title: CB-CD34+

status: Public on Dec 14 2012

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: CD34+ cord blood cells

hyb_protocol: The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes, and then injected into a GeneChip ST cartridge. The arrays were incubated at 45°C for 17 hours ± 1 hour in a rotating oven at 60 rpm. The arrays were then washed and stained according to the GeneChip Expression Wash, Stain and Scan User Manual (P/N702731).

scan_protocol: Fluorescence signals were scanned with the Affymetrix GeneChip Scaner 3000. Affymetrix GeneChip Command Console (AGCC) software was used for acquisition of the initial image of the scanned array.

data_processing: The Affymetrix Expression Console was used to normalize data and determine signal intensity (RMA-Sketch).

label_protocol: 45 μL of fragmented single-stranded DNA was mixed with 15 μL of master mix containing 5X TdT buffer, TdT and DNA Labeling reagent, and was incubated at 37°C for 60 minutes.

growth_protocol: ES cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM)-F12 (Sigma) supplemented with 1x MEM non-essential amino acids (Gibco-Invitrogen), 1x GlutaMAX-I (Gibco-Invitrogen), 20% knockout serum replacement (KSR) (Gibco-Invitrogen), 0.1 mM 2-mercaptoethanol (2-ME)(Sigma), and 5 ng/mL basic fibroblast growth factor (bFGF)(ReproCELL) either on irradiated MEF as feeder layers.

tag: cell type

value: CD34+ cord blood cells


title: Fibroblasts, mometasone, time 6h, patient 1, rep 1

status: Public on Dec 31 2012

type: RNA

city: St. Gallen

first: Florent

last: Baty

address: Rorschacherstrasse 95

department: Lung Center

country: Switzerland

institute: Cantonal Hospital St. Gallen

hyb_protocol: According to Affymetrix' instructions

scan_protocol: GeneArray Scanner

data_processing: Data were normalized using the RMA algorithm (R, Bioconductor)

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary human lung fibroblasts

label_protocol: According to Affymetrix' instructions

growth_protocol: Fibroblast proliferation for 6 hours (10-6 - 10-8M)

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

treatment_protocol: Cells were treated by mometasone furoate, some with additional formoterol

tag: tissue

value: Primary human lung fibroblasts

tag: treatment

value: Mometasone

tag: patient

tag: time


title: Micropatterned Endothelial cell #2

status: Public on Nov 29 2012

city: Stanford

first: Ngan

middle: F

last: Huang

state: CA

address: 300 Pasteur Drive

department: Cardiovascular Medicine

country: USA

institute: Stanford University

hyb_protocol: The samples were hybridized to Affymetrix Human Gene 1.0 ST GeneChips and then scanned on an Affymetrix 3000 scanner according to standard protocols (Lopez ME, Klein AD, Hong J, Dimbil UJ, Scott MP. Neuronal and epithelial cell rescue resolves chronic systemic inflammation in the lipid storage disorder niemann-pick c. Hum. Mol. Genet. 2012;21:2946-2960.)

scan_protocol: Affymetrix 3000 scanner

data_processing: log2 MAS 5.0 then  Significance Analysis of Microarrays (SAM) module in R was used to calculate a d-score used to rank the most differentially expressed genes between groups , along with the corresponding q value for significance using FDR correction for multiple testing, using a cutoff value of q<0.05.

label: biotin

source_name: Micropatterned Endothelial cell #1

label_protocol: For DNA microarray analysis, RNA purity was verified by Agilent Bioanalyzer, and then the cDNA was synthesized and labeling according based on previous publications

growth_protocol: Human microvascular Endothelial Cells (HMDEC, Lonza) were cultured in EGM2MV media (Lonza)

extract_protocol: Trizol for cell lysis, Qiagen RNEasy Kit for total RNA extraction.

treatment_protocol: Polydimethylsiloxane (PDMS) containing non-patterned surface (control) or parallel micropatterned channels were plasma treated and treated with collagen I before cell seeding.

value: primary human microvascular endothelial cells

value: micropatterned


title: Micropatterned Endothelial cell #1


title: Control Endothelial cell #2

source_name: Control Endothelial cell #2

value: control


title: Control Endothelial cell #1

source_name: Control Endothelial cell #1


title: Human_Teff_repeated_T280min

status: Public on Nov 23 2012

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

description: transcriptomic data to construct a dynamic functional network of human regulatory T cell genes

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 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 trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: human peripheral blood of healthy donor

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

growth_protocol: taken from donors, sorted, expanded ex vivo and stimulated

extract_protocol: RNeasy

treatment_protocol: Human Tregs or Teffs were mixed with anti-CD3/anti-CD28-coated Dynabeads (Invitrogen) at a ratio of 1:1 and with 100 U/ml of IL2 (Proleukin, Novartis) and were distributed with 4x106 cells into 1.5 ml microtubes (Eppendorf) for each time point. Before the cells were cultured at 37°C, they were first stored at 4°C to allow cells and beads to settle properly. Samples were taken every 20 min during the first six hours following stimulation, except for TeffGARP and TeffGFP cells, which were measured at time points 0, 100 and 360 min. The cells were centrifuged, and the cell pellets were lysed in RLT buffer (Qiagen) and immediately stored at -70°C.

value: sorted human Teff cells (CD4+CD25-) stimulated by anti-CD3/anti-CD28 Dynal beads/IL2


title: Human_Teff_repeated_T340min


title: Human_Teff_repeated_T260min


title: Human_Teff_repeated_T160min


title: Human_Teff_repeated_T200min


title: Human_Teff_repeated_T320min


title: Human_Teff_repeated_T180min


title: Human_Teff_repeated_T220min


title: Human_Teff_repeated_T360min


title: Human_Teff_repeated_T140min


title: Control (1)_HN [mRNA]

status: Public on Dec 07 2012

city: Philadelphia

first: Bassel

middle: E

last: Sawaya

state: PA

address: 3307 N. Broad Street

department: Neurology

institute: Temple University

description: CONTROL 1

hyb_protocol: Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.

data_processing:
RMA normalization using GeneSpring software.
Quality control measures were carried out to ensure that RNA isolated was not degraded or lost. Housekeeping control genes and spike controls were routinely analyzed on the GeneChip® microarrays to confirm the successful labeling of target RNAs. Preliminary data analysis was performed in conjunction with the Thomas Jefferson University Bioinformatics Program.
GeneChip® array results were also correlated with the array design and annotation information using the NetAffxTM Analysis Center. Hierarchical cluster analysis and heat maps were generated using Spotfire DecisionSite 7.2.

source_name: Primary human Neurons

growth_protocol: Primary human neurons (HN) (5 x 105) purchased from ScienCell Research Laboratories (Carlsbad, CA) were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA). 750 ng of total RNA was used for Gene expression profiling that was performed using the Affymetrix GeneChip® [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]

treatment_protocol: Cells were treated with Tat (10 ng/ml) kindly received from NIH (AIDS reagnets Bank) for 24 hours.


title: Human_Teff_T320min


title: Human_Teff_repeated_T120min


title: Human_Teff_repeated_T60min


title: Human_Teff_T300min


title: Human_Teff_repeated_T100min


title: Human_Teff_repeated_T300min


title: Human_Teff_repeated_T240min


title: Human_Teff_T340min


title: Human_Teff_repeated_T40min


title: Human_Teff_repeated_T80min


title: Human_Teff_T280min


title: Human_Teff_repeated_T0min


title: HIV-1 Vpr (1) [mRNA]

description: SAMPLE 3

scan_protocol: Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.

treatment_protocol: Cells were treated with Vpr (10 pg/ml) kindly received from Dr Eric Cohen (University of Montreal-Canada) for 24 hours.

value: Vpr


title: Human_Teff_T80min


title: Human_Teff_T260min


title: Human_Teff_T40min


title: Human_Teff_T360min


title: Human_Teff_T0min


title: Human_Teff_T160min


title: Human_Teff_T120min


title: Human_Teff_T240min


title: Human_Teff_T20min


title: Human_Treg_repeated_T240min

value: sorted human Treg cells (CD4+CD25hi) stimulated by anti-CD3/anti-CD28 Dynal beads/IL2


title: Human_Teff_T220min


title: Human_Treg_repeated_T280min


title: Human_Teff_T100min


title: Human_Teff_T60min


title: Human_Treg_repeated_T220min


title: Human_Treg_repeated_T320min


title: Human_Treg_repeated_T160min


title: Human_Treg_repeated_T360min


title: Human_Treg_repeated_T340min


title: Human_Teff_T200min


title: Human_Teff_T140min


title: Human_Treg_repeated_T300min


title: Human_Treg_repeated_T180min


title: Human_Treg_repeated_T200min


title: Human_Treg_repeated_T260min


title: Human_Treg_repeated_T60min


title: Human_Treg_repeated_T0min


title: Human_Treg_repeated_T40min


title: Human_Teff_repeated_T20min


title: Human_Treg_repeated_T140min


title: Human_Treg_repeated_T120min


title: Human_Treg_repeated_T80min


title: Human_Treg_T180min


title: Human_Treg_T100min


title: H302

status: Public on Nov 26 2012

type: genomic

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

description: Hybridized to SNP6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The SNP6.0 CEL files were imported in Genotyping Console version 4.1 (Affymetrix) and copy number/LOH analysis performed using regional GC correction and the CN baseline file generated from 270 HapMap samples; GenomeWideSNP_6.hapmap270.na32.r1.a5.ref (downloaded from Affymetrix webpage). Individual SNPs were not assessed. The resulting CNCHP-files were viewed using the software; Chromosome Analysis Suite, version 1.1 (Affymetrix). TXT files of normalized data were exported from the Chromosome Analysis Suite software. All genomic positions were annotated to the hg19 version of the human genome (NCBI build 37).
Detection of CNVs larger than 200 kb with size being the only restriction.

molecule: genomic DNA

source_name: Sample from patient with diffuse large B-cell lymphoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: The tumor sample was after removal snap frozen and stored in OCT at - 80 oC. From each OCT block, 3x20 µm cuts were obtained using a microtome; the slices were washed twice in PBS and homogenized using the TissueLyser II (Qiagen). DNA extraction was performed using the DNeasy Blood & Tissue kit (Qiagen). From one of the patients (H380) a peripheral blood sample was included as a normal control sample (BB39). Mononuclear cells were isolated from the blood sample by Ficoll-Paque Plus (GE Health Care, Uppsala, Sweden) and stored in 10 % DMSO and 20 % serum at – 80 oC. For DNA extraction, the cells were thawed, washed twice in PBS and genomic DNA extracted using the DNeasy Blood & Tissue kit (Qiagen). The DNA was eluted in water and the concentration measured using a Nanodrop (Thermo Scientific)

value: sample of diffuse large B-cell lymphoma


title: Human_Treg_T40min


title: Human_Treg_T80min


title: Human_Treg_T220min


title: Human_Treg_T200min


title: Human_Treg_T340min


title: Human_Treg_T320min


title: Human_Treg_T60min


title: Human_Treg_T360min


title: Human_Treg_T160min


title: Human_Treg_T280min


title: Human_Treg_T140min


title: Human_Treg_T260min


title: Human_Treg_T0min


title: FL2 DINO siRNA doxorubicin repeat 1

status: Public on Nov 20 2012

first: Adam

last: Schmitt

address: 269 Campus Drive

department: Department of Dermatology

description: biological replicate 1

hyb_protocol: Standard illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol

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

source_name: FL2 DINO siRNA doxorubicin repeat 1

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

growth_protocol: Cells were propogated according to standard cell culture conditions for indicated cell lines.

extract_protocol: RNA was isolated by Trizol extraction and Qiagen RNAeasy spin column. DNA contamination eliminated by DNAse treatment. RNA quality was evaluated by Agilent Bioanalyser.

treatment_protocol: Exponentially growing cells treated with 200ng/mL doxorubicin or sham for 26 hours.

value: normal diploid human fetal lung fibroblast

tag: transfection

value: FL2 DINO siRNA


title: Human_Treg_T240min


title: FL2 DINO siRNA doxorubicin repeat 2

description: biological replicate 2

source_name: FL2 DINO siRNA doxorubicin repeat 2


title: Human_Treg_T20min


title: FL2 DINO siRNA untreated repeat 3

description: biological replicate 3

source_name: FL2 DINO siRNA untreated repeat 3


title: FL2 DINO siRNA doxorubicin repeat 3

description: biological replicate 3

source_name: FL2 DINO siRNA doxorubicin repeat 3


title: Human_Teff_T180min


title: FL2 CNTRL siRNA doxorubicin repeat 2

description: biological replicate 2

source_name: FL2 CNTRL siRNA doxorubicin repeat 2

value: FL2 CNTRL siRNA


title: Human_Treg_repeated_T100min


title: HCT116 p53-/- doxorubicin repeat 2

description: biological replicate 2

source_name: HCT116 p53-/- doxorubicin repeat 2

tag: cell line

value: colon cancer

tag: genotype/variation

value: p53 mutant


title: FL2 CNTRL siRNA untreated repeat 1

description: biological replicate 1

source_name: FL2 CNTRL siRNA untreated repeat 1


title: HCT116 p53+/+ untreated repeat 2

description: biological replicate 2

source_name: HCT116 p53+/+ untreated repeat 2

value: p53 wildtype


title: HCT116 p53+/+ untreated repeat 1

description: biological replicate 1

source_name: HCT116 p53+/+ untreated repeat 1


title: HCT116 p53-/- doxorubicin repeat 1

description: biological replicate 1

source_name: HCT116 p53-/- doxorubicin repeat 1


title: FL2 CNTRL siRNA doxorubicin repeat 1

description: biological replicate 1

source_name: FL2 CNTRL siRNA doxorubicin repeat 1


title: HCT116 p53-/- untreated repeat 2

description: biological replicate 2

source_name: HCT116 p53-/- untreated repeat 2


title: HCT116 p53-/- untreated repeat 1

description: biological replicate 1

source_name: HCT116 p53-/- untreated repeat 1


title: FL2 DINO siRNA untreated repeat 2

description: biological replicate 2

source_name: FL2 DINO siRNA untreated repeat 2


title: HCT116 p53+/+ doxorubicin repeat 1

description: biological replicate 1

source_name: HCT116 p53+/+ doxorubicin repeat 1


title: HCT116 p53+/+ doxorubicin repeat 2

description: biological replicate 2

source_name: HCT116 p53+/+ doxorubicin repeat 2


title: Manipulated T(TCM), biological replicate B

status: Public on Nov 16 2012

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from CD8 T(TCM) cells

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

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and log2 expression measure calculated using median polish summarization. Probes were summarized using the revised entrez-based probe annotation of Dai (Dai 2005, the package hgu133plus2hsentrezgcdf.db, version 13)

source_name: human central memory derived-derived CD8 T cells, stimulated anti-CD3/CD28 beads, transduced with HSV-TK and cultured with IL-7 and IL-15 (5 ng/ml) for 15 days (TTCM)

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.

growth_protocol: Purified CD8 T-cell subsets were either directly used for RNA extraction or activated anti-CD3/CD28-conjugated magnetic beads in 3:1 bead/T-cell ratio and then cultured with IL-7 and IL-15 (5 ng/ml) for 15 days.

treatment_protocol: Cells were kept in culture in IMDM supplemented with 10% FBS and IL-7 and IL-15 (5 ng/ml)

tag: cell

value: activated CD8 cells of central memory origin (TTCM)

tag: protocol

value: activated


title: Central memory, biological replicate C

description: Gene expression data from control central memory CD8 cells

source_name: human purified peripheral blood CD8 central memory lymphocytes, untreated

value: unmanipulated CD8 central memory control cells

value: untreated


title: Manipulated T(TN), biological replicate B

description: Gene expression data from CD8 T(TN) cells

source_name: human naïve-derived CD8 T cells, stimulated anti-CD3/CD28 beads, transduced with HSV-TK and cultured with IL-7 and IL-15 (5 ng/ml) for 15 days (TTN)

value: activated CD8 cells of naïve origin (TTN)


title: FL2 CNTRL siRNA untreated repeat 2

description: biological replicate 2

source_name: FL2 CNTRL siRNA untreated repeat 2


title: Manipulated T(TN), biological replicate C


title: Manipulated T(TCM), biological replicate A


title: Central memory, biological replicate B


title: Naive natural, biological replicate B

description: Gene expression data from control naive CD8 cells

source_name: human purified peripheral blood CD8 naïve lymphocytes, untreated

value: unmanipulated CD8 naïve control cells


title: Manipulated T(TCM), biological replicate C


title: H385

description: Hybridized to SNP6.0

source_name: Sample from patient with diffuse large B-cell lymphoma


title: Manipulated T(TN), biological replicate A


title: Naive natural, biological replicate C


title: Naive natural, biological replicate A


title: Central memory, biological replicate A


title: Cord blood CD4+_0h_rep2

status: Public on Nov 09 2012

city: Turku

first: Tapio

last: Lonnberg

address: P.O.Box 123

country: Finland

institute: University of Turku

description: biological replicate 2

hyb_protocol: 15 ug of biotinylated and fragmented cRNA was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays overnight (16-18 hours) at 45*C. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with AutoLoader.

data_processing: The raw microarray data were processed using robust multi-array average normalization and log2-transformed in R (version 2.12.0) using the Bioconductor affy package (version 1.28.0)

source_name: human cord blood CD4+ cell, 0h

label_protocol: Amplification was started from 100 ng of total RNA using the Affymetrix Two-Cycle cDNA Synthesis Kit (P/N 900432), and cDNA/cRNA synthesis reactions and sample cleanup steps were performed according to Affymetrix´s GeneChip Expression Analysis Technical Manual.

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturers instructions.

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen) according to manufacturers instructions. In-column DNase (RNase-Free Dnase Set, Qiagen) treatment was performed for 15 minutes. RNA was eluted in dH2O.

treatment_protocol: Cells were activated on 24-well plates, 4x10^6 cells/ml Yssel´s medium, through the T cell receptor (plate bound antiCD3 500 ng/well, and soluble antiCD28 500 ng/ml, Immunotech, France). To induce Th1 polarization, IL-12 (2.5ng/ml, R&D Systems) was added. To induce Th2 polarization, both IL-4 (10ng/ml, R&D Systems) and anti-IL-12 (10µg/ml, R&D Systems) were added. At 48h timepoint IL-2 (17ng/ml, R&D Systems) was added to the culturing medium. Cells were harvested at 0.5, 1, 2, 4, 6, 12, 24, 48 and 72 h. Naive cells without any treatments were collected as 0h controls from every replicate.

value: CD4+ Th cell, cord blood


title: Cord blood CD4+_Act+IL-4_48h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 48h


title: Cord blood CD4+_Act+IL-4_72h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 72h


title: Cord blood CD4+_Act+IL-4_24h_rep2

description: biological replicate 2

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 24h


title: Cord blood CD4+_Act+IL-4_48h_rep2

description: biological replicate 2


title: Cord blood CD4+_0h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act+IL-4_48h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act+IL-4_12h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 12h


title: Cord blood CD4+_Act+IL-4_72h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act+IL-4_24h_rep1

description: biological replicate 1


title: Cord blood CD4+_0h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act+IL-4_12h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-12_72h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-12 treated, 72h


title: Cord blood CD4+_Act+IL-12_48h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated and IL-12 treated, 48h


title: Cord blood CD4+_Act+IL-12_12h_rep2

description: biological replicate 2

source_name: human cord blood CD4+ cell, activated and IL-12 treated, 12h


title: Cord blood CD4+_Act+IL-12_12h_rep1

description: biological replicate 1


title: Human_Treg_repeated_T20min

source_name: human peripheral blood of healthy donor


title: Cord blood CD4+_Act+IL-4_12h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act+IL-12_12h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act+IL-12_24h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated and IL-12 treated, 24h


title: Cord blood CD4+_Act+IL-12_48h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-12_24h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act+IL-4_24h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act+IL-4_72h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-12_24h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-12_72h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act_72h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated, 72h


title: Cord blood CD4+_Act+IL-12_48h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act_48h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated, 48h


title: Cord blood CD4+_Act_12h_rep2

description: biological replicate 2

source_name: human cord blood CD4+ cell, activated, 12h


title: Cord blood CD4+_Act_24h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated, 24h


title: Cord blood CD4+_Act_24h_rep3

description: biological replicate 3


title: FL2 DINO siRNA untreated repeat 1

description: biological replicate 1

source_name: FL2 DINO siRNA untreated repeat 1


title: Cord blood CD4+_Act_48h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act_12h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act_48h_rep2

description: biological replicate 2


title: Human_Treg_T300min


title: NCCIT-DF_2

status: Public on Oct 19 2012

city: Augusta

first: Keith

last: robertson

address: 1120 15th street

institute: Georgia Health Sciences University

description: differential NCCIT, biological rep2

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were analyzed using RMA (with quantile normalization), significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO). Gene annotation enrichment analysis was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 and Ingenuity Pathways Analysis (IPA Ingenuity® Systems) for all significantly changed genes (≥ ±1.5 fold, P < 0.01).

label: TdT

source_name: NCCIT treated with RA for 7 days

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: NCCIT cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone).

treatment_protocol: Treatment of NCCIT cells with 10 μM all-trans retinoic acid (RA) was performed for up to 7 days

tag: tumor cell line

value: NCCIT

value: embryonic cancer

tag: cell status

value: differentiated


title: NCCIT-DF_3

description: differential NCCIT, biological rep3


title: NCCIT-DF_1

description: differential NCCIT, biological rep1


title: Cord blood CD4+_Act_24h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act_72h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act_12h_rep3

description: biological replicate 3


title: Cell line SW1116

status: Public on Oct 02 2012

city: Rehovot

first: Michal

last: Sheffer

address: Herzel

country: Israel

institute: Weizmann Institute of Science

description: Cell line SW1116 SW1116

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: data was summarized using PLIER algorithm

source_name: Tissue samples taken from colorectal cancer patients

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: scan date

tag: patient id

value: Cell line

tag: included in analysis

value: No


title: Cell line MCF7

description: Cell line MCF7 MCF7


title: Cell line LNCap

description: Cell line LNCap LNCap

value: LNCap


title: NCCIT-UD_3

description: undifferential NCCIT, biological rep3

source_name: undifferential NCCIT

value: undifferentiated


title: Cell line SW620

description: Cell line SW620 SW620


title: Cell line HCT15rehyb

description: Cell line HCT15rehyb HCT15rehyb


title: Cell line HT29

description: Cell line HT29 HT29


title: Cell line LOVO

description: Cell line LOVO LOVO

value: LOVO


title: NCCIT-UD_1

description: undifferential NCCIT, biological rep1


title: Cell line HTB39

description: Cell line HTB39 HTB39


title: Cell line HCT15

description: Cell line HCT15 HCT15


title: Cell line NCM460

description: Cell line NCM460 NCM460


title: Cell line DLD1

description: Cell line DLD1 DLD1


title: Cell line WiDr

description: Cell line WiDr WiDr

value: WiDr


title: mature CD5+CD27- PB B cells CD5_naive_5

status: Public on Sep 27 2012

city: Essen

first: Marc

middle: JS

last: Seifert

state: NRW

address: Virchowstraße 173

department: IFZ

country: Germany

institute: University Hospital Essen

description: CD43 negative

hyb_protocol: cRNA was hybridized to GPL6244 Arrays with the Affymetrix GeneChip Hybridization, Wash and Stain kit, according to manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G and GeneChip Command Console 3.2 software.

data_processing: Data were normalized according to vsn and imported into Gene Spring GX 11.5.1 for further analysis.

source_name: human peripheral blood

label_protocol: Samples were processed with WT Ovation PICO RNA Amplification System, the WT Ovation Exon module and fragmented and labeled with the Encore Biotin module according to manufacturer's instructions.

growth_protocol: cell sorting, see sample title

extract_protocol: 10,000 cell samples sorted into Trizol lysis buffer, hydrous phase mixed with equal volume of 70% EtOH and loaded onto Qiagen RNeasy micro colum. Further processing according to manufacturer's instruction.

tag: tumor stage

value: non-tumor

value: mature CD5+CD27- PB B cells


title: mature CD5+CD27- PB B cells CD5_naive_2

description: CD43 negative


title: mature CD5+CD27+ PB B cells CD5_CD27_5

description: CD43 negative

value: mature CD5+CD27+ PB B cells


title: mature CD5+CD27+ PB B cells CD5_CD27_4

description: CD43 negative


title: mature CD5+CD27- PB B cells CD5_naive_1

description: CD43 negative


title: mature CD5+CD27- PB B cells CD5_naive_4

description: CD43 negative


title: mature CD5+CD27- PB B cells CD5_naive_3

description: CD43 negative


title: mature CD5+CD27+ PB B cells CD5_CD27_3

description: CD43 negative


title: RNA-Seq analysis of cDNA_Lib 3 derived from human hippocampus middle cells; cDNA_Lib 3

status: Public on Sep 05 2012

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.12080
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: transcriptomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM916094_BI.Brain_Hippocampus_Middle.mRNA-Seq.150.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 3.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Brain Hippocampus Middle, Donor 150 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13716
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 180,715,638
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.61
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM916094_BI.Brain_Hippocampus_Middle.mRNA-Seq.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 3.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Brain Hippocampus Middle, Donor 150 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13719
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BHM mRNA 50
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle mRNA-Seq Donor 150 Library cDNA_Lib 3 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 180,715,638
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.61
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; cDNA_Lib 3

extract_protocol: Library construction protocol: Strand specific cDNA libraries were constructed for Illumina sequencing using the dUTP method essentially as described in S. Zhong et al, Cold Spring Harbor Protoc 8, 940 - 949 (2011).

tag: sample alias

tag: sample common name

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD present

tag: disease

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 73.0 Years

value: 1.8X SPRI cleanup (no size selection)

value: Dynabeads mRNA purification kit (Invitrogen)

value: 95C  2mins, 10 cycles of: 98C for 30 sec, 55C for 30 sec, 72C for 1 min, then 72C for 10 min, hold 4C

value: NNNNNN

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: PFU Ultra II

value: CAAGCAGAAGACGGCATACGAGAT

value: 98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min.

value: mRNA-Seq

value: We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h.


title: polymorphonuclear leukocyte control cells time 180 replicate 1

status: Public on Sep 06 2012

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description:
3592_SFG_1_human_10_Cntl-180-1_01_3931
Gene expression data from PMN leukocyte control cells time 180 replicate 1

hyb_protocol: Samples from 3 different PMN donors were hybridized on HU133+2 GeneChips (Affymetrix, Santa Clara, CA) according to manufacturer's recommendations

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis. The trimmed mean target intensity of each array was arbitrarily set to 1250.

source_name: polymorphonuclear leukocyte control cells time 180 min

label_protocol: 12 µg of biotin-labeled cRNA target as previously described [PMID:11983860]

growth_protocol: PMNs were isolated from venous whole blood of healthy individuals as described [PMID:11983860]. Each subject gave informed consent prior to participation in the study and all work was approved by the Institutional Review Board for Human Subjects, National Institute of Allergy and Infectious Diseases, National Institutes of Health, USA.

extract_protocol: At each indicated time point, PMNs were lysed with RLT buffer and RNA was purified

treatment_protocol: PMNs (1 × 107) in RPMI/H were cultured with 1 nM PVL or iPVL at 37°C for 30, 60, or 180 min.

tag: cell type

value: polymorphonuclear leukocyte


title: polymorphonuclear leukocyte control cells time 180 replicate 2

description:
3593_SFG_1_human_11_Cntl-180-2_01_5751
Gene expression data from PMN leukocyte control cells time 180 replicate 2


title: mature CD5+CD27+ PB B cells CD5_CD27_2

description: CD43 negative

value: non-tumor

value: mature CD5+CD27+ PB B cells


title: polymorphonuclear leukocyte control cells time 180 replicate 3

description:
3594_SFG_1_human_12_Cntl-180-3_01_8460
Gene expression data from PMN leukocyte control cells time 180 replicate 3


title: polymorphonuclear leukocyte control cells time 0 replicate 3

description:
3585_SFG_1_human_03_Cntl-0-3_01_8523
Gene expression data from PMN leukocyte control cells time 0 replicate 3

source_name: polymorphonuclear leukocyte control cells time 0 min


title: DC_IFNα1_3days_rep1

status: Public on Sep 20 2012

city: Montpellier

first: Geneviève

last: Garcin

address: UM2. Place Eugene Bataillon. Bat 24.

country: France

institute: CNRS UMR5235

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with HWS kit.

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

data_processing: The values from the data matrix are MAS5 values and derived from affymetrix expression console software.

source_name: IFNα1-DC at 3 days of differentiation

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT Express protocol from 200 ng total RNA (3'IVT ExpressTechnical Manual, 2009, P/N702646 Rev1 Affymetrix).

extract_protocol: Total RNA were extracted with the High Pure RNA isolation Kit from Roche and according to manufacturer's instructions.

tag: ifn type1

tag: Stage

value: 3 days of differentiation


title: polymorphonuclear leukocyte control cells time 0 replicate 2

description:
3584_SFG_1_human_02_Cntl-0-2_01_5746
Gene expression data from PMN leukocyte control cells time 0 replicate 2


title: polymorphonuclear leukocyte control cells time 30 replicate 1

description:
3586_SFG_1_human_04_Cntl-30-1_01_3949
Gene expression data from PMN leukocyte control cells time 30 replicate 1

source_name: polymorphonuclear leukocyte control cells time 30 min


title: iPS3 (Huf5) cell derived Endothelial Cells New Method

status: Public on Sep 01 2012

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St

department: GICD

institute: J. David Gladstone Institute

description:
New Method- EB formation one day, then Aggregation medium +10% mTeSR medium + BMP4 (12ng/ml)+bFGF (5ng/ml) +ACTIVIN A (6ng/ml) until day 4. After day 4 Aggregation medium+ 10ng/ml VEGF+10ng/ml bFGF.  Day 6, MACS was performed according and KDR+ cells were plated on fibronectin in ECM medium (ScienCell, Carlsbad, CA) with 5% FBS, pen/strep and ECGS (10 mg/ml BSA, 10 mg/ml apo-transferrin, 5 mg/ml insulin, 10 ng/ml EGF, 2 ng/ml bFGF, 2 ng/ml VEGF, 2 ng/ml IGF-1, 1 mg/ml hydrocortisone and 30 ng/mL retinoic acid). KDR+ cells were allowed to grow to 80 90% confluence.
Old Method- EB formation followed by addition of 10 ng/mL VEGF from Day1 to Day14 and then CD31+ cell sorting on Day14
Unless otherwise stated, all differentiations were done with the new method.

hyb_protocol: Labeled samples were then hybridized to Affymetrix Human Gene 1.0 ST GeneChips. GeneChips were then washed and stained on Affymetrix 450 Fluidics Stations using manufacturor's instructions

scan_protocol: Arrays were scanned on an Affymetrix 3000 Scanner according to standard protocols

data_processing: Microarrays were normalized to control for array-specific effects with the Affymetrix Power Tools software using Robust Multi-Array normalization. All probe sets in which none of the groups had an average log2 intensity greater than 3.0 were removed. Linear models were fitted for each gene using the limma package (Smyth 2008) in R/Bioconductor

label_protocol: RNA was amplified, fragmented and labeled using NuGEN Technologies Applause Plus kits and the manufacturer's instructions

growth_protocol: All cells were grown in endothelial cell media (ECM) from Sciencell in 6 well plates..

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The RNA was cleaned and DNAse digested on RNeasy columns (Qiagen, Valencia, CA).

treatment_protocol: All cells were grown until completely confluent, washed with PBS and collected in Trizol

tag: differentiation protocol

value: New Method

tag: starting material

value: Human iPS Cell (Viral OSKM)

tag: source cell line

value: iPS3 (Huf5)

value: Endothelial Cell


title: DC_IFNα8_3days_rep1

source_name: IFNα8-DC at 3 days of differentiation


title: iPS 2 (3S5F) cell derived Endothelial Cells Day Y (different from Day X)

value: iPS 2 (3S5F)


title: polymorphonuclear leukocyte control cells time 60 replicate 2

description:
3590_SFG_1_human_08_Cntl-60-2_01_3961
Gene expression data from PMN leukocyte control cells time 60 replicate 2

source_name: polymorphonuclear leukocyte control cells time 60 min


title: iPS3 (Huf5) cell derived Endothelial Cells Old Method

value: Old Method


title: polymorphonuclear leukocyte control cells time 60 replicate 3

description:
3591_SFG_1_human_09_Cntl-60-3_01_3923
Gene expression data from PMN leukocyte control cells time 60 replicate 3


title: DC_IFNβ_3days_rep1

source_name: IFNβ-DC at 3 days of differentiation

value: IFNβ-DC


title: polymorphonuclear leukocyte control cells time 30 replicate 2

description:
3587_SFG_1_human_05_Cntl-30-2_01_3947
Gene expression data from PMN leukocyte control cells time 30 replicate 2


title: polymorphonuclear leukocyte control cells time 60 replicate 1

description:
3589_SFG_1_human_07_Cntl-60-1_01_5742
Gene expression data from PMN leukocyte control cells time 60 replicate 1


title: DC_IFNα2_3days_rep1

source_name: IFNα2-DC at 3 days of differentiation


title: polymorphonuclear leukocyte control cells time 30 replicate 3

description:
3588_SFG_1_human_06_Cntl-30-3_01_3940
Gene expression data from PMN leukocyte control cells time 30 replicate 3


title: polymorphonuclear leukocyte control cells time 0 replicate 1

description:
3583_SFG_1_human_01_Cntl-0-1_01_5780
Gene expression data from PMN leukocyte control cells time 0 replicate 1


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; IPS cell line 18c; CE_AM_1013094

status: Public on Aug 07 2012

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
IPS cells were differentiated in vitro from fibroblasts using standard methods; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7561
sample alias: 64.0
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2305

hyb_protocol: As recommended by Affymetrix

scan_protocol: As recommended by Affymetrix

data_processing: Processed data were not provided for this record

source_name: IPS cell line 18c; CE_AM_1013094

label_protocol: As recommended by Affymetrix

growth_protocol: tissue culture

extract_protocol: Cells were lysed and RNA extracted using Qiagen Rneasy kit

treatment_protocol: untreated cultured cells

value: Harvard University

value: Cell Line

tag: line

tag: lineage

value: induced pluripotent cells

value: induced pluripotent stem cells

value: undifferentiated

tag: passage

tag: medium

value: KSR

tag: Sex

value: Female

tag: batch


title: iPS 2 (3S5F) cell derived Endothelial Cells Day X (different from Day Y)


title: H7 ES cell derived Endothelial Cells

source_name: H7 ES cell derived Endothelial Cells

value: Human ES Cell


title: H9 ES cell derived Endothelial Cells New Method


title: H1 ES cell derived Endothelial Cells

source_name: H1 ES cell derived Endothelial Cells


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; IPS cell line 18b; CE_AM_1013093

description:
sample_term_id: NTR_0001166
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
IPS cells were differentiated in vitro from fibroblasts using standard methods; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7560
sample alias: 63
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3897

source_name: IPS cell line 18b; CE_AM_1013093


title: iPS 1 (K23F) cell derived Endothelial Cells

value: iPS 1 (K23F)


title: H9 ES cell derived Endothelial Cells Old Method


title: Human Saphenous Vein Endothelial Cell Primary Line

value: Primary Cells


title: Human Aortic Endothelial Cell Primary Line

source_name: Human Aortic Endothelial Cell Primary

value: New Method


title: Human Lymphatic Endothelial Cell Primary Line


title: NKG2D positive 2 (Biological replica 2)

status: Public on Aug 15 2012

city: Frederiksberg C

first: Helle

last: Jensen

address: Stigbojlen 7

department: Section of Biomedicine

institute: LIFE, University of Copenhagen

description: Gene expression data for HCMV stimulated memory CD4 T-cells

hyb_protocol: Performed according to standard Affymetrix protocols, at RH Microarray Center at the Center for Genomic Medicine, Copenhagen, Denmark  protocols, at RH Microarray Center at the Center for Genomic Medicine,  Copenhagen, Denmark

data_processing: Cell intensity files (CEL files) were generated in the GeneChip® Command Console® Software (AGCC); The data were modeled using the RMA (Robust Multichip Average) approach, followed by mean Probe Set summarization giving each gene a single expression value (Partek Genomics Suite 6.5).

source_name: HCMV stimulated memory CD4 T-cells

label_protocol: RNA was amplified and labeled using the Ambion WT Expression Kit (Applied Biosystems) according to manufactures instructions. Performed at RH Microarray Center at the Center for Genomic Medicine, Copenhagen, Denmark

growth_protocol: Human CD4 T-cells were isolated from buffy coat by anti-CD4 conjugated magnetic beads. Memory CD4 T-cells were sorted, labeled with CFSE and stimulated with autologous monocytes pulsed with HCMV for 20 (donor 1) or 17 (donor 2) days.

extract_protocol: Total RNA was extractet using Trizol reagent (Invitrogen), according to the manufactures instructions.

treatment_protocol: Autologous monocytes were pulsed for 5 hr with 5µg/ml HCMV before addition of the sorted memory CD4 T-cells. 50U/ml IL-2 was added at day 6 post stimulation.

value: CD4 T-cell

tag: ag specificity

value: HCMV

tag: cell surface marker

value: NKG2D positive


title: NCCIT-UD_2

description: undifferential NCCIT, biological rep2

source_name: undifferential NCCIT

tag: tumor cell line

value: NCCIT

value: embryonic cancer

tag: cell status


title: NKG2D negative 2 (Biological replica 2)

scan_protocol: Performed according to standard Affymetrix protocols, at RH Microarray Center at the Center for Genomic Medicine, Copenhagen, Denmark  protocols, at RH Microarray Center at the Center for Genomic Medicine,  Copenhagen, Denmark

value: NKG2D negative


title: PMN-LPS-2

status: Public on Aug 03 2012

city: Manhasset

first: Dennis

last: Davidson

state: New York

address: 350 Community Dr

department: Pediatrics

institute: The Feinstein Institute for Medical Research

description: Gene Expression data from the Umbilical Cord Blood Polymorphonuclear cells treated with PBS vehicle for 1 hr followed by 10ng/ml Lipopolysaccharide stimulation for 4 hrs

hyb_protocol: Fragmented cRNA (n=5) were hybridized to Affymetrix Human U133 plus 2.0 microarray chips in hybridization oven for 18hr at 45˚C, processed by Gene Chip 450 fluidics station.

scan_protocol: Chips were scanned by Gene Chip 3000 scanner

data_processing: Raw data (n=5 patients) was uploaded onto GeneSifter (internet-based microarray data analysis software), log transformed and normalized using GC-RMA (v 1.1)

source_name: Umbilical Cord blood Polymorphonucler cells; LPS

label_protocol: Total RNA was amplified and labled using Ambion MessageAmp II-Biotin enhanced kit. Total RNA and cRNA purity and integrity were monitored by 260/280 and 260/230 ratios respectively, using a Bioanalyzer .

growth_protocol: PMNs and MONOs were resuspended in RPMI 1640+10%FCS at 5x106 cells/mL.

extract_protocol: Total RNA was isolated using Qiagen RNeasy spin columns.

treatment_protocol: Cells were pre-incubated with PBS (vehicle control) or stimulated with LPS (10 ng/mL) for 4 h. Cells were harvested and suspended in RNAlater to preserve RNA.

tag: human umbilical cord blood cells

value: Polymorphonuclear cells

tag: treatment

value: LPS (10 ng/mL) for 4 h


title: NKG2D negative 1 (Biological replica 1)

tag: cell type


title: PMN-LPS-5


title: PMN-PBS-5

description: Gene Expression data from the Umbilical Cord Blood Polymorphonuclear cells treated with 10^ -8 M Dexamethasone for 1 hr followed by 10ng/ml Lipopolysaccharide stimulation for 4 hrs

source_name: Umbilical Cord blood Polymorphonucler cells; PBS

value: PBS (vehicle control)


title: mature CD5+CD27+ PB B cells CD5_CD27_1

description: CD43 negative

source_name: human peripheral blood

tag: tumor stage

value: non-tumor

value: mature CD5+CD27+ PB B cells


title: PMN-LPS-3


title: Mono-LPS-4

description: Gene Expression data from the Umbilical Cord Blood Monocytes treated with PBS vehicle for 1 hr followed by 10ng/ml Lipopolysaccharide  stimulation for 4 hrs

source_name: Umbilical Cord blood Monocytes; LPS

value: Monocytes


title: PMN-PBS-4


title: PMN-PBS-2


title: NKG2D positive 1 (Biological replica 1)


title: Mono-LPS-3


title: PMN-PBS-1


title: Mono-PBS-5

description: Gene Expression data from the Umbilical Cord Blood Monocytes treated with 10^ -8 M Dexamethasone for 1 hr followed by 10ng/ml Lipopolysaccharide  stimulation for 4 hrs

source_name: Umbilical Cord blood Monocytes; PBS


title: Mono-LPS-1


title: PMN-PBS-3


title: PMN-LPS-1


title: PMN-LPS-4


title: Mono-LPS-2


title: Mono-PBS-3


title: Mono-PBS-4


title: Mono-PBS-1


title: Mono-PBS-2


title: Monocytes from healthy donor number 8 isolated immediately after drawing blood

status: Public on Jun 14 2012

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description:
peripheral blood monocytes were isolated immediately after drawing blood. Monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 8 that were immediately isolated after drawing blood

hyb_protocol: label protocol for 14 SLE chips (including SLE test samples), 8 RA chips (RA1 to RA 11, without RA test samples) and 12 ND chips: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol. label protocol for 3 TNF_1.5h chips, 7 IFNa2a_1.5h chips, 7 IFNg_1.5h chips, 11 Un_1.5h chips and 8 Un_0h chips: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v5 protocol. label protocol for 4 RA test chips: RA_1_test, RA_18 test, RA_88_test and RA_98 test: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the FS450_0001 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database (www.bioretis.de)

source_name: peripheral blood monocytes

label_protocol:
label protocol for 14 SLE chips (including SLE test samples), 8 RA chips (RA1 to RA 11, without RA test samples) and 12 ND chips: 3-5 µg of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)
label protocol for 3 TNF_1.5h chips, 7 IFNa2a_1.5h chips, 7 IFNg_1.5h chips, 11 Un_1.5h chips and 8 Un_0h chips: 300 ng of total RNA was amplified and labelled using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit according to Affymetrix instruction
label protocol for 4 RA test chips: RA_1_test, RA_18 test, RA_88_test and RA_98 test: 100 ng of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)

extract_protocol: RNA was collected by using the RNeasy mini kit (Qiagen)

treatment_protocol: only for Affymetrix chips where monocytes were stimulated in vitro by TNFα, IFNα2a and IFNγ

tag: individual

value: healthy donor 8

tag: disease state

value: healthy


title: Monocytes from healthy donor number 4 isolated immediately after drawing blood

description:
peripheral blood monocytes were isolated immediately after drawing blood. Monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 4 that were immediately isolated after drawing blood

value: healthy donor 4


title: Monocytes from healthy donor number 10 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 10 that were incubated in whole blood without any stimulation for 1.5 hour

value: healthy donor 10


title: Monocytes from healthy donor number 6 isolated immediately after drawing blood

description:
peripheral blood monocytes were isolated immediately after drawing blood. Monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 6 that were immediately isolated after drawing blood

value: healthy donor 6


title: Monocytes from healthy donor number 3 isolated immediately after drawing blood

description:
peripheral blood monocytes were isolated immediately after drawing blood. Monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 3 that were immediately isolated after drawing blood

value: healthy donor 3


title: Monocytes from healthy donor number 7 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 7 that were incubated in whole blood without any stimulation for 1.5 hour

value: healthy donor 7


title: Monocytes from healthy donor number 2 isolated immediately after drawing blood

description:
peripheral blood monocytes were isolated immediately after drawing blood. Monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 2 that were immediately isolated after drawing blood

value: healthy donor 2


title: Monocytes from healthy donor number 9 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 9 that were incubated in whole blood without any stimulation for 1.5 hour

value: healthy donor 9


title: Monocytes from healthy donor number 1 isolated immediately after drawing blood

description:
peripheral blood monocytes were isolated immediately after drawing blood. Monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 1 that were immediately isolated after drawing blood

value: healthy donor 1


title: Monocytes from healthy donor number 5 isolated immediately after drawing blood

description:
peripheral blood monocytes were isolated immediately after drawing blood. Monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 5 that were immediately isolated after drawing blood

value: healthy donor 5


title: Monocytes from healthy donor number 6 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 6 that were incubated in whole blood without any stimulation for 1.5 hour


title: Monocytes from healthy donor number 4 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 4 that were incubated in whole blood without any stimulation for 1.5 hour


title: Monocytes from healthy donor number 7 isolated immediately after drawing blood

description:
peripheral blood monocytes were isolated immediately after drawing blood. Monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 7 that were immediately isolated after drawing blood


title: Monocytes from healthy donor number 7 stimulated with IFNγ for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNγ in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 7 that were stimulated in vitro by IFNγ for 1.5 hour

value: stimulated with IFNγ for 1.5 hour


title: Monocytes from healthy donor number 11 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 11 that were incubated in whole blood without any stimulation for 1.5 hour

value: healthy donor 11


title: Monocytes from healthy donor number 2 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 2 that were incubated in whole blood without any stimulation for 1.5 hour


title: Monocytes from healthy donor number 8 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 8 that were incubated in whole blood without any stimulation for 1.5 hour


title: Monocytes from healthy donor number 1 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 1 that were incubated in whole blood without any stimulation for 1.5 hour


title: Monocytes from healthy donor number 3 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 3 that were incubated in whole blood without any stimulation for 1.5 hour


title: Monocytes from healthy donor number 4 stimulated with IFNγ for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNγ in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 4 that were stimulated in vitro by IFNγ for 1.5 hour


title: Monocytes from healthy donor number 3 stimulated with IFNγ for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNγ in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 3 that were stimulated in vitro by IFNγ for 1.5 hour


title: Monocytes from healthy donor number 2 stimulated with IFNγ for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNγ in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 2 that were stimulated in vitro by IFNγ for 1.5 hour


title: Monocytes from healthy donor number 5 incubated for 1.5 hour without any stimulation

description:
peripheral blood monocytes were incubated at 37 °C in whole blood for 1.5 hour. Following incubation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 5 that were incubated in whole blood without any stimulation for 1.5 hour


title: Monocytes from healthy donor number 5 stimulated with IFNγ for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNγ in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 5 that were stimulated in vitro by IFNγ for 1.5 hour


title: Mono-LPS-5

description: Gene Expression data from the Umbilical Cord Blood Monocytes treated with PBS vehicle for 1 hr followed by 10ng/ml Lipopolysaccharide  stimulation for 4 hrs

value: LPS (10 ng/mL) for 4 h


title: Monocytes from healthy donor number 6 stimulated with IFNγ for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNγ in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 6 that were stimulated in vitro by IFNγ for 1.5 hour


title: Monocytes from healthy donor number 1 stimulated with IFNγ for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNγ in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 1 that were stimulated in vitro by IFNγ for 1.5 hour


title: Monocytes from healthy donor number 6 stimulated with IFNα2a for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNα2a in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 6 that were stimulated in vitro by IFNα2a for 1.5 hour

value: stimulated with IFNα2a for 1.5 hour


title: Monocytes from healthy donor number 4 stimulated with IFNα2a for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNα2a in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 4 that were stimulated in vitro by IFNα2a for 1.5 hour


title: Monocytes from healthy donor number 1 stimulated with TNFα for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by TNFα in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 1 that were stimulated in vitro by TNFα for 1.5 hour

value: stimulated with TNFα for 1.5 hour


title: Monocytes from RA patient number 98 for testing (RA_98_test)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient for testing number 98, labelled as RA_98_test

value: Monocytes

value: patient for testing number 98

value: RA


title: MAC_Sea_Rep1

status: Public on Jun 10 2012

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

hyb_protocol: The labeled DNA was added to a hybridization cocktail (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20, 0.1 mg ml-1 of HS DNA, and 0.5 mg ml-1 acetylated bovine serum albumine), then the sample was injected into the array, (GeneChip Mouse Gene 1.0 ST Array). Washed and stain processes were performed in the GeneChip Fluidics Station 450.

scan_protocol: The probe arrays were scanned using The GeneChip® Scanner 3000 7G (Affmetrix, Santa Clara CA, USA).

data_processing: Microarray rma background correction and quantile normalization was done using the Oligo package in R Bioconductor. Differentially expressed genes were  determined using the Limma package.

source_name: Macrophage Seasonal rep1

label_protocol: 1 µg of total RNA was used to generate double-stranded cDNA by reverse transcription using an oligo(dT) primer containing a T7 RNA polymerase promoter followed by an in vitro transcription to obtain cRNA molecules. A second cDNA synthesis was performed incorporating dUTP nucleotides to the newly generated strand. Then, cDNA fragmentation was performed using a combination of uracil DNA glycosylase (UDG) and apurinic/apirymidinic endonuclease 1 (APE1). The resulting fragmented DNA was labeled using terminal deoxynucleotidyl transferase (TdT) and  biotinylated nucleotides.

extract_protocol: The macrophages were obtained by the isolation of monocytes from total peripheral blood by density gradient centrifugation. CD14+ monocytes were purified using magnetic beads, and seeded in 10% FBS, 1% L-glutamine, supplemented RPMI 1640 culture medium with penicillin and streptomycin to induce differentiation into macrophages.  Differentiated macrophages were assessed by flow cytometry; in which the expression of CD11b, HLA-DR and CD14 were measured.  Finally the macrophages were treated with 5x105 TCID of the pandemic A/H1N1. RNA was extracted with commercial method based in columns, following the manufacture procedure. Briefly the cells were homogenized to obtain the nucleic acid. The RNA was washing with ethanol and eluted in 30ul of free RNase water. The RNA concentration was determined using a spectrophotometer and its integrity was evaluated on an Agilent 2100 Bioanalyzer

tag: sample

value: 5 treated macrophages from five independent experiments were pooled.

tag: infection (virus strain)

value: Influenza seasonal virus A/PR/8/34 strain


title: Monocytes from healthy donor number 7 stimulated with IFNα2a for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNα2a in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 7 that were stimulated in vitro by IFNα2a for 1.5 hour

value: healthy


title: Monocytes from healthy donor number 3 stimulated with IFNα2a for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNα2a in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 3 that were stimulated in vitro by IFNα2a for 1.5 hour

value: healthy donor 3


title: Monocytes from healthy donor number 2 stimulated with IFNα2a for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNα2a in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 2 that were stimulated in vitro by IFNα2a for 1.5 hour


title: MAC_H1N1_Rep1

source_name: Macrophage H1N1 rep1

value: Influenza A/H1N1 virus isolated from a patient with fatal pneumonia during the first outbreak in Mexico City in April 2009.


title: Monocytes from healthy donor number 5 stimulated with IFNα2a for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNα2a in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 5 that were stimulated in vitro by IFNα2a for 1.5 hour


title: Monocytes from healthy donor number 2 stimulated with TNFα for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by TNFα in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 2 that were stimulated in vitro by TNFα for 1.5 hour

value: healthy donor 2


title: Monocytes from RA patient number 18 for testing (RA_18_test)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient for testing number 18, labelled as RA_18_test

value: patient for testing number 18


title: Monocytes from healthy donor number 1 stimulated with IFNα2a for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by IFNα2a in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 1 that were stimulated in vitro by IFNα2a for 1.5 hour

value: healthy donor 1


title: Th17-enriched_Donor3

status: Public on May 13 2012

city: New Haven

first: Wei

last: Zhang

state: Connecticut

institute: Yale School of Medicine

description:
SAMPLE 11
Gene expression data from in vitro expanded Th17-enriched effector T cells

hyb_protocol: Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.

scan_protocol: The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.

data_processing: The data was RMA normalized using Partek Genomics suite.

label_protocol: High quality total RNA is subjected to the Ambion Whole Transcript Expression Kit where their patented primer is used to prime for mRNA and coding RNA’s only. The RNAs that have been primed are then amplified to create cDNA and which is used in in vitro transcription to create cRNA. The cRNA is cleaned using Ambion’s bead purification that comes within the WT Expression kit and quantitated. 10ug of amplified cRNA is placed into a reaction with a random primer and then onto to generate a second cycle of 1st strand sense direction cDNA. The cDNA is purified using the Ambion bead cleanup as described previously and quantitated. 5.5ug of sscDNA is then enzymatically fragmented using ADP and UDG using the Affymetrix Terminal Labeling kit and ran on the Agilent bioanalyzer to ensure proper transcript size. The fragmented material is then labeled using TdT and then placed into a hybridization cocktail.

growth_protocol: Human PBMDs were isolated by Ficoll separation, and then FACS-sorted to naïve and CD161-CCR6-, CD161+CCR6+ CD4 T cells.

extract_protocol: Total RNA isolation was done with Qiagen Rneasy Kit according to manufacturer's manual.

treatment_protocol: Naïve T cells were in vitro differentiated to Th1 with IL-12 and anti-IFNgamma for 7 days. CD161-CCR6- and CD161+CCR6+ memory T cells were in vitro expanded with IL-1b and IL-23 for 7 days.

value: lymphocytes


title: Th17-negative_Donor4

description:
SAMPLE 17
Gene expression data from in vitro expanded Th17-negative effector T cells


title: MAC_H1N1_Rep2

source_name: Macrophage H1N1 rep2


title: Th17-negative_Donor3

description:
SAMPLE 16
Gene expression data from in vitro expanded Th17-negative effector T cells


title: Th17-negative_Donor2

description:
SAMPLE 15
Gene expression data from in vitro expanded Th17-negative effector T cells


title: Th17-enriched_Donor5

description:
SAMPLE 13
Gene expression data from in vitro expanded Th17-enriched effector T cells


title: Monocytes from healthy donor number 3 stimulated with TNFα for 1.5 hour

description:
peripheral blood monocytes were stimulated in vitro by TNFα in whole blood for 1.5 hour. Following stimulation, monocyte were depleted from granulocytes by CD15 MACS beads, and subsequently they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes from healthy donor 3 that were stimulated in vitro by TNFα for 1.5 hour


title: Th17-negative_Donor5

description:
SAMPLE 18
Gene expression data from in vitro expanded Th17-negative effector T cells


title: Monocytes from RA patient number 1 for testing (RA_1_test)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient for testing number 1, labelled as RA_1_test

value: patient for testing number 1


title: Th17-enriched_Donor4

description:
SAMPLE 12
Gene expression data from in vitro expanded Th17-enriched effector T cells


title: Monocytes from RA patient number 88 for testing (RA_88_test)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient for testing number 88, labelled as RA_88_test

value: patient for testing number 88


title: Th17-negative_Donor1

description:
SAMPLE 14
Gene expression data from in vitro expanded Th17-negative effector T cells


title: Th17-enriched_Donor2

description:
SAMPLE 10
Gene expression data from in vitro expanded Th17-enriched effector T cells


title: MAC_Sea_Rep2

source_name: Macrophage Seasonal rep2

extract_protocol: The macrophages were obtained by the isolation of monocytes from total peripheral blood by density gradient centrifugation. CD14+ monocytes were purified using magnetic beads, and seeded in 10% FBS, 1% L-glutamine, supplemented RPMI 1640 culture medium with penicillin and streptomycin to induce differentiation into macrophages.  Differentiated macrophages were assessed by flow cytometry; in which the expression of CD11b, HLA-DR and CD14 were measured.  Finally the macrophages were treated with 5x105 TCID of the seasonal A/PR/8/34 strain. RNA was extracted with commercial method based in columns, following the manufacture procedure. Briefly the cells were homogenized to obtain the nucleic acid. The RNA was washing with ethanol and eluted in 30ul of free RNase water. The RNA concentration was determined using a spectrophotometer and its integrity was evaluated on an Agilent 2100 Bioanalyzer


title: Th17-enriched_Donor1

description:
SAMPLE 9
Gene expression data from in vitro expanded Th17-enriched effector T cells


title: Th1_Donor4

description:
SAMPLE 8
Gene expression data from in vitro differentiated Th1 cells

source_name: in vitro dfferentiated Th1


title: Th1_Donor3

description:
SAMPLE 7
Gene expression data from in vitro differentiated Th1 cells


title: Naïve_Donor1

description:
SAMPLE 1
Gene expression data from human naïve T cells

source_name: peripheral naïve T cells


title: Naïve_Donor4

description:
SAMPLE 4
Gene expression data from human naïve T cells


title: Th1_Donor2

description:
SAMPLE 6
Gene expression data from in vitro differentiated Th1 cells


title: Th1_Donor1

description:
SAMPLE 5
Gene expression data from in vitro differentiated Th1 cells


title: Naïve_Donor3

description:
SAMPLE 3
Gene expression data from human naïve T cells


title: BEAS-2B_V-transformed_Clone_rep_2

status: Public on Mar 22 2012

city: Tuxedo

first: Hailey

last: Clancy

state: NY

address: 57 Old Forge Road

department: Environmental Medicine

institute: New York University

hyb_protocol: cRNA generated by the labeling procedure was hybridized for 16 hr to the Affymetrix array according to the manufacturer's manual. Genechips were processed using protocol FS450_0007 for Genechip® fluidics station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files; data from cel files were batch normalized in R using the COMBAT package.   The probe-level analysis of the batch-normalized data was done by the RMA-16 algorithm using GeneSpring GX11.5 program.

source_name: 10.0uM NaVO4_30 days_metal removed_clone isolated from agar (4 wks)_grown in monolayer (3 wks)

label_protocol: The cDNA probes were synthesized using the WT Expression Kit for Affymetrix Whole Transcript Expression Arrays (Ambion), fragmented, and labeled using Affymetrix Whole Transcript Terminal Labeling Kit (Affymetrix).

growth_protocol: cell were grown under standard laboratory conditions in DMEM supplemented with 10% FBS and 1% PenStrep; a single cell suspension of 5,000 cells per 9.6 square cm was seeded in soft agar at a concentration of 0.35%

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s protocol and purified using RNeasy Plus Micro Kit (Qiagen).

treatment_protocol: Cells were treated with an aqueous filter-sterlized solution of metals at the concentrations and days indicated prior to seeding in soft agar; metal was removed before seeding in soft agar and for the remainder of the experiment.

tag: cell line background

tag: background cell type

value: immortalized human bronchial epithelial cell

value: clone isolated from agar (4 wks) and grown in monolayer (3 wks)

tag: exposed to

value: 10.0uM NaVO4 for 30 days


title: Naïve_Donor2

description:
SAMPLE 2
Gene expression data from human naïve T cells


title: BEAS-2B_V-transformed_Clone_rep_4


title: HMC-1_cell_RNA_1

status: Public on Apr 16 2012

city: Gothenburg

first: Karin

last: Ekström

address: Medicinaregatan 1G

country: Sweden

institute: Krefting Research Centre

hyb_protocol: The experiment was performed by SweGene (http://www.lth.se/index.php?id=7789) according to Affymetrix guidelines. Briefly, a hybridisation cocktail was prepared with the biotinylated and fragmented cRNA, control oligonucleotide, herring sperm DNA, acetylated BSA, 4-morpholinepropanesulfonic acid (MES), Tween 20, and bacterial cRNA controls respectively. The hybridisation cocktail was heated to 99°C for 5 min and to 45°C for 5 min, and was briefly centrifuged before hybridization. The pre-wet GeneChipTM probe array cartridge was filled with the hybridisation cocktail and incubated on rotation, 60 rpm at 45°C for 16–18 h. The cartridge was then subjected to an automated washing procedure, using the GeneChipTM Fluidics Station 400 and with a non stringent wash buffer, containing saline, sodium, phosphate, EDTA (SSPE), Tween 20 and antifoam according to the Affymetrix manual. A final wash with the stringent buffer, containing MES-sodium salt and Tween 20 was performed. The probe array was then stained with a solution of acetylated BSA, streptavidin and R-phycoerythrin in stain buffer, containing sodium-MES and Tween 20 and antifoam, followed by non stringent wash buffer. A second stain was performed with a solution of acetylated BSA, normal goat IgG and biotinylated goat antistreptavidin antibody in stain buffer. A third staining step with streptavidin R-phycoerythrin was performed as described above, before a final one with non-stringent wash buffer at 30°C.

scan_protocol: The probe arrays were scanned with the Gene Array Scanner (Affymetrix, Inc. www.affymetrix.com) and controlled by the software GenChip Operating System 1.2 (GCOS; Affymtrix Inc.).

data_processing: The expression level Signals were scaled in GCOS 1.2 to give a median array intensity of 100. This was done to enable different arrays to be compared. The program Spotfire DecisionSite 8.2 (www.spotfire.com) was used for gene-profiling analysis, genes only present in exosomes and expression differences. For the network analysis to identify biological mechanisms, the program Ingenuity was used (www.ingenuity.com).

source_name: HMC-1 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix). The experiment was performed by SweGene (http://www.lth.se/index.php?id=7789) according to the Affymetrix guidelines.

growth_protocol: Cell culture and exosome release  The human mast cell line HMC-1 (Dr Joseph Butterfield, Mayo Clinic, USA), was cultured in IMDM containing 10% depleted fetal bovine serum (FBS), 100 U ml-1 penicillin, 100 µg ml-1 streptomycin, 2 mM L-glutamine and 1.2 mM alpha-thioglycerol (all from Sigma-Aldrich). To eliminate exosomes present in serum, FBS was ultracentrifuged at 120 000 g for 90 min using a Ti70 rotor (Beckman optima LE-80k Ultracentrifuge). Peripheral blood mononuclear cells (PBMC) were prepared from peripheral blood of healthy subjects by Ficoll-Plaque density separation. The CD34 cells were obtained from the PBMC by positive isolation using magnetic separation according to the manufacturer’s instruction (Miltenyi Biotec, Germany). CD34 cells were cultured in IMDM (Sigma-Aldrich) containing 10% FBS, 100 U ml-1 penicillin, 100 µg ml-1 streptomycin, 2 mM L-glutamine and 1mM sodium pyruvate. The purity of the separations ranged between 60-85%, as analyzed by flow cytometry using antibody against CD34 (BD Biosciences) in combination with 7-AAD for viability. Exosomes were isolated according to Valadi et al., 2007. Briefly, cells were stimulated with 1 µM calcium ionophore (Sigma-Aldrich) for 30 min, centrifuged at 500 g for 10 min to eliminate cells and at 16 500 g for 20 min, followed by filtration through 0.22 µm filter to remove cell debris. Exosomes were pelleted by ultracentrifugation (Beckman Ti70 rotor) at 120 000 g for 70 min. For PKH67 transfer experiments, exosomes were washed once in a large volume PBS. For electron microscopy, the exosome pellet was diluted in a large volume PBS, filtrated through 0.1 µm filters and pelleted by ultracentrifugation. Exosomes were measured for their protein content using BCA™ Protein Assay Kit (Pierce). Cell viability was assessed using trypan blue exclusion or 7-AAD.

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

treatment_protocol: Growth under normal conditions

tag: cell line

value: mast cell line HMC-1

tag: total rna source

value: whole cell


title: BEAS-2B_Cr-transformed_Clone_rep_3

description:
Cr-3
reanalysis of GSM591435

source_name: 0.50uM K2CrO4_60 days_metal removed_clone isolated from agar (4 wks)_grown in monolayer (3 wks)

value: 0.50uM K2CrO4 for 60 days


title: Proband4 18h in vitro

status: Public on May 01 2012

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: CD4+ T-Cells from peripheral blood of proband4 after 18h in vitro

hyb_protocol: Sense-strand DNA was hybridized on Affymetrix GeneChip Human Gene 1.0 ST Array.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 System.

data_processing: Microarray data were analyzed with Affymetrix GeneChip Command Console Software (Affymetrix). The advanced analysis was done with R (version 2.9) with package limma.

label_protocol: Biotinylated sense-strand DNA was generated from 100 ng of total RNA with WT Sense Target Labeling and Control Reagent (Affymetrix).

growth_protocol: After venipuncture at 10.30 o'clock the cells were cultivated at 12.00 o'clock.

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

tag: time

tag: tissue

value: peripheral blood

value: CD4+ T-Cells

tag: proband age

value: 22 years

tag: proband sex

value: male


title: Proband3 6h in vitro

description: CD4+ T-Cells from peripheral blood of proband3 after 6h in vitro

value: 25 years


title: Proband2 30h in vitro

description: CD4+ T-Cells from peripheral blood of proband2 after 30h in vitro

value: 31 years


title: Proband3 18h in vitro

description: CD4+ T-Cells from peripheral blood of proband3 after 18h in vitro


title: HMC-1_cell_RNA_3


title: Proband4 30h in vitro

description: CD4+ T-Cells from peripheral blood of proband4 after 30h in vitro


title: BEAS-2B_V-transformed_Clone_rep_3


title: Proband4 6h in vitro

description: CD4+ T-Cells from peripheral blood of proband4 after 6h in vitro


title: BEAS-2B_Cr-transformed_Clone_rep_4

description:
Cr-4
reanalysis of GSM591436


title: BEAS-2B_V-transformed_Clone_rep_5


title: Proband2 18h in vitro

description: CD4+ T-Cells from peripheral blood of proband2 after 18h in vitro


title: BEAS-2B_V-transformed_Clone_rep_1


title: BEAS-2B_Ni-transformed_Clone_rep_6

source_name: 250.0uM NiSO4_60 days_metal removed_clone isolated from agar (4 wks)_grown in monolayer (3 wks)

value: 250.0uM NiSO4 for 60 days


title: BEAS-2B_Ni-transformed_Clone_rep_7


title: HMC-1_cell_RNA_2


title: Proband3 30h in vitro

description: CD4+ T-Cells from peripheral blood of proband3 after 30h in vitro


title: BEAS-2B_Cr-transformed_Clone_rep_5

description:
Cr-5
reanalysis of GSM591437


title: BEAS-2B_Cr-transformed_Clone_rep_2

description:
Cr-2
reanalysis of GSM591434


title: Proband2 6h in vitro

description: CD4+ T-Cells from peripheral blood of proband2 after 6h in vitro


title: HMC-1_cell_RNA_4


title: BEAS-2B_Cr-transformed_Clone_rep_1

description:
Cr-1
reanalysis of GSM591433


title: BEAS-2B_Ni-transformed_Clone_rep_2


title: BEAS-2B_Ni-transformed_Clone_rep_3


title: BEAS-2B_As-transformed_Clone_rep_7

source_name: 2.0uM NaAsO2_60 days_metal removed_clone isolated from agar (4 wks)_grown in monolayer (3 wks)

value: 2.0uM NaAsO2 for 60 days


title: BEAS-2B_Ni-transformed_Clone_rep_4


title: BEAS-2B_Ni-transformed_Clone_rep_5


title: BEAS-2B_As-transformed_Clone_rep_6


title: BEAS-2B_As-transformed_Clone_rep_3


title: BEAS-2B_Contrl_Clone_rep_11

source_name: agar-derived clone_not treated_paired with V clones

value: agar-derived control clone


title: BEAS-2B_Contrl_Clone_rep_9


title: BEAS-2B_As-transformed_Clone_rep_1


title: BEAS-2B_Contrl_Clone_rep_10


title: BEAS-2B_Contrl_Clone_rep_5

source_name: agar-derived clone_not treated_paired with As and Ni clones


title: BEAS-2B_Ni-transformed_Clone_rep_1


title: BEAS-2B_As-transformed_Clone_rep_5


title: BEAS-2B_As-transformed_Clone_rep_4


title: BEAS-2B_Contrl_Clone_rep_1


title: BEAS-2B_Contrl_Clone_rep_7

description:
Ctrl-7
reanalysis of GSM591431

source_name: agar-derived clone_not treated_paired with Cr clones


title: BEAS-2B_Contrl_Clone_rep_2


title: BEAS-2B_Contrl_Clone_rep_6

description:
Ctrl-6
reanalysis of GSM591430


title: BEAS-2B_Contrl_Clone_rep_4


title: BEAS-2B_As-transformed_Clone_rep_2


title: BEAS-2B_rep_2

description:
P-2
reanalysis of GSM591439

source_name: parental cell line used for Cr exposures


title: BEAS-2B_rep_3

source_name: parental cell line used for V exposures

value: parental cell line used for V exposures


title: BEAS-2B_rep_1

source_name: parental cell line used for As and Ni exposures


title: BEAS-2B_Contrl_Clone_rep_8

description:
Ctrl-8
reanalysis of GSM591432


title: ZR-75-30

status: Public on Mar 20 2012

first: Nicolas

last: Stransky

address: 7 Cambridge center

department: Cancer Program

description: Gene expression data from the CCLE

hyb_protocol: Fragmentation of the biotin-labeled cRNA prepared the sample for hybridization on the GeneChip Human U133 2.0 (PN 900467). The washing and staining was performed on the GeneChip Fluidics station using standard Affymetrix protocols outlined in the Expression Analysis Technical Manual, 2001, Affymetrix.

scan_protocol: The GeneChip® Scanner 3000 was used for scanning the arrays.

data_processing: The data were analyzed with 2.14.0, using the packages affyio_1.22.0 and affy_1.32.0, and RMA as normalization method. rma() was used with default options (normalize=TRUE, background=TRUE) and with the package hgu133plus2hsentrezgcdf_15.0.0 from Brainarray for the CDF file.

source_name: ATCC

label_protocol: The Affymetrix One-Cycle Target labeling assay was used to synthesize hybridization target using 1 mg of total RNA. Labeled cRNA hybridization target was produced using a 3-day, semi-automated workflow

growth_protocol: Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached.  Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.

extract_protocol: RNA was isolated from frozen cell pellets, containing an average cell count of 4.5 million cells, via Trizol (Invitrogen) extraction following the manufacturers instructions. Samples were quantified using both the Nanodrop 8000 spectrophotometer (ThermoScientific) and via Agilent 2100 Bioanalyzer.

tag: primary site

value: breast

tag: histology

value: carcinoma

tag: histology subtype1


title: ZR-75-1

description: Gene expression data from the CCLE


title: BEAS-2B_Contrl_Clone_rep_3

value: immortalized human bronchial epithelial cell

tag: cell type


title: YMB-1

description: Gene expression data from the CCLE

source_name: HSRRB


title: YD-8

description: Gene expression data from the CCLE

source_name: KCLB


title: YD-10B

description: Gene expression data from the CCLE


title: YKG1

description: Gene expression data from the CCLE

value: glioma


title: WM-983B

description: Gene expression data from the CCLE

source_name: Academic Lab

value: skin


title: WM-266-4

description: Gene expression data from the CCLE


title: WM-793

description: Gene expression data from the CCLE


title: WM-88

description: Gene expression data from the CCLE


title: YH-13

description: Gene expression data from the CCLE


title: WM1799

description: Gene expression data from the CCLE


title: YAPC

description: Gene expression data from the CCLE

source_name: DSMZ

value: pancreas


title: WM-115

description: Gene expression data from the CCLE


title: VMRC-RCW

description: Gene expression data from the CCLE

source_name: RIKEN

value: kidney


title: YD-38

description: Gene expression data from the CCLE


title: VM-CUB1

description: Gene expression data from the CCLE


title: UACC-812

description: Gene expression data from the CCLE


title: VCaP

description: Gene expression data from the CCLE

value: prostate

value: adenocarcinoma


title: UACC-62

description: Gene expression data from the CCLE

source_name: NCI/DCTD


title: UM-UC-3

description: Gene expression data from the CCLE


title: UACC-893

description: Gene expression data from the CCLE


title: UACC-257

description: Gene expression data from the CCLE


title: TYK-nu

description: Gene expression data from the CCLE

value: ovary


title: TUHR14TKB

description: Gene expression data from the CCLE


title: U-2 OS

description: Gene expression data from the CCLE

value: bone

value: osteosarcoma


title: U-87 MG

description: Gene expression data from the CCLE

value: astrocytoma


title: U-138 MG

description: Gene expression data from the CCLE


title: U-251 MG

description: Gene expression data from the CCLE


title: VMRC-RCZ

description: Gene expression data from the CCLE


title: TUHR10TKB

description: Gene expression data from the CCLE


title: TGBC11TKB

description: Gene expression data from the CCLE

value: stomach


title: T.T

description: Gene expression data from the CCLE

value: oesophagus


title: TM-31

description: Gene expression data from the CCLE


title: TOV-21G

description: Gene expression data from the CCLE


title: TOV-112D

description: Gene expression data from the CCLE


title: TT2609-C02

description: Gene expression data from the CCLE

value: thyroid


title: TUHR4TKB

description: Gene expression data from the CCLE


title: TE-9

description: Gene expression data from the CCLE


title: TE-6

description: Gene expression data from the CCLE


title: TE-8

description: Gene expression data from the CCLE


title: TEN

description: Gene expression data from the CCLE

value: endometrium


title: TE-1

description: Gene expression data from the CCLE


title: TT

description: Gene expression data from the CCLE


title: TE 441.T

description: Gene expression data from the CCLE

value: rhabdomyosarcoma


title: TE-11

description: Gene expression data from the CCLE

value: carcinoma


title: TE-5

description: Gene expression data from the CCLE


title: TE-15

description: Gene expression data from the CCLE