title: AA_3

city: Dalian

first: Zhiguang

last: Li

state: Liaoning

address: 9 Lvshun South Road

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: Array was made by LC Sciences at Houston, Texas based on Sanger miRBase Release 12.0. It included probes for 1292 unique mature miRNAs with 856, 617, and 349 from human, mouse, and rat respectively.  Each probe was repeated 2x times. Sixty-one control probles with 4-16 repeats were also present on the array.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Raw intensities experienced the adjustments of data-filtering, log 2 transformation, gene centering and normalization with a cyclic LOWESS (locally weighted regression). MiRNAs with at least one of the 12 intensities larger than the intensity threshold of 32 were considered detectable.

organism: Rattus norvegicus

source_name: Liver

label_protocol: To perform the miRNA array experiment, total RNA (2 to 5 µg) was first size fractionated using a YM-100 Microcon centrifugal filter (Millipore). The small RNAs (< 300 nt) were then 3’-extended with a poly(A) tail using poly(A) polymerase.  Thereafter, an oligonucleotide tags was ligated to the poly(A) tail for later staining with fluorescent dye Cy3.

growth_protocol: All animal procedures followed the recommendations of the NCTR Institutional Animal Care and Use Committee for the handling, maintenance, treatment, and sacrifice of the rats.

extract_protocol: miRNAs were isolated from kidney, liver, and testis of rats using mirVana™ miRNA isolation kit (Ambion, Austin, TX). RNA concentrations were determined using NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, Delaware). The quality of RNA samples was characterized on an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) using an RNA6000 Nano Chip (Agilent).

treatment_protocol: AA was purchased from Sigma (St. Louis, MO). The AA content of the test agent was 96% (40% AAI and 56% AAII). Male Big Blue transgenic rats were obtained from Taconic Laboratories (Germantown, NY).  The treatment protocol was based on a previous carcinogenesis study in which AA induced kidney tumors in rat in 3 months        (Mei et al., 2006; Mengs et al., 1982b). Six-week-old Big Blue rats were treated with 0.1, 1.0, or 10.0 mg AA/kg body weight by gavage, five times per week for 12 weeks; Vehicle control rats were gavaged with 0.9% sodium chloride using the same schedule as for the AA-treated rats. Six rats from each treatment group were sacrificed one day after the last treatment. The kidney and liver tissues that were collected and used for the DNA adduct and mutation study (Mei et al, 2006) were used for the miRNA profiling and real-time PCR in this study, which allow us to compare the different endpoints at the same conditions.

value: Male

value: 6 weeks

value: Fisher 344

tag: genetics

value: Big Blue Transgenic


title: AA_2

status: Public on Nov 10 2013

type: RNA

country: China

molecule: total RNA

tag: gender

tag: age

tag: strain


title: AA_5


title: AA sample5 vs. control sample5 for rat kidney

description: Array was made by LC Sciences at Houston, Texas based on Sanger miRBase Release 10.0. It included probes for 1094 unique mature miRNAs with 711, 568, and 348 from human, mouse, and rat respectively.  Each probe was repeated 3 x times. Sixty-three control probles with variable repeats were also present on the array.

source_name: Kidney control

source_name: Kidney AA-treatment


title: AA sample4 vs. control sample4 for rat kidney


title: AA_4


title: AA sample3 vs. control sample3 for rat kidney


title: AA sample6 vs. control sample6 for rat kidney


title: HPAG-HLJ193-CGH

type: genomic

city: Beijing

first: yuanhai

last: you

address: Changbai road 155,Changping district

institute: intitute of communicable disease control and prevention,China CDC

description: chronic superficial gastritis (HLJ220,HLJ215),atrophic gastritis (HLJ193,HLJ256), gastric ulcer (HLJ271,HLJ253), gastric cancer (HLJ038,HLJ005),reference strain (26695)

hyb_protocol: Microarrays were pre-hybridized with 6×SSPE containing 0.05% Tween-20, 5×Denhardt’s solution, and 100 ng salmon sperm DNA for 30 min at 50°C. TheCy5-ULS labeled DNA fragments were then hybridized in the hybridizing solution(6× SSPE and 0.05% SDS) by denaturing at 95°C for 3 min and then incubating for16 h at 50°C. Post-hybridization wash steps were 6× SSPET for 5 min at 50°C,3×SSPET for 1 min, 0.5× SSPET for 1 min, and PBST for 1 min at room temperature. After hybridization and imaging, the microarray was stripped using CustomArrayTM Stripping Solution.

scan_protocol: Hybridized microarrays were covered with imaging solution and scanned with an Axon GenePixTM 4000B.

data_processing: Data was extracted by using Microarray_Imager_5.9.3 software. The foreground median of each spot was taken into following analysis. Information of probe location and corresponding hybridization signals were extracted for further analysis. For ease of analysis, all genes were separated into two independent files, one including genes located in H.pylori P12 genome, another including strain specific genes in each of the other strains which are named chromosome 1~6 respectively (also including P12 strain specific genes). Isolates of gastric cancer were represented as GC, isolates of gastric ulcer were represented as GU, isolates of chronic superficial gastritis were represented as SG, and isolates of atrophic gastritis were represented as AG. Signal comparison were performed between the two strains in GC,GU,SG and AG group respectively.and by GC vs GU,GU vs AG,GC vs SG and AG vs SG. Signal ratios of two hybridized strains were log2 transformed and imported into a web tool ADaCGH, which was used for the analysis of microarray datasets to obtain gains and losses of genes between two genomes. The data was centered and segmented in ADaCGH by employing a position-dependent segmentation algorithm CBS (circular binary segmentation) to partition data points into absent, present and no change sequence segments

molecule: genomic DNA

organism: Helicobacter pylori

label_protocol:
Four microgram of heated DNA from each H.pylor strain was labeled with
Cy5-ULS using the Kreatech ULS array CGH Labeling kit (EA-005, Kreatech,Netherlands) according to the manufacturer’s instructions and then hybridized to the microarray. Experiments were performed according to CombiMatrix protocol.

growth_protocol: H. pylori strains were routinely cultured for 24 h on Columbia agar plates (Oxoid) containing 5% goat blood under microaerophilic conditions at 37℃, following a wash in sterile PBS.

treatment_protocol:
Genomic DNA was extracted by using the Dneasy Blood & Tissue Kit (QIAGEN)according to the manufacturer’s instructions. The concentration of genomic DNA wasadjusted to 120ng/μl with nuclease-free water and to a volume of 40μl. DNA washeated in a PCR machine (Biorad, USA) at 95℃ for 10min to obtain DNA fragments
with sizes of 100bp to 600bp for genomic labeling. The results were visualized by 1% agarose gel electrophoresis.

value: HLJ193 (atrophic gastritis)


title: HPGU-HLJ253-CGH

extract_protocol: Genomic DNA was extracted by using the Dneasy Blood & Tissue Kit (QIAGEN)according to the manufacturer’s instructions

value: HLJ253 (gastric ulcer)


title: AA_1


title: HPGC-HLJ005-CGH

value: HLJ005 (gastric cancer)


title: Control_6


title: AA sample2 vs. control sample2 for rat kidney


title: AA sample1 vs. control sample1 for rat kidney


title: AA_6


title: 23GFP+ EC biological replicate 1

status: Public on Nov 11 2013

city: Oxford

first: Stephen

last: Taylor

address: Headington

country: United Kingdom

institute: CBRG

description: Gene expression data for 23GFP+ endothelial cells isolated from pooled E8.5 mouse concepti

hyb_protocol: Hybridisation for 16 hr at 45C onto Affymetrix Mouse Genome 430 2.0 arrays by standard protocols at the Stanford Protein and Nucleic Acid facility

scan_protocol: Genechip Scanner 3000 7G

data_processing: CEL files were normalised using RMA normalisation in the affy package.

label: biotin

organism: Mus musculus

source_name: VE-Cad+ Ter119- CD45- CD41- 23GFP+ cells from E8.5 conceptus

label_protocol: Labelled and fragmented using WT Ovation cDNA Biotin Module v2 (NuGEN)

growth_protocol: E8.5 embryos were genotyped and staged by counting somite pairs.

extract_protocol: Trizol extraction of total RNA according to manufacturers instructions and purified using RNeasy Micro kit. Samples were amplified using WT-Ovation Pico RNA amplification system (NuGEN).

treatment_protocol: Concepti were pooled and incubated for 20 mins at 37 degrees C in PBS with 10%FCS, 50U/ml penicillin and 50ug/ml streptomycin and 0.12% collagenase type I. A single cell suspension was generation by manual pipetting. Antibody staining was performed, and specific cell populations were isolated by FACS.

tag: genetic background

value: mixed (CBA x C57BL/6)

tag: cell type


title: HPGU-HLJ271-CGH

value: HLJ271 (gastric ulcer)


title: Control_5


title: HP26695 reference

value: 26695 (reference strain)


title: Control_2


title: Control_1


title: Control_4


title: Barrestin_Si_Serum Starved

city: Tampa

first: Jonathan

last: Nguyen

state: FL

department: Tumor Biology

country: USA

institute: Moffitt Cancer Centre & Research Institute

description: Beta arrestin depleted-Serum starved

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scaner.

data_processing:
The data were analyzed with the Affymetrix GCOS 1.4 software using the MAS 5.0 alorighthm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.  Additonal analysis was performed by by log2 transformation of the expression values, and the mean center expression level for each gene was determined
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0

label: Biotin

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the Ambion Message Amp Premier protocl using 100 ng of total RNA (Ambion).

growth_protocol: Human NSCLC cell lines A549 was used in this study. The cell line was maintained in Ham’s F-12K(Cellgro) supplemented with 10% FBS (Cellgro). Nicotine used in the study was 1µM. A549 cells were grown to 70% confluency in  medium with serum for 24 hours, transfected with control siRNA and Beta arrestin siRNA next day and then rendered quiescent by serum starvation for 36 hours and stimulated with nicotine for 24 hours.RNA was prepared from the treated samples with Qiagen RNeasy Kit and then sent for microarray analysis. The RNA samples were subjected to heat inactivation to check the purity and validated the same on 1%  agarose gel by electrophoresis. Total RNA extracted  were used to generate cRNA targets, which were subsequently hybridized to Human Genome U133A plus 2.0 oligonucleotide probe arrays (Affymetrix, Santa Clara, CA) according to standard protocols. Raw data was processed by log2 transformation of the expression values. Genes with significant expression levels above 2 fold downregulated or upregulated were chosen for further study.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

tag: cell line

value: NSCLC cell line A549

tag: genotype/variation

value: Beta arrestin depletion

tag: agent

value: untreated


title: Control_SI_Nicotine

description: Nicotine treated

value: control

value: Nicotine


title: Control_SI_Serum Starved

description: Serum starved


title: C2ATF2 replicate3

city: Manchester

first: steve

last: lyons

address: Wilmslow Rd

department: Cell Regulation

institute: CRUK Manchester

hyb_protocol: The products were hybridized to GeneChip Mouse Gene Array 1.0 ST (Affymetrix) microarray chips. Hybridized arrays were washed using a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Scanned using a GeneChip Scanner 30007G (Affymetrix).

data_processing: The data were analyzed with RMA implemented in the software apt-probeset-summarize with the default settings.

source_name: Hepatoblasts expressing active ATF2 8hrs

label_protocol: RNA was reverse transcribed using an Ovation Pico WTA kit (NuGen, 3300-12) to produce an amplified cDNA. Second strand synthesis was achieved using a WT-Ovation Exon module version 1.0 kit (NuGen, 2000-12), after which the cDNA was fragmented and labelled using Encore Biotin Module reagents (NuGen, 4200-12).

growth_protocol: Hepatoblasts were seeded onto gelatin coated plates. Medium was DMEM (sigma D0819), plus 10% FBS, 1% penicillin/streptomycin, HGF 10ng/ml, EGF 20 ng/ml, dexamethasone 1uM.

extract_protocol: Total RNA was extracted using Rneasy columns (QIAgen 74104)

value: Embryonic hepatoblasts


title: Control_3


title: GFP replicate 3

source_name: Hepatoblasts expressing GFP 8hrs


title: GFP replicate 2


title: GFP replicate 1


title: Normal Cornea 2

status: Public on Nov 09 2013

city: Los Angeles

first: Vincent

middle: Anthony

last: Funari

state: CA

address: 8700 Beverly Drive

department: Medical Genetics

institute: Cedars Sinai

hyb_protocol: Affymetrix protocol (FlashTag Biotin HSR RNA Labeling Kit).

data_processing: Data was normalized using miRNA QC tool and log2 transformed.

source_name: Cornea, normal

extract_protocol: RNeasy

tag: tissue

value: cornea

tag: disease state

value: normal


title: Normal Cornea 1

scan_protocol: Affymetrix protocol (FlashTag Biotin HSR RNA Labeling Kit).


title: Normal Cornea 5

label_protocol: Affymetrix protocol (FlashTag Biotin HSR RNA Labeling Kit).


title: Normal Cornea 6


title: C2ATF2 replicate2


title: Diabetic Retinopathy 3

source_name: Cornea, diabetic retinopathy

value: diabetic retinopathy


title: Normal Cornea 3


title: Normal Cornea 4


title: Diabetic Retinopathy 1


title: Mouse 102, HF diet, Irradiated

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

country: France

institute: IRSN

description: HF diet, Irradiated

hyb_protocol: Labeled RNA was hybridized to miRCURY LNA microRNA arrays according to the manufacturer's instructions.

scan_protocol: Slides were scanned using a laser scanner (Molecular Devices, Sunnyvale, CA, USA) and the resulting images were analyzed using Array-Pro v.4.5 (Media Cybernetics, Bethesda, MD, USA).

data_processing: Following background correction, quantile normalization was applied, so that the distribution remains the same across arrays.

label_protocol: RNA was labeled with Hy3 using the miRCURY labelling kit, according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from the livers of C57BL/6J mice (n = 3 per experimental condition) using TRIZol reagent.

treatment_protocol: C57BL/6J mice were fed a normal or a high-fat diet and exposed to 4 x 0.75 Gy X-rays.

tag: irradiation

tag: diet

value: High-fat diet


title: CD14-CD45-EpCAM+ cells In bone marrow, non liver metastasis group, replicate 6

city: Suita

first: Hiroshi

last: Takeyama

state: Osaka

address: Yamada-oka 2-2

department: Gastroenterological Surgery

country: Japan

institute: Graduate School of Medicine, Osaka University

hyb_protocol: Cy3-labeled samples were hybridized with the miRNA Complete Labeling and Hyb Kit(Agilent, Santa Clara,CA,USA) acording to the manufacture's procedure.

scan_protocol: Microarray slides were scanned with Agilent G2505C scanner. The sanned image files were analyzed using Agilent FeatureExtraction software ver 10.7.3.1.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1(Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid:021827_D_F_20100604) to obtain background subtracted and spatially detrended Processed Signal intensities.  The signal values were 90 percentile normalization with Agilent GeneSpring ver11.5.1

label_protocol: 100 ng totalRNA samples  were labeled and hybridized with the miRNA Complete Labeling and Hyb Kit(Agilent, Santa Clara,CA,USA) in accordance with the manufacture's procedure.

extract_protocol: Total RNA was isolated using the miRNeasy kit (Applied Biosystems, Carlsbad, CA) following the manufacturer’s protocol. Total RNA concentration and purity were assessed with a spectrophotometer. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Colorectal cancer patients were administered anesthesia and 20 mL BM was taken from the right and left anterior iliac crests before surgery. Mononucleated cells were collected using a standard Ficoll-Hypaque gradient technique. To enrich for EpCAM+ cells, CD14+ cells were removed from the whole bone marrow using auto MACSTM pro (Milteny Biotec, Bergisch Gladbach, Germany) with anti-CD14 immunomagnetic beads (clone; TÜK4, Milteny Biotec). Next, CD45+ cells were removed by treatment with anti-CD45 immunomagnetic beads (clone; 5B1; Milteny Biotec). The residual CD14−CD45− cells were then incubated with FcR blocking reagent (Milteny Biotec), followed by incubation with anti-EpCAM immunomagnetic beads (clone; HEA-125, Milteny Biotec), and the CD14−CD45−EpCAM+ cells were taken up.

value: CD14-CD45-EpCAM+ cells

tag: group

value: non liver metastasis

value: female


title: Mouse 113, Irradiated

description: Irradiated

value: Normal diet


title: Diabetic Retinopathy 2


title: Mouse 111, Irradiated

description: Irradiated


title: Diabetes Mellitus 1

source_name: Cornea, diabetes mellitus

value: diabetes mellitus


title: Mouse 101, HF diet, Irradiated

description: HF diet, Irradiated


title: Diabetes Mellitus 3


title: Mouse 112, Irradiated

description: Irradiated


title: Diabetes Mellitus 2


title: Mouse 103, HF diet, Irradiated

description: HF diet, Irradiated


title: Mouse 108, HF diet

description: HF diet

value: 0 Gy


title: Mouse 118, Control

description: Control


title: Wnt1CreEzh2lox/lox, branchial arch 1, biological replicate 2

city: Zurich

first: Michal

middle: J

last: Okoniewski

state: Zurich

address: Binzmühlestrasse 130

country: Switzerland

institute: ETH Zurich

description: Branchial arch1 (one brnachial arch per embryo)

hyb_protocol: Samples were hybridized according to Affymetrix manuals,in a Affymetrix hybridization station.  Then washings were performed in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data have been processed using R/Bioconductor.

source_name: Wnt1CreEzh2lox/lox; Branchial arch 1

label_protocol: biotin

growth_protocol: Mouse branchial arch dissected from day 11.5 mouse embryos

extract_protocol: Qiagen RNeasy

treatment_protocol: not applicable

value: Branchial arch 1

tag: genotype

value: Wnt1Cre Ezh2lox/lox


title: Ezh2lox/lox, Branchial arch 1, biological replicate 3

source_name: Ezh2lox/lox; Branchial arch1


title: Mouse 106, HF diet

description: HF diet


title: Ezh2lox/lox, Branchial arch 1, biological replicate 2


title: Wnt1CreEzh2lox/lox, branchial arch 1, biological replicate 3


title: Wnt1CreEzh2lox/lox, branchial arch 1, biological replicate 1


title: Mouse 117, Control

description: Control


title: SL1344_swap_BR3

type: mixed

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

description: Sample 6; biological replicate 3

hyb_protocol: Cy3 labeled cDNA and Cy5 labeled control genomic DNAs were co-precipitated using standard sodium acetate/ethanol procedures and resuspended in hybridization buffer (Oxford Gene Technologies), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridiized for 24 hours at 55oC in an Agilent hybiridization oven at 5 rpm. After hybridization, slides were washed according to instructions provided by Oxford Gene Technologies

scan_protocol: The microarray slides were scanned using a GenePix 4000B scanner (Axon Instruments). Cy3 and Cy5 images were acquired at 5 micron resolution.

data_processing: Quantification of fluorescent spot intensities and local background data was performed using the GenePix 3.0 software supplied.  The Cy3/Cy5 ratio and median Cy3/Cy5 ratio were determined for each probe. Cy3/Cy5 values were median normalised and the intensities of the multiple probes across each gene were averaged

label: Cy3 dCTP

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: RNA_SL1344(swap) cells grown to OD600nm 0.3

label_protocol: Fluorescent labeling of genomic DNA  and cDNA samples were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ul of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ul). *[200 ng of  cDNA and 200 ng of Input DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ml of stop buffer added to terminate the reaction. Labeled DNAs were purified using G-50 columns (GE-healthcare), according to manufacturers instructions.

growth_protocol: SL1344(swap) cells were inoculated 1:100 into 25 ml fresh Luria Broth (LB) and grown at 37degrees celsius in a shaking waterbath at 200 rpm until OD600 0.3

extract_protocol: For transcriptome experiments 2.0 OD600nm units of bacterial cultures were harvested during mid-exponential growth (OD600nm= 0.3). Total RNA was extracted as above using a Promega SV Total RNA Isolation kit according to manufacturer guidelines. RNA samples were quantified using a Nanodrop ND-1000 and checked for purity and degradation by gel electrophoresis. Total RNA samples were then converted to double stranded cDNA pools in a two-step process using a Superscript™ Double-Stranded cDNA synthesis kit (Invitrogen) according to manufacturer guidelines

label: Cy5 dCTP

source_name: genomic DNA_SL1344 cells grown to OD600nm 0.3

growth_protocol: SL1344 cells were inoculated 1:100 into 25 ml fresh Luria Broth (LB) and grown at 37degrees celsius in a shaking waterbath at 200 rpm until OD600 0.3


title: Mouse 116, Control

description: Control


title: SL1344_swap_BR2

description: Sample 5; biological replicate 2


title: SL1344_swap_BR1

description: Sample 4; biological replicate 1


title: SL1344_wildtype_BR3

description: Sample 3; biological replicate 3

source_name: RNA_SL1344 cells grown to OD600nm 0.3

value: SL1344 wild type


title: C2ATF2 replicate1


title: LPS6 hrs

city: Ann Arbor

first: Paul

middle: Edward

last: Makidon

state: MI

address: 9340 MSRB III, 1150 W. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

description: Global gene expression in vitro

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment version 2.15.0. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: 6hrs with 1ug/ml LPS treatment

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

growth_protocol: Jaws II cells were grown according ATCC protocol

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

treatment_protocol: JAWS II dendritic cells (10^7 cells/culture in 10 ml plates) were incubated with 0.001% W805EC NE alone or mixed with 10 µg/ml rPA. Control cultures were either untreated (PBS) or incubated with 10 µg/ml rPA or with 1 µg/ml of TLR4 ligand LPS K12

tag: background strain

value: JAWS II dendritic cells


title: Mouse 107, HF diet

description: HF diet


title: NE 24hrs

description: Global gene expression in vitro

source_name: 24hrs with 0.001% NE treatment


title: NE/rPA 6hrs

description: Global gene expression in vitro

source_name: 6hrs with 0.001% NE/10ug rPA treatment


title: 5mM_32h

description: Gene expression in fibroblasts 32h after H2O2 treatment

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays Ver2.0 (G4846A) 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 using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NIH3T3:Per2-Luc fibroblasts, 5 mM H2O2, 32h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low Input Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: NIH-3T3:Per2-Luc fibroblasts were established and cultured as described previously (Tamaru et al., 2011).

extract_protocol: Total RNA was extracted using the Trizol Plus RNA Purification Kit (Ambion, USA).

treatment_protocol: Cells were treated with 5 mM H2O2 for 10 min.

value: NIH-3T3:Per2-Luc fibroblasts

tag: h2o2 treatment

value: 5 mM

tag: time after h2o2 treatment


title: LPS 12hrs

description: Global gene expression in vitro

source_name: 24hrs with 1ug/ml LPS treatment


title: rPA 6hrs

description: Global gene expression in vitro

source_name: 6hrs with 10ug rPA treatment


title: rPA 24hrs

description: Global gene expression in vitro

source_name: 24hrs with 10ug rPA treatment


title: NE/rPA 24hrs

description: Global gene expression in vitro

source_name: 24hrs with 0.001% NE/10ug rPA treatment


title: SL1344_wildtype_BR2

description: Sample 2; biological replicate 2


title: PBS control 6hrs

description: Global gene expression in vitro

source_name: 6hrs with PBS treatment


title: OGIB-patient-15

status: Public on Nov 08 2013

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

institute: Kinki university School of Medicine

hyb_protocol: Labeled DNA products were hybridized onto DMET Plus arrays at 49° C and 35 rpm for 16 h. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Scanned in an Affymetrix GeneChip Scanner 3000 7G (Santa Clara, CA).

data_processing:
Data extraction was done by the Affymetrix Command Console v1.3. Algorithm is Fixed Genotype Boundaries version 2 that is built in Command Console.
4 matrix tables as indicated below.
[1] aspirin-cont-all_GT.txt: SNPs of 18 control patients
[2] aspirin-posi-all_GT.txt: SNPs of 17 OGIB patients
[3] aspirin-cont-all_CN.txt: copy number variation of 18 control patients
[4] aspirin-posi-all_GT.txt: copy number variation of 17 OGIB patients

source_name: blood, aspirin, obscure gastrointestinal bleeding

label_protocol: Genomic DNA fragments were biotinylated at 3' end using terminal deoxynucleotidyl transferase according to the standard Affymetrix protocol.

extract_protocol: Genomic DNA was extracted from 200 μL of peripheral blood using QIAamp DNA Blood Mini kits.

treatment_protocol: Aspirin

value: blood

tag: treatment

value: enteric-coated low-dose aspirin (LDA)

tag: condition

value: obscure gastrointestinal bleeding (OGIB)


title: OGIB-patient-17


title: 5mM_20h

description: Gene expression in fibroblasts 20h after H2O2 treatment

source_name: NIH3T3:Per2-Luc fibroblasts, 5 mM H2O2, 20h


title: PBS control

description: Global gene expression in vitro

source_name: 24hrs with PBS treatment


title: Ezh2lox/lox, Branchial arch 1, biological replicate 1

tag: age


title: NE 6hrs

description: Global gene expression in vitro

source_name: 6hrs with 0.001% NE treatment


title: 5mM_4h

description: Gene expression in fibroblasts 4h after H2O2 treatment

source_name: NIH3T3:Per2-Luc fibroblasts, 5 mM H2O2, 4h


title: VC

city: Boston

first: Yongsheng

state: MA

address: 77 Ave Louis Pasteur, HIM836

department: Anethesiology

institute: Brigham and Women's Hospital

description:
Profiling of inflammation related genes involved in human macrophages transfected with lentiviral vector control (VC), miR-466l, anti-miR-negative (anti-miR-neg) or anti-miR-466l (37 °C, 72h)
VC, miR-466l, anti-miR-neg, or anti-miR-466l transfections for 12 donors (n1-n12).
Total RNA was isolated for reverse transcription. cDNA were used for real-time PCR

scan_protocol: Reactions were carried out with an ABI 7900HT thermal cycler (Applied Biosystems, Foster City, CA).

data_processing: Results were analyzed using 2-∆Ct and 2-∆∆Ct relative quantification methods. mRNAs that displayed threshold cycles (Ct) >35 were excluded from the analysis. GAPDH was used as housekeeping gene. Data were analyzed with Statminer software (Integromics, Philadelphia, PA) and normalized against vector control or anti-miR-negative.

label: SYBR Green I

source_name: human whole blood

label_protocol: 3 ng cDNA was added into each 20 μL reaction mix.

extract_protocol: Total RNA was extracted using the Roche Applied Science (Indianapolis, IN) according to the manufacturer's instructions. Reverse transcription to cDNA was performed with miScript II RT kit (Qiagen, Germantown, MD).

value: human macrophages

tag: status after 2 years

value: Alive

tag: transfection


title: miR-466l

tag: cell type


title: OGIB-patient-14


title: 0mM_4h

description: Gene expression in control fibroblasts

source_name: NIH3T3:Per2-Luc fibroblasts, 0 mM H2O2, 4h

value: 0 mM


title: OGIB-patient-13


title: OGIB-patient-12


title: SL1344_wildtype_BR1

description: Sample 1; biological replicate 1

source_name: RNA_SL1344 cells grown to OD600nm 0.3

tag: strain

source_name: genomic DNA_SL1344 cells grown to OD600nm 0.3


title: OGIB-patient-10


title: OGIB-patient-6


title: OGIB-patient-7


title: OGIB-patient-9


title: OGIB-patient-8


title: OGIB-patient-4


title: OGIB-patient-5


title: OGIB-patient-16


title: OGIB-patient-2


title: anti-miR-neg

value: anti-miR-neg (37 °C, 72h)


title: C-patient-18

source_name: blood, aspirin, control

value: aspirin

value: control


title: OGIB-patient-1


title: C-patient-17


title: C-patient-15


title: C-patient-16


title: HelaCont1_20120607

city: Montpellier

first: Edouard

last: BERTRAND

address: 1919 Route de Mendes

institute: CNRS

description: result file: IPIRBM7mHELA_signal.txt

hyb_protocol: Samples were prepared and hybridized according to Affymetrix specifications. (kit Hybridization Wash and Stain kit réf: 900720)

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1) using parameters: one side upper, 90 bp bandwidth and perfect match only. Output txt files (i.e. result file).
TASParam* files include parameter settings and input file information for the TAS analysis for each result file.

source_name: HeLa_control IP

label_protocol: Samples were prepared and hybridized according to Affymetrix specifications. (Tilling with WT Amplified Double-Stranded cDNA Synthesis Kit)

growth_protocol: HeLa cells were grown to sub-confluency in DMEM, 10% FCS, at 37°C.

extract_protocol: RNAs from beads or cell extracts were homogenized in Trizol and purified with RNeasy mini kit (Qiagen).

treatment_protocol: Cells were extracted in HNTG buffer (20 mM HEPES, pH 7.9, 150 mM NaCl, 1% Triton, 10% glycerol, 1 mM MgCl2, 1 mM EGTA, and protease inhibitors) for 30 min at 4°C. Cellular debris were removed by centrifugation (10 min at 9000 g). Extracts were put on antibody-coated beads for 2h at 4°C (M2 -Sigma). Beads were washed twice in HNTG and three times in PBS, and pelleted materials were Trizol.

tag: cell line

value: HeLa Kyoto

tag: ip antibody

value: GFP Trap


title: C-patient-14

tag: tissue


title: IpCBP20_1602N0_20111123

description: result file: IPCbpVsIPHela_signal.txt

source_name: HeLa_Flag-CBP20 IP

value: HeLa H9

value: anti-Flag Antibody

tag: antibody vendor

value: Sigma

tag: antibody cat. #

tag: antibody lot #


title: C-patient-13


title: OGIB-patient-11


title: anti-miR-466l


title: C-patient-12


title: IpCBP20_2302N0_20111123

description: result file: IPCbpVsIPHela_signal.txt


title: Barrestin_Si_Nicotine

description: Beta arrestin depleted- Nicotine treated

value: NSCLC cell line A549

tag: genotype/variation

value: Beta arrestin depletion

tag: agent

value: Nicotine


title: IP Flag ARS2 6 18.03

description: result file: Ars2VsHeLa_signal.txt

source_name: HeLa_Flag- Ars2 IP


title: HelaCont2_20120607

description: result file: IPIRBM7mHELA_signal.txt


title: OGIB-patient-3

value: blood


title: IpRBM7_2_20120607

description: result file: IPIRBM7mHELA_signal.txt

source_name: HeLa_GFP-RBM7 IP


title: C-patient-11


title: C-patient-10


title: IpRBM7_1_20120607

description: result file: IPIRBM7mHELA_signal.txt


title: IP_ARS2_6.03

description: result file: Ars2VsHeLa_signal.txt


title: C-patient-9


title: IP Flag HeLa 9 18.03

description: result file: Ars2VsHeLa_signal.txt; IPCbpVsIPHela_signal.txt


title: IP_HeLa_6.03


title: SiARS2_090309_20110630

description: result file: SiARSvsFFL_signal.txt

hyb_protocol: Tilling Samples were prepared and hybridized to Tiling Array according to Affymetrix specifications (Tilling with WT Amplified Double-Stranded cDNA Synthesis Kit). HuGene Samples were prepared and hybridized according to Affymetrix specifications : WTGene termlabel manuelrev1

scan_protocol: The arrays were scanned using an Affymetrix GeneChip Scanner  according to manufacturer's instruction : GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays rev.1

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1) using parameters: one side upper, 90 bp bandwidth and perfect match only.
SiARSvsFFL_signal.txt contains the signal intensities coming from the TAS Software (2 SiARS2 arrays versus 2 SiFFL arrays) and the 'AffyParamSiARSVsSiFFL.txt' file contains parameter settings and input file information for the TAS analysis.

source_name: HeLa_siRNA Ars2

growth_protocol: HeLa H9 cells were grown to sub-confluency in DMEM, 10% FCS, at 37°C.

treatment_protocol: For siRNAs, cells were transfected 48h using Lipofectamine and Plus reagent (InVitrogen), at a concentration of 50nM, and cells were homogeneized in Trizol. For IPs, cells were extracted in HNTG buffer (20 mM HEPES, pH 7.9, 150 mM NaCl, 1% Triton, 10% glycerol, 1 mM MgCl2, 1 mM EGTA, and protease inhibitors) for 30 min at 4°C. Cellular debris were removed by centrifugation (10 min at 9000 g). Extracts were put on antibody-coated beads for 2h at 4°C (M2 -Sigma). Beads were washed twice in HNTG and three times in PBS, and pelleted materials were Trizol.

tag: transfected with

value: Ars2 siRNA


title: C-patient-8


title: SiFFL1_090309_20110630

description: result file: SiARSvsFFL_signal.txt

source_name: HeLa_control FFL siRNA

label_protocol: Tilling Samples were prepared and hybridized to Tiling Array according to Affymetrix specifications (Tilling with WT Amplified Double-Stranded cDNA Synthesis Kit). HuGene Samples were prepared and hybridized according to Affymetrix specifications : WTGene termlabel manuelrev1

value: control FFL siRNA


title: C-patient-7


title: C-patient-6


title: C-patient-4


title: C-patient-5


title: pHTE65p0

city: Chicago

first: Ann

last: Harris

state: IL

address: 2430 N Halsted Street Box 211

institute: Lurie Children's Hospital of Chicago Research Center

description: Expression values for human genes in HTE cells

hyb_protocol: Hybridization was performed by NimbleGen following their standard operating protocol. See www.NimbleGen.com.

scan_protocol: Scanning was performed by NimbleGen following their standard operating protocol. See www.NimbleGen.com.

data_processing: Data were processed by NimbleGen following their standard operating protocol. See www.NimbleGen.com.

source_name: Human tracheal epithelial cells

label_protocol: Labeling was performed by NimbleGen following their standard operating protocol. See www.NimbleGen.com.

growth_protocol: Growth conditions as described in Davis PB, Silski CL, Kercsmar CM, et al. Beta-adrenergic receptors on human tracheal epithelial cells in primary culture. Am J Physiol 1990;258:C71–6.

extract_protocol: RNA was isolated by Trizol extraction from two primary cultures of HTE (human tracheal epithelial) cells. Total RNA was purified by Millipore Microcon YM-100 filter centrifugation.

treatment_protocol: No treatment

tag: developmental stage

value: adult

value: trachea

value: epithelia


title: C-patient-3

tag: treatment


title: SiFFL1_220709_20110630

description: result file: SiARSvsFFL_signal.txt


title: pHTE63p1


title: C-patient-2

tag: condition


title: C-patient-1


title: Rapamycin + Dietary Restriction 12

city: Saint Louis

first: Wilson

middle: Chun Yim

last: Fok

state: MO

address: 660 S Euclid Ave

department: Hematology

institute: Washington University in St. Louis

description: Rapa+DR 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed in R by log2 transformation and z-normalization

source_name: Rapamycin + Dietary Restriction 12

label_protocol: Biotinylated cRNA were prepared using Ambion kit- Illumina TotalPrep RNA Amplification Kit

extract_protocol: Total RNA was extracted from 25 mg of liver in each sample using Qiagen Rneasy kit following manufacturer’s protocol.  RNA quantity was assessed by Nanodrop and RNA quality was assessed by Agilent Bioanalyzer.

value: Liver

tag: age

value: 8 months

tag: Sex

value: Male

tag: protocol

value: 14 ppm Rapamycin + 40% Dietary Restriction


title: Rapamycin + Dietary Restriction 11

description: Rapa+DR 11

source_name: Rapamycin + Dietary Restriction 11


title: Rapamycin + Dietary Restriction 5

description: Rapa+DR 5

source_name: Rapamycin + Dietary Restriction 5


title: HSC,WT,rep3

city: Rochester

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: Arrays were hybridized overnight with 2.8 ug cDNA using using an Affymetrix hyb station, with hybridization solutions and conditions recommended by the kit manufacturer (Nugen).

scan_protocol: After arrays were washed they were stained with phycoerythrin-streptavidin as recommended by Affymetrix (including anti-SAPE antibody enhancement), and phycoerythrin fluorescence was determined with an Affymetrix scanner. Affymetrix Cammand Console software was used to control the scanner and generate raw image files (DAT) and to consolidate data from individual pixels into array features (CEL files).

data_processing: CEL files were quantile normalized and background subtracted with the Iterplier algorithm of Affymetrix Expression Console.

source_name: hematopoietic stem cells, wild-type mouse

label_protocol: Biotinylated cDNA was prepared from total RNA with the Nugen WT-Ovation PicoSL Kit.

growth_protocol: Mice were weaned at 3 weeks and fed ad libitum thereafter.

extract_protocol: Mice were killed by carbon dioxide inhalationat 8 weeks of age. Bone marrow was depleted of Lin+ cells as described by Singh et al. 2009 (Carcinogenesis 30;11-19). SLAM+ HSC were extracted from Lin- cells as described by Kiel et al. 2005 (Cell 121;1109-1121). Selected cells were collected in RNAlater reagent (Ambion) and frozen at -80C until total RNA was extracted with a Micro RNeasy kit (Qiagen).

tag: genotype

value: wild-type Ahr

tag: genetic background

tag: cell type

value: hematopoietic stem cells


title: Rapamycin + Dietary Restriction 6

description: Rapa+DR 6

source_name: Rapamycin + Dietary Restriction 6

tag: strain


title: Rapamycin + Dietary Restriction 10

description: Rapa+DR 10

source_name: Rapamycin + Dietary Restriction 10

tag: tissue


title: HSC,AhrKO,rep1

source_name: hematopoietic stem cells, Ahr-KO mouse

value: Ahr knockout


title: control genital epithelium 2

city: Umeå

first: Karin

last: Danielsson

address: Byggnad 6M

department: Medicalbiosciences

country: Sweden

institute: Umeå University

description: laser microdissected epithelium

hyb_protocol: standard Illumina hybridization protocol

data_processing: Data were normalized and background corrected  in Limma Neqc

source_name: human genital epithelium

label_protocol: Biotinylated cRNA was prepared with the TargetAmp-Nano labeling kit for Illumina Expression BeadChip

extract_protocol: RNA was extracted by the use of trizol reagent,followed by clean up with Qiagen Rneasy mini kit as described in protocol included in the kit. Quality was assed by the use of Agilent Bioanalyzer

tag: gender

value: female

value: genital epithelium


title: HSC,WT,rep4


title: control genital epithelium 4

description: laser microdissected epithelium


title: genital lichen planus epithelium 5

description: laser microdissected epithelium


title: HSC,AhrKO,rep3


title: SiARS2_1_220709_20110630

description: result file: SiARSvsFFL_signal.txt

tag: cell line

value: HeLa H9


title: Rapamycin + Dietary Restriction 4

description: Rapa+DR 4

source_name: Rapamycin + Dietary Restriction 4


title: Rapamycin + Dietary Restriction 9

description: Rapa+DR 9

source_name: Rapamycin + Dietary Restriction 9


title: Rapamycin + Dietary Restriction 8

description: Rapa+DR 8

source_name: Rapamycin + Dietary Restriction 8


title: Rapamycin + Dietary Restriction 3

description: Rapa+DR 3

source_name: Rapamycin + Dietary Restriction 3


title: Rapamycin + Dietary Restriction 7

description: Rapa+DR 7

source_name: Rapamycin + Dietary Restriction 7


title: HSC,AhrKO,rep2


title: control genital epithelium 3

description: laser microdissected epithelium


title: HSC,WT,rep1


title: genital lichen planus epithelium 4

description: laser microdissected epithelium


title: HSC,WT,rep2


title: Rapamycin 12

description: Rapa 12

source_name: Rapamycin 12

value: 14 ppm Rapamycin


title: Rapamycin + Dietary Restriction 2

description: Rapa+DR 2

source_name: Rapamycin + Dietary Restriction 2


title: Rapamycin + Dietary Restriction 1

description: Rapa+DR 1

source_name: Rapamycin + Dietary Restriction 1


title: control genital epithelium 1

description: laser microdissected epithelium


title: genital lichen planus epithelium 1

description: laser microdissected epithelium


title: Rapamycin 11

description: Rapa 11

source_name: Rapamycin 11


title: FAO hepatoma_PA+Met+NaS-treated_replicate17

city: Geelong

first: Bradley

last: Hayward

state: VIC

address: Pigdons Road

country: Australia

institute: Deakin University

description:
Treated for 24 h with 0.075mM PA in RPMI-1640 containing 10% (v/v) FBS (Invitrogen) followed by co-treatment for a further 24 h with 0.075 mM PA, 0.25 mM Met and 2 mM NaS in glucose-free RPMI-1640 containing 0.1% (w/v) BSA (USB Corporation), 2mM Sodium Pyruvate (GIBCO Invitrogen) and 20 mM Sodium L-lactate (Sigma-Aldrich)
To capture the biological variability, replicates were collected over 8 independent days with LDH cellular cytotoxicity analysis.

hyb_protocol: The hybridization solution (100 µl) was then applied to coverslips and mounted onto the array slide. Hybridization was conducted in humid hybridization chambers in a hybridization oven at 65°C for 16-20 h.

scan_protocol: Slides were scanned immediately after washing using the GenePix 4000B scanner (Molecular Devices) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent’s Feature Extraction software (version 9.5.1) was used to extract the data. The data files were then normalised using the 75th percentile value and further scaled so that the median of each array was equal to 1.0. The data used for normalisation had to meet the following filtering criteria; the processing signal be 2-fold above the background, saturated pixels < 50%, the feature must be ‘present’  and only ‘Feature’ probes/genes were used.

source_name: FAO hepatoma PA+Met+NaS-treated

label_protocol: Fluorescently labelled cDNA was prepared from 800 ng total RNA using Agilent Quick Amp Labeling Kit (5190-0424) and Agilent One Color DNA Spike-In Kit (5188-5282) as per manufacturers instructions.

growth_protocol: FAO hepatoma cells were maintained in RPMI-1640 containing 10% FBS (Invitrogen). Maintainence cells were passaged thrice weekly.

extract_protocol: Total RNA was extracted from 3T3-L1 adipocytes using TRIzol reagent (Invitrogen) and purified using Rneasy Mini Kit Columns (Quiagen) as per manufacturer’s instructions

treatment_protocol: FAO hepatoma cells were treated for 24 h with 0.075mM PA in RPMI-1640 containing 10% (v/v) FBS (Invitrogen). FAO hepatoma cells were co-treated for a further 24 h with 0.075 mM PA, 0.25 mM Met and 2 mM NaS in glucose-free RPMI-1640 containing 0.1% (w/v) BSA (USB Corporation), 2mM Sodium Pyruvate (GIBCO Invitrogen) and 20 mM Sodium L-lactate (Sigma-Aldrich)

value: FAO Hepatoma Cells

value: 0.075 mM PA, 0.25 mM Met and 2 mM NaS


title: FAO hepatoma_PA+Met+NaS-treated_replicate20


title: X2C-H3K4me3-ChIP

city: Xiamen

first: Shubin

last: Gao

address: Chengzhi building 110,Xiang'an South Road

department: Basic Medical Sciences

institute: Medical College,Xiamen University

description: H3K4me3 ChIP in HCC specimens X2C

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: H3K4me3 ChIP DNA from HCC specimens X2C

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Fresh HCC specimens were at -80°C.

extract_protocol: Grind the tissue(50-100mg) into a fine powder by Biopulverizer. Add 10ml of culture medium and tissue to the dish. Crosslink by adding 270ul of 37% formaldehyde to a final concentration of 1% to the dish in the hood. Incubate for 10 minutes at  room temperature(RT) on orbital shaker. Followed by quenching with 0.125 M glycine for 5 min. The tissue were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: HCC specimens were transported by dry ice.

value: HCC specimens and their adjacent tissues

source_name: Input DNA from HCC specimens X2C


title: genital lichen planus epithelium 2

description: laser microdissected epithelium


title: Rapamycin 10

description: Rapa 10

source_name: Rapamycin 10


title: FAO hepatoma_PA+Met+NaS-treated_replicate18


title: FAO hepatoma_PA+Met+NaS-treated_replicate15


title: FAO hepatoma_PA+Met+NaS-treated_replicate16


title: FAO hepatoma_PA+Met+NaS-treated_replicate13


title: FAO hepatoma_PA+Met+NaS-treated_replicate19


title: Rapamycin 9

description: Rapa 9

source_name: Rapamycin 9


title: Rapamycin 7

description: Rapa 7

source_name: Rapamycin 7


title: X1N-H3K4me3-ChIP

description: H3K4me3 ChIP in HCC specimens X1N

source_name: H3K4me3 ChIP DNA from HCC specimens X1N

source_name: Input DNA from HCC specimens X1N


title: FAO hepatoma_PA+Met+NaS-treated_replicate14


title: X4N-H3K4me3-ChIP

description: H3K4me3 ChIP in HCC specimens X4N

source_name: H3K4me3 ChIP DNA from HCC specimens X4N

source_name: Input DNA from HCC specimens X4N


title: X4C-H3K4me3-ChIP

description: H3K4me3 ChIP in HCC specimens X4C

source_name: H3K4me3 ChIP DNA from HCC specimens X4C

source_name: Input DNA from HCC specimens X4C


title: X2N-H3K4me3-ChIP

description: H3K4me3 ChIP in HCC specimens X2N

source_name: H3K4me3 ChIP DNA from HCC specimens X2N

source_name: Input DNA from HCC specimens X2N


title: genital lichen planus epithelium 3

description: laser microdissected epithelium

source_name: human genital epithelium


title: FAO hepatoma_PA+Met+NaS-treated_replicate09


title: Rapamycin 8

description: Rapa 8

source_name: Rapamycin 8


title: FAO hepatoma_PA+Met+NaS-treated_replicate10


title: Rapamycin 5

description: Rapa 5

source_name: Rapamycin 5


title: Rapamycin 6

description: Rapa 6

source_name: Rapamycin 6


title: FAO hepatoma_PA+Met+NaS-treated_replicate07

source_name: FAO hepatoma PA+Met+NaS-treated


title: FAO hepatoma_PA+Met+NaS-treated_replicate06


title: FAO hepatoma_PA+Met+NaS-treated_replicate08


title: Rapamycin 4

description: Rapa 4

source_name: Rapamycin 4


title: FAO hepatoma_PA+Met+NaS-treated_replicate02


title: FAO hepatoma_PA+Met+NaS-treated_replicate03


title: Dietary Restriction 11

description: DR 11

source_name: Dietary Restriction 11

value: 40% Dietary Restriction


title: oral lichen planus epithelium 6

description: laser microdissected epithelium

source_name: human oral epithelium

value: oral epithelium


title: Rapamycin 1

description: Rapa 1

source_name: Rapamycin 1


title: X1C-H3K4me3-ChIP

description: H3K4me3 ChIP in HCC specimens X1C

source_name: H3K4me3 ChIP DNA from HCC specimens X1C

source_name: Input DNA from HCC specimens X1C


title: FAO hepatoma_PA-treated_replicate20

description:
Treated for 24 h with 0.075mM PA in RPMI-1640 containing 10% (v/v) FBS (Invitrogen) followed by co-treatment for a further 24 h with 0.075 mM PA in glucose-free RPMI-1640 containing 0.1% (w/v) BSA (USB Corporation), 2mM Sodium Pyruvate (GIBCO Invitrogen) and 20 mM Sodium L-lactate (Sigma-Aldrich)
To capture the biological variability, replicates were collected over 8 independent days with LDH cellular cytotoxicity analysis.

source_name: FAO hepatoma PA-treated


title: oral lichen planus epithelium 7

description: laser microdissected epithelium

value: male


title: FAO hepatoma_PA-treated_replicate16


title: FAO hepatoma_PA+Met+NaS-treated_replicate01


title: FAO hepatoma_PA+Met+NaS-treated_replicate04


title: Rapamycin 3

description: Rapa 3

source_name: Rapamycin 3

value: Liver


title: oral lichen planus epithelium 5

description: laser microdissected epithelium


title: FAO hepatoma_PA-treated_replicate18


title: FAO hepatoma_PA-treated_replicate15


title: FAO hepatoma_PA+Met+NaS-treated_replicate05


title: Rapamycin 2

description: Rapa 2

source_name: Rapamycin 2

value: 8 months


title: oral lichen planus epithelium 4

description: laser microdissected epithelium


title: FAO hepatoma_PA-treated_replicate14


title: oral lichen planus epithelium 3

description: laser microdissected epithelium


title: FAO hepatoma_PA-treated_replicate17


title: FAO hepatoma_PA-treated_replicate19


title: FAO hepatoma_PA+Met+NaS-treated_replicate11


title: FAO hepatoma_PA-treated_replicate13


title: 20100723_CBC20_1_(HuGene-1_0-st-v1)

description: total RNA

data_processing: Sample data table contains all the RMA normalized signal intensity for each affymetrix probesets using Affymetrix Expression Console (v.1.0). The supplementary processed data contains summarized Log2(IP_tests/IP_Cont) data (i.e. ProcessedDatas_EA.xls)

source_name: HeLa_Flag-CBP20 IP

tag: ip antibody

value: anti-Flag Antibody

tag: antibody vendor

value: Sigma

tag: antibody cat. #

tag: antibody lot #


title: Dietary Restriction 10

description: DR 10

source_name: Dietary Restriction 10

value: Male


title: 20100723_CBC20_2_(HuGene-1_0-st-v1)

description: total RNA


title: FAO hepatoma_PA-treated_replicate06


title: FAO hepatoma_PA-treated_replicate09


title: Dietary Restriction 6

description: DR 6

source_name: Dietary Restriction 6


title: oral lichen planus epithelium 1

description: laser microdissected epithelium


title: FAO hepatoma_PA-treated_replicate12


title: IP Flag ARS2 6_(HuGene-1_0-st-v1)

description: total RNA

source_name: HeLa_Flag- Ars2 IP


title: IP ARS2 11.06_(HuGene-1_0-st-v1)_Rep2

description: total RNA


title: FAO hepatoma_PA-treated_replicate08


title: FAO hepatoma_PA-treated_replicate05


title: FAO hepatoma_PA-treated_replicate03


title: FAO hepatoma_PA-treated_replicate11


title: Dietary Restriction 9

description: DR 9

source_name: Dietary Restriction 9


title: FAO hepatoma_PA-treated_replicate04


title: FAO hepatoma_PA-treated_replicate07


title: Dietary Restriction 4

description: DR 4

source_name: Dietary Restriction 4


title: Dietary Restriction 3

description: DR 3

source_name: Dietary Restriction 3


title: FAO hepatoma_PA-treated_replicate10


title: FAO hepatoma_PA-treated_replicate02


title: Dietary Restriction 5

description: DR 5

source_name: Dietary Restriction 5


title: FAO hepatoma_vehicle_replicate08

description:
Treated for 24 h in RPMI-1640 containing 10% (v/v) FBS (Invitrogen) followed by co-treatment for a further 24 h with glucose-free RPMI-1640 containing 0.1% (w/v) BSA (USB Corporation), 2mM Sodium Pyruvate (GIBCO Invitrogen) and 20 mM Sodium L-lactate (Sigma-Aldrich)
To capture the biological variability, replicates were collected over 8 independent days with LDH cellular cytotoxicity analysis.

source_name: FAO hepatoma vehicle

value: vehicle


title: FAO hepatoma_vehicle_replicate07


title: Dietary Restriction 8

description: DR 8

source_name: Dietary Restriction 8


title: FAO hepatoma_PA-treated_replicate01


title: FAO hepatoma_PA+Met+NaS-treated_replicate12

source_name: FAO hepatoma PA+Met+NaS-treated


title: Dietary Restriction 7

description: DR 7

source_name: Dietary Restriction 7


title: oral lichen planus epithelium 2

description: laser microdissected epithelium

source_name: human oral epithelium


title: IP HeLa 5.06_(HuGene-1_0-st-v1)

description: total RNA

source_name: HeLa_control IP


title: FAO hepatoma_vehicle_replicate06


title: Dietary Restriction 1

description: DR 1

source_name: Dietary Restriction 1


title: FAO hepatoma_vehicle_replicate03


title: FAO hepatoma_vehicle_replicate02


title: E17.5 Pax7-nGFP+ cells, biological replicate C

city: Paris

first: Shahragim

last: Tajbakhsh

address: 25 rue du Dr Roux

department: Dept. of Developmental & Stem Cell Biology

institute: Pasteur Institute

description: Gene expression data from E17.5 Pax7-nGFP+ cells from limbs.

hyb_protocol: Fragmented biotin-labeled cRNA samples were hybridized on GeneChip Mouse Genome 430_2 arrays, according to the manufacturer’s protocol

scan_protocol: Not available

data_processing: Raw data were pre-processed using the GC-Robust Multichip Analysis (GCRMA) algorithm in order to correct the background, to adjust the intensity distribution over the arrays and to convert probe intensity summarisation into a unique probe set signal. The mean of Log2 expression signals from biological triplicates were used to make heat maps using MeV software. Local Pooled Error (LPE*) tests were performed in order to identify significant differences in gene expression between groups. The Benjamini-Hochberg (BH**) multiple correction test was applied to control for the number of false positives with an adjusted 5% statistical significance threshold.

source_name: Mouse E17.5 limb buds

label_protocol: cRNA obtained from 100ng of RNA was amplified by using the GeneChip Expression Two-Cycle 3’amplification system (Affymetrix)

extract_protocol: Total RNA was isolated using Qiagen Rneasy Plus micro kit according to the manufacturer's instructions.

treatment_protocol: Embryo limbs were dissected and enzymatically digested in 0.1% trypsin/PBS for 15min at 37°C. Dissociated cells were filtered (40um) and Pax7-GFP+ cells were isolated by FACS.

value: Limb skeletal muscle


title: Dietary Restriction 2

description: DR 2

source_name: Dietary Restriction 2


title: Ad Libitum 9

description: AL 9

source_name: Ad Libitum 9

value: Ad Libitum


title: MPEC wild-type rep1

city: New York

first: Willey

last: Liao

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

description: Gene expression from wild-type KLRG1lo OT-I MPEC T cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0 genome arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using GeneChip Affymetrix scanner 3000 7G

data_processing: The data was analyzed using the RMA and limma methods to assess differential expression

source_name: MPEC wild-type

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

extract_protocol: miRNeasy kit extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

value: OT-I MPEC T cells

tag: genotype/variation

value: wild-type KLRG1lo


title: MPEC wild-type rep2


title: MPEC Foxo1fl/fl rep2

description: Gene expression from GzmB-cre Foxo1fl/fl KLRG1lo OT-I MPEC T cells

source_name: MPEC Foxo1fl/fl

value: GzmB-cre Foxo1fl/fl KLRG1lo


title: SLEC wild-type

description: Gene expression from wild-type KLRG1hi OT-I SLEC T cells

source_name: SLEC wild-type

value: OT-I SLEC T cells

value: wild-type KLRG1hi


title: FAO hepatoma_vehicle_replicate01

value: FAO Hepatoma Cells

tag: treatment


title: Ad Libitum 7

description: AL 7

source_name: Ad Libitum 7


title: E12.5 Pax7-nGFP+ cells, biological replicate C

description: Gene expression data from E12.5 Pax7-nGFP+ cells from limbs.

source_name: Mouse E12.5 limb buds


title: Ad Libitum 10

description: AL 10

source_name: Ad Libitum 10


title: Ad Libitum 8

description: AL 8

source_name: Ad Libitum 8


title: E12.5 Pax7-nGFP+ cells, biological replicate A


title: E17.5 Pax7-nGFP+ cells, biological replicate A


title: E17.5 Pax7-nGFP+ cells, biological replicate B


title: Ad Libitum 4

description: AL 4

source_name: Ad Libitum 4


title: MPEC Foxo1fl/fl rep1


title: Ad Libitum 11

description: AL 11

source_name: Ad Libitum 11


title: FAO hepatoma_vehicle_replicate04

source_name: FAO hepatoma vehicle


title: Ad Libitum 5

description: AL 5

source_name: Ad Libitum 5


title: FAO hepatoma_vehicle_replicate05


title: Ad Libitum 3

description: AL 3

source_name: Ad Libitum 3


title: E12.5 Pax7-nGFP+ cells, biological replicate B


title: Ad Libitum 2

description: AL 2

source_name: Ad Libitum 2


title: Ad Libitum 6

description: AL 6

source_name: Ad Libitum 6


title: Ad Libitum 1

description: AL 1

source_name: Ad Libitum 1


title: Patient 37,Normal,Pre

status: Public on Nov 07 2013

city: Bronx

first: Juan

last: Lin

address: 1300 Morris Park Ave.

institute: Albert Einstein College of Medicine

description: Gene expression data

hyb_protocol: 15 ug of fragmented cRNA  was hybridized to human HG-U133A (Affymetrix) according the manufacturer’s instructions.

scan_protocol: HU133A chips were washed, stained and scanned using the Affymetrix Gene Chip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual

data_processing: In order to compare expression profiles of groups interested (tumor tissues pre- vs. post- bortezomib treatment; tumor tissues pre- vs. post- bortezomib-irinotecan treatment, and pre- treatment normal vs. tumor tissue), related chips were picked out to assemble three sub-datasets. The gene expression measures from these three subsets were then normalized by the robust multi-array analysis (RMA) approach in the Expression Console v1.1 (Affymetrix) software package, separately. Ranking of genes by degree of differential expression was performed using Bioconductor package Limma and in-house R code. Data was analyzed using general linear models, adjusting for matched pairs and including unmatched subjects. Selection of significantly different gene expression profiles between the two experimental conditions was based on the empirical Bayes moderated t-statistic and Benjamini-Hochberg method was applied to correct for multiple testing. Significant genes were identified by adjusted-P value ≤0.05.  Ingenuity Pathway Analysis (version 8.5, Ingenuity Systems, Redwood City, CA) was also performed evaluating differences in gene expression between tumor and normal tissue (N=8 patients), and between post treatment and pretreatment specimens for bortezomib alone (N=2 patients) and bortezomib plus irinotecan (N= 10patients).

source_name: Bortezomib-Irinotecan, Normal

label_protocol: 250-500 ng of total RNA was amplified using the Affymetrix small sample protocol, labled with Biotin.  20ug of cRNA was fragmented according to Affyfetrix manufacturer's protocol (affymetrix)

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini prep kits (Qiagen)  according to the manufacturer's protocol.

treatment_protocol: Tumor samples were placed in RNA later and left at room temperature for 30 minutes, refrigerated overnight, and then frozen at -20 C.

tag: tissue type

value: Normal

tag: tissue site

value: Esophagus

tag: array date


title: Patient 24,Tumor,Pre

description: Gene expression data

source_name: Bortezomib-Irinotecan, Tumor

value: Tumor

value: GE Junction


title: Patient 23,Tumor,Pre

description: Gene expression data


title: Patient 24,Normal,Post

description: Gene expression data


title: Patient 37,Tumor,Post

description: Gene expression data


title: Patient 26,Tumor,Pre

description: Gene expression data


title: Patient 24,Normal,Pre

description: Gene expression data


title: HDFs

city: yokohama-shi

first: yuichi

last: yashiro

state: kanagawa

department: orthodontic department

institute: tsurumi university

hyb_protocol: 1Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Make sure that the gasket slide is flush with the chamber base and is not ajar.2Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.3Grip the slide on either end and slowly put the slide “active side” down, parallel to the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Make sure that the sandwich-pair is properly aligned.4Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.5Firmly hand-tighten the clamp onto the chamber.  6Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. If necessary, tap the assembly on a hard surface to move stationary bubbles.7Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 × g when using 2× Hi-RPM Hybridization Buffer.8Hybridize at 65°C for 17 hours.

scan_protocol: 1Put assembled slide holders with or without the ozone-barrier slide cover into scanner carousel.2Select Start Slot m End Slot n where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.3Select Profile AgilentG3_GX_1color (for SurePrint G3 formats) or Profile AgilentHD_GX_1color (for SurePrint HD formats).4Verify scan settings for one-color scans.5Verify that Output Path Browse is set for desired location.  6Verify that the Scanner status in the main window says Scanner Ready.7Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing:
When comparing data across a set of one-color microarrays, a simple linear scaling of the data is usually sufficient for most experimental applications.Agilent has determined that the signal value of the 75th percentile of all of non-control probes on the microarray is a more robust and representative value of the overall microarray signal as compared to the median or 50th percentile signal. Therefore, use the 75th percentile signal value to normalize Agilent one-color microarray signals for inter-array comparisons. To do downstream analysis of Agilent microarray data, We Uue GeneSpring GX 9.0 or later.
To normalize Agilent one-color microarray data without the GeneSpring program, use the 75th percentile value for each microarray assay in the Agilent Feature Extraction text file.  1Generate a Feature Extraction text file. 2Find the “STATS Table” in the middle section of the text file. This section describes the results from the array-wide statistical calculations. 3Find the 75th percentile value of the non-control signals under the column with the heading gPercentileIntensityProcessedSignal. 4Divide each of the green processed signals (gProcessedSignal) by the 75th percentile signal (gPercentileIntensityProcessedSignal) to generate the 75th percentile normalized microarray processed signals.

source_name: normal human dermal fibroblasts (HDFs)

label_protocol: 1Equilibrate water bath to 60°C. 2For each microarray, add each of the components as indicated in Cyanine 3-labeled, linearly amplified cRNA 5.00 μg to a 1.5 mL nuclease-free microfuge tube: 3Mix well but gently on a vortex mixer.4Incubate at 60°C for exactly 30 minutes to fragment RNA.5Immediately cool on ice for one minute.6Add 2× Hi-RPM Hybridization Buffer to stop the fragmentation reaction.7Mix well by careful pipetting part way up and down. Do not introduce bubbles to the mix. The surfactant in the 2× Hi-RPM Hybridization Buffer easily forms bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.8Spin for 1 minute at room temperature at 13,000 × g in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.Use immediately. Do not store.9Place sample on ice and load onto the array as soon as possible.

growth_protocol: Normal human periodontal ligament fibroblasts (HPDLFs) derived from a 16-year-old male (Lonza Biosciences, Basel, Switzerland) were maintained in stromal cell basal medium (SCBM™, Takara Bio Inc., Otsu, Japan) supplemented with growth factors (basic fibroblast growth factor, insulin), 10% FBS, and gentamicin/amphotericin-B. Normal human dermal fibroblasts (HDFs) (KURABOU Co., Ltd., Osaka, Japan) were maintained in Medium106S supplemented with low serum growth supplement (LSGSTM Life Technologies, Carlsbad, CA). Normal human gingival  fibroblasts (HGFs)  were maintained in DMEM supplemented with low serum growth supplement (LSGSTM Life Technologies, Carlsbad, CA).

extract_protocol: Total RNAs were extracted from the above cell lines using Isogen (Nippon Gene Co., Ltd., Toyama, Japan).

value: dermal

value: fibroblast


title: Patient 37,Tumor,Pre

description: Gene expression data


title: Patient 19,Normal,Post

description: Gene expression data


title: Patient 20,Tumor,Post

description: Gene expression data


title: Patient 26,Normal,Post

description: Gene expression data


title: Patient 26,Tumor,Post

description: Gene expression data


title: Patient 26,Normal,Pre

description: Gene expression data


title: Patient 19,Tumor,Post

description: Gene expression data


title: Patient 23,Tumor,Post

description: Gene expression data


title: Patient 23,Normal,Post

description: Gene expression data


title: Patient 19,Tumor,Pre

description: Gene expression data


title: Patient 14,Tumor,Pre

description: Gene expression data

value: Gastric


title: Patient 15,Tumor,Post

description: Gene expression data


title: Patient 20,Normal,Pre

description: Gene expression data


title: HPDLFs

source_name: normal human periodontal ligament fibroblasts (PDLFs)

value: periodontal ligament


title: Patient 15,Normal,Post

description: Gene expression data


title: Patient 20,Normal,Post

description: Gene expression data


title: Patient 15,Normal,Pre

description: Gene expression data


title: Patient 15,Tumor,Pre

description: Gene expression data


title: Patient 23,Normal,Pre

description: Gene expression data


title: Patient 24,Tumor,Post

description: Gene expression data


title: Patient 14,Normal,Pre

description: Gene expression data


title: Patient 20,Tumor,Pre

description: Gene expression data


title: HGFs

source_name: normal human gingival fibroblasts (HGFs)

value: gingiva


title: Patient 12,Tumor,Post

description: Gene expression data

source_name: Bortezomib alone, Tumor

value: Peri-umbilical lymph node


title: Patient 9,Tumor,Post

description: Gene expression data

value: Lymph Node FNA


title: Patient 6,Tumor,Pre

description: Gene expression data


title: Patient 6,Tumor,Post

description: Gene expression data


title: Patient 7,Tumor,Pre

description: Gene expression data


title: Patient 10,Tumor,Post

description: Gene expression data


title: Patient 4,Tumor,Pre

description: Gene expression data


title: Patient 9,Tumor,Pre

description: Gene expression data


title: Patient 12,Tumor,Pre

description: Gene expression data


title: 9_Hep3_GATA4,6_Cre

city: Philadelphia

first: Rena

last: Zheng

state: PA

address: 3615 Civic Center Blvd. Abramson Research Center 315A

institute: Children's Hospital of Philadelphia

description:
SAMPLE 9
replicate3

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay system  was used to hybridize Biotin -aRNA to the Illumina Mouse WG-6 v 2 Expression Beadchip

scan_protocol: Illumina BeadArray Reader  with Illumina BeadScan

data_processing: The data were quantile normalized between each other and filtered to remove non-informative probes (with detection p-value >0.05 in all samples)

source_name: Mouse hepatocytes

label_protocol: Total RNA was labeled with Epicentre TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip

extract_protocol: Total RNA was extracted with TRIzol reagent from hepatocytes.  RNA quality was determined by Bioanalyzer and only samples with RNA integrity number (RIN) of >7.5 were used.

treatment_protocol: GATA4,6 fl/fl mice were either intravenously injected with AAV8-Tbg-Cre or AAV8-Tbg-GFP two weeks prior to harvesting of RNA

tag: age

value: postnatal 2.5-4.5 months

value: Hepatocytes from liver


title: 8_Hep2_GATA4,6_Cre

description:
SAMPLE 8
replicate2

tag: genotype


title: 3_Hep3_GATA4,6_GFP

description:
SAMPLE 3
replicate3

value: AAV-Tbg-GFP


title: 7_Hep1_GATA4,6_Cre

description:
SAMPLE 7
replicate1


title: 11_Hep5_GATA4,6_Cre

description:
SAMPLE 11
replicate5


title: 7_Hep7_GATA4_Cre

description:
replicate 3
SAMPLE 7

treatment_protocol: GATA4 fl/fl mice were either intravenously injected with AAV8-Tbg-Cre or AAV8-Tbg-GFP two weeks prior to harvesting of RNA

value: GATA4 depleted

value: CD1 x 129S1/SvImJ

value: postnatal 2-3 months


title: 6_Hep6_GATA4_Cre

description:
replicate 2
SAMPLE 6


title: 10_Hep4_GATA4,6_Cre

description:
SAMPLE 10
replicate4


title: 5_Hep5_GATA4_Cre

description:
replicate 1
SAMPLE 5


title: 12_Hep6_GATA4,6_Cre

description:
SAMPLE 12
replicate6


title: Patient 5,Tumor,Post

description: Gene expression data


title: 4_Hep4_GATA4_GFP

description:
replicate 4
SAMPLE 4

value: GFP


title: 8_Hep8_GATA4_Cre

description:
replicate 4
SAMPLE 8


title: 5_Hep5_GATA4,6_GFP

description:
SAMPLE 5
replicate5


title: 4_Hep4_GATA4,6_GFP

description:
SAMPLE 4
replicate4


title: 3_Hep3_GATA4_GFP

description:
replicate 3
SAMPLE 3


title: 6_Hep6_GATA4,6_GFP

description:
SAMPLE 6
replicate6


title: 1_Hep1_GATA4_GFP

description:
replicate 1
SAMPLE 1


title: 2_Hep2_GATA4,6_GFP

description:
SAMPLE 2
replicate2


title: Holoclone_PC3-2G7_vs_PC3

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
Holoclone PC3/2G7 versus Parent PC3 cells
Total RNA was prepared from a combination of each of four sequential cell passages for each PC3-derived parental cell line or holoclone, as indicated.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software.

data_processing: Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1)

label: Alexa 555

source_name: PC3 Holoclone 2G7

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

growth_protocol: PC3 cells, obtained from the American Type Culture Collection (Manassas, VA), and PC3-derived holoclones, were cultured in RPMI 1640 medium containing 2.05 mM L-glutamine, 2 g/liter sodium bicarbonate and 2 g/liter glucose (Invitrogen, Carlsbad, CA) together with 7% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Trizol extraction of total RNA. Total RNA was prepared from each of four sequential cell passages for each PC3-derived holoclone, and from four passages of parental PC3 cells, 48 h after seeding the cells at 100,000 cells per well of a 6-well plate. For each sample (holoclones or parental PC3 cells), a pool of RNA was prepared by combining equal amounts of RNA from each passage to minimize the effects of passage number and inter-sample variability

tag: colony morphology

value: Holoclone

label: Alexa 647

source_name: PC3 parental

value: Mixed


title: 2_Hep2_GATA4_GFP

description:
replicate 2
SAMPLE 2

tag: cell type


title: Oligodendroglioma o-0484

city: Beijing

first: Tao

last: Jiang

address: Tiantan Xili No.6, Dongcheng District

department: Neurosurgery

institute: Beijing Tiantan Hospital, Capital Medical University

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Data were acquired using the Agilent G2565BA Microarray Scanner System and Agilent Feature Extraction Software (version 9.1).

data_processing: Probe intensities were normalized using GeneSpring GX 11.0.

source_name: Human oligodendroglioma

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA from frozen tumor samples was extracted using the mirVana miRNA Isolation kit (Ambion) according to the manufacturers protocol. RNA concentration and quality were measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies).

tag: individual

value: Chinese patient

value: brain tumor

tag: tumor grade

value: WHO grade 2

tag: disease state

value: oligodendroglioma

tag: patient age

tag: patient gender

value: female


title: 1_Hep1_GATA4,6_GFP

description:
SAMPLE 1
replicate1

tag: strain

tag: tissue


title: Oligodendroglioma o-0672

value: male


title: Holoclone_PC3-1A8_vs_PC3

description:
Holoclone PC3/1A8 versus Parent PC3 cells
Total RNA was prepared from a combination of each of four sequential cell passages for each PC3-derived parental cell line or holoclone, as indicated.

tag: cell line

source_name: PC3 Holoclone 1A8


title: Holoclone_PC3-2H10_vs_PC3

description:
Holoclone PC3/2H10 versus Parent PC3 cells
Total RNA was prepared from a combination of each of four sequential cell passages for each PC3-derived parental cell line or holoclone, as indicated.

source_name: PC3 Holoclone 2H10


title: Oligodendroglioma o-0387


title: Oligodendroglioma o-0485


title: Oligodendroglioma o-0543


title: Holoclone_PC3-5A2_vs_PC3

description:
Holoclone PC3/5A2 versus Parent PC3 cells
Total RNA was prepared from a combination of each of four sequential cell passages for each PC3-derived parental cell line or holoclone, as indicated.

source_name: PC3 Holoclone 5A2


title: Glioblastoma gbm-0518

source_name: Human glioblastoma

value: WHO grade 4

value: glioblastoma


title: Oligodendroglioma o-0579


title: Oligodendroglioma o-0659


title: Oligodendroglioma o-0275


title: Oligodendroglioma o-0633


title: Oligodendroglioma o-0589


title: Oligodendroglioma o-0639


title: Glioblastoma gbm-0462


title: Oligodendroglioma o-0323


title: Oligodendroglioma o-0446


title: Glioblastoma gbm-0822


title: Anaplastic oligodendrocytoma aoa-0596

source_name: Human anaplastic oligodendrocytoma

value: WHO grade 3

value: anaplastic oligodendrocytoma


title: Glioblastoma gbm-0104


title: Anaplastic oligodendrocytoma aoa-0562


title: Anaplastic oligodendrocytoma aoa-0492


title: Anaplastic oligodendrocytoma aoa-0406


title: Anaplastic oligodendrocytoma aoa-0391


title: Anaplastic oligodendrocytoma aoa-0513


title: Anaplastic oligodendrocytoma aoa-0438


title: Anaplastic oligodendrocytoma aoa-0352


title: Anaplastic oligodendrocytoma aoa-0498


title: Anaplastic oligodendrocytoma aoa-0351


title: Anaplastic oligodendroglioma ao-0508

source_name: Human anaplastic oligodendroglioma

value: anaplastic oligodendroglioma


title: Anaplastic oligodendroglioma ao-0558


title: Anaplastic oligodendroglioma ao-0403


title: Anaplastic astrocytoma aa-0405

source_name: Human anaplastic astrocytoma

value: anaplastic astrocytoma


title: Anaplastic oligodendroglioma ao-0474


title: Anaplastic oligodendrocytoma aoa-0329


title: Anaplastic oligodendroglioma ao-0260


title: Anaplastic astrocytoma aa-0331


title: Anaplastic oligodendrocytoma aoa-0393


title: Anaplastic astrocytoma aa-0334


title: Anaplastic oligodendrocytoma aoa-0259


title: Anaplastic oligodendrocytoma aoa-0232


title: Anaplastic astrocytoma aa-0353


title: Anaplastic oligodendroglioma ao-0598


title: Anaplastic oligodendroglioma ao-0364


title: Astrocytoma a-0776

source_name: Human astrocytoma

value: astrocytoma


title: Anaplastic astrocytoma aa-0412


title: Anaplastic oligodendroglioma ao-0489


title: Anaplastic oligodendroglioma ao-0490


title: Anaplastic oligodendrocytoma aoa-0231


title: Anaplastic oligodendroglioma ao-0314


title: Astrocytoma a-0767


title: Astrocytoma a-0792


title: Anaplastic astrocytoma aa-0476


title: Anaplastic astrocytoma aa-0354


title: Astrocytoma a-0753


title: Astrocytoma a-0770


title: Anaplastic astrocytoma aa-0249


title: Astrocytoma a-0746


title: Astrocytoma a-0743


title: Astrocytoma a-0712


title: Astrocytoma a-0673


title: Astrocytoma a-0692


title: Astrocytoma a-0708


title: Astrocytoma a-0718


title: Astrocytoma a-0663


title: Astrocytoma a-0711


title: Astrocytoma a-0736


title: Astrocytoma a-0583


title: Astrocytoma a-0548


title: Astrocytoma a-0552


title: Astrocytoma a-0648


title: Astrocytoma a-0469


title: Astrocytoma a-0542


title: Astrocytoma a-0522


title: Astrocytoma a-0595


title: Astrocytoma a-0571


title: Astrocytoma a-0601


title: Astrocytoma a-0544


title: Astrocytoma a-0688


title: SK-MEL-28.20µMBRD32048/16h.rep1

first: Marius

last: Pop

address: 450 Brookline ave

institute: DFCI

hyb_protocol: Hybridization and scanning were conducted using the Affymetrix GeneTitan (MC) instrument (Affymetrix PN 00-0372), according to the attached standard protocol.http://www.affymetrix.com/estore/esearch/search.jsp?Ntt=titan&basic=1

scan_protocol: CEL files were produced using the Affymetrix GeneChip Command Console software (Affymetrix PN agcc01) integrated with the GeneTitan. http://www.affymetrix.com/estore/browse/products.jsp?productId=131429#1_1

data_processing: The data were analyzed with R 3.0.2, using the package affy_1.40.0, and RMA as normalization method. RMA was used with default options (normalize=TRUE, background=TRUE) and with the package hthgu133ahsentrezgcdf v17.1.0 from Brainarray for the CDF file.

label_protocol: Labeling was conducted manually, using the Affymetrix 3' IVT Express Kit (Affymetrix PN 901253) according to the attached standard protocol. Reactions were cycled on the Thermo Hybaid MBS Satellite 0.2G cycler. http://www.affymetrix.com/estore/esearch/search.jsp?pd=131549&N=429496729

growth_protocol: Cells were grown in RPMI media supplemented with 10% FBS

extract_protocol:
QIAgen kit according to manufacturer protocol
Total RNA from the samples was normalized to 50 ng/ul and the GeneChip® 3’ IVT Express Kit (Affymetrix PN 901253) was used for amplification according to the standard protocol. The total RNA underwent reverse transcription to synthesize first-strand cDNA. This cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-conjugated nucleotide. The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the samples for hybridization to Affymetrix HT-HG U133 A peg arrays (Affymetrix PN 900751).

treatment_protocol: shRNA expression was performed for 4 days. Coumpound treatment was 20 µM for 16 hours. Final DMSO concentration (treatment and control) was at 0.2%.

tag: cell line type

value: melanoma cell line


title: SK-MEL-28.20µMBRD32048/16h.rep3

tag: treatment


title: brown-like adipocytes differentiated from Lgr4 mutant  SVF, biological rep2

city: Shanghai

first: ruixin

last: liu

address: 2nd Ruijin Road, Building 11, 925

institute: ruixin liu

description: Gene expression data from brown-like adipocytes differentiated from Lgr4 mutant eWAT SVF

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 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 analyzed with Partek Genomics Suite 6.6 using RMA as normalization method.

source_name: brown-like adipocytes differentiated from eWAT SVF of Lgr4 homozygous mutant mice

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix 3' IVT Expression Kit protocol from 500 ng total RNA.

growth_protocol: Stromal vascular fraction (SVF) of epididymal WAT (eWAT) was isolated and cultured in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin (Invitrogen), and 10 ng/ml murine bFGF (R&D systems).

extract_protocol: Total RNA was extracted from cells using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: SVF cells of the two genotypes were plated in 12-well plates to reach confluency and then differentiated to brown adipocyte in growth medium supplemented with 5 μg/ml insulin, 0.5 mM isobutylmethylxanthine (IBMX) (Sigma), 1 μM dexamethasone (Sigma), 50 nM T3 (Sigma), and 5 μM troglitazone (Sigma) for 48 h, and further in growth medium supplemented with insulin, T3 and troglitazone for 6 days.

tag: genotype/variation

value: Lgr4 homozygous mutant

tag: gender

value: 4 months


title: Astrocytoma a-0505


title: Astrocytoma a-0592


title: SK-MEL-28.20µMBRD32048/16h.rep2


title: Astrocytoma a-0590


title: brown-like adipocytes differentiated from Lgr4 mutant  SVF, biological rep1

value: brown-like adipocytes differentiated from eWAT SVF


title: brown-like adipocytes differentiated from wild-type SVF, biological rep2

description: Gene expression data from brown-like adipocytes differentiated from wild-type eWAT SVF

source_name: brown-like adipocytes differentiated from eWAT SVF of wild-type mice

value: wild-type


title: Astrocytoma a-0626

value: Chinese patient

value: brain tumor


title: Astrocytoma a-0461

value: WHO grade 2


title: SK-MEL-28.DMSO/16h.rep3

source_name: SK-MEL-28, DMSO control/16h, rep3

value: DMSO control/16h


title: SK-MEL-28.DMSO/16h.rep2

source_name: SK-MEL-28, DMSO control/16h, rep2


title: SK-MEL-28.ETV1-sh5.rep1

source_name: SK-MEL-28, ETV1-sh5, 4 days, rep1

treatment_protocol:
24 hours post-lentiviral infection add 1µg/ml puromycin for 4 days
shRNA expression was performed for 4 days. Coumpound treatment was 20 µM for 16 hours. Final DMSO concentration (treatment and control) was at 0.2%.

value: ETV1-sh5, 4 days


title: SK-MEL-28.ETV1-sh3.rep2

source_name: SK-MEL-28, ETV1-sh3, 4 days, rep2

value: ETV1-sh3, 4 days


title: Astrocytoma a-0459

value: male


title: Astrocytoma a-0434


title: SK-MEL-28.ETV1-sh3.rep1

source_name: SK-MEL-28, ETV1-sh3, 4 days, rep1


title: SK-MEL-28.DMSO/16h.rep1

source_name: SK-MEL-28, DMSO control/16h, rep1


title: SK-MEL-28.ETV1-sh5.rep2

source_name: SK-MEL-28, ETV1-sh5, 4 days, rep2


title: brown-like adipocytes differentiated from wild-type SVF, biological rep1


title: SK-MEL-28.ETV1-sh5.rep3

source_name: SK-MEL-28, ETV1-sh5, 4 days, rep3


title: Astrocytoma a-0433


title: Astrocytoma a-0402


title: Astrocytoma a-0407


title: SK-MEL-28.ETV1-sh3.rep3

source_name: SK-MEL-28, ETV1-sh3, 4 days, rep3


title: Astrocytoma a-0396


title: Astrocytoma a-0447


title: SK-MEL-28.GFP-sh.rep2

source_name: SK-MEL-28, GFP-sh, 4 days, rep2

value: GFP-sh, 4 days


title: Astrocytoma a-0399


title: SK-MEL-28.GFP-sh.rep3

source_name: SK-MEL-28, GFP-sh, 4 days, rep3


title: SR1 MHG, rep1

city: Stanford

first: Kyle

middle: M.

last: Loh

address: 265 Campus Drive

department: Department of Developmental Biology

institute: Stanford University School of Medicine

description:
MHG_1
Cultured cells.
Gene expression data.

hyb_protocol: Microarray processing was conducted per the in-house guidelines of the Stanford PAN Facility.

data_processing: The data were RMA normalized using the Broad Institute's online GenePattern pipeline (http://genepattern.broadinstitute.org/) using default parameters (quantile normalized and background corrected).

source_name: Midgut/hindgut (SR1-induced), day 7

growth_protocol: Prior to differentiation, uncommitted HES3 hESCs were maintained in an undifferentiated state by cultivation in mTeSR1 (StemCell Technologies) on tissue culture plates coated with Matrigel (BD Biosciences).

extract_protocol: High-quality RNA was extracted using the RNeasy Plus Mini Kit (Qiagen), and RNA integrity was validated by Bioanalyzer on-chip electrophoresis.

treatment_protocol: hESCs were differentiated into anterior primitive streak, definitive endoderm, anterior foregut, posterior foregut or midgut/hindgut using the defined, serum-free SR1 system as described in the accompanying paper (KM Loh and LT Ang). hESCs were also differentiated towards endodermal populations using the pre-existing serum-based (D'Amour et al., 2005; Nature Biotechnology) or AFBLy-based (Touboul et al., 2010; Hepatology) protocols.

value: midgut/hindgut (SR1-induced)

tag: day of in vitro differentiation


title: SK-MEL-28.GFP-sh.rep1

source_name: SK-MEL-28, GFP-sh, 4 days, rep1


title: SR1 MHG, rep3

description:
MHG_3
Cultured cells.
Gene expression data.

scan_protocol: Microarray processing was conducted per the in-house guidelines of the Stanford PAN Facility.


title: Astrocytoma a-0357

value: female


title: SR1 PFG, rep3

description:
PFG_3
Cultured cells.
Gene expression data.

source_name: Posterior foregut (SR1-induced), day 7

label_protocol: Microarray processing was conducted per the in-house guidelines of the Stanford PAN Facility.

value: posterior foregut (SR1-induced)


title: SR1 MHG, rep2

description:
MHG_2
Cultured cells.
Gene expression data.


title: Astrocytoma a-0379

source_name: Human astrocytoma

value: astrocytoma


title: Astrocytoma a-0321


title: LNCaP.872.DOX4d.rep3

source_name: LNCaP.872, doxicyclin 4days, rep3

treatment_protocol:
100ng/ml dox for 4 days
shRNA expression was performed for 4 days. Coumpound treatment was 20 µM for 16 hours. Final DMSO concentration (treatment and control) was at 0.2%.

value: prostate cancer cell line

value: LNCap

value: sh872, doxicyclin 4days


title: LNCaP.872.DOX4d.rep2

source_name: LNCaP.872, doxicyclin 4days, rep2


title: Astrocytoma a-0365


title: SR1 PFG, rep2

description:
PFG_2
Cultured cells.
Gene expression data.


title: LNCaP.872.DOX4d.rep1

source_name: LNCaP.872, doxicyclin 4days, rep1


title: LNCaP.872.DMSO.rep2

source_name: LNCaP.872, DMSO control/16h, rep2

value: sh872, DMSO control/16h


title: LNCaP.872.DMSO.rep3

source_name: LNCaP.872, DMSO control/16h, rep3


title: LNCaP.872.DMSO.rep1

source_name: LNCaP.872, DMSO control/16h, rep1


title: SR1 PFG, rep1

description:
PFG_1
Cultured cells.
Gene expression data.


title: Astrocytoma a-0281


title: Serum, rep3

description:
Serum_3
Cultured cells.
Gene expression data.

source_name: Serum-differentiated hESCs, day 3

value: serum-differentiated hESCs


title: LNCaP.872.20µM16h.rep3


title: Astrocytoma a-0317

value: Chinese patient


title: SR1 AFG, rep2

description:
AFG_2
Cultured cells.
Gene expression data.

source_name: Anterior foregut (SR1-induced), day 7

value: anterior foregut (SR1-induced)


title: SR1 AFG, rep1

description:
AFG_1
Cultured cells.
Gene expression data.


title: Astrocytoma a-0316

value: brain tumor

value: WHO grade 2


title: Astrocytoma a-0258


title: Serum, rep2

description:
Serum_2
Cultured cells.
Gene expression data.


title: Astrocytoma a-0285


title: Serum, rep1

description:
Serum_1
Cultured cells.
Gene expression data.


title: SR1 AFG, rep3

description:
AFG_3
Cultured cells.
Gene expression data.


title: Astrocytoma a-0253


title: LNCaP.872.20µM16h.rep1


title: AFBLy, rep3

description:
AFBLy_3
Cultured cells.
Gene expression data.

source_name: AFBLy-differentiated hESCs, day 3

value: AFBLy-differentiated hESCs


title: LNCaP.872.20µM16h.rep2


title: LNCaP.1117.DOX4d.rep3

source_name: LNCaP.1117, doxicyclin 4days, rep3

value: sh1117, doxicyclin 4days


title: LNCaP.1117.DMSO.rep3

source_name: LNCaP.1117, DMSO control/16h, rep3

value: sh1117, DMSO control/16h


title: LNCaP.1117.DOX4d.rep2

source_name: LNCaP.1117, doxicyclin 4days, rep2


title: LNCaP.1117.DOX4d.rep1

source_name: LNCaP.1117, doxicyclin 4days, rep1


title: LNCaP.1117.DMSO.rep2

source_name: LNCaP.1117, DMSO control/16h, rep2


title: SR1 DE, rep3

description:
DE_3
Cultured cells.
Gene expression data.

source_name: Definitive endoderm (SR1-induced), day 3

value: definitive endoderm (SR1-induced)


title: AFBLy, rep2

description:
AFBLy_2
Cultured cells.
Gene expression data.


title: LNCaP.1117.DMSO.rep1

source_name: LNCaP.1117, DMSO control/16h, rep1


title: SR1 DE, rep1

description:
DE_1
Cultured cells.
Gene expression data.


title: SR1 APS, rep1

description:
APS_1
Cultured cells.
Gene expression data.

source_name: Anterior primitive streak (SR1-induced), day 1

value: anterior primitive streak (SR1-induced)


title: SR1 APS, rep3

description:
APS_3
Cultured cells.
Gene expression data.


title: LNCaP.1117.20µM16h.rep3


title: AFBLy, rep1

description:
AFBLy_1
Cultured cells.
Gene expression data.


title: SR1 APS, rep2

description:
APS_2
Cultured cells.
Gene expression data.


title: LNCaP.1117.20µM16h.rep1


title: LNCaP.1117.20µM16h.rep2


title: SR1 DE, rep2

description:
DE_2
Cultured cells.
Gene expression data.


title: hESC, rep3

description:
hESC_3
Cultured cells.
Gene expression data.

source_name: Human embryonic stem cells, undifferentiated

value: embryonic stem cells


title: DU145_VprBPsh_rep2

city: Los Angeles

first: Kyunghwan

last: Kim

state: California

address: 1450 Biggy Street NRT6517

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were processed and anlayzed by the Array Pipe software.

source_name: Bladder cancer cells

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina array.

extract_protocol: Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.

value: Bladder cancer

value: VprBP-depleted


title: DU145_NCsh_rep2

description: replicate 2

value: mock


title: hESC, rep2

description:
hESC_2
Cultured cells.
Gene expression data.


title: DU145_VprBPsh_rep1

description: replicate 1


title: hESC, rep1

description:
hESC_1
Cultured cells.
Gene expression data.


title: rph1-YPD-rep3

status: Public on Nov 06 2013

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

description:
BH239-4
Gene expression profile from rph1-deleted strain.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on Yeast Genome 2.0. GeneChips were washed and stained in the Affymetrix® GeneChip® Fluidics Station 450 according to the Mini_euk2v3_450 protocol.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The further analysis was performed using GeneSpring 11.

organism: Saccharomyces cerevisiae

source_name: W303 background, rph1, YPD, log phase

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Yeasts were grown in rich medium (YPD) at 30C to log phase.

extract_protocol: Total RNA was extracted by the Geneaid MiniRNA kit according to the manufacturer's instructions.

treatment_protocol: The cell pellets were harvested by centrifugation and washed twice with TBS pH 7.4. The pellets were stored at -80C.

tag: strain/background

value: rph1 deletion

tag: medium

value: rich

tag: growth phase

value: log


title: WT-YPD-rep3

description:
BH239-3
Gene expression profile from WT.

source_name: W303 background, wildtype, YPD, log phase

tag: genotype

value: wild-type


title: DU145_NCsh_rep1

description: replicate 1

tag: cell type


title: rph1-YPD-rep1

description:
1011
Gene expression profile from rph1-deleted strain.


title: rph1-YPD-rep2

description:
BH239-2
Gene expression profile from rph1-deleted strain.


title: WT-YPD-rep2

description:
BH239-1
Gene expression profile from WT.


title: WT-YPD-rep1

description:
1013
Gene expression profile from WT.