title: Bcell_activated-gp120pp_3hrs, AF6

source_name: Bcell, activated, gp120++, 3hrs


title: Bcell_activated-gp120pp_30min, AF3

status: Public on Oct 17 2013

type: RNA

city: Frederick

first: Richard

last: Lempicki

state: MD

address: 1050 Boyles Street / P.O. Box B

country: USA

institute: NCI-Frederick

hyb_protocol: Labeled cRNA was hybridized to the Affymetrix Human Gene 1.0 ST microarray according to the manufacturer's recommended standard protocol.

scan_protocol: Hybridized Affymetrix human gene microarrays were scanned according to the manufacturer's recommended standard protocol.

data_processing: Gene expression profiles were analyzed using Partek Genomic Suite 6.6.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Bcell, activated, gp120++, 30min

label_protocol: cRNA was labelled according to the manufacturer's recommended standard protocol for the Affymetrix Human Gene 1.0 ST microarray.

growth_protocol: Freshly isolated PBMCs were obtained from healthy donors and separated by Ficoll-Hypaque. Purified CD4+ T cells or B cells were obtained by negative selection using magnetic beads (StemCell Technologies, Vancouver, Canada). Cultured CD4+ cells were activated with OKT3, IL2 (20IU/ml) and all-trans retinoic acid (RA, 10nM) unless otherwise specified. RA was obtained from Sigma (St. Louis, MO) and discarded 1 month after reconstitution.

extract_protocol: cDNA of each sample was generated with Ambion WT Expression Kit.

treatment_protocol: Isolated B cells were treated with gp120 proteins of different affinity or mock protein. The exposure time points included 30min, 3hrs and 6hrs.

tag: disease status

value: healthy

tag: cell type

value: B cells

tag: gp120 treatment

tag: time point


title: Bcell_activated-gp120m_3hrs, AE7

source_name: Bcell, activated, gp120-, 3hrs


title: Bcell_activated-gp120pp_3hrs, AE6


title: Bcell_activated_6hrs, AE8

source_name: Bcell, activated, 6hrs


title: Bcell_activated_3hrs, AE5

source_name: Bcell, activated, 3hrs


title: Bcell_activated-gp120m_6hrs, AE10

source_name: Bcell, activated, gp120-, 6hrs


title: Bcell_activated-gp120m_30min, AE4

source_name: Bcell, activated, gp120-, 30min


title: Bcell_activated-gp120pp_6hrs, AE9

source_name: Bcell, activated, gp120++, 6hrs


title: Bcell_mock_0hrs, AF1

source_name: Bcell, mock, 0hrs

value: mock


title: Bcell_activated_30min, AF2

source_name: Bcell, activated, 30min


title: Bcell_activated-gp120m_6hrs, AD10


title: Bcell_activated-gp120pp_6hrs, AD9


title: Bcell_activated_30min, AE2


title: Bcell_activated-gp120pp_30min, AE3


title: Bcell_mock_0hrs, AE1


title: Bcell_activated-gp120m_30min, AD4


title: Bcell_activated_3hrs, AD5


title: Bcell_activated_6hrs, AD8


title: EPN_416_1

status: Public on Aug 30 2013

city: Aurora

first: Lindsey

middle: M.

last: Hoffman

state: Colorado

address: 12800 East 19th Avenue

department: Pediatric Neuro-Oncology

institute: University of Colorado Denver

description:
included_in_corresponding_manuscript:yes
Gene expression data from surgical tumor sample of ependymoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 17,664 genes.

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: group

value: Primary

tag: tissue

value: brain tumor (ependymoma)


title: Bcell_activated-gp120m_3hrs, AD7


title: EPN_333_1


title: Bcell_activated-gp120pp_30min, AD3


title: Bcell_activated_30min, AD2


title: Bcell_mock_0hrs, AD1


title: EPN_135_1


title: EPN_388_1


title: Bcell_activated-gp120pp_3hrs, AD6


title: EPN_285_1


title: Th1, patient 676

status: Public on Aug 26 2013

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

description: Gene expression data from circulating Th1 cells

hyb_protocol: Briefly, the quality of total RNA was first tested using an Agilent 2100 Bioanalyzer chip. Then, high quality RNA was reverse transcribed and hybridized on the GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix).

scan_protocol: GeneChip scan was carried out at McGill University & Genome Quebec Innovation Centre according to the Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4).

data_processing: Gene expression data was analyzed using Bioconductor limma package. The R software package was used to preprocess and normalize the probes intensities using RMA.

source_name: Peripheral blood mononuclear cells (PBMC)

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

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol and quantified by Pearl nanophotometer (Implen, Munich, Germany) (typically, 106 cells yielded 3-5 µg RNA).

treatment_protocol: Sorted Th1Th17 and Th1 subsets were stimulated with immobilized CD3 and soluble CD28 Abs (1 µg/ml) for 3 days

tag: donor

value: CD4+ Th cells

tag: cell subset

value: Th1 cells


title: Th1, patient 580


title: Th1Th17, patient 580

description: Gene expression data from circulating Th1Th17 cells

value: Th1Th17 cells


title: Th1Th17, patient 661


title: Th1Th17, patient 676


title: Th1, patient 661


title: Th1Th17, patient 674


title: PA-631

status: Public on Aug 25 2013

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description:
Gene expression data from surgical tumor sample of pilocytic astrocytoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 21,050 genes.

source_name: brain tumor (pilocytic astrocytoma)

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

tag: disease state

value: brain tumor

value: pilocytic astrocytoma


title: PA-563


title: PA-519


title: PA-378


title: PA-476


title: PA-249


title: PA-257


title: PA-653


title: PA-363


title: NORMAL-605-Frontal

description:
Gene expression data from surgical tumor sample of normal brain
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

source_name: normal brain (frontal lobe of cerebral cortex)

value: normal

value: frontal lobe of cerebral cortex


title: PA-160


title: NORMAL-E3-Frontal


title: GBM-281

description:
Gene expression data from surgical tumor sample of glioblastoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

source_name: brain tumor (glioblastoma)

value: glioblastoma


title: NORMAL-514-Frontal


title: GBM-434


title: GBM-089


title: GBM-000


title: NORMAL-514-Temporal

source_name: normal brain (temporal lobe of cerebral cortex)

value: temporal lobe of cerebral cortex


title: GBM-637


title: GBM-309


title: GBM-098


title: GBM-057


title: GBM-391


title: Pulmonary fibroblasts_scleroderma-associated interstitial lung disease_ biological rep5

status: Public on Aug 05 2013

city: London

first: Carmel

last: Stock

address: 1b Manresa Road

department: Interstitial Lung Disease

country: United Kingdom

institute: National Heart and Lung Institute

description: Gene expression data from pulmonary fibroblasts in individuals with scleroderma-associated interstitial lung disease.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Homo sapiens U133A1. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 30007G scanner.

data_processing: The data were analyzed with dCHIP using the invariant set normalisation method.

label: Biotin

source_name: Primary pulmonary fibroblasts from scleroderma-associated interstitial lung disease patient 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary fibroblasts were cultured from lung biopsies as previously described (Abraham, D.J., et al. J.Biol.Chem 2000;275:15220-25).

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

treatment_protocol: Prior to RNA extraction confluent cultures were serum-deprived for 42 hours (media changed at 18 hours) in 0.1% bovine serum albumin.

value: Pulmonary fibroblasts

value: Scleroderma associated interstitial lung disease


title: GBM-271


title: Pulmonary fibroblasts_Usual Interstitial Pneumonia_ biological rep1

description: Gene expression data from pulmonary fibroblasts in individuals with Usual Interstitial Pneumonia.

source_name: Primary pulmonary fibroblasts from Usual Interstitial Pneumonia patient 1

value: Usual Interstitial Pneumonia


title: Pulmonary fibroblasts_scleroderma-associated interstitial lung disease_ biological rep8

source_name: Primary pulmonary fibroblasts from scleroderma-associated interstitial lung disease patient 8


title: Pulmonary fibroblasts_scleroderma-associated interstitial lung disease_ biological rep7

source_name: Primary pulmonary fibroblasts from scleroderma-associated interstitial lung disease patient 7


title: Pulmonary fibroblasts_scleroderma-associated interstitial lung disease_ biological rep6

source_name: Primary pulmonary fibroblasts from scleroderma-associated interstitial lung disease patient 6


title: Pulmonary fibroblasts_control individual_ biological rep8

description: Gene expression data from pulmonary fibroblasts in individuals without lung disease.

source_name: Primary pulmonary fibroblasts from control individual 8

value: Control


title: Pulmonary fibroblasts_control individual_ biological rep10

source_name: Primary pulmonary fibroblasts from control individual 10


title: Pulmonary fibroblasts_scleroderma-associated interstitial lung disease_ biological rep2

source_name: Primary pulmonary fibroblasts from scleroderma-associated interstitial lung disease patient 2


title: Pulmonary fibroblasts_scleroderma-associated interstitial lung disease_ biological rep1

source_name: Primary pulmonary fibroblasts from scleroderma-associated interstitial lung disease patient 1


title: Pulmonary fibroblasts_control individual_ biological rep9

source_name: Primary pulmonary fibroblasts from control individual 9


title: Pulmonary fibroblasts_scleroderma-associated interstitial lung disease_ biological rep3

source_name: Primary pulmonary fibroblasts from scleroderma-associated interstitial lung disease patient 3


title: Pulmonary fibroblasts_control individual_ biological rep2

source_name: Primary pulmonary fibroblasts from control individual 2


title: Pulmonary fibroblasts_control individual_ biological rep3

source_name: Primary pulmonary fibroblasts from control individual 3


title: Pulmonary fibroblasts_control individual_ biological rep4

source_name: Primary pulmonary fibroblasts from control individual 4


title: Pulmonary fibroblasts_control individual_ biological rep1

source_name: Primary pulmonary fibroblasts from control individual 1


title: Pulmonary fibroblasts_scleroderma-associated interstitial lung disease_ biological rep4

source_name: Primary pulmonary fibroblasts from scleroderma-associated interstitial lung disease patient 4


title: Th1, patient 674

source_name: Peripheral blood mononuclear cells (PBMC)


title: Pulmonary fibroblasts_control individual_ biological rep7

source_name: Primary pulmonary fibroblasts from control individual 7


title: Pulmonary fibroblasts_control individual_ biological rep5

source_name: Primary pulmonary fibroblasts from control individual 5


title: Human T cell HIV tat exposed 24hr Sample Pair 5

status: Public on Aug 02 2013

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Human T cell HIV tat exposed 24hr Sample 5

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs was hybridized to The Affymetrix Human Genome ST 1.0 GeneChip. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin(Vector Laboratories, Burlingame, CA).

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using Affymetrix AGCC software.

data_processing: The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 33,297 RMA normalized gene fragment expression values for each hybridized cRNA.

label_protocol: Samples were prepared according to Affymetrix protocols (Affymetrix, Inc). RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc) respectively. Per RNA labeling, 200 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 1.0 ST chips.

growth_protocol: PBMCs from HIV-uninfected healthy volunteers were obtained by leukapheresis. T-cells were isolated using a Pan T-cell II isolation kit (Miltenyl Biotec Inc.) and maintained in Iscove's Modified Dulbecco's Media (IMDM) with 10% (v/v) human serum and 1% (v/v) antibiotic and antimycotic solution at 37°C with 5% CO2.

extract_protocol: RNA extraction was performed using Qiagen RNeasy kit (Qiagen) per manufacturer’s instructions.

treatment_protocol: After isolation T-cells were seeded into a 96-well round bottom plate at 5x105 cells/ well and challenged with either no peptide (negative control), 200 nM Tat peptide/ well, or 1 ug/ml phytohaemagglutinin (PHA) as a positive control (Invitrogen). Recombinant Tat was obtained from Phillip Dale Ray, University of Kentucky (Lexington, KY) as a lyophilized powder. Tat was resuspended with IMDM at 1 ug/ul.

tag: condition

value: healthy donor

tag: time

tag: sample pair

tag: treatment

value: HIV tat

value: T cell


title: Human T cell HIV tat exposed 24hr Sample Pair 6

description: Human T cell HIV tat exposed 24hr Sample 6


title: Human T cell HIV tat exposed 24hr Sample Pair 4

description: Human T cell HIV tat exposed 24hr Sample 4


title: Human T cell HIV tat exposed 24hr Sample Pair 3

description: Human T cell HIV tat exposed 24hr Sample 3


title: Human T cell HIV tat exposed 0hr Sample Pair 4

description: Human T cell HIV tat exposed 0hr Sample 4


title: Human T cell HIV tat exposed 0hr Sample Pair 5

description: Human T cell HIV tat exposed 0hr Sample 5


title: Human T cell HIV tat exposed 0hr Sample Pair 3

description: Human T cell HIV tat exposed 0hr Sample 3


title: Human T cell HIV tat exposed 0hr Sample Pair 6

description: Human T cell HIV tat exposed 0hr Sample 6


title: Human T cell HIV tat exposed 24hr Sample Pair 1

description: Human T cell HIV tat exposed 24hr Sample 1


title: Human T cell HIV tat exposed 24hr Sample Pair 2

description: Human T cell HIV tat exposed 24hr Sample 2


title: CD 14 5

status: Public on Aug 01 2013

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R [version 2.15.1 (2012-06-22)]. Additional software packages (affy [version 2.10], geneplotter, multtest, and vsn [version 2.10]) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: Unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: CD14+ monocytes

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

extract_protocol: RNA was amplified directly from cells using the One-direct-Kit from NUGEN applied for 250 microdissected cells

treatment_protocol: Cells were microdissected from HE stained kryosections

value: CD14+ monocytes


title: CD 14-16 2

source_name: CD14+CD16+ monocytes

value: CD14+CD16+ monocytes


title: CD 14-16 3


title: CD 14 4


title: CD 14-16 4


title: CD 14 3


title: CD 14-16 1


title: CD 14 1


title: TCHRBCL_M8

source_name: TCHRCBL macrophages

value: TCHRCBL macrophages


title: Human T cell HIV tat exposed 0hr Sample Pair 2

description: Human T cell HIV tat exposed 0hr Sample 2


title: Human T cell HIV tat exposed 0hr Sample Pair 1

description: Human T cell HIV tat exposed 0hr Sample 1


title: TCHRBCL_M5


title: TCHRBCL_M1


title: TCHRBCL_M3


title: TCHRBCL_M2


title: TCHRBCL_M4


title: TCHRBCL_M6


title: KZM1

source_name: Germinal center macrophages

value: Germinal center macrophages


title: KZM2


title: KZM3


title: KZM6


title: SM5

source_name: Sinus macrophages

value: Sinus macrophages


title: SM4


title: SM2


title: SM6


title: SM1


title: KZM4


title: SM3


title: CD 14 2


title: Normal Fibroblast GM03440 rep2

status: Public on Jul 11 2013

first: Hoi Hung

last: Cheung

address: 49 Convent Dr, Rm.2C08 Bldg.49

institute: NICHD

description: Gene expression data from normal skin fibroblast culture

hyb_protocol: cDNA was hybridization at 45C overnight. Wash and staining was performed by GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Arrays were scanned by GeneChip Scanner 3000 7G controlled AGCC Scan Control (Affymetrix)

data_processing: Microarray data were analyzed by Partek Genomics Suite 6.6 with quantile normalization and RMA background correction. A batch effect due to scan date was removed before One-way ANOVA analysis for differentially expressed genes between normal and WS fibroblasts.

source_name: Normal Fibroblast

label_protocol: cDNA was labeled by biotin using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Fibroblast culture was maintained in alpha MEM medium containing 15% FBS. iPSC/hESC culture was maintained on Matrigel with mTeSR1 medium.

extract_protocol: Total RNA was extracted by Trizol and purified by Direct-zol RNA MiniPrep (Zymo Research). RNA integrity was assessed by BioAnalyzer.

tag: gender

value: Male

tag: age

tag: genotype

value: WT

value: Normal Fibroblast


title: WS Fibroblast AG03141 rep2

description: Gene expression data from WS skin fibroblast culture

source_name: WS Fibroblast

value: WRN mutant

value: Werner Syndrome Fibroblast


title: WS Fibroblast AG12797 rep1


title: WS Fibroblast AG12797 rep2


title: WS Fibroblast AG00780 rep1


title: WS Fibroblast AG06300 rep1


title: Normal Fibroblast BC rep2


title: Normal Fibroblast GM03440 rep1


title: WS Fibroblast AG03141 rep1


title: WS Fibroblast AG05229 rep1


title: Normal Fibroblast AN3 rep1


title: Normal Fibroblast AN3 rep2


title: WS Fibroblast AG00780 rep2


title: Normal Fibroblast AN2 rep2


title: WS Fibroblast AG06300 rep2


title: Normal Fibroblast BC rep1


title: Normal Fibroblast AN1 rep1


title: Normal T cell-12

status: Public on Jul 06 2013

city: Baltimore

first: Yezhou

last: Sun

address: 620 W. Lexington St.

institute: U. of Maryland, Baltimore

description: Gene Expression Data from T Cells

hyb_protocol: Following fragmentation, 5 ug of labled DNA was hybridized for 16 hr at 45C on HuGene-1_0-st-v1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000 and software AffyMetrix Genechip Command Console .

data_processing: The data were analyzed using the affy R package to load the data before using the quantile method in the limma R package from Bioconductor to normalize all of the data

source_name: T Cells

label_protocol: DNA was labeled by teriminal deoxynucleotidyl transferase (TdT) with the Affymetrix propritary DNA labeling reagent that is covalently linked to biotin. (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All the leukemia cell lines were culture in vitro under appropriate cell cutlure conditions according to the supplier recommondataion. Normal mature hematopoietic cells were purifed from normal healthy donor peripheral blood using Ficoll gradiant centrifugation followed by FACS sorting.

extract_protocol: Cell were lysed in Trizol and total RNA was purifed using miRNAeasy kit  according to the manufacturer's instructions.

tag: phenotype

value: Normal


title: Normal T cell-15

description: Gene Expression Data from T Cells


title: Normal T cell-14

description: Gene Expression Data from T Cells


title: Normal T cell-10

description: Gene Expression Data from T Cells


title: Normal Fibroblast AN2 rep1


title: Normal T cell-16

description: Gene Expression Data from T Cells


title: WS Fibroblast AG05229 rep2


title: Normal T cell-17

description: Gene Expression Data from T Cells


title: Normal Monocyte-5

description: Gene Expression Data from Monocytes

source_name: Monocytes


title: Normal Monocyte-6

description: Gene Expression Data from Monocytes


title: Normal B cell-8

description: Gene Expression Data from B Cells

source_name: B Cells


title: Normal Granulocyte-12

description: Gene Expression Data from Granulocytes

source_name: Granulocytes


title: Normal Monocyte-4

description: Gene Expression Data from Monocytes


title: Normal T cell-13

description: Gene Expression Data from T Cells


title: Normal B cell-11

description: Gene Expression Data from B Cells


title: Normal Monocyte-3

description: Gene Expression Data from Monocytes


title: Normal B cell-9

description: Gene Expression Data from B Cells


title: Normal B cell-5

description: Gene Expression Data from B Cells


title: Normal B cell-7

description: Gene Expression Data from B Cells


title: Normal Granulocyte-9

description: Gene Expression Data from Granulocytes


title: Normal T cell-9

description: Gene Expression Data from T Cells


title: Normal B cell-6

description: Gene Expression Data from B Cells


title: Normal Granulocyte-10

description: Gene Expression Data from Granulocytes


title: Normal Granulocyte-11

description: Gene Expression Data from Granulocytes


title: Normal B cell-10

description: Gene Expression Data from B Cells


title: Normal Granulocyte-8

description: Gene Expression Data from Granulocytes


title: Normal Fibroblast AN1 rep2


title: Normal Granulocyte-6

description: Gene Expression Data from Granulocytes


title: Normal Granulocyte-7

description: Gene Expression Data from Granulocytes


title: Normal Granulocyte-5

description: Gene Expression Data from Granulocytes


title: Normal B-cell-2

description: Gene Expression Data from B Cells


title: Normal T cell-4

description: Gene Expression Data from T Cells


title: Normal Monocyte-2

description: Gene Expression Data from Monocytes


title: Normal Monocyte-1

description: Gene Expression Data from Monocytes


title: Normal T cell-6

description: Gene Expression Data from T Cells


title: Normal Granulocyte-4

description: Gene Expression Data from Granulocytes


title: Normal B-cell-1

description: Gene Expression Data from B Cells


title: Normal T cell-1

description: Gene Expression Data from T Cells


title: Normal B cell-4

description: Gene Expression Data from B Cells


title: Normal T cell-8

description: Gene Expression Data from T Cells


title: Normal T cell-5

description: Gene Expression Data from T Cells


title: Normal Granulocyte-2

description: Gene Expression Data from Granulocytes


title: Normal B cell-3

description: Gene Expression Data from B Cells


title: Normal Granulocyte-3

description: Gene Expression Data from Granulocytes


title: Normal T cell-7

description: Gene Expression Data from T Cells


title: Normal T cell-3

description: Gene Expression Data from T Cells


title: Normal Granulocyte-1

description: Gene Expression Data from Granulocytes


title: Nx

status: Public on Jun 30 2013

city: La Jolla

first: Zhen

last: Chen

address: 9500 Gilman Dr.

institute: UCSD

description:
HUVEC-Ago1 IP RNA
The intensity of Ago1 bound mRNA of nomoxia HUVECs.

hyb_protocol: 5.2ug cDNA that were labeled were hybridized for 16hr at 45C on HumanGene 1.0 ST GeneChips. The GeneChips were stained and washed on the Affymetrix Fluidics Station 450, following the recommended protocol.

scan_protocol: The scanning was done by using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with RMA with default parameters.

source_name: normoxic HUVEC-Ago1 IP

label_protocol: Ambion WT Expression kit (PN 4411973) was used to prepare RNA samples, generating sense-strand cDNA from total RNA for fragmentation and labeling using the Affymetrix GeneChip WT Terminal Labeling kit (PN 900671). It uses a reverse transcription prming method that specifically primes non-ribosomal RNA from the samples, including both poly(A) and non-poly(A) mRNA. After fragmentation of 5.5ug single-stranded cDNA, 5.2ug were labeled .

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured in M199 medium supplemented with 15% FBS following standard protocol.

extract_protocol: HUVECs were lysed with a buffer containing 50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.1% NP-40, 1 mM EDTA, and 100 units/μl RNase inhibitor.  The lysates were incubated with anti-Ago1 (Wako Chemicals, Clone 2A7) at 4°C overnight at 5 ug/mg total protein and then protein G Dynabeads for 4 hr.  The beads were then spun down, and the immunoprecipitated RNAs were extracted with Trizol following the manufacterer's manual.

treatment_protocol: Cells were subjected to 2% oxygen for 24 hr. The control cells were cultured at normal oxygen condition (21% oxygen) for the same time.

value: umbilical vein endothelial cells

value: normoxia

tag: rip antibody

value: anti-Ago1 (Wako Chemicals, Clone 2A7)


title: Normal T cell-2

description: Gene Expression Data from T Cells


title: Total CD4 NS + SN016 at 24h

status: Public on Jun 17 2013

city: Brussels

first: Chunyan

last: GU

address: Bld de Waterloo 127

department: Medecine (Jules Bordet Institute)

country: Belgium

institute: Free University of Brussels

description:
Gene expression data from total CD4+ T cells from healthy donor blood treated with SN for 24h
Total CD4+ T cells were negatively purified from a healthy donor (D5) blood using CD4+ T Cell Isolation Kit II (Myltenyi Biotec).

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data (CEL files) were analyzed in R version 2.5.1 for RMA normalization (together with 9 other samples of the same experiments which are not included in this study).

source_name: purified CD4+ T cells from a healthy donor (+ 24h treatment with SN from breast cancer patient 016)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit Manual, 2009, Affymetrix).

treatment_protocol: Cells (2x106 cells/ml) were incubated in X-VIVO 20 (Lonza) overnight following isolation. Cell viability was controlled the following day by flow cytometry (>95%) and then an equal volume of tumor SN (diluted; concentrations normalized to total RNA quantity of non-CD4 cells in each tumor) or X-VIVO was added.

tag: source tissue

value: peripheral blood

tag: cell type

value: healthy


title: Hx

description:
HUVEC-Ago1 IP RNA
The intensity of Ago1 bound mRNA of hypoxia HUVECs.

source_name: hypoxic HUVEC-Ago1 IP

value: hypoxia


title: Total CD4 NS + SN034 at 24h

source_name: purified CD4+ T cells from a healthy donor (+ 24h treatment with SN from breast cancer patient 034)


title: Total CD4 NS at 24h, biological rep3

description:
Gene expression data from total CD4+ T cells from healthy donor blood at 24h
Total CD4+ T cells were negatively purified from a healthy donor (D5) blood using CD4+ T Cell Isolation Kit II (Myltenyi Biotec).

source_name: purified CD4+ T cells from a healthy donor (24h)


title: Total CD4 NS + SN014 at 24h

source_name: purified CD4+ T cells from a healthy donor (+ 24h treatment with SN from breast cancer patient 014)


title: Total CD4 NS at 24h, biological rep1


title: RO at T0

description:
Gene expression data from purified memory CD4+ T cells from healthy donor blood at T0
CD4+ T cells were positively purified from patient tumors using Dynabeads CD4 (Invitrogen);  Memory CD4+ cells were purified from a healthy donor (D6) by CD45RA depletion [Dynabeads M-450 Epoxy coupled to anti-CD45RA (#304102, Biolegend) followed by Dynabeads CD4 (Invitrogen) positive selection.

data_processing: The data (CEL files) were analyzed in R version 2.10.1 for RMA normalization.

source_name: purified CD45RA-CD4+ T cells from a healthy donor at T0

treatment_protocol: Cells were immediately processed for RNA extraction following isolation or were incubated without stimulation in X-VIVO 20 (Lonza) for 24h before RNA extraction.

value: purified CD45RA-CD4+ T cells


title: TIL064 at 24h

description:
Gene expression data from purified CD4+ T cells from patient tumor at 24h
CD4+ T cells were positively purified from patient tumors using Dynabeads CD4 (Invitrogen);  Memory CD4+ cells were purified from a healthy donor (D6) by CD45RA depletion [Dynabeads M-450 Epoxy coupled to anti-CD45RA (#304102, Biolegend) followed by Dynabeads CD4 (Invitrogen) positive selection.

source_name: purified CD4+ T cells from breast cancer patient 064 at 24h

value: breast tumor

value: purified CD4+ T cells

value: breast cancer

value: 24 h incubation in X-VIVO 20


title: RO at 24h

description:
Gene expression data from purified memory CD4+ T cells from healthy donor blood at 24h
CD4+ T cells were positively purified from patient tumors using Dynabeads CD4 (Invitrogen);  Memory CD4+ cells were purified from a healthy donor (D6) by CD45RA depletion [Dynabeads M-450 Epoxy coupled to anti-CD45RA (#304102, Biolegend) followed by Dynabeads CD4 (Invitrogen) positive selection.

source_name: purified CD45RA-CD4+ T cells from a healthy donor at 24h


title: Memory CD4 S + SN019 at 24h

description:
Gene expression data from memory CD4+ T cells from healthy donor blood stimulated and treated with SN for 24h
Memory CD4+ T cells were negatively purified from a healthy donor (D6) blood using Memory CD4+ T Cell Isolation Kit (Myltenyi Biotec).

source_name: purified CD45RA-CD4+ T cells from a healthy donor (+ 24h stimulation & treatment with SN from breast cancer patient 019)

treatment_protocol: Cells (2x106 cells/ml) were incubated in X-VIVO 20 (Lonza) overnight following isolation. Cell viability was controlled the following day by flow cytometry (>95%) and then an equal volume of tumor SN (undiluted) or X-VIVO was added ± anti-CD3 (#317304, clone OKT3; Biolegend) and anti-CD28 (#555725, clone CD28.2; BD Pharmingen), each at 1µg/ml.

value: + 24h stimulatin (anti-CD3 + anti-CD28) & treatment with SN from breast cancer patient 019


title: TCHRBCL_M7

source_name: TCHRCBL macrophages

value: TCHRCBL macrophages


title: Memory CD4 NS at 24h, biological rep3

description:
Gene expression data from memory CD4+ T cells from healthy donor blood at 24h
Memory CD4+ T cells were negatively purified from a healthy donor (D6) blood using Memory CD4+ T Cell Isolation Kit (Myltenyi Biotec).

source_name: purified CD45RA-CD4+ T cells from a healthy donor (24h)

value: untreated


title: TIL064 at T0

description:
Gene expression data from purified CD4+ T cells from patient tumor at T0
CD4+ T cells were positively purified from patient tumors using Dynabeads CD4 (Invitrogen);  Memory CD4+ cells were purified from a healthy donor (D6) by CD45RA depletion [Dynabeads M-450 Epoxy coupled to anti-CD45RA (#304102, Biolegend) followed by Dynabeads CD4 (Invitrogen) positive selection.

source_name: purified CD4+ T cells from breast cancer patient 064 at T0


title: Memory CD4 S + SN034 at 24h

source_name: purified CD45RA-CD4+ T cells from a healthy donor (+ 24h stimulation & treatment with SN from breast cancer patient 034)

value: + 24h stimulatin (anti-CD3 + anti-CD28) & treatment with SN from breast cancer patient 034


title: LN Patient 9

description:
Gene expression data from purified CD4+ T cells from patient lymph node at T0
CD4+ T cells were positively purified from patient samples or healthy donor blood using Dynabeads CD4 (Invitrogen).

data_processing: The data (CEL files) were analyzed in R version 2.3.0 for RMA normalization.

source_name: purified CD4+ T cells from breast cancer patient 9

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

treatment_protocol: no treatment

value: lymph node


title: Memory CD4 S + SN027 at 24h

source_name: purified CD45RA-CD4+ T cells from a healthy donor (+ 24h stimulation & treatment with SN from breast cancer patient 027)

value: + 24h stimulatin (anti-CD3 + anti-CD28) & treatment with SN from breast cancer patient 027


title: Memory CD4 S at 24h, biological rep2

description:
Gene expression data from memory CD4+ T cells from healthy donor blood stimulated for 24h
Memory CD4+ T cells were negatively purified from a healthy donor (D6) blood using Memory CD4+ T Cell Isolation Kit (Myltenyi Biotec).

source_name: purified CD45RA-CD4+ T cells from a healthy donor (+ 24h stimulation)

value: + 24h stimulation


title: Memory CD4 NS + SN034 at 24h

description:
Gene expression data from memory CD4+ T cells from healthy donor blood treated with SN for 24h
Memory CD4+ T cells were negatively purified from a healthy donor (D6) blood using Memory CD4+ T Cell Isolation Kit (Myltenyi Biotec).

source_name: purified CD45RA-CD4+ T cells from a healthy donor (+ 24h treatment with SN from breast cancer patient 034)


title: LN Patient 10

source_name: purified CD4+ T cells from breast cancer patient 10


title: Memory CD4 NS + SN019 at 24h

source_name: purified CD45RA-CD4+ T cells from a healthy donor (+ 24h treatment with SN from breast cancer patient 019)


title: Memory CD4 S at 24h, biological rep1


title: Total CD4 NS at 24h, biological rep2


title: LN Patient 8

source_name: purified CD4+ T cells from breast cancer patient 8


title: Memory CD4 NS at 24h, biological rep1


title: Memory CD4 NS + SN043 at 24h

source_name: purified CD45RA-CD4+ T cells from a healthy donor (+ 24h treatment with SN from breast cancer patient 043)


title: Memory CD4 NS + SN027 at 24h

source_name: purified CD45RA-CD4+ T cells from a healthy donor (+ 24h treatment with SN from breast cancer patient 027)


title: LN Patient 6

source_name: purified CD4+ T cells from breast cancer patient 6


title: Memory CD4 S + SN043 at 24h

source_name: purified CD45RA-CD4+ T cells from a healthy donor (+ 24h stimulation & treatment with SN from breast cancer patient 043)

value: + 24h stimulatin (anti-CD3 + anti-CD28) & treatment with SN from breast cancer patient 043


title: Memory CD4 NS at 24h, biological rep2


title: LN Patient 7

source_name: purified CD4+ T cells from breast cancer patient 7


title: LN Patient 5

source_name: purified CD4+ T cells from breast cancer patient 5


title: LN Patient 3

source_name: purified CD4+ T cells from breast cancer patient 3


title: Normal T cell-11

description: Gene Expression Data from T Cells

source_name: T Cells

value: Normal


title: PB Patient 10

description:
Gene expression data from purified CD4+ T cells from patient blood at T0
CD4+ T cells were positively purified from patient samples or healthy donor blood using Dynabeads CD4 (Invitrogen).

value: peripheral blood


title: LN Patient 2

source_name: purified CD4+ T cells from breast cancer patient 2


title: PB Patient 5


title: PB Patient 8


title: LN Patient 1

source_name: purified CD4+ T cells from breast cancer patient 1


title: Memory CD4 S at 24h, biological rep3

value: healthy


title: PB Patient 3


title: PB Patient 4

source_name: purified CD4+ T cells from breast cancer patient 4


title: LN Patient 4


title: PB Donor 3

description:
Gene expression data from purified CD4+ T cells from healthy donor blood at T0
CD4+ T cells were positively purified from patient samples or healthy donor blood using Dynabeads CD4 (Invitrogen).

source_name: purified CD4+ T cells from healthy donor 3


title: PB Patient 9

source_name: purified CD4+ T cells from breast cancer patient 9


title: PB Patient 2


title: PB Patient 7


title: PB Patient 6


title: PB Donor 4

source_name: purified CD4+ T cells from healthy donor 4


title: PB Donor 1

source_name: purified CD4+ T cells from healthy donor 1


title: PB Patient 1


title: PB Donor 2

source_name: purified CD4+ T cells from healthy donor 2


title: MDA-MB-231 transfected with miR-200c mimic

status: Public on Jun 03 2013

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

hyb_protocol: The array hybridization followed the standard affymetrix protocols.

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

data_processing: CEL files was uploaded into Partek Genomics Suites 6.5 and processed using the mRNA expression pipeline. The data was quantile-normalized, summarized (median polish), and log2-transformed.

source_name: MDA-MB-231 miR-200c

label_protocol: The cRNA was synthesized using Ambion WT Expression Kit and labeled using Affymetix GeneChip WT Terminal Labeling Kit.

growth_protocol: Breast cancer cell line MDA-MB-231was cultured in DMEM media with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: miRNA mimic was transfected into MDA-MB-231 cells using Lipofectamine™ 2000 reagent (Invitrogen).

value: breast

tag: cell lines

value: Breast cancer cells

tag: transfected with

value: miR-200c mimic


title: MDA-MB-231 transfected with miR-205 mimic

tag: tissue

value: miR-205 mimic


title: MDA-MB-231 transfected with miR-375 mimic

value: miR-375 mimic


title: MEF2C adenovirus-infected HUVEC, 32h

status: Public on Jun 01 2013

city: Vienna

first: Caterina

last: Sturtzel

address: Lazarettgasse 19

department: Dep f Vasc Bio

country: Austria

institute: Medical Univ Vienna

description: Gene expression data from HUVEC infected with Ad.MEF2C for 32h

hyb_protocol: Affymetrix GeneChip® Human Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Fluidics Protocol FS450_0007).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console

source_name: HUVEC, MEF2C adenovirus, 32h

label_protocol: 100ng of total RNA were amplified and labeled with biotin using the Whole Transcript (WT) Sense Target Labeling Protocol.

growth_protocol: Isolated HUVEC, passage 3, were grown in 6 wells to subconfluent density.

treatment_protocol: HUVEC received fresh medium and were infected with adenovirus of MOI 10 for indicated time points, cells were harvested in Trizol.

value: human umbilical vein endothelial cells (HUVECs)

tag: passage

value: MEF2C adenovirus infection

tag: treatment duration


title: MDA-MB-231 mock control

description: MIR-Ctrl

source_name: MDA-MB-231 mock control


title: Control adenovirus-infected HUVEC, 16h

description: Gene expression data from HUVEC infected with Ad.con for 16h

source_name: HUVEC, control adenovirus, 16h

value: control adenovirus infection


title: dn MEF2 adenovirus-infected HUVEC, 16h

description: Gene expression data from HUVEC infected with Ad.DNMEF2 for 16h

source_name: HUVEC, dn MEF2 adenovirus, 16h

value: dn MEF2 adenovirus infection


title: MEF2C adenovirus-infected HUVEC, 16h

description: Gene expression data from HUVEC infected with Ad.MEF2C for 16h

source_name: HUVEC, MEF2C adenovirus, 16h


title: Control adenovirus-infected HUVEC, 32h

description: Gene expression data from HUVEC infected with Ad.con for 32h

source_name: HUVEC, control adenovirus, 32h


title: dn MEF2 adenovirus-infected HUVEC, 8h

description: Gene expression data from HUVEC infected with Ad.DNMEF2 for 8h

source_name: HUVEC, dn MEF2 adenovirus, 8h


title: Non-lesional fibroblast, biological rep 4

status: Public on May 28 2013

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Non-lesional sample from individual with keloid scar

hyb_protocol: Labeling and hybridization to Affymetrix Human Gene 1.0 ST microarray chips

scan_protocol: CEL files were generated using Expresison Console v1.1.1

data_processing: Expression values were subjected to RMA normalization using Affymetrix CDF probeset definition and GeneSpringGX v7.3.1.

source_name: Fibroblast from non-lesional sample in individual with keloid scar

growth_protocol: Normal full thickness skin samples and excised keloid scars were incubated overnight at 4 degrees in Dispase II.  Fibroblasts were isolated by mincing dermal components followed by collagenase digestion.  Keratinocytes were released from epidermis using 0.025% trypsin.  Fibroblasts were cultered in Dubecco's modified Eagle's medium supplemented with 10ng/ml EGF, f ug/ml insulin, 0.5 ug/ml hydrocortisone, 0.1 mM ascorbic acid-2=phosphate, 4% fetal bovine serum, and 1X penicillin-streptomucin-fungizone.  Primary keratinocyte cultures were initiated using tissue culture flasks coated with collagen, in medium containing reduced calcium.  Keratinocyte medium consisted of MCDB153 supplemented with 0.2% bovine pituitary extract, 1ng/ml EGF, 5ug/ml insulin, 0.5ug/ml hydrocortisone, 0.1mM AA2P, and 1X PPSF.  All cells were subcultured or harvested at 80-90% confluence.

extract_protocol: RNA was isolated using Rneasy and quality verified by Agilent 2100 Bioanalyzer

treatment_protocol: Keloid skars were exised from pediatric and young adult patients undergoing elective scar excision surgeries; for some patients adjacent non-lesional skin samples were also obtained.  Non-keloid skin biopsies were not collected due to ethical concerns of further keloid scar development.  Normal skin samples were obtained from pateints undergoing elective plastic surgery.

value: Non-lesional fibroblast

value: M

tag: ethnicity

value: Caucasian

tag: excision location

value: Chin


title: Control adenovirus-infected HUVEC, 8h

description: Gene expression data from HUVEC infected with Ad.con for 8h

source_name: HUVEC, control adenovirus, 8h


title: Uninfected HUVEC

description: Gene expression data from uninfected HUVEC

source_name: HUVEC, uninfected


title: Non-lesional keratinocyte, biological rep 2

source_name: Keratinocyte from non-lesion sample from individual with keloid scar

label_protocol: Labeling and hybridization to Affymetrix Human Gene 1.0 ST microarray chips

value: Non-lesional keratinocyte

value: African American

value: Face


title: MEF2C adenovirus-infected HUVEC, 8h

description: Gene expression data from HUVEC infected with Ad.MEF2C for 8h

source_name: HUVEC, MEF2C adenovirus, 8h


title: Non-lesional fibroblast, biological rep 3

value: Ear


title: Keloid fibroblast, biological rep 5

description: Subject with keloid scar

source_name: Fibroblast from keloid scar sample

value: Keloid fibroblast

value: Face-cheek


title: Control fibroblast, biological rep 1

description: normal

source_name: Fibroblast from indivual without keloid scar

value: Control fibroblast

value: F

value: Breast


title: Non-lesional keratinocyte, biological rep 1

value: Neck


title: Control fibroblast, biological rep 3

description: normal


title: Non-lesional fibroblast, biological rep 2


title: Non-lesional keratinocyte, biological rep 4


title: Non-lesional fibroblast, biological rep 1


title: Non-lesional keratinocyte, biological rep 3


title: dn MEF2 adenovirus-infected HUVEC, 32h

description: Gene expression data from HUVEC infected with Ad.DNMEF2 for 32h

source_name: HUVEC, dn MEF2 adenovirus, 32h

value: human umbilical vein endothelial cells (HUVECs)


title: Control fibroblast, biological rep 2

description: normal

value: Torso


title: Keloid fibroblast, biological rep 7

description: Subject with keloid scar


title: Keloid fibroblast, biological rep 8

description: Subject with keloid scar


title: Keloid fibroblast, biological rep 6

description: Subject with keloid scar


title: Keloid fibroblast, biological rep 9

description: Subject with keloid scar


title: Keloid fibroblast, biological rep 3

description: Subject with keloid scar


title: Keloid fibroblast, biological rep 4

description: Subject with keloid scar


title: Keloid fibroblast, biological rep 1

description: Subject with keloid scar


title: HUVEC Telmisartan+Amlodipine biological rep2

status: Public on May 14 2013

city: New Haven

first: Mauro

last: Siragusa

address: 10 Amistad Street

institute: Yale University School of Medicine

hyb_protocol: Samples were then hybridized for 16 hours at 45°C to the Affymetrix Whole Transcript GeneChip Human Gene 1.0 ST array using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 7G using the Affymetrix Genechip Command Console for image processing, following the user manual's instructions.

data_processing: Data were analyzed with the Affimetrix Expression Console Software 1.2, using the GC-RMA processing algorithm, following the user manual's instructions.

source_name: HUVEC treated with 100 umol/L telmisartan and 5 umol/L amlodipine

label_protocol: In order to generate sense-strand cDNA, samples (250ng total RNA) were processed using The Ambion® WT Expression Kit (Applied Biosystems), followed by the GeneChip® WT Terminal Labeling Kit (Affymetrix) for fragmentation and biotin labeling, according to the manufacturer’s protocol.

growth_protocol: HUVEC were plated on 0.1% gelatin coated dishes in M199 media supplemented with endothelial cell growth supplement (ECGS), 10% fetal bovine serum (FBS), penicillin-streptomycin and glutamine and used between passages 2 and 4.

extract_protocol: Total RNA was isolated using the miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions. RNA samples were assessed with a NanoDrop 2000c spectrophotometer (Thermo Scientific) and run on a bioanalyzer to determine acceptable quality and quantity.

treatment_protocol: Culture media were supplemented with 100 µmol/L telmisartan or 5 µmol/L amlodipine or both in dimethyl sulfoxide (DMSO) or an equivalent volume of DMSO alone, as control, for 24 hours.

value: HUVEC

tag: sample type

value: primary human umbilical vein endothelial cells between passage 2 and 4


title: HUVEC DMSO biological rep1

source_name: HUVEC treated with DMSO

value: DMSO


title: HUVEC Telmisartan biological rep2

source_name: HUVEC treated with 100 umol/L telmisartan

value: 100 umol/L telmisartan


title: HUVEC DMSO biological rep2


title: NCF DGOct10--709-2010--2NCF

status: Public on May 10 2013

city: L'Hospitalet de Llobregat

first: david

middle: g

last: mollevi

address: Av Gran Via 197-203

country: Spain

institute: IDIBELL

hyb_protocol: Samples were hybridized with GeneChip Human Gene1.0 ST Arrays (Affymetrix) and scanned at the IRB Microarray Core Facility.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: We used RMA background correction, quantile normalization and RMA summarization

source_name: normal colonic fibroblast

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

growth_protocol: We obtained fibroblast cultures from fresh surgical specimen ressected from patients with primary colorectal carcinoma: normal colonic fibroblasts (NCF=9) from the normal colonic mucosa at least 5-10cm from the surgical margin, carcinoma-associated fibroblasts from the primary tumor (CAF-PT=14) and carcinoma-associated fibroblasts (CAF-LM=11) from fresh surgical specimens of liver metastases. All samples were collected under the supervision of the Ethics Committee of the Hospital Universitari de Bellvitge. To establish primary cultures, firstly we homogenated surgical specimens with Collagenase IV and Dispase in a MACS separation unit (Milteny Biotech, Auburn, CA, USA), depleted homogenates from epithelial cells using anti-EPCAM Dynabeads (Invitrogen) and positively selected fibroblasts using anti-fibroblasts microbeads (Milteny Biotech, Auburn, CA, USA). Cells were then cultured in DMEMF12+10%FBS (Gibco) with added penicillin/streptomycin.

extract_protocol: Total RNA was isolated from fresh cells using Qiagen Rneasy mini kit

tag: disease state

value: primary colorectal carcinoma

value: colorectal cancer NORMAL ASSOCIATED MUCOSA

value: normal colonic fibroblast

tag: Stage

value: NORMAL COLONIC MUCOSA

value: MALE


title: NCF DGOct10--723-2010--9NCF

tag: gender


title: NCF DGOct10--713-2010--4NCF

tag: age


title: CAF-PT DGOct10--819-2010--B09-732T

source_name: carcinoma-associated fibroblast primary tumour

value: colorectal cancer PRIMARY TUMOUR


title: CAF-PT DGOct10--820-2010--994489T

value: carcinoma-associated fibroblast primary tumour


title: NCF DGOct10--721-2010--8NCF

value: FEMALE


title: CAF-PT DGOct10--722-2010--B4T


title: HUVEC Telmisartan biological rep1

tag: treatment


title: NCF DGOct10--707-2010--1NCF


title: NCF DGOct10--715-2010--5NCF


title: CAF-PT DGOct10--821-2010--1399068T


title: CAF-PT DGOct10--718-2010--B2T


title: CAF-PT DGOct10--818-2010--B08-22886T


title: CAF-PT DGOct10--716-2010--B1T


title: NCF DGOct10--711-2010--3NCF


title: NCF DGOct10--719-2010--7NCF


title: NCF DGOct10--717-2010--6NCF


title: Keloid fibroblast, biological rep 2

description: Subject with keloid scar

value: Keloid fibroblast

value: M

value: Caucasian

value: Ear


title: HUVEC Telmisartan+Amlodipine biological rep1

value: 100 umol/L telmisartan and 5 umol/L amlodipine


title: CAF-PT DGOct10--724-2010--C1T


title: CAF-PT DGOct10--822-2010--1505300T


title: CAF-PT DGOct10--710-2010--A2T


title: CAF-PT DGOct10--720-2010--B3T


title: CAF-PT DGOct10--712-2010--A3T


title: CAF-PT DGOct10--708-2010--A1T


title: CAF-PT DGOct10--714-2010--A4T


title: CAF-LM DGOct10--828-2010--D11T-10290T

source_name: carcinoma-associated fibroblast liver metastasis

value: colorectal cancer LIVER MET


title: CAF-LM DGOct10--827-2010--D10T-8293T

value: carcinoma-associated fibroblast liver metastasis


title: CAF-LM DGOct10--823-2010--D6T-15565T


title: CAF-LM DGOct10--826-2010--D9T-12321T


title: CAF-LM DGOct10--824-2010--D7T-9014T


title: B1_Cells_rep3

status: Public on May 01 2013

city: Leuven

first: Leentje

last: Van Lommel

address: Herestraat 49 bus 901

department: Molecular cell biology

institute: KULeuven

hyb_protocol: Following fragmentation, the cRNA was hybridized for 17 hr at 45C on human gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using  the affymetrix 3000 gene scanner.

data_processing: The data were analyzed with RMA sketch in expression console (v.1.2.0.20).

source_name: Human Peripheral  Blood B cell subset

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting from 50-100 ng total RNA (Expression Analysis Technical Manual, 4425209Rev.B, Affymetrix).

growth_protocol: PBMC from fresh donor blood were isolated by standard density centrifugation procedures, CD19+ B Cells were isolated by magnetic separation (Miltenyi) and B cell subsets purified by fluorescence activted cells sorted.

extract_protocol: RNA was extracted using the agilent absolutely RNA nanoprep kit (400753) according to the protocol

tag: tissue source

value: human peripheral blood

tag: cell type origin

value: peripheral blood mononuclear cells (PBMCs)

tag: b cell subset type

value: B1 cell


title: memory_B_Cells_rep1

value: memory B cell


title: CAF-LM DGOct10--728-2010--D3T

value: primary colorectal carcinoma

tag: cell type


title: CAF-LM DGOct10--825-2010--D8T-10659T


title: I_MAC3

status: Public on Mar 29 2013

first: Xiaojun

last: Hu

address: 1050 Boyles St.

department: CSP

institute: SAIC_Frederick, INc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

data_processing:
Data were processed using Partek software. RMA background correction with quantile normalization
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: microphage treated with M-CSF

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: CD14+ monocytes were isolated from healthy donor peripheral blood enriched leukopacks (Blood Bank, National Institute of Health, Bethesda, MD, USA) using MACS CD14 MicroBeads (Miltenyi Biotec, Auburn, CA, USA). Monocytes were differentiated into macrophages using 25 ng/ml M-CSF (R&D Systems, Minneapolis, MN, USA) (M-Mac) or a combination of M-CSF and 100 ng/ml IL-27 (R&D Systems) (I-Mac). Initially the monocytes were in Macrophage serum free media (Invitrogen, Carlsbad, CA, USA) which was replaced after three days with DMEM (Invitrogen) with 10% FBS (HyClone Laboratories, Logan, UT, USA), 25 mM HEPES (Quality Biology, Gaithersburg, MD, USA) and 5 µg/ml Gentamicin (Invitrogen) containing the same concentration of IL-27. Cells were incubated at 37°C in a 5% CO2 incubator for a total 7 days.

extract_protocol: Cells were collected in RLT buffer. Total RNA was isolated using Qiagen Rneasy kit. cDNA synthesis and amplification used Ambion  WT expression kit.

value: CD14+ monocytes

value: M-CSF + IL-27


title: PB_Cells_rep3

value: plasmablast


title: naïve_B_Cells_rep1

value: naïve B cell


title: PB_Cells_rep2


title: B1_Cells_rep2


title: CAF-LM DGOct10--829-2010--D12T-16236T

value: MALE


title: CAF-LM DGOct10--726-2010--D1T


title: naïve_B_Cells_rep3


title: PB_Cells_rep1


title: I_MAC1


title: naïve_B_Cells_rep2


title: memory_B_Cells_rep2


title: B1_Cells_rep1


title: M_MAC2

source_name: micropahge treated with M-CSF + IL-27

value: M-CSF


title: M_MAC3


title: M_MAC1


title: CAF-LM DGOct10--729-2010--D4T


title: I_MAC2


title: mDC-IL27_2

first: Richard

middle: A

last: Lempicki

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

source_name: iDCs were stimulated by IL-27

growth_protocol: Monocyte derived immature DCs (iDCs) were generated by incubating 500000/ml  monocytes in G4 medium (RPMI 1640 containing 10% fetal bovine serum (Hyclone, UT, USA), 2 mM glutamine, 25 mM HEPES [N-2-hydroxyethylpiperazine-N’-2-ethanesulfonic acid] (Quality Biological, Gaithersburg, MD, USA), 10 µg/ml gentamicin, 50 ng/mL GM-CSF (R&D Systems, Minneapolis, MN, USA) and 50 ng/mL IL-4 (R&D Systems) at 37°C in a CO2 (5%) incubator for 7 days. The culture media was changed with fresh G4 media every 3-4 days.

treatment_protocol: 1000000 DCs were stimulated in the presence or absence of 100 ng/ml IL-27 for 48 hours. The iDCs were then washed with cold PBS prior to RNA extraction (Qiagen RNeasy)

value: IL-27 treated iDCs


title: memory_B_Cells_rep3


title: mDC-IL27_3


title: mDC-iDC_1

source_name: Monocyte derived immature DCs

value: mock treated iDCs


title: mDC-IL27_1


title: mDC-iDC_2


title: Donor-2, T cells (CD3+)

status: Public on Mar 28 2013

city: Gaithersburg

first: Christopher

middle: Allen

last: Morehouse

address: One Medimmune Way

institute: Medimmune LLC

description: HGU133 Plus array data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed in R.

source_name: T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion MessageAmp II-Biotin Enhanced Single Round aRNA Amplification protocol from 75 ng total RNA.

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

treatment_protocol: To examine gene expression in purified cellular fractions, normal human blood was collected from 2 donors as per institutional policy. The granulocyte (CD15+), monocyte (CD14+), T cell (CD3+), B cell (Non-PC gated, CD19+), and PC (CD27++CD38++) fractions from peripheral blood were separated. White blood cells were washed with FACS buffer (PBS + 0.5%BSA + 2mM EDTA (Gibco)) and incubated with 20% heat-inactivated FBS for 10-15 minutes on ice. The following mAbs were added directly to the cells: CD15 (HI98); CD14 (M5E2), CD3 (UCHT1), CD27 (M-T271), CD38 (HB7), and DAPI (Molecular probes). Cells were sorted on a Becton Dickinson FACS Aria II flow cytometer. All sorted fractions were collected in FACS buffer, centrifuged, and the resulting cell pellet was suspended in RNA lysis buffer (Ambion).

value: T cells

tag: markers


title: Donor-2, B cells (CD19+CD20+)

description: HGU133 Plus array data

source_name: B cells

value: B cells


title: Donor-2, Monocytes (CD14+)

description: HGU133 Plus array data

source_name: Monocytes

value: Monocytes


title: Donor-2, Granulocytes (CD15+)

description: HGU133 Plus array data

source_name: Granulocytes

value: Granulocytes


title: Donor-2, Plasma cells (CD38+CD27+)

description: HGU133 Plus array data

source_name: Plasma cells

value: Plasma cells


title: Donor-1, Plasma cells (CD38+CD27+)

description: HGU133 Plus array data


title: CD14-CD19+CD3-.TMP195.PHA#2

status: Public on Mar 24 2013

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

description:
FACS-sorted CD19+ cells from PBMC cultured 60 hours ex vivo, 1 ug/ml PHA stimulation, 3 uM TMP195 treated
RNA by Qiagen RNeasy with on-column DNase treatment method

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 1.0ST for 16-18 hours in GeneChip Hybridization oven 640 at 45 °C with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450. The first stain with streptavidin-R-phycoerythrin (SAPE) was followed by signal amplification using a biotinilated goat anti-streptavidin antibody and another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix).

scan_protocol: Standard Affymetrix protocol on an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix).

data_processing:
Samples were RMA* normalized using Affymetrix Power Tools (*gcbg background correction, quantile normalization, median polish)
Only annotated probes were included in the normalization (i.e. probes having a gene symbol according to Affymetrix's annotation).  HuGene-1_0-st-v1.r4 (annotated only).mps Affymetrix file specifically designed to define the probesets that will be included in a normalization (via the parameter --meta-probesets <file name>.mps) was used.

source_name: human CD19+ B cells, TMP195 treated, PHA-stimulated culture

label_protocol: standard Affymetrix protocol

growth_protocol: Human PBMC were cultured in standard medium (10% FBS, 2 mM L-glutamine, 1 mM Pyruvate, 10 mM HEPES, 10 U/10 mg Penicillin/Streptomycin) at a density of 3x10^6 per mL.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy with on-column DNase treatment method.

treatment_protocol: HDAC inhibitor (3 uM vorinostat or 3 uM TMP195) or vehicle control (0.2% v/v DMSO) were added to the cells in culture immediately before the addition of 1 ug/ml phyohemagglutinin (PHA).  For sorted cell populations, cultured PBMCs were concurrently stained with anti-CD3, anti-CD19, and anti-CD14 antibodies and subjected to FACS (Aria2, BD Biosciences).  Sorted cells were snap frozen prior to RNA extraction.

value: CD19+ B cells


title: mDC-iDC_3

city: Frederick


title: CD14+CD19-CD3-.TMP195.PHA#2

description:
FACS-sorted CD14+ cells from PBMC cultured 60 hours ex vivo, 1 ug/ml PHA stimulation, 3 uM TMP195 treated
RNA by Qiagen RNeasy with on-column DNase treatment method

source_name: human CD14+ monocytes, TMP195 treated, PHA-stimulated culture


title: Donor-1, Monocytes (CD14+)

description: HGU133 Plus array data


title: Donor-1, B cells (CD19+CD20+)

description: HGU133 Plus array data


title: CD14-CD19+CD3-.DMSO.PHA#1

description:
FACS-sorted CD19+ cells from PBMC cultured 60 hours ex vivo, 1 ug/ml PHA stimulation, no HDAC inhibitor
RNA by Qiagen RNeasy with on-column DNase treatment method

source_name: human CD19+ B cells, vehicle treated, PHA-stimulated culture

value: vehicle


title: CD14-CD19-CD3+.DMSO.PHA#1

description:
FACS-sorted CD3+ cells from PBMC cultured 60 hours ex vivo, 1 ug/ml PHA stimulation, no HDAC inhibitor
RNA by Qiagen RNeasy with on-column DNase treatment method

source_name: human CD3+ T cells, vehicle treated, PHA-stimulated culture

value: CD3+ T cells


title: CD14-CD19-CD3+.TMP195.PHA#2

description:
FACS-sorted CD3+ cells from PBMC cultured 60 hours ex vivo, 1 ug/ml PHA stimulation, 3 uM TMP195 treated
RNA by Qiagen RNeasy with on-column DNase treatment method

source_name: human CD3+ T cells, TMP195 treated, PHA-stimulated culture


title: Donor-1, T cells (CD3+)

description: HGU133 Plus array data


title: CD14-CD19+CD3-.DMSO.PHA#2


title: CD14-CD19+CD3-.TMP195.PHA#1


title: CD14+CD19-CD3-.TMP195.PHA#1


title: CD14-CD19-CD3+.TMP195.PHA#1


title: CD14+CD19-CD3-.DMSO.PHA#2

description:
FACS-sorted CD14+ cells from PBMC cultured 60 hours ex vivo, 1 ug/ml PHA stimulation, no HDAC inhibitor
RNA by Qiagen RNeasy with on-column DNase treatment method

source_name: human CD14+ monocytes, vehicle treated, PHA-stimulated culture


title: CD14-CD19-CD3+.DMSO.PHA#2


title: PBMC.TMP195.PHA#1

description:
PBMC cultured 60 hours ex vivo, 1 ug/ml PHA stimulation, 3 uM TMP195 treated
RNA by Qiagen RNeasy with on-column DNase treatment method

source_name: human PBMC, 3uM TMP195 treated, PHA-stimulated culture

value: 3uM TMP195

value: PBMC


title: PBMC.TMP195.PHA#2


title: Donor-1, Granulocytes (CD15+)

description: HGU133 Plus array data


title: CD14+CD19-CD3-.DMSO.PHA#1

value: CD14+ monocytes


title: PBMC.DMSO.PHA#2

description:
PBMC cultured 60 hours ex vivo, 1 ug/ml PHA stimulation, no HDAC inhibitor
RNA by Qiagen RNeasy with on-column DNase treatment method

source_name: human PBMC, vehicle treated, PHA-stimulated culture


title: PBMC.vorinostat.PHA#2

description:
PBMC cultured 60 hours ex vivo, 1 ug/ml PHA stimulation, 3 uM vorinostat treated
RNA by Qiagen RNeasy with on-column DNase treatment method

source_name: human PBMC, 3uM vorinostat treated, PHA-stimulated culture

value: 3uM vorinostat


title: PBMC.DMSO.PHA#1


title: PBMC.DMSO#1

description:
PBMC cultured 60 hours ex vivo, resting, no HDAC inhibitor
RNA by Qiagen RNeasy with on-column DNase treatment method

source_name: human PBMC, vehicle treated, resting culture


title: PBMC.vorinostat.PHA#1


title: PBMC.DMSO#2


title: shCDK19, hypoxia, replicate 1

status: Public on Mar 01 2013

city: Aurora

first: Matthew

middle: D

last: Galbraith

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description: Gene expression data from HCT116 shCDK19 cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Differential gene expression was determined with Partek software using one-way ANOVA.

source_name: HCT116 shCDK19, 24hrs hypoxia

growth_protocol: Hct116 cells were plated in McCoys 5A medium supplemented with 10% fetal calf serum 24hrs prior to treatment as indicated

extract_protocol: total RNA was extracted from cells using a Qiagen Rneasy kit according to manufacturer's instructions

treatment_protocol: normal growth; DMSO/0.375M 5-fluorouracil 12hrs; High/Low glucose DMEM media 24hrs; normoxia/1% O2 24hrs

tag: cell line

tag: shRNA

value: hypoxia


title: shControl, hypoxia, replicate 1

description: Gene expression data from HCT116 shControl cells

source_name: HCT116 shControl, 24hrs hypoxia

value: non-target


title: shCDK8, hypoxia, replicate 1

description: Gene expression data from HCT116 shCDK8 cells

source_name: HCT116 shCDK8, 24hrs hypoxia


title: shControl, high glucose, replicate 1

source_name: HCT116 shControl, high glucose

value: high glucose


title: shControl, hypoxia, replicate 2


title: shControl, low glucose, replicate 1

source_name: HCT116 shControl, low glucose

value: low glucose


title: shCDK19, low glucose, replicate 2

source_name: HCT116 shCDK19, low glucose


title: shCDK19, hypoxia, replicate 2


title: shCDK19, low glucose, replicate 1


title: shControl, low glucose, replicate 3


title: shCDK8, low glucose, replicate 3

source_name: HCT116 shCDK8, low glucose


title: shCDK19, low glucose, replicate 3


title: shCDK8, low glucose, replicate 1


title: shCDK19, 5FU, replicate 1

source_name: HCT116 shCDK19, 0.375M 5FU 12hrs


title: shControl, high glucose, replicate 2


title: shCDK8, hypoxia, replicate 2


title: shCDK8, low glucose, replicate 2


title: shControl, 5FU, replicate 1

source_name: HCT116 shControl, 0.375M 5FU 12hrs


title: shCDK8, 5FU, replicate 1

source_name: HCT116 shCDK8, 0.375M 5FU 12hrs


title: shCDK19, 5FU, replicate 2


title: donor 1 control conditions

status: Public on Mar 07 2013

first: Markus

last: Kleinewietfeld

address: 300 George St

institute: Yale

description: Gene expression data from naive CD4+ T cells differentiated into Th17 cells

hyb_protocol: Standard hybridisation at Yale Center for Genome Analysis (YCGA)  for 16 hours at 45C to Affymetrix HG-U133 plus 2.0 arrays according to Affymetrix guidelines.

scan_protocol: Standard scan at Yale Center for Genome Analysis (YCGA) according to Affymetrix guidelines.

data_processing: The image data were analyzed using Affymetrix Command Console Viewer and metric analyses was carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console and standard MAS5.0 processing at Yale Center for Genome Analysis (YCGA).

source_name: CD4+ T cells differentiated under control conditions, day7

label_protocol: Standard 3´IVT and biotin labelling at Yale Center for Genome Analysis (YCGA) according to Affymetrix guidelines.

growth_protocol: FACS sorted naive human CD4+ T cells (CD45RA+CD45RO-CD25-CD127+) were differentiated into Th17 cells by stimulation with aCD3 and aCD28 and IL-1beta, IL-6, IL-21, IL-23 and TGF-beta1 in the presence (nacl) or absence (none) of additional 40mM NaCl. RNA was extracted after 7 days of culture.

extract_protocol: Total RNA was extracted by Trizol according to the manufacturer (Invitrogen).

treatment_protocol: plate bound aCD3 (10µg/ml) and soluble aCD28 (1µg/ml) and soluble IL-1beta (12.5ng/ml), IL-6 (25ng/ml), IL-21 (25ng/ml), IL-23 (25ng/ml) and TGF-beta1(5ng/ml) in the presence (nacl) or absence (none) of additional 40mM NaCl in X-VIVO cell culture media (LONZA). RNA was extracted after 7 days of culture.

tag: tissue

value: lymphocyte


title: shControl, high glucose, replicate 3


title: shControl, low glucose, replicate 2


title: donor 2 control conditions


title: shCDK8, 5FU, replicate 2


title: shControl, DMSO, replicate 2

source_name: HCT116 shControl, DMSO 12hrs

value: DMSO


title: shControl, 5FU, replicate 2


title: donor 2 high salt conditions

description: Gene expression data from naive CD4+ T cells differentiated into Th17 cells in the presence of high-salt

source_name: CD4+ T cells differentiated under high-salt conditions, day7


title: donor 1 high salt conditions


title: shControl, DMSO, replicate 1


title: shCDK19, normal growth, replicate 3

source_name: HCT116 shCDK19, normal growth

value: untreated


title: shCDK19, normal growth, replicate 2


title: shControl, normal growth, replicate 3

source_name: HCT116 shControl, normal growth


title: shCDK8, normal growth, replicate 3

source_name: HCT116 shCDK8, normal growth


title: shCDK19, normal growth, replicate 1


title: shControl, normal growth, replicate 2


title: SKOV3 - proliferating-rep1

status: Public on Jan 26 2013

city: Melbourne

first: Karen

middle: Elizabeth

last: Sheppard

state: Victoria

address: St Andrews Place

department: Research

country: Australia

institute: Perter MacCallum Cancer Centre

hyb_protocol: Hybridization was for 16hrs andaccording to the standard Affymetrix protocol

scan_protocol: GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450 using standard Fluidics Protocol ((Fluidics protocol FS450_007)). GeneChips were scanned using the Affymetrix 7G Scanner

data_processing: The data was  gc-rma normalised using the R Bioconductor package affy.

source_name: SKOV3 - proliferating

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Ovarian cancer cell lines were plated and harvested when 50-80% confluent.    RNA was extracted and hybridized on Affymetrix microarrays. At least 3 biological repeats were performed for each cell line.

extract_protocol: QIAgen Rneasy was used to extract RNA

treatment_protocol: No treatment

value: Exponentially proliferating ovarian cancer cells


title: RMG1 - proliferating-rep1

source_name: RMG1 - proliferating


title: RMG1 - proliferating-rep2


title: shCDK8, normal growth, replicate 2


title: TOV21G - proliferating-rep2

source_name: TOV21G - proliferating


title: SKOV3 - proliferating-rep4


title: SKOV3 - proliferating-rep3


title: OVCAR8 - proliferating-rep3

source_name: OVCAR8 - proliferating


title: TOV112D - proliferating-rep2

source_name: TOV112D - proliferating


title: TOV112D - proliferating-rep1


title: RMG.II - proliferating-rep1

source_name: RMG.II - proliferating


title: OVCAR8 - proliferating-rep2


title: shCDK8, normal growth, replicate 1


title: RMG.II - proliferating-rep3


title: SKOV3 - proliferating-rep2


title: RMG1 - proliferating-rep3


title: TOV21G - proliferating-rep3


title: shControl, normal growth, replicate 1


title: TOV21G - proliferating-rep1


title: OVCAR5 - proliferating-rep2

source_name: OVCAR5 - proliferating


title: OVCAR5 - proliferating-rep1


title: OVCAR8 - proliferating-rep1


title: OVCAR4 - proliferating-rep3

source_name: OVCAR4 - proliferating


title: RMG.II - proliferating-rep2


title: OVCAR4 - proliferating-rep2


title: OVCAR3 - proliferating-rep2

source_name: OVCAR3 - proliferating


title: TOV112D - proliferating-rep3


title: OV90 - proliferating-rep2

source_name: OV90 - proliferating


title: OAW28 - proliferating-rep1

source_name: OAW28 - proliferating


title: OV90 - proliferating-rep4


title: OAW28 - proliferating-rep3


title: OVCA432 - proliferating-rep1

source_name: OVCA432 - proliferating


title: MCAS - proliferating-rep2

source_name: MCAS - proliferating

value: MCAS


title: OVCA432 - proliferating-rep2


title: OV90 - proliferating-rep1


title: OVCAR3 - proliferating-rep1


title: OAW42 - proliferating-rep2

source_name: OAW42 - proliferating


title: OV90 - proliferating-rep3


title: OAW42 - proliferating-rep1


title: KURAMOCHI - proliferating-rep1

source_name: KURAMOCHI - proliferating

value: KURAMOCHI


title: MCAS - proliferating-rep3


title: OAW28 - proliferating-rep2


title: OVCA432 - proliferating-rep3


title: OAW42 - proliferating-rep3


title: KURAMOCHI - proliferating-rep2


title: KURAMOCHI - proliferating-rep3


title: MCAS - proliferating-rep1


title: JHOM.1 - proliferating-rep2

source_name: JHOM.1 - proliferating


title: JHOS.3 - proliferating-rep4

source_name: JHOS.3 - proliferating


title: JHOS.3 - proliferating-rep2


title: JHOS.3 - proliferating-rep3


title: JHOM.1 - proliferating-rep1


title: JHOM.1 - proliferating-rep3


title: JHOC.9 - proliferating-rep2

source_name: JHOC.9 - proliferating


title: JHOS.3 - proliferating-rep1


title: JHOC.9 - proliferating-rep3


title: JHOC.7 - proliferating-rep1

source_name: JHOC.7 - proliferating


title: JHOC.5 - proliferating-rep2

source_name: JHOC.5 - proliferating


title: JHOC.9 - proliferating-rep1


title: JHOC.5 - proliferating-rep1


title: ES.2 - proliferating-rep3

source_name: ES.2 - proliferating


title: IGROV1- proliferating-rep2

source_name: IGROV1- proliferating


title: FU.OV.1 - proliferating-rep1

source_name: FU.OV.1 - proliferating


title: IGROV1- proliferating-rep3


title: OVCAR3 - proliferating-rep3


title: JHOC.7 - proliferating-rep3


title: JHOC.7 - proliferating-rep2


title: FU.OV.1 - proliferating-rep2


title: EFO.21 - proliferating-rep3

source_name: EFO.21 - proliferating


title: FU.OV.1 - proliferating-rep3


title: JHOC.5 - proliferating-rep3


title: ES.2 - proliferating-rep2


title: EFO.27 - proliferating-rep3

source_name: EFO.27 - proliferating


title: EFO.27 - proliferating-rep2


title: ES.2 - proliferating-rep1


title: EFO.27 - proliferating-rep1


title: Colo.720E - proliferating-rep3

source_name: Colo.720E - proliferating


title: EFO.21 - proliferating-rep2


title: COLO.704 - proliferating-rep3

source_name: COLO.704 - proliferating


title: Colo.720E - proliferating-rep1


title: EFO.21 - proliferating-rep1


title: OVCAR4 - proliferating-rep1

source_name: OVCAR4 - proliferating


title: CH1 - proliferating-rep1

source_name: CH1 - proliferating


title: Caov3 - proliferating-rep3

source_name: Caov3 - proliferating


title: CH1 - proliferating-rep3


title: 59M - proliferating-rep1

source_name: 59M - proliferating


title: 59M - proliferating-rep3


title: COLO.704 - proliferating-rep2


title: A2780- proliferating-rep3

source_name: A2780- proliferating


title: 59M - proliferating-rep2


title: Caov3 - proliferating-rep2


title: Colo.720E - proliferating-rep2


title: A2780- proliferating-rep1


title: Caov3 - proliferating-rep1


title: CH1 - proliferating-rep2


title: COLO.704 - proliferating-rep1


title: 2008 - proliferating-rep3

source_name: 2008 - proliferating


title: 2008 - proliferating-rep2


title: peripheral blood T-cells Patient7 [mRNA]

status: Public on Jan 22 2013

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: gene expression data from T-cell

hyb_protocol: Following fragmentation,15 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridisation (according to the Minimum Information About a Microarray Experiment guideline, the arrays were scanned using an Affymetrix confocal laser scanner (Affymetrix, GeneArray scanner GCS3000) and visualised using GeneChip Operating Software (GCOS, Affymetrix).

data_processing: The raw expression signals were preprocessed following the method of Probe Logarithmic Intensity Error (PLIER) based on perfect match only (pm-only) calculation (Affymetrix).The robust quantile method was applied to get normalized expression values.

source_name: peripheral blood T-cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was prepared using Chomczynski's method (Anal Biochem 162, 156-9 (1987))

treatment_protocol: Cells were snap frozen in -80 C

tag: group

value: ITP patient


title: peripheral blood T-cells Patient5 [mRNA]

description: gene expression data from T-cell


title: A2780- proliferating-rep2


title: 2008 - proliferating-rep1


title: peripheral blood T-cells Patient2 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Patient3 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Patient9 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Patient1 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control8 [mRNA]

description: gene expression data from T-cell

value: Control


title: peripheral blood T-cells Control9 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Patient4 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Patient6 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Patient8 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control5 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control7 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control6 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control2 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control4 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control3 [mRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control1 [mRNA]

description: gene expression data from T-cell


title: MED, ID00241

status: Public on Jan 21 2013

first: Diane

middle: K

last: Birks

department: Neurosurgery

institute: University of Colorado, Denver - Anschutz Medical Campus

hyb_protocol: Standard Affymetrix procedure.

scan_protocol: Standard Affymetrix procedure.

data_processing: Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).

source_name: brain tumor, medulloblastoma, large-cell

label_protocol: For most samples, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer.  For a few samples, limited amount of starting RNA precluded use of this protocol. Instead, RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems) according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.

growth_protocol: All samples were collected at time of surgery.

extract_protocol: RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions.

value: medulloblastoma, large-cell


title: MED, ID00401


title: MED, ID00231


title: AT/RT, ID00737

source_name: brain tumor, AT/RT

value: atypical teratoid / rhabdoid tumor


title: peripheral blood T-cells Control10 [mRNA]

description: gene expression data from T-cell


title: AT/RT, ID00517


title: AT/RT, ID00514


title: CD8+BTLA- TIL_Patient #2549

status: Public on Jan 03 2013

city: Houston

first: Laszlo

middle: G

last: Radvanyi

state: Texas

address: 1515 Holcombe Blvd

department: Melanoma Medical Oncology

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

description:
Gene expression data from sorted CD8+BTLA- TIL from Patient #2549
TIL 2549 CD8+BTLA-

hyb_protocol: Samples were hybridized to Human Gene ST 1.0 Arrays (Affymetrix) in a GeneChip Hybridization Oven 640 for >16 hours, at +45°C, 60 rpm, and stained on a GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Raw data passed QC assessment were generated with Affymetrix GeneChip Command Console. The resulting data were imported into BRB-ArrayTools (NCI, v4.2.1) using Affymetrix default analysis settings, normalized with robust multi-array average (RMA) method, and log2 transformed.

source_name: Sorted CD8+BTLA- TIL from Patient #2549 after 2 weeks of expansion with high-dose IL-2

label_protocol: The single strand cDNA was fragmented by restriction digestion and terminal labeled using GeneChip WT Terminal Label kit (Affymetrix) in the presence of controls

growth_protocol: TILs were isolated by enzymatically digest the melanoma tumor fragments obtained from Stage IIIc/IV melanoma patients at M.D. Anderson Cancer Center.  The TILs were expanded ex vivo with high-dose IL-2 for two weeks

extract_protocol: RNA were extracted from sorted cells (ranging from 0.5x10^6 to 1.0x10^6 cells) using Qiagen Rneasy Mini Kit with removal of genomic DNA with DNase according to the manufacturer's instruction

treatment_protocol: The IL-2 expanded TILs were sorted by fluorescent-activated cell sorter (FACS) for CD8+BTLA+ and CD8+BTLA- TIL subsets. Post-sort purity were determined by flow cytometry.

tag: tumor staging

value: Stage IIIc

tag: locations of metastatic tumor specimens

value: Lymph node (groin) metastases

value: Female

tag: patient id

value: CD8+BTLA- TIL


title: AT/RT, ID00404


title: CD8+BTLA+ TIL_Patient #2549

description:
Gene expression data from sorted CD8+BTLA+ TIL from Patient #2549
TIL 2549 CD8+BTLA+

source_name: Sorted CD8+BTLA+ TIL from Patient #2549 after 2 weeks of expansion with high-dose IL-2

value: CD8+BTLA+ TIL


title: AT/RT, ID00504


title: PMN NS, rep4

status: Public on Jan 10 2013

city: Denver

first: Ken

last: Malcolm

address: 1400 Jackson St

institute: National Jewish Health

description:
C4
Gene expression data from neutrophils after 2h.

hyb_protocol: Affymetrix HG-U133 Plus 2.0 microarrays were hybridized with 10µg cRNA.

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The data were analyzed with Command Console Microarray Suite version 5.0 (MAS 5.0)(Affymetrix).

source_name: neutrophils, control

label_protocol: Microarray sample labeling was carried out using standard methods for reverse transcription and one round of in vitro transcription.

growth_protocol: Freshly isolated human neutrophils from healthy donors were incubated in RPMI containing 2% heat-inactivated platelet-poor plasma.

extract_protocol: RNA was isolated using Trizol Reagent (Invitrogen).

treatment_protocol: Bacteria (or saline) were incubated at 10 bacteria per neutrophil for 2 hours.

value: blood neutrophils

tag: disease status

value: healthy

value: saline

value: 2 hrs


title: AT/RT, ID00413


title: AT/RT, ID00119


title: CD8+BTLA- TIL_Patient #2538

description:
Gene expression data from sorted CD8+BTLA- TIL from Patient #2538
TIL 2538 CD8+BTLA-

source_name: Sorted CD8+BTLA- TIL from Patient #2538 after 2 weeks of expansion with high-dose IL-2

value: Left axillary node metastases


title: AT/RT, ID00003


title: CD8+BTLA- TIL_Patient #2547

description:
Gene expression data from sorted CD8+BTLA- TIL from Patient #2547
TIL 2547 CD8+BTLA-

source_name: Sorted CD8+BTLA- TIL from Patient #2547 after 2 weeks of expansion with high-dose IL-2

value: Stage IV

value: Pulmonary metastases


title: AT/RT, ID00343


title: PMN R-Mab, rep3

description:
R3
Gene expression data from neutrophils after 2h R-Mab.

source_name: neutrophils, rough Mab

value: rough M. abscessus


title: CD8+BTLA+ TIL_patient #2538

description:
Gene expression data from sorted CD8+BTLA+ TIL from Patient #2538
TIL 2538 CD8+BTLA+

source_name: Sorted CD8+BTLA+ TIL from Patient #2538 after 2 weeks of expansion with high-dose IL-2


title: CD8+BTLA+ TIL_Patient #2547

description:
Gene expression data from sorted CD8+BTLA+ TIL from Patient #2547
TIL 2547 CD8+BTLA+

source_name: Sorted CD8+BTLA+ TIL from Patient #2547 after 2 weeks of expansion with high-dose IL-2


title: PMN Sa, rep3

description:
Sa3
Gene expression data from neutrophils after 2h Sa.

source_name: neutrophils, S. aureus

value: S. aureus


title: PMN Sm-Mab, rep4

description:
Sm4
Gene expression data from neutrophils after 2h Sm-Mab.

source_name: neutrophils, smooth Mab

value: smooth M. abscessus


title: PMN R-Mab, rep4

description:
R4
Gene expression data from neutrophils after 2h R-Mab.


title: PMN Sm-Mab, rep3

description:
Sm3
Gene expression data from neutrophils after 2h Sm-Mab.


title: PMN R-Mab, rep2

description:
R2
Gene expression data from neutrophils after 2h R-Mab.


title: AT/RT, ID00370


title: PMN Sa, rep4

description:
Sa4
Gene expression data from neutrophils after 2h Sa.


title: PMN Sm-Mab, rep2

description:
Sm2
Gene expression data from neutrophils after 2h Sm-Mab.


title: PMN NS, rep1

description:
C1
Gene expression data from neutrophils after 2h.


title: PMN Sa, rep2

description:
Sa2
Gene expression data from neutrophils after 2h Sa.


title: PMN NS, rep3

description:
C3
Gene expression data from neutrophils after 2h.


title: PMN NS, rep2

description:
C2
Gene expression data from neutrophils after 2h.


title: CD8+BTLA- TIL_Patient #2532

description:
Gene expression data from sorted CD8+BTLA- TIL from Patient #2532
TIL 2532 CD8+BTLA-

source_name: Sorted CD8+BTLA- TIL from Patient #2532 after 2 weeks of expansion with high-dose IL-2

value: Metastatic tumor mass, left upper back

value: Male


title: PMN Sm-Mab, rep1

description:
Sm1
Gene expression data from neutrophils after 2h Sm-Mab.


title: PMN Sa, rep1

description:
Sa1
Gene expression data from neutrophils after 2h Sa.


title: CD8+BTLA+ TIL_Patient #2529

description:
Gene expression data from sorted CD8+BTLA+ TIL from Patient #2529
TIL 2529 CD8+BTLA+

source_name: Sorted CD8+BTLA+ TIL from Patient #2529 after 2 weeks of expansion with high-dose IL-2

value: Lymph node metastases


title: CD8+BTLA- TIL_Patient #2529

description:
Gene expression data from sorted CD8+BTLA- TIL from Patient #2529
TIL 2529 CD8+BTLA-

source_name: Sorted CD8+BTLA- TIL from Patient #2529 after 2 weeks of expansion with high-dose IL-2


title: CD8+BTLA+ TIL_Patient #2532

description:
Gene expression data from sorted CD8+BTLA+ TIL from Patient #2532
TIL 2532 CD8+BTLA+

source_name: Sorted CD8+BTLA+ TIL from Patient #2532 after 2 weeks of expansion with high-dose IL-2


title: PMN R-Mab, rep1

description:
R1
Gene expression data from neutrophils after 2h R-Mab.


title: Sarcoma Cell Line SK-N-AS

status: Public on Jan 01 2013

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

institute: UCL

description: human sarcoma and primary mesenchymal cell lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Hgu133av2 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: For pre-processing of raw data (background correction, normalisation, and probeset summarisation) we used the Bioconductor affy package for the R prgramming language specifically the 'rma' algorithm

source_name: ATCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary cells and cell lines were grown accrding to standard protocols and used at passage 4-7.

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

treatment_protocol: Undifferentiated human osteoblasts (HOB) were grown to 60% confluency in proliferation medium according to the manufacturer's (Clonetics) instructions. Differentiated HOB were grown for 21 days in differentiation mediua (Clonetics) and test samples were stained for Alakine Phosphatase, Alizarin S and Von Kossa staining to determine levels of differentiation. MSC were grown in adipogenic medium for 7 days.

value: tumour cell line

tag: sarcoma and primary cell type

value: neuroblastoma (metastatic)

tag: other

value: Full details are available at the ATCC website


title: Sarcoma Cell Line TASK1

source_name: Wolfson Insitute for Biomedical Research Cell bank, UCL, London, U.K.

value: ewing sarcoma


title: Sarcoma Cell Line JNDSCRT

source_name: Gift from Dr. Jun Nishio, Department of Pathology, School of Medicine, Fukuoka University, Fukuoka, Japan.

value: desmoplastic round cell tumor

value: Nishio et al., 2002


title: Sarcoma Cell Line LiSa-2

source_name: Gift from Dr. Peter Moller, University of Ulm, Germany.

value: poorly differentiated liposarcoma cell line

value: Wabitsch et al., 2000


title: Sarcoma Cell Line KELLY


title: Sarcoma Cell Line SAOS-2

value: osteosarcoma


title: Sarcoma Cell Line CCA

value: rhabdomyosarcoma


title: Sarcoma Cell Line SAOS-2ICRF


title: Sarcoma Cell Line HT-1080

value: fibrosarcoma


title: Sarcoma Cell Line MHH-NB-11

source_name: DSMZ

value: Full details are available at the DSMZ website


title: Sarcoma Cell Line SK-ES-1


title: Sarcoma Cell Line RH30

value: alveolar rhabdomyosarcoma


title: Sarcoma Cell Line SAOS-2PL


title: Sarcoma Cell Line SK-N-SH


title: Sarcoma Cell Line MG-63


title: Sarcoma Cell Line CBOSM1


title: Sarcoma Cell Line TC71


title: Sarcoma Cell Line RH1


title: Sarcoma Cell Line U-2 OS


title: Sarcoma Cell Line G-292


title: Sarcoma Cell Line CAL-72


title: Sarcoma Cell Line HOS


title: Fibroblasts, mometasone, time 1.5h, patient 2, rep 1

status: Public on Dec 31 2012

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)

source_name: Primary human lung fibroblasts

label_protocol: According to Affymetrix' instructions

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

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

value: Primary human lung fibroblasts

value: Mometasone

tag: patient

tag: time


title: Fibroblasts, mometasone, time 0.3h, patient 2, rep 1

tag: treatment


title: Fibroblasts, mometasone, time 3h, patient 2, rep 1


title: Fibroblasts, baseline, time 0, patient 2, rep 2

value: Baseline


title: Fibroblasts, mometasone, time 0.7h, patient 2, rep 1


title: Fibroblasts, mometasone, time 6h, patient 2, rep 1


title: Fibroblasts, mometasone, time 2h, patient 2, rep 1


title: Fibroblasts, formoterol, time 6h, patient 2, rep 1

value: Formoterol


title: Fibroblasts, mometasone, time 1.5h, patient 1, rep 1


title: Fibroblasts, formoterol, time 3h, patient 2, rep 1


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


title: Fibroblasts, baseline, time 0, patient 1, rep 2


title: Fibroblasts, baseline, time 0, patient 1, rep 1


title: Fibroblasts, mometasone, time 0.7h, patient 1, rep 1


title: Fibroblasts, mometasone, time 2h, patient 1, rep 1


title: Fibroblasts, mometasone, time 3h, patient 1, rep 1


title: Fibroblasts, formoterol, time 3h, patient 1, rep 1


title: Sarcoma Cell Line 143B

value: tumour cell line


title: Fibroblasts, mometasone + R, time 6h, patient 2, rep 1


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


title: Fibroblasts, baseline, time 0, patient 2, rep 1


title: Fibroblasts, mometasone, time 0.3h, patient 1, rep 1


title: Fibroblasts, mometasone, time 1h, patient 2, rep 1


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


title: HepaRG+miR-371-3 rep2

city: Evry

first: stefano

last: cairo

address: 4 rue Pierre Fontaine

country: France

institute: Xentech

hyb_protocol: hybridization was performed as described in Affymetrix GeneChipÂ® Whole Transcript (WT) Sense Target Labeling Assay Manual

scan_protocol: scanning was performed as described in Affymetrix GeneChipÂ® Whole Transcript (WT) Sense Target Labeling Assay Manual

data_processing: Normalized expression was calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) in R. The script is attached to the Series record as a supplemantary file.

source_name: HepaRG cells

label_protocol: 100ng of total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: On average, 1x106 cells were resuspended in Trizol, and RNA extraction was performed according to maunfacturer's instructions.

tag: sex

value: F

value: Liver

value: HepaRG

tag: genome/variation

value: ectopically express miR-371-3 cluster


title: HepaRG+control vector rep3

value: control empty vector


title: HepaRG+control vector rep2


title: HepaRG+miR-371-3 rep1


title: Control (2)_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 2

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.

value: control


title: HIV-1 Vpr (2) [mRNA]

description: SAMPLE 4

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: HepaRG+miR-371-3 rep3


title: HepaRG+control vector rep1