title: CTRL_sponge-rep1

status: Public on Oct 15 2014

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

hyb_protocol: GeneChip WT labeling and Hybridization kit from Ambion was used according to manufacturer instructions

scan_protocol: GeneChips were scanned using the 7G Scanner

data_processing: Affymetrix .CEL files were separately processed for each replicate using the Robust Multi-array Average (RMA) algorithm with quantile normalization as implemented in the Bioconductor package 'oligo'.

source_name: CD4+ T-lymphocytes

label_protocol: Ambion WT Expression kit was used according to manufacturer instructions

growth_protocol: primary T-lymphocytes were grown in RPMI supplemented with 10% FBS, L-glutamine, pen/strep and IL-2

extract_protocol: Total RNA was extracted using Tri-reagent (Sigma) according o manufacturer instructions

treatment_protocol: CD4+ naïve T-lymphocytes were stimulated by anti CD3-CD28 beads(dynal) at a 1:1 cell to beads ratio. 5 days later (48 hrs before harvest) cells were re-stimulated with the same protocol

tag: construct

value: Control


title: miR21_sponge-rep3

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

value: MiR-21 sponge


title: miR21_sponge-rep1


title: human macrophages (si control) 16h without treatment, 4h 21% oxygen [1N1]

status: Public on Nov 30 2014

city: Frankfurt

first: Nathalie

last: Dehne

address: Theodor-Stern-Kai 7

department: Faculty of Medicine, Institute of Biochemestry I

country: Germany

institute: Goethe-University Frankfurt

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. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al.
Unsupported Human Gene 1.0 ST Array CDF Files
HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

label_protocol: Samples were labelled with Ambion WT Expression Kit washed and stained using the HWS Kit (Affymetrix).

growth_protocol: primary human leukocytes were isloated from Buffy-coated blood using Leucosept tubes and LSM 1077. Cells were differentiated to macrophages by addition of human serum to RPMI medium containing pencecilin/steptomycin for 5 days.

extract_protocol: total RNA was isolated using Quiagen RNeasy Kit, RNA was amplified using Ambion WT Expression Kit

treatment_protocol: primary human macrophages were petreated with or without IL-10 (20ng/ml) for 16h and aditionally 4h under 21% or 1% oxygen. RNA was isolated using the Quiagen RNeasy Micro Kit.

tag: cell type

value: macrophages


title: CTRL_sponge-rep2


title: CTRL_sponge-rep3


title: IGTB1130 Th17 48hr

status: Public on Oct 10 2014

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner.

data_processing:
Data were processed using Affymetrix PowerTools, RMA package.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB1130 profiled at 48hr

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit.

growth_protocol: RosettaSep-purified CD4+ T cells were thawed and resuspended in RPMI-1640 supplemented with 10% FCS.

extract_protocol: Total RNA was isolated using Trizol extraction.

treatment_protocol: Thawed T cells were activated with anti-CD3 and anti-CD28 beads, with or without IFNb (30 U/ml) or with Th17 cocktail (anti-IFNg 10ng/ml, anti-IL4 10mg/ml, IL6 50ng/ml, IL23 20ng/ml, IL1b 10ng/ml, TGFb 5ng/ml).

tag: stimulation

tag: hour

tag: age

tag: height

tag: weight

tag: bmi

tag: systolic

tag: diastolic

tag: ethnicity

value: Asian

tag: Sex

value: F

tag: individual id


title: IGTB1393 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB1393 profiled at 48hr

value: European


title: IGTB231 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB231 profiled at 48hr

value: M


title: IGTB1393 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB1393 profiled at 4hr

value: IFNb


title: IGTB1130 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB1130 profiled at 4hr


title: miR21_sponge-rep2


title: RISC-free control transfected, biological rep 1

status: Public on Oct 17 2014

city: Philadelphia

first: Zhewei

last: Shen

state: PA

address: BRB II/III Rm 527, 421 Curie Blvd.,

institute: University of Pennsylvania

hyb_protocol: standard Affymetrix protocol, performed by Penn Genomic Analysis Core

data_processing:
standard Affymetrix protocol, conducted by Penn Bioinformatics Core and Dr. John Tobias
Expression level of genes in RISC-free or siYAP treated HUVEC

source_name: Human umbilical vein endothelial cell

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were cultured in culture dishes pre-coated with 0.1% gelatin with commercial EGM2 media from Lonza

extract_protocol: Qiagen miRNeasy kit was used for extraction

treatment_protocol: siRNA was synthesized as duplex by Life Technology and transfected directly using Invitrogen RNAiMAX. All steps were conducted according to the included vendor protocol.

tag: treatment

value: RISC-free control transfected

value: Primary cell line


title: IGTB1119 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB1119 profiled at 48hr


title: IGTB1088 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB1088 profiled at 48hr

value: African American


title: IGTB1088 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB1088 profiled at 4hr


title: IGTB231 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB231 profiled at 4hr


title: IGTB1119 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB1119 profiled at 4hr


title: IGTB1355 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB1355 profiled at 48hr


title: IGTB1355 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB1355 profiled at 4hr


title: IGTB853 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB853 profiled at 48hr


title: IGTB1061 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB1061 profiled at 48hr


title: IGTB1162 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB1162 profiled at 48hr


title: IGTB853 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB853 profiled at 4hr


title: IGTB1047 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB1047 profiled at 48hr

value: European/Asian


title: IGTB1162 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB1162 profiled at 4hr


title: siYAP RNA #2 transfected, biological rep 2

scan_protocol: standard Affymetrix protocol, performed by Penn Genomic Analysis Core

value: siYAP RNA #2 transfected


title: IGTB1047 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB1047 profiled at 4hr


title: IGTB1061 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB1061 profiled at 4hr


title: IGTB920 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB920 profiled at 4hr


title: IGTB565 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB565 profiled at 48hr


title: IGTB565 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB565 profiled at 4hr


title: IGTB920 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB920 profiled at 48hr


title: IGTB581 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB581 profiled at 48hr


title: IGTB19 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB19 profiled at 4hr


title: IGTB19 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB19 profiled at 48hr


title: IGTB581 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB581 profiled at 4hr


title: Sorted CD38- naive CD4 T cells from adult 4

status: Public on Sep 21 2014

city: London

first: Deena

middle: L

last: Gibbons

state: UK

address: 2nd Floor Borough Wing

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: Kings College London

hyb_protocol: Following fragmentation and labelling, 1.85ug of biotin-cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450, using the Hybridization Wash Stain (HWS) kit (Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner GCS3000.

data_processing: Raw data (CEL files) were processed using the RMA-sketch algorithm (gene level) implemented in Affymetrix’s Expression Console package to produce CHP files for further analysis.

label_protocol: Biotinylated cDNA were prepared according to the recommended protocol from 50ng total RNA, using NuGEN's Ovation Pico WTA V2 kit.

growth_protocol: Primary cells were used, cultured as below in RPMI/10% FCS

extract_protocol: RNA was extracted using the Rneasy kit (Qiagen) as per the manufacturer's instructions and amplified using the NuGen amplification kit

treatment_protocol: Cells were set up at 2x106/ml with 10ng/ml PMA and 1mg/ml Ionomycin for 1.5hrs. Cells were then surface stained for TCRab, CD4, CD45RA and CD38. TCRab+, CD4+, CD45RA+ cells that were +ve or -ve for CD38 were sorted by flow cytometry.

value: Adult CD4 T cells


title: IGTB1132 Th17 48hr

source_name: Anti-CD3/CD28+Th17 polarization CD4+ T cells from individual IGTB1132 profiled at 48hr


title: IGTB1132 IFNb 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells from individual IGTB1132 profiled at 4hr


title: Sorted CD38+ naive CD4 T cells from adult 3


title: Sorted CD38+ naive CD4 T cells from adult 4


title: Sorted CD38- naive CD4 T cells from adult 1


title: Sorted CD38- naive CD4 T cells from adult 2


title: Sorted CD38- naive CD4 T cells from adult 3


title: wild type infected hMDMs, biological rep 3

status: Public on Sep 19 2014

city: Louisville

first: Christopher

last: Price

address: 505 S HANCOCK ST CTR ROOM 633

department: Microbiology and Immunology

institute: University of Louisville

description: Gene expression data from hMDMS infected with Legionella pneumophila AA100

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Human GeneArray 1.0 ST v1 arrays according to the GeneChip WT Terminal Labeling and Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 3.2 (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.6 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization on a gene level. A one-way ANOVA was set up for the different cell types.

source_name: Primary human monocyte derived macrophages infected with Legionella pneumophila AA100 for 8h

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion WT Expression kit protocol followed by the Terminal Labeling and Control Kit (Affymetrix) from 250 ng total RNA

growth_protocol: Human monocytes were isolated from whole blood and allowed to adhere to low adherence cell culture plates for 3 days in RPMI 1640 supplemented with 20% FBS at 37°C and 5% CO2. The monocytes were then counted and resuspended RPMI 1640 supplemented with 10% FBS and plated at a density of 3 X 10^6 cells per well of a 6 well cell culture plate and incubated for a further 2 days. The cell culture media was then replaced with RPMI 1640 supplemented with 5% FBS for one day, and then with RPMI 1640 supplemented with 1% FBS for one day. The mature hMDMs were then used for infection by L. pneumophila. L. pneumophila was grown on BCYE plates for 3 days at 37°C prior to infection.

extract_protocol: Total RNA was isolated from the infected hMDM monolayers using the Qiagen RNeasy Mini kit with on-column DNaseI treatment according to the manufacturer's (Qiagen) instructions

treatment_protocol: The hMDM monolayers plated at density of 3 X 10^6 cells per well in a 6 well plate were either uninfected or infected in triplicate with either the wild type L. pneumophila or the ankB or T2SS mutant at an MOI of 20 for 1 h and.  The hMDMs were then treated for 1h with gentamicin to kill remaining extracellular bacteria and incubated at 37°C and 5% CO2. The infections were allowed to proceed for a total of 8h prior to isolation of total RNA..

value: primary human monocyte-derived macrophages

tag: infection

value: Legionella pneumophila AA100 for 8h


title: Sorted CD38+ naive CD4 T cells from cord blood 1

value: Cord blood CD4 T cells


title: Sorted CD38+ naive CD4 T cells from adult 1


title: wild type infected hMDMs, biological rep 1


title: uninfected hMDMs, biological rep 1

description: Gene expression data from hMDMS

source_name: Primary human monocyte derived macrophages

value: uninfected


title: Sorted CD38+ naive CD4 T cells from cord blood 3


title: ankB mutant infected hMDMS, biological rep 3

description: Gene expression data from hMDMS infected with an ankB mutant of Legionella pneumophila AA100

source_name: Primary human monocyte derived macrophages infected with an ankB mutant of Legionella pneumophila AA100 for 8h


title: Sorted CD38+ naive CD4 T cells from adult 2


title: uninfected hMDMs, biological rep 3

description: Gene expression data from hMDMS


title: t2ss mutant infected hMDMs, biological rep 3

description: Gene expression data from hMDMS infected with an T2SS mutant of Legionella pneumophila AA100

source_name: Primary human monocyte derived macrophages infected with an T2SS mutant of Legionella pneumophila AA100 for 8h


title: Sorted CD38+ naive CD4 T cells from cord blood 2


title: ankB mutant infected hMDMS, biological rep 2

value: ankB mutant of Legionella pneumophila AA100 for 8h


title: Sorted CD38+ naive CD4 T cells from cord blood 4


title: wild type infected hMDMs, biological rep 2


title: t2ss mutant infected hMDMs, biological rep 2

value: T2SS mutant of Legionella pneumophila AA100 for 8h


title: uninfected hMDMs, biological rep 2

description: Gene expression data from hMDMS


title: ankB mutant infected hMDMS, biological rep 1


title: t2ss mutant infected hMDMs, biological rep 1


title: HuVEC with JK exosomes replicate#2

status: Public on Sep 01 2014

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

description: HuVEC-JK exosome treated replicate#2

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cRNAs was hybridized to The Affymetrix Human Gene 1.0 ST 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: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software.

label: Biotin

source_name: HuVEC endothelial cell line

label_protocol: Per RNA labeling, 300 nanograms  of total RNA was used in conjunction with the Affymetrix recommended protocol GeneChip WT Terminal Labeling and Controls Kit (Cat#901525) and Ambion WT Expression Kit (cat#4411973)

growth_protocol: Jurkat T cells and the corresponding CD47-deficient Jurkat mutant JinB8 were maintained at 2.0 x 105 cells per ml in RPMI 1640 medium (Life technologies) supplemented with 10% human serum AB, glutamine, penicillin, and streptomycin.  Jurkat cells were maintained for a maximum of 4 weeks for experiments.  Before exosome isolation, the cells were cultured using low human AB serum in their respective media for at least one passage.  The T cells were cultured in 75 cm3 flasks (Corning) and conditioned medium from ~40x106 cells (~100 ml) was collected. The conditioned medium was further centrifuged for 10 min at 1530×g to remove cell debris.  The supernatants were transferred to new 50 ml tubes. The supernatants were concentrated using centrifugal filter device YM-10 (Centricon). The final volume of supernatant was ~1 ml.  The concentrated supernatants  (~250 μl) from the respective cells were used to purify exosomes. The exosomes were isolated using the exoQuick kit (SBI System Biosciences) according to the manufactures instructions.  The supernatant was completely removed via centrifugation 2 times for 30 min at 1500×g. The white exosome pellet was diluted into 1 ml of ultra-pure water (~10×106 cells).   HUVEC were incubated with Jurkat and JinB8 T cell-derived exosomes using EGM2 media for 6 hours.

extract_protocol: Exosome pellets were purified from Jurkat and Jinb8 T cell conditioned medium using the Exo Quick kit TC (SBI Biosciences).  The pellets were dissolved into 100 μl of IXPBS. Total RNAs from cells or Exosomes (including small and long RNAs) was extracted using miRNeasy Mini kit (Qiagen). (cat. no. 217004)

treatment_protocol: No treatments were performed.

value: JK exosome

tag: cell line

value: HuVEC


title: HuVEC with JK exosomes replicate#1

description: HuVEC-JK exosome treated replicate#1


title: HuVEC replicate#3

description: HuVEC untreated replicate#3


title: HuVEC with JINB8 exosomes replicate#3

description: HuVEC-JINB8 exosome treated replicate#3

value: JINB8 exosomes


title: HuVEC replicate#2

description: HuVEC untreated replicate#2


title: HuVEC with JINB8 exosomes replicate#1

description: HuVEC-JINB8 exosome treated replicate#1


title: HUVEC-high phosphate concentration-24hour-rep1

status: Public on Aug 30 2014

city: Shanghai

first: Ling

last: Qin

address: No.301,Middle Yanchang Road

department: Nephrology

country: China

institute: Shanghai Tenth People's Hospital,Tongji University School of medicine

description: Random variance model (RVM) t -test was used to effectively increase the degree of freedom for small sample sizes. After a significance analysis and a false discovery rate (FDR) analysis, P values and FDRs of less than 0.05 were considered statistically significant.

hyb_protocol: Following fragmenting and labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip HuGene1.0 ST Arrays in Hybridization Oven 640. GeneChips were washed  in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.1) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

label_protocol: Total RNA was amplified into cDNA using the Ambion WT Expression kit. 5.5 ug of cDNA was fragmented and labeled with biotin using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured in Endothelial Cell Growth Medium (EGM ) (Lonza, Walkersville, MD) in a humidified incubator set at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using standard Affymetrix.

tag: phosphate concentration

value: high

value: HUVEC


title: HUVEC-high phosphate concentration-24hour-rep2


title: HUVEC-low phosphate concentration-24hour-rep3

value: low


title: HUVEC-high phosphate concentration-24hour-rep3


title: HuVEC with JK exosomes replicate#3

description: HuVEC-JK exosome treated replicate#3


title: IGTB1162 Activated 48hr

status: Public on Aug 28 2014

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1162 profiled at 48hr

value: Activated

value: F


title: HUVEC-normal phosphate concentration-24hour-rep2

value: normal


title: HUVEC-low phosphate concentration-24hour-rep2


title: IGTB1132 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1132 profiled at 48hr

value: African American

value: M


title: IGTB1130 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1130 profiled at 48hr

value: Asian


title: IGTB1119 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1119 profiled at 48hr


title: IGTB1393 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1393 profiled at 48hr

value: European


title: HUVEC-low phosphate concentration-24hour-rep1


title: HUVEC-normal phosphate concentration-24hour-rep3


title: IGTB1355 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1355 profiled at 48hr


title: IGTB1047 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1047 profiled at 48hr

value: European/Asian


title: IGTB1061 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1061 profiled at 48hr


title: IGTB1088 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1088 profiled at 48hr


title: HuVEC with JINB8 exosomes replicate#2

description: HuVEC-JINB8 exosome treated replicate#2


title: HUVEC-normal phosphate concentration-24hour-rep1


title: IGTB581 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB581 profiled at 48hr


title: IGTB853 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB853 profiled at 48hr


title: IGTB1355 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1355 profiled at 4hr


title: IGTB565 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB565 profiled at 48hr


title: IGTB1162 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1162 profiled at 4hr


title: IGTB920 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB920 profiled at 48hr


title: IGTB1132 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1132 profiled at 4hr


title: IGTB231 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB231 profiled at 48hr


title: IGTB1393 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1393 profiled at 4hr


title: IGTB1061 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1061 profiled at 4hr


title: IGTB1047 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1047 profiled at 4hr


title: IGTB1130 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1130 profiled at 4hr


title: IGTB231 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB231 profiled at 4hr


title: IGTB1119 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1119 profiled at 4hr


title: IGTB1162 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB1162 profiled at 4hr

value: Unstim


title: IGTB1355 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB1355 profiled at 4hr


title: IGTB1088 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB1088 profiled at 4hr


title: IGTB19 Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB19 profiled at 48hr


title: IGTB581 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB581 profiled at 4hr


title: IGTB853 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB853 profiled at 4hr


title: IGTB19 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB19 profiled at 4hr


title: IGTB1132 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB1132 profiled at 4hr


title: IGTB1047 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB1047 profiled at 4hr


title: IGTB1088 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB1088 profiled at 4hr


title: IGTB1061 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB1061 profiled at 4hr


title: IGTB920 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB920 profiled at 4hr


title: IGTB853 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB853 profiled at 4hr


title: IGTB920 Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB920 profiled at 4hr


title: IGTB565 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB565 profiled at 4hr


title: IGTB1119 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB1119 profiled at 4hr


title: IGTB581 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB581 profiled at 4hr


title: IGTB1130 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB1130 profiled at 4hr


title: IGTB19 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB19 profiled at 4hr


title: IGTB1393 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB1393 profiled at 4hr


title: IFNb stimulated 48hr

scan_protocol: Affymetrix GeneChip Scanner

data_processing:
Data were processed using Bioconductor RMA package.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells profiled at 48hr

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

growth_protocol: Frozen T cells were thawed and resuspended with RPMI-1640 supplemented with 10% FCS.

treatment_protocol: Thawed T cells were activated with anti-CD3 and anti-CD28 beads, with or without IFNb (1, 30, 100 or 1000 U/ml) or with Th17 cocktail (anti-IFNg 10ng/ml, anti-IL4 10mg/ml, IL6 50ng/ml, IL23 20ng/ml, IL1b 10ng/ml, TGFb 5ng/ml.

value: IFNb


title: IFNb stimulated 72hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells profiled at 72hr


title: IFNb stimulated 10hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells profiled at 10hr


title: Activated 48hr

source_name: Anti-CD3/CD28 activated CD4+ profiled at 48hr


title: IFNb stimulated 1U 10hr

source_name: Anti-CD3/CD28+IFNb (1U) stimulated CD4+ T cells profiled at 10hr


title: Activated 24hr

source_name: Anti-CD3/CD28 activated CD4+ profiled at 24hr


title: Th17 activated 24hr

source_name: Anti-CD3/CD28+Th17 polarizing activated CD4+ T cells profiled at 24hr


title: Th17 activated 72hr

source_name: Anti-CD3/CD28+Th17 polarizing activated CD4+ T cells profiled at 72hr


title: IFNb stimulated 4hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells profiled at 4hr


title: IFNb stimulated 24hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells profiled at 24hr


title: Activated 10hr

source_name: Anti-CD3/CD28 activated CD4+ profiled at 10hr


title: Th17 activated 10hr

source_name: Anti-CD3/CD28+Th17 polarizing activated CD4+ T cells profiled at 10hr


title: Th17 activated 4hr

source_name: Anti-CD3/CD28+Th17 polarizing activated CD4+ T cells profiled at 4hr


title: Th17 activated 48hr

source_name: Anti-CD3/CD28+Th17 polarizing activated CD4+ T cells profiled at 48hr


title: Unstimulated 4hr

source_name: Unstimulated CD4+ T cells profiled at 0hr


title: Activated 72hr

source_name: Anti-CD3/CD28 activated CD4+ profiled at 72hr


title: Unstimulated 72hr

source_name: Unstimulated CD4+ T cells profiled at 72hr


title: Unstimulated 24hr

source_name: Unstimulated CD4+ T cells profiled at 24hr


title: Th17 activated 2hr

source_name: Anti-CD3/CD28+Th17 polarizing activated CD4+ T cells profiled at 2hr


title: IFNb stimulated 1000U 10hr

source_name: Anti-CD3/CD28+IFNb (1000U) stimulated CD4+ T cells profiled at 10hr


title: Activated 4hr

source_name: Anti-CD3/CD28 activated CD4+ profiled at 4hr


title: Th17 activated 45min

source_name: Anti-CD3/CD28+Th17 polarizing activated CD4+ T cells profiled at 45min


title: Activated 2hr

source_name: Anti-CD3/CD28 activated CD4+ profiled at 2hr


title: IFNb stimulated 1000U 45min

source_name: Anti-CD3/CD28+IFNb (1000U) stimulated CD4+ T cells profiled at 45min


title: IFNb stimulated 2hr

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells profiled at 2hr


title: IFNb stimulated 1U 45min

source_name: Anti-CD3/CD28+IFNb (1U) stimulated CD4+ T cells profiled at 45min


title: IFNb stimulated 45min

source_name: Anti-CD3/CD28+IFNb stimulated CD4+ T cells profiled at 45min


title: Activated 45min

source_name: Anti-CD3/CD28 activated CD4+ profiled at 45min


title: Unstimulated 0hr


title: UWB1.289(-)

status: Public on Jul 29 2014

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
SMhu185
Gene expression data from cultured ovarian cancer cell line.

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized by Robust Multichip Average (RMA) using Affymetrix Powertools.

source_name: Cultured ovarian cancer cell line UWB1.289, untreated

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA.

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

treatment_protocol: Cells were seeded in 96-well plates at an optimal density (ranges 4,000 ~ 12,000; 80% confluency). Following an overnight incubation, cells were treated with GI50 concentrations of cisplatin for 48 h.

value: ovarian cancer cell line

tag: batch


title: SKOV-6(+)

description:
SMhu176
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line SKOV-6, Cisplatin treated

tag: cell type

value: Cisplatin


title: TAYA(-)

description:
SMhu179
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line TAYA, untreated

value: TAYA


title: UWB1.289(+)

description:
SMhu186
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line UWB1.289, Cisplatin treated


title: SKOV-3-(1)

description:
SMhu172
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line SKOV-3, untreated


title: SKOV-4(-)

description:
SMhu170
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line SKOV-4, untreated


title: TOV-112D(-)

description:
SMhu181
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line TOV-112D, untreated


title: TAYA(+)

description:
SMhu180
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line TAYA, Cisplatin treated


title: SKOV-3(+)

description:
SMhu174
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line SKOV-3, Cisplatin treated


title: TOV-21G(+)

description:
SMhu184
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line TOV-21G, Cisplatin treated


title: SKOV-8(+)

description:
SMhu178
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line SKOV-8, Cisplatin treated


title: SKOV-8(-)

description:
SMhu177
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line SKOV-8, untreated


title: SKOV-6(-)

description:
SMhu175
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line SKOV-6, untreated


title: RMG-II(+)

description:
SMhu169
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line RMG-II, Cisplatin treated

value: RMG-II


title: SKOV-4(+)

description:
SMhu171
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line SKOV-4, Cisplatin treated


title: RMG-I(+)

description:
SMhu167
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line RMG-I, Cisplatin treated

value: RMG-I


title: TOV-21G(-)

description:
SMhu183
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line TOV-21G, untreated


title: TOV-112D(+)

description:
SMhu182
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line TOV-112D, Cisplatin treated


title: RMG-I(-)

description:
SMhu166
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line RMG-I, untreated


title: PEO1(-)

description:
SMhu164
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line PEO1, untreated


title: OVK-18(+)

description:
SMhu162
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVK-18, Cisplatin treated


title: PEO1(+)

description:
SMhu165
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line PEO1, Cisplatin treated


title: RMG-II(-)

description:
SMhu168
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line RMG-II, untreated


title: SKOV-3-(2)

description:
SMhu173
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line SKOV-3, untreated


title: OVK-18(-)

description:
SMhu161
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVK-18, untreated


title: OVCAR-5(+)

description:
SMhu160
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-5, Cisplatin treated


title: PA-1(-)

description:
SMhu163
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line PA-1, untreated


title: OVCAR-5(-)

description:
SMhu159
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-5, untreated


title: HuVEC replicate#1

description: HuVEC untreated replicate#1

source_name: HuVEC endothelial cell line

value: HuVEC


title: OVCAR-3(+)

description:
SMhu151
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-3, Cisplatin treated


title: OVCAR-2(+)

description:
SMhu157
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-2, Cisplatin treated


title: OVCAR-3(-)

description:
SMhu158
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-3, untreated


title: OVCA433b(+)

description:
SMhu155
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA433, Cisplatin treated


title: OVCA432(+)

description:
SMhu153
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA432, Cisplatin treated


title: OAW42(+)

description:
SMhu146
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OAW42, Cisplatin treated


title: OV56(+)

description:
SMhu150
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OV56, Cisplatin treated


title: OV56(-)

description:
SMhu149
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OV56, untreated


title: OAW28(+)

description:
SMhu144
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OAW28, Cisplatin treated


title: DOV13A(-)

description:
SMhu147
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line DOV13A, untreated


title: DOV13A(+)

description:
SMhu148
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line DOV13A, Cisplatin treated


title: OVCA432(-)

description:
SMhu152
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA432, untreated


title: OVCAR-2(-)

description:
SMhu156
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-2, untreated


title: JHOS-2(+)

description:
SMhu140
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line JHOS-2, Cisplatin treated


title: JHOS-3(-)

description:
SMhu141
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line JHOS-3, untreated


title: OAW42(-)

description:
SMhu145
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OAW42, untreated


title: JHOS-3(+)

description:
SMhu142
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line JHOS-3, Cisplatin treated


title: JHOS-2(-)

description:
SMhu139
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line JHOS-2, untreated


title: OVCA433b(-)

description:
SMhu154
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA433, untreated


title: Caov-2(-)

description:
SMhu133
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line Caov-2, untreated


title: Caov-2(+)

description:
SMhu134
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line Caov-2, Cisplatin treated


title: Caov-3(-)

description:
SMhu135
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line Caov-3, untreated


title: OAW28(-)

description:
SMhu143
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OAW28, untreated


title: Caov-3(+)

description:
SMhu136
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line Caov-3, Cisplatin treated


title: ovary1847(+)

description:
SMhu132
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line ovary1847, Cisplatin treated


title: ovary1847(-)

description:
SMhu131
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line ovary1847, untreated


title: Hey(+)

description:
SMhu138
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line Hey, Cisplatin treated

value: Hey


title: Hey(-)

description:
SMhu137
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line Hey, untreated


title: M41(-)

description:
SMhu127
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line M41, untreated


title: OVCAR-8+(3)

description:
SMhu126
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-8, Cisplatin treated


title: IGROV-1+(3)

description:
SMhu120
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line IGROV-1, Cisplatin treated


title: OVCAR-8+(2)

description:
SMhu125
Gene expression data from cultured ovarian cancer cell line.


title: A2780cisR(+)

description:
SMhu130
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line A2780cisR, Cisplatin treated


title: A2780cisR(-)

description:
SMhu129
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line A2780cisR, untreated


title: M41(+)

description:
SMhu128
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line M41, Cisplatin treated


title: OVCAR-8-(1)

description:
SMhu121
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-8, untreated


title: IGROV-1+(2)

description:
SMhu119
Gene expression data from cultured ovarian cancer cell line.


title: OVCAR-8+(1)

description:
SMhu124
Gene expression data from cultured ovarian cancer cell line.


title: OVCAR-8-(2)

description:
SMhu122
Gene expression data from cultured ovarian cancer cell line.


title: OVCAR-8-(3)

description:
SMhu123
Gene expression data from cultured ovarian cancer cell line.


title: IGROV-1-(3)

description:
SMhu117
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line IGROV-1, untreated


title: IGROV-1-(1)

description:
SMhu115
Gene expression data from cultured ovarian cancer cell line.


title: C13+(3)

description:
SMhu114
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line C13, Cisplatin treated


title: IGROV-1-(2)

description:
SMhu116
Gene expression data from cultured ovarian cancer cell line.


title: C13+(1)

description:
SMhu112
Gene expression data from cultured ovarian cancer cell line.


title: C13+(2)

description:
SMhu113
Gene expression data from cultured ovarian cancer cell line.


title: C13-(3)

description:
SMhu111
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line C13, untreated


title: IGROV-1+(1)

description:
SMhu118
Gene expression data from cultured ovarian cancer cell line.


title: C13-(1)

description:
SMhu109
Gene expression data from cultured ovarian cancer cell line.


title: C13-(2)

description:
SMhu110
Gene expression data from cultured ovarian cancer cell line.


title: IGTB231 Unstimulated 4hr

source_name: Unstimulated CD4+ T cells from individual IGTB231 profiled at 4hr

tag: stimulation


title: DOV13B+(3)

description:
SMhu108
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line DOV13B, Cisplatin treated


title: DOV13B+(2)

description:
SMhu107
Gene expression data from cultured ovarian cancer cell line.


title: DOV13B+(1)

description:
SMhu106
Gene expression data from cultured ovarian cancer cell line.


title: DOV13B-(3)

description:
SMhu105
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line DOV13B, untreated


title: OVCAR-10+(3)

description:
SMhu102
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-10, Cisplatin treated


title: DOV13B-(1)

description:
SMhu103
Gene expression data from cultured ovarian cancer cell line.


title: OVCA433+(3)

description:
SMhu096
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA433, Cisplatin treated


title: OVCAR-10+(1)

description:
SMhu100
Gene expression data from cultured ovarian cancer cell line.


title: DOV13B-(2)

description:
SMhu104
Gene expression data from cultured ovarian cancer cell line.


title: OVCA433+(1)

description:
SMhu094
Gene expression data from cultured ovarian cancer cell line.


title: OVCA433-(2)

description:
SMhu092
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA433, untreated


title: DOV13+(3)

description:
SMhu090
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line DOV13, Cisplatin treated


title: OVCAR-10-(2)

description:
SMhu098
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCAR-10, untreated


title: DOV13-(3)

description:
SMhu087
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line DOV13, untreated


title: DOV13-(2)b

description:
SMhu086b
Gene expression data from cultured ovarian cancer cell line.


title: OVCAR-10+(2)

description:
SMhu101
Gene expression data from cultured ovarian cancer cell line.


title: DOV13+(1)

description:
SMhu088
Gene expression data from cultured ovarian cancer cell line.


title: A2008+(3)

description:
SMhu084
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line A2008, Cisplatin treated


title: A2008+(2)

description:
SMhu083
Gene expression data from cultured ovarian cancer cell line.


title: OVCAR-10-(3)

description:
SMhu099
Gene expression data from cultured ovarian cancer cell line.


title: DOV13-(1)b

description:
SMhu085b
Gene expression data from cultured ovarian cancer cell line.


title: DOV13-(2)

description:
SMhu086
Gene expression data from cultured ovarian cancer cell line.


title: DOV13-(1)

description:
SMhu085
Gene expression data from cultured ovarian cancer cell line.


title: OVCA433-(1)

description:
SMhu091
Gene expression data from cultured ovarian cancer cell line.


title: OVCAR-10-(1)

description:
SMhu097
Gene expression data from cultured ovarian cancer cell line.


title: A2008-(2)

description:
SMhu080
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line A2008, untreated


title: A2008+(1)

description:
SMhu082
Gene expression data from cultured ovarian cancer cell line.


title: DOV13+(2)

description:
SMhu089
Gene expression data from cultured ovarian cancer cell line.


title: FU-OV-1+(3)

description:
SMhu072
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line FU-OV-1, Cisplatin treated


title: A2008-(3)

description:
SMhu081
Gene expression data from cultured ovarian cancer cell line.


title: A2008-(1)

description:
SMhu079
Gene expression data from cultured ovarian cancer cell line.


title: FU-OV-1-(2)

description:
SMhu068
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line FU-OV-1, untreated


title: FU-OV-1+(2)

description:
SMhu071
Gene expression data from cultured ovarian cancer cell line.


title: FU-OV-1-(3)

description:
SMhu069
Gene expression data from cultured ovarian cancer cell line.


title: OV90-(3)

description:
SMhu063
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OV90, untreated


title: FU-OV-1-(1)

description:
SMhu067
Gene expression data from cultured ovarian cancer cell line.


title: OV90+(2)

description:
SMhu065
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OV90, Cisplatin treated


title: OV90+(3)

description:
SMhu066
Gene expression data from cultured ovarian cancer cell line.


title: FU-OV-1+(1)

description:
SMhu070
Gene expression data from cultured ovarian cancer cell line.


title: CH1+(1)

description:
SMhu052
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line CH1, Cisplatin treated


title: CH1+(2)

description:
SMhu053
Gene expression data from cultured ovarian cancer cell line.


title: OV90-(2)

description:
SMhu062
Gene expression data from cultured ovarian cancer cell line.


title: CH1-(3)

description:
SMhu051
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line CH1, untreated


title: CH1-(2)

description:
SMhu050
Gene expression data from cultured ovarian cancer cell line.


title: OV90-(1)

description:
SMhu061
Gene expression data from cultured ovarian cancer cell line.


title: TYK-nu+(2)

description:
SMhu041
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line TYK-nu, Cisplatin treated

value: TYK-nu


title: CH1-(1)

description:
SMhu049
Gene expression data from cultured ovarian cancer cell line.


title: TYK-nu+(3)

description:
SMhu042
Gene expression data from cultured ovarian cancer cell line.


title: TYK-nu-(3)

description:
SMhu039
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line TYK-nu, untreated


title: TYK-nu+(1)

description:
SMhu040
Gene expression data from cultured ovarian cancer cell line.


title: TYK-nu-(1)

description:
SMhu037
Gene expression data from cultured ovarian cancer cell line.


title: TYK-nu-(2)

description:
SMhu038
Gene expression data from cultured ovarian cancer cell line.


title: PA-1+(3)

description:
SMhu036
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line PA-1, Cisplatin treated


title: PA-1+(2)

description:
SMhu035
Gene expression data from cultured ovarian cancer cell line.


title: PA-1-(3)

description:
SMhu033
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line PA-1, untreated


title: PA-1+(1)

description:
SMhu034
Gene expression data from cultured ovarian cancer cell line.


title: PA-1-(2)

description:
SMhu032
Gene expression data from cultured ovarian cancer cell line.


title: PA-1-(1)

description:
SMhu031
Gene expression data from cultured ovarian cancer cell line.


title: OVCA429+(3)

description:
SMhu030
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA429, Cisplatin treated


title: OVCA429+(1)

description:
SMhu028
Gene expression data from cultured ovarian cancer cell line.


title: OVCA429+(2)

description:
SMhu029
Gene expression data from cultured ovarian cancer cell line.


title: OVCA429-(1)

description:
SMhu025
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA429, untreated


title: OVCA420+(2)

description:
SMhu023
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA420, Cisplatin treated


title: OVCA429-(2)

description:
SMhu026
Gene expression data from cultured ovarian cancer cell line.


title: OVCA429-(3)

description:
SMhu027
Gene expression data from cultured ovarian cancer cell line.


title: OVCA420-(3)

description:
SMhu021
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA420, untreated


title: OVCA420-(2)

description:
SMhu020
Gene expression data from cultured ovarian cancer cell line.


title: OVCA420+(3)

description:
SMhu024
Gene expression data from cultured ovarian cancer cell line.


title: OVCA420-(1)

description:
SMhu019
Gene expression data from cultured ovarian cancer cell line.


title: OVCA420+(1)

description:
SMhu022
Gene expression data from cultured ovarian cancer cell line.


title: A2780+(3)

description:
SMhu018
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line A2780, Cisplatin treated


title: A2780-(1)

description:
SMhu013
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line A2780, untreated


title: A2780-(3)

description:
SMhu015
Gene expression data from cultured ovarian cancer cell line.


title: A2780-(2)

description:
SMhu014
Gene expression data from cultured ovarian cancer cell line.


title: HeyC2+(2)

description:
SMhu011
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line HeyC2, Cisplatin treated


title: A2780+(1)

description:
SMhu016
Gene expression data from cultured ovarian cancer cell line.


title: HeyC2-(3)

description:
SMhu009
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line HeyC2, untreated


title: HeyC2+(3)

description:
SMhu012
Gene expression data from cultured ovarian cancer cell line.


title: A2780+(2)

description:
SMhu017
Gene expression data from cultured ovarian cancer cell line.


title: R848 CD34-MoDC #4

status: Public on Jul 23 2014

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Human Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package. Four compendia were generated to address 4 different questions: i) what is the nature of the DC subsets from the FS3T cultures as compared to CD34-MoDCs and to bDC subsets (Matrix 1)? ii) How close are the DC subsets from FS3T versus FS36 cultures (Matrix 2)? iii) What is the impact of TLR stimulations on the CD34-DC subsets from FS3T cultures as compared to the CD34-MoDCs (Matrix 3)? and iv) How do the responses to TLR stimulations of FS3T XCR1+ CD34-DCs versus FS3T XCR1-CD34-DCs comapre to the responses of XCR1+ bDCs and of CD1c+ bDCs (Matrix 4)?

label_protocol: Except for sample  SB_(4,5,6,7,10,20,21,22,30,33,34,35,46 ), 10-D1, and 12-D1 where only 1-2 ng was available, 20ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.

growth_protocol: For the generation of XCR1+ and XCR1- DC subsets, cord blood CD34+ cells were cultured in the presence of FLT3-L, SCF, IL-3 and IL-6 (FS36) or FLT3-L, SCF, IL-3 and TPO (FS3T) for 7 days and further differentiated with FLT3-L, SCF, GM-CSF and IL-4 for 11 to 3 days. MoDCs were generated from CD34+ cells by an initial expansion phase of 21 days with FLT3-L, SCF and TPO, followed by enrichment of the CD14+ cells with MACS and their differentiation with GM-CSF and IL-4 for 7 days. DC subsets from peripheral blood were enriched by depleting the lineage-positive cells by MACS and each subset was then purified by FACS sorting.

extract_protocol: Total RNA was extracted from between1,8x10E4 and 3x10E5 cells for each DC subset with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.

treatment_protocol: Sorted and purified DC subsets were cultured for 16 hrs in RPMI+10% FCS with FLT3-L, SCF, GM-CSF (5 x 10 E5 cells/mL in U bottom 96 well plate) and IL-4 in medium alone or with PolyI:C (5µg/mL), R848 (10µg/mL) or LPS (1µg/mL). The cells were then used for RNA extraction, for immunophenotyping or for other functional analyses.

tag: origin

value: cord blood culture

tag: cord blood or blood donor

tag: culture condition


title: LPS CD34-MoDC #4

value: LPS


title: PIC CD34-MoDC #2

value: PIC


title: UN CD34-MoDC #3

value: Unstimulated


title: UN CD34-MoDC #4


title: R848 CD34-MoDC #3


title: PIC CD34-MoDC #4


title: LPS CD34-MoDC #3


title: PIC CD34-MoDC #3


title: R848 CD34-MoDC #1


title: PIC CD34-MoDC #1


title: LPS CD34-MoDC #1


title: LPS XCR1_bDC #2

value: blood

value: Ex vivo


title: UN bpDC

value: bpDC


title: R848 XCR1_bDC #2


title: UN CD34-MoDC #1


title: R848 CD1c_bDC #1


title: PIC FS3T XCR1- CD34-DC #6

value: XCR1- CD34-DC


title: LPS XCR1_bDC #1


title: UN CD1c_bDC #2


title: PIC XCR1_bDC #1


title: PIC XCR1_bDC #2


title: UN XCR1_bDC #1


title: LPS CD1c_bDC #1


title: UN CD1c_bDC #1


title: LPS CD1c_bDC #2


title: PIC CD1c_bDC #1


title: PIC CD1c_bDC #2


title: R848 XCR1_bDC #1


title: UN XCR1_bDC #2


title: R848 CD1c_bDC #2


title: UN FS3T XCR1- CD34-DC #6


title: LPS FS3T XCR1- CD34-DC #5


title: LPS FS3T XCR1+ CD34-DC #6

value: XCR1+ CD34-DC


title: PIC FS3T XCR1- CD34-DC #5


title: R848 FS3T XCR1- CD34-DC #5


title: HeyC2-(1)

description:
SMhu007
Gene expression data from cultured ovarian cancer cell line.

value: ovarian cancer cell line


title: HeyA8+(3)

description:
SMhu006
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line HeyA8, Cisplatin treated

value: Cisplatin


title: PIC FS3T XCR1- CD34-DC #3


title: UN FS3T XCR1+ CD34-DC #6


title: PIC FS3T XCR1+ CD34-DC #6


title: UN FS3T XCR1+ CD34-DC #5


title: LPS FS3T XCR1- CD34-DC #4


title: UN FS3T XCR1- CD34-DC #4


title: PIC FS3T XCR1- CD34-DC #4


title: R848 FS3T XCR1+ CD34-DC #5


title: PIC FS3T XCR1+ CD34-DC #5


title: UN FS3T XCR1- CD34-DC #3


title: HeyC2-(2)

description:
SMhu008
Gene expression data from cultured ovarian cancer cell line.


title: HeyC2+(1)

description:
SMhu010
Gene expression data from cultured ovarian cancer cell line.


title: UN FS3T XCR1- CD34-DC #5


title: R848 FS3T XCR1- CD34-DC #3


title: OVCA433-(3)

description:
SMhu093
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA433, untreated


title: LPS FS3T XCR1+ CD34-DC #4


title: PIC FS3T XCR1+ CD34-DC #4


title: UN FS3T XCR1+ CD34-DC #4


title: OVCA433+(2)

description:
SMhu095
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OVCA433, Cisplatin treated


title: HeyA8-(2)

description:
SMhu002
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line HeyA8, untreated


title: HeyA8-(1)b

description:
SMhu001b
Gene expression data from cultured ovarian cancer cell line.


title: CH1+(3)

description:
SMhu054
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line CH1, Cisplatin treated


title: OV90+(1)

description:
SMhu064
Gene expression data from cultured ovarian cancer cell line.

source_name: Cultured ovarian cancer cell line OV90, Cisplatin treated


title: HeyA8-(1)

description:
SMhu001
Gene expression data from cultured ovarian cancer cell line.


title: R848 FS3T XCR1- CD34-DC #1


title: PIC FS3T XCR1- CD34-DC #2


title: R848 FS3T XCR1+ CD34-DC #3


title: LPS FS3T XCR1- CD34-DC #2


title: UN FS3T XCR1+ CD34-DC #3


title: PIC FS3T XCR1+ CD34-DC #3


title: UN FS3T XCR1- CD34-DC #2


title: PIC FS3T XCR1- CD34-DC #1


title: R848 FS3T XCR1+ CD34-DC #1


title: UN FS3T XCR1+ CD34-DC #1


title: HeyA8-(2)b

description:
SMhu002b
Gene expression data from cultured ovarian cancer cell line.


title: HeyA8-(3)

description:
SMhu003
Gene expression data from cultured ovarian cancer cell line.


title: HeyA8+(1)

description:
SMhu004
Gene expression data from cultured ovarian cancer cell line.


title: UN FS3T XCR1+ CD34-DC #2


title: PIC FS3T XCR1+ CD34-DC #1


title: LPS FS3T XCR1+ CD34-DC #2


title: UN FS36 XCR1+ CD34-DC #3


title: UN FS36 XCR1+ CD34-DC #1


title: UN FS36 XCR1+ CD34-DC #2


title: UN FS36 CD141- XCR1- CD34-DC #3

value: CD141- XCR1- CD34-DC


title: UN FS36  CD141+ XCR1- CD34-DC #3

value: CD141+ XCR1- CD34-DC


title: UN FS36  CD141+ XCR1- CD34-DC #1


title: UN FS3T XCR1- CD34-DC #1


title: UN FS36  CD141+ XCR1- CD34-DC #2


title: UN FS36 CD141- XCR1- CD34-DC #1


title: UN FS36 CD141- XCR1- CD34-DC #2


title: Normal Volunteer, Replicate 43

status: Public on Jun 30 2014

city: Bethesda

first: Eric

last: Billings

state: MD

address: 10 Center Drive

institute: NHLBI

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing: The data were analyzed with Affymetrix apt version 1.12, GeneSpring 11.5.1 .  Apt was used to determine present/absent calls and GeneSpring RMA normalization was applied.

source_name: Alveolar macrophage isolated from Normal Volunteer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Affymetrix Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: Total RNA extraction.

tag: diagnosis

value: Normal

tag: tissue

value: Alveolar Macrophage


title: Spontaneous IPF, Replicate 11

source_name: Alveolar macrophage isolated from Spontaneous IPF

value: Spontaneous Idiopathic Pulmonary Fibrosis (IPF)


title: Normal Volunteer, Replicate 33


title: Normal Volunteer, Replicate 37


title: Normal Volunteer, Replicate 34


title: Spontaneous IPF, Replicate 8


title: Spontaneous IPF, Replicate 14


title: Normal Relative, Replicate 16

source_name: Alveolar macrophage isolated from Normal Relative


title: Normal Volunteer, Replicate 35


title: Normal Volunteer, Replicate 36


title: Normal Relative, Replicate 15


title: Normal Volunteer, Replicate 31


title: Normal Volunteer, Replicate 40


title: Spontaneous IPF, Replicate 15


title: Normal Volunteer, Replicate 42


title: Familial IPF, Replicate 8

source_name: Alveolar macrophage isolated from Familial IPF

value: Familial Idiopathic Pulmonary Fibrosis (IPF)


title: Spontaneous IPF, Replicate 12


title: Normal Volunteer, Replicate 45


title: Normal Volunteer, Replicate 38


title: Normal Volunteer, Replicate 32


title: Spontaneous IPF, Replicate 13


title: Normal Volunteer, Replicate 39


title: Spontaneous IPF, Replicate 9


title: Familial IPF, Replicate 7


title: Normal Relative, Replicate 14


title: Normal Volunteer, Replicate 41


title: Normal Volunteer, Replicate 44


title: Normal Volunteer, Replicate 30


title: Spontaneous IPF, Replicate 10


title: Spontaneous IPF, Replicate 7


title: Familial IPF, Replicate 4


title: Normal Volunteer, Replicate 28


title: Spontaneous IPF, Replicate 3


title: Familial IPF, Replicate 5


title: Normal Volunteer, Replicate 29


title: Spontaneous IPF, Replicate 5


title: Normal Relative, Replicate 12


title: Normal Volunteer, Replicate 24


title: Spontaneous IPF, Replicate 2


title: Spontaneous IPF, Replicate 6


title: Spontaneous IPF, Replicate 4


title: Normal Volunteer, Replicate 26


title: Normal Volunteer, Replicate 27


title: Normal Volunteer, Replicate 23


title: Normal Relative, Replicate 13


title: Familial IPF, Replicate 6


title: Spontaneous IPF, Replicate 1


title: Familial IPF, Replicate 2


title: Familial IPF, Replicate 1


title: Normal Relative, Replicate 11


title: Normal Volunteer, Replicate 25


title: Familial IPF, Replicate 3


title: Normal Volunteer, Replicate 20


title: Normal Volunteer, Replicate 19


title: Normal Volunteer, Replicate 15


title: Normal Volunteer, Replicate 17


title: Normal Volunteer, Replicate 22


title: Normal Volunteer, Replicate 18


title: Normal Relative, Replicate 10


title: Normal Relative, Replicate 8


title: Normal Volunteer, Replicate 14


title: Normal Relative, Replicate 5


title: Normal Volunteer, Replicate 12


title: Normal Volunteer, Replicate 16


title: Normal Relative, Replicate 9


title: Normal Volunteer, Replicate 9


title: Normal Volunteer, Replicate 13


title: Normal Relative, Replicate 1


title: Normal Volunteer, Replicate 8


title: Normal Relative, Replicate 4


title: Normal Relative, Replicate 3


title: Normal Volunteer, Replicate 11


title: Normal Relative, Replicate 2


title: Normal Relative, Replicate 7


title: Normal Volunteer, Replicate 7


title: Normal Volunteer, Replicate 6


title: Normal Relative, Replicate 6


title: Normal Volunteer, Replicate 5


title: Normal Volunteer, Replicate 10


title: Normal Volunteer, Replicate 2


title: Normal Volunteer, Replicate 1


title: Normal Volunteer, Replicate 3


title: Normal Volunteer, Replicate 4


title: SS1-28z at T96, biological rep3

status: Public on Jun 26 2014

first: Carl

last: June

state: Pennsylvania

address: 3400 Civic Center Blvd, TRC 8th Floor 8-110E

department: Pathology and laboratory medicine

description: Gene expression data from CAR-redirected Th17 cells following antigen recognition

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and 80 ul of the hybridization cocktail hybridized to Human Gene 1.0 SHuman Gene 1.0ST arrays were scan in a GeneChip 3000 7G scannerT GeneChips (Affymetrix Inc., Santa Clara CA)for 16 h at 45ºC in a 645 GeneChip Hybridization Oven

data_processing: RMA applied to cel files using Partek Genomics Suite v6.6

source_name: SS1-28z at T96

label_protocol: Biotinylated sense-strand cDNA prepared from 250 ng total RNA at the UPENN molecular profiling core using the Ambion WT Expression Kit

growth_protocol: Peripheral blood CD4+ T cells were negatively isolated using RosetteSep Kits, stimultated with activating beads coated with anti-CD3 and anti-ICOS antibodies and cultured under TH17 conditions. 24h upon stimulation, T cells were transduced with lentiviral vectors expressing CARs. The CAR constructs used in this study contain the SS1 scFv that recognizes human mesothelin

extract_protocol: RNA isolation with the Qiazol/miRNeasy mini protocol

treatment_protocol: Redirected T cells from 3 different normal human donors were stimulated with immobilized yeast-derived recombinant mesothelin. Cell pellets were collected and frozen at indicated time points upon antigen recognition

value: Th17 cells

tag: normal donor

value: NDC

tag: car

tag: time point


title: SS1-BBz at T96, biological rep 3

scan_protocol: Human Gene 1.0ST arrays were scan in a GeneChip 3000 7G scanner

source_name: SS1-BBz at T96

value: BBZ


title: SS1-ICOSz at T96, biological rep2

source_name: SS1-ICOSz at T96

value: NDB

value: icosZ


title: SS1-ICOSz at T96, biological rep3


title: SS1-BBz at T24, biological rep 3

source_name: SS1-BBz at T24


title: SS1-BBz at T96, biological rep 2


title: SS1-ICOSz at T96, biological rep1

value: NDA


title: SS1-28z at T96, biological rep1


title: SS1-28z at T24, biological rep3

source_name: SS1-28z at T24


title: SS1-ICOSz at T24, biological rep2

source_name: SS1-ICOSz at T24


title: SS1-BBz at T8, biological rep 3

source_name: SS1-BBz at T8


title: SS1-BBz at T24, biological rep1


title: SS1-BBz at T96, biological rep1


title: SS1-ICOSz at T8, biological rep3

source_name: SS1-ICOSz at T8


title: SS1-28z at T24, biological rep1


title: SS1-28z at T8, biological rep3

source_name: SS1-28z at T8


title: SS1-28z at T24, biological rep2


title: SS1-28z at T96, biological rep2


title: SS1-28z at T8, biological rep2


title: SS1-ICOSz at T8, biological rep2


title: SS1-BBz at T24, biological rep 2


title: SS1-ICOSz at T8, biological rep1


title: SS1-ICOSz at T24, biological rep3


title: SS1-BBz at T8, biological rep1


title: SS1-ICOSz at T4, biological rep3

source_name: SS1-ICOSz at T4


title: SS1-28z at T8, biological rep1


title: SS1-ICOSz at T24, biological rep1


title: SS1-28z at T4, biological rep2

source_name: SS1-28z at T4


title: SS1-ICOSz at T0, biological rep3

description: Gene expression data from CAR-redirected Th17 cells before activation

source_name: SS1-ICOSz at T0


title: SS1-BBz at T4, biological rep1

source_name: SS1-BBz at T4


title: SS1-28z at T4, biological rep3


title: SS1-BBz at T4, biological rep 3


title: SS1-BBz at T8, biological rep 2


title: SS1-ICOSz at T4, biological rep2


title: SS1-ICOSz at T4, biological rep1


title: SS1-28z at T4, biological rep1


title: bLAF_4

status: Public on Jun 15 2014

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

institute: Roslin Institute, University of Edinburgh

description:
ch1:Hy3 array = 1_Exiqon_14326026_S01.txt
ch2:Hy5 array = 0_Exiqon_14326026_S01.txt
ch1 = Test
ch2 = Reference

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 16.0.

scan_protocol: The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in  order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing:
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
Values in processed data table ("Log2_FoldChanges_Test_v_Reference.txt") represent lowess normalized log2 ratio (test/reference)

organism: Bos taurus

source_name: Whole Large Atretic follicle

label_protocol: Six-hundred ng of total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: Total RNA from whole follicles devoid of follicular fluid was extracted using miRNeasy mini kit (Qiagen) according to manufacturer’s instructions (Qiagen, UK) and analysed using the Nano Drop and Agilent Bioanalyzer 2100 (Agilent Technologies).

value: Whole follicle

tag: developmental stage

value: LargeAtretic

source_name: Pooled follicle sample (equal RNA amount from each sample)

value: Small+Large Healthy+Large Atretic


title: bLAF_3

description:
ch1:Hy3 array = 1_Exiqon_14326029_S01.txt
ch2:Hy5 array = 0_Exiqon_14326029_S01.txt
ch1 = Test
ch2 = Reference


title: bLAF_5

description:
ch1:Hy3 array = 1_Exiqon_14326024_S01.txt
ch2:Hy5 array = 0_Exiqon_14326024_S01.txt
ch1 = Test
ch2 = Reference


title: bLAF_1

description:
ch1:Hy3 array = 1_Exiqon_14326014_S01.txt
ch2:Hy5 array = 0_Exiqon_14326014_S01.txt
ch1 = Test
ch2 = Reference


title: bLAF_2

description:
ch1:Hy3 array = 1_Exiqon_14326017_S01.txt
ch2:Hy5 array = 0_Exiqon_14326017_S01.txt
ch1 = Test
ch2 = Reference


title: bLHF_5

description:
ch1:Hy3 array = 1_Exiqon_14326007_S01.txt
ch2:Hy5 array = 0_Exiqon_14326007_S01.txt
ch1 = Test
ch2 = Reference

source_name: Whole Large Healthy follicle

value: LargeHealthy


title: SS1-BBz at T0, biological rep 3

source_name: SS1-BBz at T0


title: SS1-BBz at T4, biological rep 2


title: SS1-BBz at T0, biological rep1


title: SS1-28z at T0, biological rep1

source_name: SS1-28z at T0


title: bLHF_2

description:
ch1:Hy3 array = 1_Exiqon_14326023_S01.txt
ch2:Hy5 array = 0_Exiqon_14326023_S01.txt
ch1 = Test
ch2 = Reference


title: SS1-28z at T0, biological rep2


title: bLHF_4

description:
ch1:Hy3 array = 1_Exiqon_14326006_S01.txt
ch2:Hy5 array = 0_Exiqon_14326006_S01.txt
ch1 = Test
ch2 = Reference


title: SS1-BBz at T0, biological rep 2


title: bLHF_1

description:
ch1:Hy3 array = 1_Exiqon_14326012_S01.txt
ch2:Hy5 array = 0_Exiqon_14326012_S01.txt
ch1 = Test
ch2 = Reference


title: SS1-28z at T0, biological rep3


title: SS1-ICOSz at T0, biological rep1


title: SS1-ICOSz at T0, biological rep2


title: bSF_1

description:
ch1:Hy3 array = 1_Exiqon_14326019_S01.txt
ch2:Hy5 array = 0_Exiqon_14326019_S01.txt
ch1 = Test
ch2 = Reference

source_name: Whole small follicle

value: Small


title: bSF_5

description:
ch1:Hy3 array = 1_Exiqon_14326005_S01.txt
ch2:Hy5 array = 0_Exiqon_14326005_S01.txt
ch1 = Test
ch2 = Reference


title: bSF_2

description:
ch1:Hy3 array = 1_Exiqon_14326021_S01.txt
ch2:Hy5 array = 0_Exiqon_14326021_S01.txt
ch1 = Test
ch2 = Reference


title: bSF_6

description:
ch1:Hy3 array = 1_Exiqon_14326009_S01.txt
ch2:Hy5 array = 0_Exiqon_14326009_S01.txt
ch1 = Test
ch2 = Reference


title: bLAF_6

description:
ch1:Hy3 array = 1_Exiqon_14326018_S01.txt
ch2:Hy5 array = 0_Exiqon_14326018_S01.txt
ch1 = Test
ch2 = Reference


title: bSF_3

description:
ch1:Hy3 array = 1_Exiqon_14326031_S01.txt
ch2:Hy5 array = 0_Exiqon_14326031_S01.txt
ch1 = Test
ch2 = Reference


title: bSF_4

description:
ch1:Hy3 array = 1_Exiqon_14326032_S01.txt
ch2:Hy5 array = 0_Exiqon_14326032_S01.txt
ch1 = Test
ch2 = Reference


title: bLHF_3

description:
ch1:Hy3 array = 1_Exiqon_14326004_S01.txt
ch2:Hy5 array = 0_Exiqon_14326004_S01.txt
ch1 = Test
ch2 = Reference


title: bLHF_6

description:
ch1:Hy3 array = 1_Exiqon_14326016_S01.txt
ch2:Hy5 array = 0_Exiqon_14326016_S01.txt
ch1 = Test
ch2 = Reference


title: Klon8, 48h r1

status: Public on May 31 2014

city: Berlin

first: Angela

last: Relogio

address: Invalidenstraße 43

department: Institute for Theoretical Biology (ITB)

institute: Humboldt University of Berlin and Charité Medical University of Berlin

hyb_protocol: The  Human Gene 1.0 ST microarrays (Affymetrix, Santa Clara, CA, USA) comprises 21,307 probesets, associated to 19,942 distinct human genes. Labeling of RNA targets, hybridization and post-hybridization procedures were performed according to protocols provided by Affymetrix.

scan_protocol: Following washing and staining, probe arrays were scanned twice at 3 µm resolution using a confocal argon laser scanner (Hewlett-Packard, Santa Clara, CA), controlled by Microarray Suite 5.0 software (Affymetrix). Photoemission was detected by a photomultiplier tube through a 570-nm long-pass filter. Computer-generated array images were overlaid with a virtual grid, controlled by Microarray Suite 5.0 software. This step allowed definition of each feature and alignment within known array dimensions. About 40 pixels within each feature were averaged after discarding outliers and pixels close to feature boundaries.  The data were normalized to compensate for variability in hybridizations and hybridization artifacts.

data_processing: Data analysis and statistical evaluations were performed with customized R codes (version 2.15.3, http://www.r-project.org/). Normalization was performed using RMA. Differential Expression has been determined by moderated t-test using R-package limma. For each cell-line we excluded both samples (0 and 48 hour time points) once and determined the 100 most significant probe sets, allowing the identification of two clock groups. We used moderated t-test to select the most discriminative genes ranked by confidence (p-value).metallia

source_name: Klon8, 48h r1

growth_protocol: HCT116 human colorectal carcinoma cells were maintained in McCoy’s 5A culture medium. HaCaT keratinocytes and its derivatives HaCaT I7, II4 and A5RT3, the osteosarcoma U2OS and the human colon carcinoma HT-29, RKO, SW480, LIM1512 and CaCo2 cell lines were cultured in Dulbecco’s modified medium (Gibco). All culture media were supplemented with 10% fetal calf serum and 1% penicillin-streptomycin (Biochrom). Stable-transduced cell populations were selected and maintained in medium containing puromycin (Sigma). For live-cell bioluminescence recording (evaluation/ analysis/ monitoring), cells were maintained in phenol red-free DMEM (Gibco) containing 10% fetal calf serum, 1% penicillin-steptomycin and 0.1 mM D-luciferin (PJK). Cell morphology and density were controlled by light microscopy. All cells were incubated at 37°C with 5% CO2 atmosphere.

extract_protocol: Cells were seeded in 35 mm dishes with a density of 2 x 10 5cells/dish and synchronized for 1 hour with dexamethasone. 24 hours later, cells were collected every three hours and total RNA was extracted. The measurement was started 24h after synchronization to avoid an influence of the immediate early gene response that may not reflect an accurate result of the oscillator. Total RNA was isolated using the RNeasy extraction kit (Qiagen), including DNAse digestion, according to manufacturer’s instructions. Cells were lysed with 350 μl RLT buffer (with 1% ß-mercaptoethanol) and lysate was homogenized with a syringe. Total RNA concentration was determined by OD260 using an UV Spectrophotometer Ultrospec 3000 and stored at -80°C.

treatment_protocol: no treatment was performed

tag: cellline

tag: timepoint

value: colon carcinoma


title: 6123 - IFN-gamma - mAdbID:120223

status: Public on Jun 01 2014

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 120223

hyb_protocol: Affymetrix Hybrization Protocol Other: Terminally labeled cDNA were hybridized to the Human GeneChip 1.0 ST array (Affymetrix) according to the manufacturers' instructions.

scan_protocol: Affymetrix Scanning Protocol Other: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Affymetrix RMA Data Processing
Calculation Method: After Robust Multichip Average (RMA) normalization, differentially expressed genes were identified by One-Way Repeated Measures ANOVA (p<0.01) corrected by Benjamini-Hochberg's False Discovery Rate method (p<0.05) and this gene list was further filtered for between-group alpha levels of p<0.01, p<0.005, and p<0.001 for genes differentially expressed from moDCs differentiated with GM-CSF and IL-4 or GM-CSF, IL-4 and 1 IU of IFN-gamma. The statistically significant gene expression changes were functionally analyzed using Ingenuity Pathways Analysis (Ingenuity Systems) software.

source_name: 6123 - IFN-gamma

label_protocol:
Affymetrix Terminal Labeling Kit
Other: Affymetrix Terminal Labeling Kit according to manufacturer's protocol.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was isolated using the RNeasy kit (Qiagen) and was amplified using the Ambion WT expression kit (Invitrogen) according to the manual.

treatment_protocol:
Agent: GM-CSF, IL-4, INF-gamma
Treatment dose: GM-CSF (800 IU/mL), IL-4 (1000 IU/mL), INF-gamma (1 IU)
Treatment time: 6 days
In-vitro treatment: Elutriated monocytes were prepared from 20-80 year old healthy donors. Elutriated monocytes were plated onto 24 well plates and differentiated into moDCs with RPMI-1640 (+glutamine; Invitrogen) supplemented with 10% heat-inactivated FCS, 0.5% HEPES, 1% Penicillin/Streptomycin, and 0.01% gentamycin, in the presence of GM-CSF (800 IU/mL), IL-4 (1000 IU/mL) and IFN-gamma (1 IU) for 6 days.

value: blood

value: monocyte-derived dendritic cells

tag: individual


title: 305 - IFN-gamma - mAdbID:120209

description: mAdb experiment ID: 120209

source_name: 305 - IFN-gamma


title: 11310 - no IFN-gamma - mAdbID:120210

description: mAdb experiment ID: 120210

source_name: 11310 - no IFN-gamma

treatment_protocol:
Agent: GM-CSF and IL-4
Treatment dose: GM-CSF (800 IU/mL) and IL-4 (1000 IU/mL)
Treatment time: 6 days
In-vitro treatment: Elutriated monocytes were prepared from 20-80 year old healthy donors. Elutriated monocytes were plated onto 24 well plates and differentiated into moDCs with RPMI-1640 (+glutamine; Invitrogen) supplemented with 10% heat-inactivated FCS, 0.5% HEPES, 1% Penicillin/Streptomycin, and 0.01% gentamycin, in the presence of GM-CSF (800 IU/mL) and IL-4 (1000 IU/mL) for 6 days.


title: 82406 - IFN-gamma - mAdbID:120215

description: mAdb experiment ID: 120215

source_name: 82406 - IFN-gamma


title: sml1_delta_35min_rep2

type: genomic

city: Los Angeles

first: Jared

middle: M

last: Peace

state: CA - California

address: 1050 Childs Way RRI 203

department: Molecular and Computational Biology

institute: University of Southern California

hyb_protocol: Standard Nimblegen Protocol

scan_protocol: Genepix Personal 4100A Scanner (Axon Instruments)

data_processing: HU array experiments (arrays 1-6) were within array normalized as in Knott et al. BMC Bioinformatics 2009. Within array normalization for time course experiments (arrays 7-18) was performed as previously described in Knott et al Cell 2012. Final matrix data for all samples is normalized as indicated above and median smoothed over a 2500bp window

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: BrdU IP DNA from S. cerevisiae

label_protocol: Standard Nimblegen Protocol

growth_protocol: Cells were grown in YEPD to OD ~0.5

extract_protocol: Genomic DNA was extracted from 25ml of culture using standard phenol chloroform extraction

treatment_protocol: cells were arrested for 4 hours at 23 degrees C with 7.5 nM alpha factor and then released into fresh media containing  200ug/ml Pronase, 400 ug/ml BrdU

tag: genotype/variation

value: sml1 delta

tag: drug

value: no drug

value: 35 minutes

tag: antibody

value: BrdU antibody (Invitrogen, catalog#033900, lot#1462116A)

source_name: Total DNA from S. cerevisiae

value: WT

value: G1 arrest


title: sml1_delta_25min_rep2

value: 25 minutes

treatment_protocol: cells were arrested for 4 hours at 23 degrees C with 7.5 nM alpha factor


title: sml1_delta_mec1_delta_35min_rep2

value: sml1 delta mec1 delta


title: 11310 - IFN-gamma - mAdbID:120211

description: mAdb experiment ID: 120211

source_name: 11310 - IFN-gamma

tag: cell type


title: 305 - no IFN-gamma - mAdbID:120208

description: mAdb experiment ID: 120208

source_name: 305 - no IFN-gamma


title: sml1_delta_25min_rep1


title: HKE3, 48h r1

source_name: HKE3, 48h r1

label_protocol: The  Human Gene 1.0 ST microarrays (Affymetrix, Santa Clara, CA, USA) comprises 21,307 probesets, associated to 19,942 distinct human genes. Labeling of RNA targets, hybridization and post-hybridization procedures were performed according to protocols provided by Affymetrix.


title: sml1_delta_35min_rep1


title: Klon8, 0h

source_name: Klon8, 0h


title: sml1_delta_rif1_delta_25min_rep1

value: sml1 delta rif1 delta


title: HKE3, 0h

source_name: HKE3, 0h


title: Klon8, 48h r2

source_name: Klon8, 48h r2


title: HKE3, 48h r2

source_name: HKE3, 48h r2


title: HCT116, 48h r2


title: 6123 - no IFN-gamma - mAdbID:120212

description: mAdb experiment ID: 120212

source_name: 6123 - no IFN-gamma


title: sml1_delta_mec1_delta_35min_rep1


title: HCT116, 0h r2


title: sml1_delta_mec1_delta_25min_rep2


title: HaCat, 48h

source_name: HaCat, 48h

value: HaCat

value: keratinocyte


title: 82406 - no IFN-gamma - mAdbID:120214

description: mAdb experiment ID: 120214

source_name: 82406 - no IFN-gamma


title: HaCat, 0h

source_name: HaCat, 0h


title: sml1_delta_rif1_delta_35min_rep2


title: sml1_delta_rif1_delta_25min_rep2


title: sml1_delta_mec1_delta_25min_rep1


title: sml1_delta_rif1_delta_35min_rep1


title: SW480, 48h

tag: cell line


title: A5RT3, 48h

value: keratinocyte, derived form HaCat


title: HCT116, 48h


title: LIM1215, 48h


title: HT29, 0h


title: Caco, 0h r2

source_name: Caco, 0h

value: Caco


title: SW620, 48h


title: Caco, 0h


title: COLO205, 0h

source_name: COLO205, 0h


title: A5RT3, 0h

source_name: A5RT3, 0h


title: Caco, 48h

source_name: Caco, 48h


title: RKO, 0h

source_name: RKO, 0h

value: RKO


title: SW403, 48h

value: colon carcinoma


title: RKO, 48h

source_name: RKO, 48h


title: SW403, 0h


title: SW480, 0h


title: HCT116, 0h


title: COLO205, 48h


title: LIM1215, 0h


title: Caco, 48h r2


title: SW620, 0h


title: HT29, 48h


title: U2OS, 0h

source_name: U2OS, 0h

value: osteosarcoma


title: Intraepithelial CD8 Tem cells - patient 6

status: Public on May 06 2014

city: Cambridge

first: Tim

last: Raine

address: Addenbrooke's Hospital, Hills Road

department: Medicine

institute: University of Cambridge

description: Gene expression data from T effector memory cells sorted by flow cytometry

hyb_protocol: Used Affymetrix GeneChip hybridization and stain kit following the manufacturer’s instructions

scan_protocol: GeneChips scanned with Affymetrix GeneChip Scanner 3000 7G Plus using Affymetrix GeneChip Command Console 3.2.3.1515 software and Affymetrix preset settings.

data_processing:
Microarray data was preprocessed using RMA implemented in R with affy package
log2 RMA signal after batch correction according to the methods ofJohnson et al. Biostatistics 8, 118-127 (2007). Presence/absence calls are based upon the Affymetrix Power Tools Detection Above BackGround (DABG) algorithm: Every probeset is assigned a p value representing the probability of the signal representing background noise, based upon the comparison of the signal from each of the probes in a given probeset and from non-expressed control probes matched for GC-content. We define a transcript ID as detected in any given sampe if ≥50% of probesets mapped to a given transcript ID have a DABG p value ≤0.01. Presence/absence calls are not made (left blank) for transcript IDs mapping to control or cross-hybridising probesets, or those not mapped to an either an autosome or to chromosome X.

source_name: Terminal ileal biopsy, healthy control

label_protocol: Amplified RNA was biotinylated using the Encore Biotin Module (NuGen) according to standard manufacturer's protocol

extract_protocol: RNA extraction was performed using RNeasy micro kits (Qiagen) in an automated manner on the QIAcube platform (Qiagen). Extracted RNA was subject to quantification and quality assurance using an Agilent 2100 Bioanalyzer (Agilent Technologies) and samples checked for a RNA Integrity Value (RIN) >7 prior to further analysis. RNA amplification was performed using the Ovation Pico system (NuGen Technologies) with 1ng starting material from all samples.

treatment_protocol: Subjects received a standardised bowel preparation and underwent the procedure in the morning. 8 pinch biopsies were collected pairwise from the terminal ileum, within 10cm of the ileocaecal valve and with visual avoidance of Peyer’s patches as well as of previously sampled areas. Biopsies were collected into RPMI medium (Invitrogen) on ice and processed immediately. 10ml of peripheral blood was also collected into tubes containing 15mg EDTA (Sigma).    Terminal ileal biopsies were suspended in calcium and magnesium free medium with 2mM EDTA and 1mM DTT (Sigma) and agitated for 30 minutes with 3 changes of media. At each stage, supernatants (containing the IEL fraction) were separated off using a 70μm cell strainer (Greiner Bio-One). After the last media change, the remaining fragments were dissociated through incubation with 200U/ml collagenase IV (Sigma) for 1 hour, prior washing through a 70μm cell strainer. PBMC were separated by centrifugation over a Nycodenz density gradient (Axis-Shield). All isolation steps with the exception of enzymatic digestion were performed at 4C. Cells were stained with an antibody cocktail comprising monoclonal antibodies (mAb) to CD19 (HIB19), CD326 (9C4), TCRab (IP26), CD62L (DREG-56), CD45RO (UCHL1), CD8a (HIT8a), CD4 (RPA-T4) (all from Biolegend), mAb to CD3 (SK7, from eBioscience), and mAb to CD8b (2ST8.5H7, from BD Biosciences). After the final antibody wash step, 4',6-diamidino-2-phenylindole (DAPI, Sigma) was added to washed cells, to enable live/dead discrimination. Cell separation was performed using a BD Facs Aria III cell sorter (BD Biosciences) with cells sorted directly into chilled cell lysis and RNA stabilisation buffer (Buffer RLT, Qiagen) prior to storage at -80C. Sort purity was verified to >99% prior to and after each sort. To minimise cellular perturbation, sorting was performed using a 100µm nozzle at the low sorting pressures using chilled, preservative free PBS.

tag: gender

value: Female

value: Terminal ileum - epithelial layer

value: CD8+ T effector memory cell


title: Lamina propria CD4 Tem cells - patient 6

value: Terminal ileum - lamina propria

value: CD4+ T effector memory cell


title: Lamina propria CD8 Tem cells - patient 6


title: Blood CD4 Tem cells - patient 6

source_name: Peripheral blood, healthy control

value: Blood


title: Lamina propria CD8 Tem cells - patient 5


title: Lamina propria CD4 Tem cells - patient 5


title: Intraepithelial CD4 Tem cells - patient 6


title: Intraepithelial CD4 Tem cells - patient 5


title: Blood CD8 Tem cells - patient 5


title: Blood CD4 Tem cells - patient 5


title: Lamina propria CD8 Tem cells - patient 4


title: Blood CD4 Tem cells - patient 3


title: Lamina propria CD4 Tem cells - patient 3


title: Blood CD8 Tem cells - patient 4


title: Lamina propria CD8 Tem cells - patient 2


title: Intraepithelial CD4 Tem cells - patient 3


title: Intraepithelial CD4 Tem cells - patient 4


title: Blood CD4 Tem cells - patient 4


title: Intraepithelial CD8 Tem cells - patient 5


title: Blood CD8 Tem cells - patient 2


title: Intraepithelial CD4 Tem cells - patient 2


title: Lamina propria CD8 Tem cells - patient 1


title: Blood CD4 Tem cells - patient 2


title: Lamina propria CD4 Tem cells - patient 2


title: Lamina propria CD8 Tem cells - patient 3


title: Intraepithelial CD8 Tem cells - patient 3


title: Intraepithelial CD4 Tem cells - patient 1


title: Lamina propria CD4 Tem cells - patient 4


title: Blood CD8 Tem cells - patient 1


title: Blood CD8 Tem cells - patient 3


title: Blood CD4 Tem cells - patient 1


title: Intraepithelial CD8 Tem cells - patient 1


title: Intraepithelial CD8 Tem cells - patient 4


title: Intraepithelial CD8 Tem cells - patient 2


title: CD4+ T cells, stimulated + 3.3 µg/ml edelfosine - rep3

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description:
Donor3_stim+3.3 µg/ml edelfosine
Gene expression data from CD4+ T cells

hyb_protocol: Probes were prepared using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) and analyzed by microarray technology (Affymetrix GeneChip Human Gene 1.0 ST Array).

scan_protocol: The gene-expression scan was performed with the GeneChip Command Console 3.0 Software (Affymetrix).

data_processing:
The robust multi-array average (RMA) algorithm was applied for background correction, using the Expression Console 1.1 Software (Affymetrix). The samples were quantile normalized, followed by mean signal summarization.
The samples were quantile normalized, followed by mean signal summarization. Hierarchical clustering, t-test and significance analysis of microarrays (SAM) were performed using the TIGR multi experiment viewer (MeV) 4.6.1 Software (TM4 Development Group).

source_name: from PBMCs, 30 h

label_protocol: Reverse transcription of RNA to synthesize cDNA was done by using the WT Expression Kit (Ambion). cDNA fragmentation and labeling was performed by applying the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: CD4+ T cells were prepared from 2 male and 2 female donors, enriched by negative selection (BD IMag) and cultured at 37°C, 5% CO2 for 30 h.

extract_protocol: RNA was isolated by chloroform/isopropanol extraction. For RNA concentration and purification the RNeasy MinElute Cleanup Kit (Qiagen) was used as recommended by the manufacturer.

treatment_protocol: CD4+ T cells of each approach were pooled, counted and resuspended in TRIzol reagent.

value: Immune cells

value: CD4+ T cells

tag: treatment

value: stimulated + 3.3 µg/ml edelfosine


title: CD4+ T cells, stimulated + 3.3 µg/ml edelfosine - rep4

description:
Donor4_stim+3.3 µg/ml edelfosine
Gene expression data from CD4+ T cells


title: CD4+ T cells, stimulated - rep3

description:
Donor3_stim
Gene expression data from CD4+ T cells

value: stimulated


title: CD4+ T cells, unstimulated + 10 µg/ml edelfosine - rep3

description:
Donor3_unstim+10 µg/ml edelfosine
Gene expression data from CD4+ T cells

value: unstimulated + 10 µg/ml edelfosine


title: CD4+ T cells, stimulated - rep4

description:
Donor4_stim
Gene expression data from CD4+ T cells


title: CD4+ T cells, stimulated - rep2

description:
Donor2_stim
Gene expression data from CD4+ T cells


title: CD4+ T cells, unstimulated + 10 µg/ml edelfosine - rep4

description:
Donor4_unstim+10 µg/ml edelfosine
Gene expression data from CD4+ T cells


title: CD4+ T cells, stimulated + 3.3 µg/ml edelfosine - rep2

description:
Donor2_stim+3.3 µg/ml edelfosine
Gene expression data from CD4+ T cells


title: CD4+ T cells, unstimulated + 10 µg/ml edelfosine - rep2

description:
Donor2_unstim+10 µg/ml edelfosine
Gene expression data from CD4+ T cells


title: CD4+ T cells, stimulated + 3.3 µg/ml edelfosine - rep1

description:
Donor1_stim+3.3 µg/ml edelfosine
Gene expression data from CD4+ T cells


title: Lamina propria CD4 Tem cells - patient 1


title: CD4+ T cells, unstimulated + 3.3 µg/ml edelfosine - rep2

description:
Donor2_unstim+3.3 µg/ml edelfosine
Gene expression data from CD4+ T cells

value: unstimulated + 3.3 µg/ml edelfosine


title: CD4+ T cells, stimulated - rep1

description:
Donor1_stim
Gene expression data from CD4+ T cells


title: CD4+ T cells, unstimulated + 3.3 µg/ml edelfosine - rep3

description:
Donor3_unstim+3.3 µg/ml edelfosine
Gene expression data from CD4+ T cells


title: CD4+ T cells, unstimulated - rep2

description:
Donor2_unstim
Gene expression data from CD4+ T cells

value: unstimulated


title: CD4+ T cells, unstimulated + 3.3 µg/ml edelfosine - rep4

description:
Donor4_unstim+3.3 µg/ml edelfosine
Gene expression data from CD4+ T cells


title: CD4+ T cells, unstimulated - rep1

description:
Donor1_unstim
Gene expression data from CD4+ T cells


title: CD4+ T cells, unstimulated + 10 µg/ml edelfosine - rep1

description:
Donor1_unstim+10 µg/ml edelfosine
Gene expression data from CD4+ T cells


title: IGTB1672.F14TR2

status: Public on May 02 2014

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: healthy individual_monocytes from PBMCs

extract_protocol: TriZol

tag: age (yrs)

tag: Sex

value: monocytes from peripheral blood mononuclear cells (PBMCs)

tag: batch

tag: inclusion markers

tag: exclusion markers

tag: phenotype markers

tag: separation method

value: Aria Sorter


title: CD4+ T cells, unstimulated - rep3

description:
Donor3_unstim
Gene expression data from CD4+ T cells

tag: tissue


title: CD4+ T cells, unstimulated + 3.3 µg/ml edelfosine - rep1

description:
Donor1_unstim+3.3 µg/ml edelfosine
Gene expression data from CD4+ T cells


title: CD4+ T cells, unstimulated - rep4

description:
Donor4_unstim
Gene expression data from CD4+ T cells


title: IGTB1672.F14TR1


title: IGTB1501.14

value: Male


title: IGTB1386.14


title: IGTB1593.14


title: IGTB1528.F14


title: IGTB1625.14


title: IGTB1389.F14


title: IGTB1253.14


title: IGTB1387.14


title: IGTB1249.14


title: IGTB1238.14


title: IGTB1530.14


title: IGTB1330.14


title: IGTB1178.14


title: IGTB1218.14


title: IGTB1388.14


title: IGTB1262.14


title: IGTB1210.14


title: IGTB1090.14BR1


title: IGTB1153.14


title: IGTB1048.14


title: IGTB1117.14


title: IGTB1214.14


title: IGTB1090.14


title: IGTB1047.14


title: IGTB1031.14


title: IGTB1017.14


title: IGTB986.14BR1


title: IGTB995.14


title: IGTB986.14


title: IGTB1233.14


title: IGTB896.14


title: IGTB884.14


title: IGTB860.F14


title: IGTB823.14


title: IGTB708.F14


title: IGTB151.14


title: IGTB308.F14


title: IGTB495.14


title: IGTB692.14


title: IGTB71.14


title: IGTB800.F14


title: IGTB708.14


title: IGTB71.14BR1


title: IGTB1672.F4 [CD4]

source_name: healthy individual_CD4 T-Cells from PBMCs

tag: age

value: T4 Naive cells from human peripheral blood mononuclear cells (PBMCs)

value: CD3+ CD4+ CD62L+


title: IGTB151.14BR1


title: IGTB1539.F4 [CD4]

value: Female


title: IGTB514.F14


title: IGTB1528.4 [CD4]


title: IGTB1593.4 [CD4]


title: IGTB1530.4 [CD4]


title: IGTB1528.F4 [CD4]


title: IGTB105.14


title: IGTB1386.4 [CD4]


title: IGTB1501.4TR2 [CD4]


title: IGTB1501.4TR1 [CD4]


title: IGTB1389.F4 [CD4]


title: IGTB1387.4 [CD4]


title: IGTB1249.4 [CD4]


title: IGTB1253.4 [CD4]


title: IGTB1262.4 [CD4]


title: IGTB1330.4 [CD4]


title: IGTB1238.4 [CD4]


title: IGTB1388.4 [CD4]


title: IGTB1117.4 [CD4]


title: IGTB1178.4 [CD4]


title: IGTB896.4 [CD4]


title: IGTB1214.4 [CD4]


title: IGTB1233.4 [CD4]


title: IGTB1090.4BR1 [CD4]


title: IGTB1625.4 [CD4]


title: IGTB1047.4 [CD4]


title: IGTB1023.4 [CD4]


title: IGTB1153.4 [CD4]


title: IGTB1218.4 [CD4]


title: IGTB708.F4 [CD4]


title: IGTB860.F4 [CD4]


title: IGTB1090.4 [CD4]


title: IGTB708.4 [CD4]


title: IGTB1031.4 [CD4]


title: IGTB1048.4 [CD4]


title: IGTB615.4 [CD4]


title: IGTB1017.4 [CD4]


title: IGTB819.4 [CD4]


title: IGTB151.4 [CD4]


title: IGTB1698.14


title: IGTB823.4 [CD4]


title: IGTB151.4BR1 [CD4]


title: IGTB884.4 [CD4]


title: IGTB1683.14


title: IGTB308.F4 [CD4]


title: IGTB495.4 [CD4]


title: IGTB1680.14


title: IGTB1686.14


title: IGTB1652.14TR2


title: IGTB1654.14


title: IGTB1652.14TR1


title: IGTB1671.F14


title: IGTB1662.14


title: IGTB71.4 [CD4]


title: IGTB1647.14


title: IGTB1688.14


title: IGTB514.F4 [CD4]


title: IGTB1650.F14


title: IGTB1651.F14


title: IGTB1669.14


title: IGTB1646.F14


title: IGTB105.4 [CD4]


title: IGTB1640.14


title: IGTB1630.F14TR1


title: IGTB1627.14


title: IGTB1623.F14


title: IGTB1611.14


title: IGTB1630.F14TR2


title: IGTB1617.F14


title: IGTB1608.14TR2


title: IGTB1610.14


title: IGTB1608.14TR1