cytokines in every two groups have been compared by paired- samples T-Test, which is detailed in the excel table.
Normalization was performed against housekeeping genes.
Fold Change worksheet reports IFN-α/control,  IFN-α+LPS/LPS. Fold change ＞ 1.5 and P ＜0.05 were thought to be differential expression.

molecule: protein

source_name: C57BL/6 mice derived spleen, IFN-α+LPS

treatment_protocol: 12 wild-type C57BL/6 (B6) mice were divided into 4 groups: control group, IFN-α group, LPS group, and IFN-α+ LPS group, every group contained 3 mice (n=3). IFN-α was administrated i.p. to IFN-α group and IFN-α+ LPS group once daily (QD) for 7 days at a dose of 105units/kg weight, PBS was administrated i.p. to control group and LPS group QD for 7 days at the same volume. LPS group and IFN-α+ LPS group were injected i.v. with 10 μg LPS for one mouse on the 8th day. Control group and IFN-α group were injected i.v. with PBS at the same volume. 6 h later, mice were sacrificed to harvest spleens for protein microarray experiment

tag: background strain

value: male

value: spleen


title: pb treated mouse 3 liver 5hmC profile (1d)

description: PB exposed mouse liver tissue

value: Active Motif


title: KARPAS-231, non-targeting siRNA, REP3

description:
KARPAS-231_SC_R3
Gene expression data from a DLBCL cell line.

source_name: DLBCL cell line KARPAS-231 transfected with a non-targeting siRNA


title: LPS activated spleen with IFN-alpha pretreament (4-1)

description: test

label_protocol: see linked Experimental Procedures PDF file


title: pb treated mouse 5 liver 5hmC profile (1d)

description: PB exposed mouse liver tissue


title: pb treated mouse 1 liver 5hmC profile (1d)

description: PB exposed mouse liver tissue


title: KARPAS-231, non-targeting siRNA, REP2

description:
KARPAS-231_SC_R2
Gene expression data from a DLBCL cell line.


title: LPS activated spleen (3-3)

description: test

source_name: C57BL/6 mice derived spleen, LPS

extract_protocol: see linked Experimental Procedures PDF file


title: control mouse 5 liver 5hmC profile (1d)

description: normal whole liver genomic DNA

source_name: normal whole liver


title: KARPAS-231, non-targeting siRNA, REP1

description:
KARPAS-231_SC_R1
Gene expression data from a DLBCL cell line.


title: LPS activated spleen with IFN-alpha pretreament (4-2)

description: test


title: SC-1 with doxycycline-induced LITAF expression REP2

description:
SC1_LITAF_DOX_R2
Gene expression data from a DLBCL cell line.

source_name: DLBCL cell line SC-1 stably transfected with a tetracycline-inducible LITAF expression vector, presence of doxycycline

value: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector

value: doxycycline


title: LPS activated spleen (3-2)

description: test


title: VAL, non-targeting siRNA, REP1

description:
VAL_SC_R1
Gene expression data from a DLBCL cell line.

value: non-targeting siRNA


title: pb treated mouse 2 liver 5mC profile (91d)

description: PB exposed mouse liver tissue

value: M

value: phenobarbital


title: LPS activated spleen (3-1)

description: test


title: pb treated mouse 2 liver 5hmC profile (1d)

description: PB exposed mouse liver tissue

value: liver


title: IFN-alpha treated spleen (2-3)

description: test

source_name: C57BL/6 mice derived spleen, IFN-α


title: SC-1 with doxycycline-induced LITAF expression REP1

description:
SC1_LITAF_DOX_R1
Gene expression data from a DLBCL cell line.


title: WB muscle, biological replicate 4

city: Boston

first: Susan

last: Kandarian

state: MA

address: 635commonwealth ave, Rm444

department: Health Sciences

institute: Boston University

description: Whole transcript expression profiling

hyb_protocol: Fragmented, biotinylated DNA samples were hybridized on a mouse Gene 1.0 ST array according to manufacture's recommendation.

scan_protocol: A total of 8 array images were acquired by GeneChip Scanner 3000 7G and quality assessed by Affymetrix Expression Console (Santa Clara, CA).

data_processing: Gene expression signals were generated by robust multi-array analysis (RMA) using Brainarray MoGene 1.0ST custom CDF files v.13.  Differential gene expression was computed using the Comparative Marker Selection module in Genepattern database (Broad Institute, Cambridge, MA) which compares mean differences between control and unloaded groups by two-way parametric t-test.  P-value ≤ 0.05 and q-value ≤ 0.05 were used to identify genes that were significantly differentially expressed with hindlimb unloading.

source_name: Gastrocnemius and plantaris from a 7-wk-old C57BL/6J mouse with hind limbs in full weight bearing

label_protocol: Whole-transcript expression profiling experiments were carried out by the Boston University Microarray Core Facility.  The Affy standard WT Sense Target Labeling assay protocol was followed to synthesize biotinylated DNA.

growth_protocol: 7-week-old female wild type mice (C57BL/6J) were purchased from the Jackson Laboratory (Bar Harbor, ME).  Animals were provided with chow and water ad libitum and housed individually in Boston University Animal Care Facility.  After 3 days of acclimation, mice were randomly assigned to weight-bearing (WB) or hind limb unloaded (HU) groups.

extract_protocol: Gastrocnemius and plantaris muscles harvested from anesthetized mice from both groups were snap frozen in liquid nitrogen and stored at -80ºC before use.  Total RNA was isolated using the Qiagen miRNeasy Mini kit (Valencia, CA) according to manufacturer’s instructions.  Extracted total RNA was treated with RNase-Free DNase I (Qiagen, Valencia, CA), quantitated by UV spectrophotometry, and quality checked by a 1% denaturing agarose gel as previously described. Each group (WB and HU) included 4 independent total RNA samples with a minimal RIN number 8.0 verified by Bioanalyzer 2100 (Agilent Technology, Palo Alto, CA).

treatment_protocol: Mice in the HU group had their hind limbs elevated off the cage floor for 5 days to induce unloading induced muscle atrophy, as described previously [Wu et al. 2011]. The use of animals in this study was approved by the Institutional Animal Care and Use Committee of Boston University (protocol number 12-012)

value: Healthy weight bearing muscle

value: 7 wk old

tag: muscles

value: Gastrocnemius and plantaris


title: WB muscle, biological replicate 3

description: Whole transcript expression profiling


title: control mouse 3 liver 5hmC profile (1d)

description: normal whole liver genomic DNA

value: control

value: none (Input)


title: SC-1 control REP2

description:
SC1_LITAF_CTRL_R2
Gene expression data from a DLBCL cell line.

source_name: DLBCL cell line SC-1 stably transfected with a tetracycline-inducible LITAF expression vector, absence of doxycycline


title: IFN-alpha treated spleen (2-2)

description: test


title: IFN-alpha treated spleen (2-1)

description: test


title: control mouse 2 liver 5hmC profile (1d)

description: normal whole liver genomic DNA


title: spleen (1-3)

description: control

source_name: C57BL/6 mice derived spleen, control


title: HU muscle, biological replicate 4

description: Whole transcript expression profiling

source_name: Gastrocnemius and plantaris from a 7-wk-old C57BL/6J mouse subjected to 5-days of hind limb unloading

value: Atrophied muscle due to 5-day unloading


title: WB muscle, biological replicate 1

description: Whole transcript expression profiling


title: WB muscle, biological replicate 2

description: Whole transcript expression profiling


title: HU muscle, biological replicate 3

description: Whole transcript expression profiling


title: control mouse 1 liver 5hmC profile (91d)

description: normal whole liver genomic DNA


title: RL with doxycycline-induced LITAF expression REP1

description:
RL_LITAF_DOX_R1
Gene expression data from a DLBCL cell line.

source_name: DLBCL cell line RL stably transfected with a tetracycline-inducible LITAF expression vector, presence of doxycycline

value: RL


title: pb treated mouse 5 liver 5hmC profile (7d)

description: PB exposed mouse liver tissue

source_name: 7 day PB exposed whole liver

source_name: PB exposed mouse liver tissue


title: RL control REP2

description:
RL_LITAF_CTRL_R2
Gene expression data from a DLBCL cell line.

source_name: DLBCL cell line RL stably transfected with a tetracycline-inducible LITAF expression vector, absence of doxycycline


title: spleen (1-1)

description: control


title: HU muscle, biological replicate 2

description: Whole transcript expression profiling


title: HU muscle, biological replicate 1

description: Whole transcript expression profiling


title: RL control REP1

description:
RL_LITAF_CTRL_R1
Gene expression data from a DLBCL cell line.


title: control mouse 4 liver 5hmC profile (1d)

description: normal whole liver genomic DNA


title: r22

status: Public on Nov 09 2012

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

description: Gene expression data from human colon biopsies; involved area UC active patient

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: The data were analyzed with Bioconductor tools in R (http://www.r-project.org) using GC-RMA as normalization method. Next we employ a conservative probe-filtering step excluding those probe sets not reaching a log2 expression values of 5 in at least 1 sample.

source_name: Human colon biopsies from UC patient with active disease (involved mucosa)

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

extract_protocol: Total RNA was extracted by Rneasy Kit (Qiagen) according to the manufacturer's instructions.

tag: age (years)

tag: evolution time (years)

tag: disease extension

value: Pancolitis

value: Azathioprine


title: r24

value: female

value: Left-sided colitis


title: r19


title: r13


title: B137+

value: male

value: No treatment


title: r04


title: r18


title: r07

value: Systemic steroids


title: RL with doxycycline-induced LITAF expression REP2

description:
RL_LITAF_DOX_R2
Gene expression data from a DLBCL cell line.

value: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector

value: doxycycline


title: SC-1 control REP1

description:
SC1_LITAF_CTRL_R1
Gene expression data from a DLBCL cell line.


title: X78-

description: Gene expression data from human colon biopsies; non-involved area UC active patient

source_name: Human colon biopsies from UC patient with active disease (non-involved mucosa)


title: b78+


title: b86+


title: b86-


title: pb treated mouse 3 liver 5hmC profile (7d)

description: PB exposed mouse liver tissue

value: M

value: Active Motif

value: phenobarbital

value: liver


title: pb treated mouse 2 liver 5hmC profile (7d)

description: PB exposed mouse liver tissue


title: control mouse 1 liver 5mC profile (7d)

description: normal whole liver genomic DNA

value: Eurogentec

value: control


title: b45+


title: b66+


title: pb treated mouse 4 liver 5hmC profile (7d)

description: PB exposed mouse liver tissue

value: none (Input)


title: b45-


title: b44-


title: b36+


title: b23.2

description: Gene expression data from human colon biopsies; UC patient in remission

source_name: Human colon biopsies from UC patient in remission (involved mucosa)


title: b12.2


title: b38-


title: b38+


title: b44+


title: b9.2


title: b36-


title: pb treated mouse 4 liver 5hmC profile (91d)

description: PB exposed mouse liver tissue

source_name: 91 day PB exposed whole liver


title: b10.2


title: control mouse 4 liver 5hmC profile (7d)

description: normal whole liver genomic DNA


title: b8.2


title: b2.2


title: b6.2


title: b158

description: Gene expression data from human colon biopsies; non-inflammatory control

source_name: Human colon biopsies from non-inflammatory control


title: b147


title: b156


title: b7.2


title: spleen (1-2)

description: control

value: spleen


title: b146


title: control mouse 1 liver 5hmC profile (1d)

description: normal whole liver genomic DNA


title: control mouse 3 liver 5hmC profile (7d)

description: normal whole liver genomic DNA


title: b106


title: pb treated mouse 1 liver 5hmC profile (7d)

description: PB exposed mouse liver tissue


title: b138


title: b93


title: b105


title: b72


title: 964N

city: Brussels

first: Gil

last: Tomas

address: 808 route de Lennik

department: IRIBHM

institute: ULB

description:
patient-matched nontumor control
964N-Plus.CEL

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were normalized with RMA using the affy Bioconductor package

source_name: patient-matched non-tumor control

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted from thyroid tissues using Trizol reagent (Invitrogen), followed by purification on RNeasy columns (Qiagen). The RNA concentration was spectrophotometrically quantified, and its integrity was verified using an automated gel electrophoresis system (Experion, Biorad).

tag: pathological diagnostic

value: patient-matched non-tumor control

tag: tissue type

value: patient-matched non-tumor


title: b89

tag: treatment


title: b76


title: 771N

description:
patient-matched nontumor control
771N-35-Plus.CEL


title: X66-

value: female

value: Azathioprine


title: 939N

description:
patient-matched nontumor control
939N-Plus.CEL


title: 954N

description:
patient-matched nontumor control
954N-41-Plus.CEL


title: ATC11

description:
anaplastic thyroid carcinoma
1-ATC11-Plus.CEL

source_name: tumour

value: anaplastic thyroid carcinoma (ATC)

value: tumour


title: 886N

description:
patient-matched nontumor control
886N-37-Plus.CEL


title: control mouse 1 liver 5hmC profile (7d)

description: normal whole liver genomic DNA

source_name: normal whole liver


title: control mouse 5 liver 5hmC profile (7d)

description: normal whole liver genomic DNA


title: 758N

description:
patient-matched nontumor control
758N-33-Plus.CEL


title: ch128.1Av U266 tx 24A

city: Los Angeles

first: Manuel

last: Penichet

department: Department of Surgery

institute: University of California, Los Angeles

description: SAMPLE 16

scan_protocol: Standard Illumina scan protocol

data_processing: Quantile normalization, probe detection, fold-change comparison in R and Matlab

source_name: U266 cells

label_protocol: Standard Illumina labeling protocol

growth_protocol: IM-9 (a human EBV-transformed B-lymphoblastoid cell line) and U266 (a human MM cell line) were purchased from the American Type Culture Collection (ATCC, Manassas, VA). Both malignant B-cell lines were grown in RPMI 1640 medium (Life Technologies, Carlsbad, CA) supplemented with 10% heat inactivated fetal bovine serum (Atlanta Biologicals Inc., Lawrenceville, GA) and grown in 5% CO2 and 37 °C.

extract_protocol: Total mRNA was collected from all samples using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: IM-9 and U266 cells were incubated for 1, 3, 9, or 24 h with 10 nM ch128.1Av alone or conjugated to b-SO6. Control samples consisted of cells incubated with an equal volume of buffer alone for the same time points.

tag: cell line

value: U266 cells


title: 905N

description:
patient-matched nontumor control
905N-39-Plus.CEL


title: ch128.1Av U266 tx 1A

description: SAMPLE 10


title: ch128.1Av conjugated to b-SO6 U266 tx 3B

description: SAMPLE 13

value: ch128.1Av conjugated to b-SO6


title: ch128.1Av U266 tx 3A

description: SAMPLE 12


title: ch128.1Av conjugated to b-SO6 U266 tx 1B

description: SAMPLE 11


title: ch128.1Av conjugated to b-SO6 U266 tx 9B

description: SAMPLE 15


title: ch128.1Av U266 tx 9A

description: SAMPLE 14


title: ch128.1Av conjugated to b-SO6 U266 tx 24B

description: SAMPLE 17


title: ch128.1Av IM9 tx 24A

description: SAMPLE 8

source_name: IM-9 cells

value: IM-9 cells


title: 686N

description:
patient-matched nontumor control
686N-Plus.CEL


title: ch128.1Av conjugated to b-SO6 IM9 tx 24B

description: SAMPLE 9


title: ch128.1Av IM9 tx 9A

description: SAMPLE 6


title: ch128.1Av conjugated to b-SO6 IM9 tx 9B

description: SAMPLE 7


title: ch128.1Av conjugated to b-SO6 IM9 tx 3B

description: SAMPLE 5


title: 601N

description:
patient-matched nontumor control
601N-Plus.CEL


title: 710N

description:
patient-matched nontumor control
710N-Plus.CEL


title: 615N

description:
patient-matched nontumor control
615N-Plus.CEL


title: 574N

description:
patient-matched nontumor control
574N-29-Plus.CEL


title: 501N

description:
patient-matched nontumor control
501N-47-Plus.CEL


title: ch128.1Av conjugated to b-SO6 IM9 tx 1B

description: SAMPLE 2


title: 691N

description:
patient-matched nontumor control
691-N-Plus.CEL


title: ch128.1Av IM9 tx 3A

description: SAMPLE 4


title: 502N

description:
patient-matched nontumor control
502N-Plus.CEL


title: 446N

description:
patient-matched nontumor control
446N-Plus.CEL


title: 515N

description:
patient-matched nontumor control
515N-45-Plus.CEL


title: ch128.1Av conjugated to b-SO6 IM9 tx 1Br

description: SAMPLE 3


title: 366N

description:
patient-matched nontumor control
366N-Plus.CEL


title: 343N

description:
patient-matched nontumor control
343N-Plus.CEL


title: b143

description: Gene expression data from human colon biopsies; non-inflammatory control


title: Mouse embryo, 44 hours, Nanog MO-injected, biological rep 1

city: Stanford

first: Kin Fai

last: Au

address: James H. Clark Center, 1st Floor East, 318 Campus Drive,

department: Statistics

institute: Stanford

description:
Gene expression data
Mouse_44h_NN_R1

hyb_protocol: The arrays were hybridized in an Affymetrix GeneChip Hybridization Oven 640 for 40 hours.

scan_protocol: The arrays were scanned using a Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were processed using dChip.

source_name: Preimplantation embryos (Nanog MO-injected) collected at 44 hours post-injection

label_protocol: The RNA was reverse transcribed and amplified using the WT-Ovation One-Direct Amplification System (NuGEN). The cDNA was then fragmented and labelled using the FL-Ovation cDNA Biotin Module (NuGEN).

growth_protocol: Embryos were cultured in drops of Human Tubal Fluid with 10% serum supplement (SAGE In-Vitro Fertilization Inc.) under mineral oil (Sigma) in 5% CO2 at 37oC.

extract_protocol: RNA was extracted using the PicoPure RNA Isolation Kit (Arcturus) according to manufacturer's instructions.

treatment_protocol: Embryos were injected with either a morpholino targeting Oct4, Sall4, or Nanog or a control morpholino targeting a sequence that does not exist in the mouse genome or transcriptome.

tag: developmental stage

value: preimplantation embryo

tag: condition

value: Nanog

tag: time (post-injection)

value: 44 hours


title: Mouse embryo, 44 hours, control-injected (for Nanog experiment), biological rep 2

description:
Gene expression data
Mouse_44h_HG(NN)_R2

source_name: Preimplantation embryos (control-injected) collected at 44 hours post-injection

value: Control (HG)


title: 249N

description:
patient-matched nontumor control
249N-43-Plus.CEL


title: Mouse embryo, 44 hours, Nanog MO-injected, biological rep 3

description:
Gene expression data
Mouse_44h_NN_R3


title: ch128.1Av IM9 tx 1A

description: SAMPLE 1

tag: time


title: Mouse embryo, 44 hours, uninjected (for Nanog experiment), biological rep 3

description:
Gene expression data
Mouse_44h_UI(NN)_R3

source_name: Preimplantation embryos (uninjected) collected at 44 hours post-injection

value: Uninjected


title: 307N

description:
patient-matched nontumor control
307N-Plus.CEL


title: Mouse embryo, 44 hours, uninjected (for Nanog experiment), biological rep 2

description:
Gene expression data
Mouse_44h_UI(NN)_R2


title: 243N

description:
patient-matched nontumor control
243N-Plus.CEL


title: Mouse embryo, 44 hours, control-injected (for Nanog experiment), biological rep 1

description:
Gene expression data
Mouse_44h_HG(NN)_R1


title: 1502N

description:
patient-matched nontumor control
1502N-5-Plus.CEL


title: 147N

description:
patient-matched nontumor control
147N-Plus.CEL


title: Mouse embryo, 44 hours, control-injected (for Nanog experiment), biological rep 3

description:
Gene expression data
Mouse_44h_HG(NN)_R3