title: DMSO_rep2

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: human monocyte derived cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit.    WT   Expression Kit

growth_protocol: Monocytes were purified from PBMCs using anti-CD14 microbeads (Miltenyi Biotech) and then cultured at 37°C in 24-well plates (5x10^5 cells per well) in 1 mL of RPMI-1640 Medium (PAA) with 10% (vol/vol) FCS (PAA) containing 100 ng/mL human GM-CSF and 20 ng/mL human IL-4 (R&D Systems，Minneapolis, MN). Half medium was replaced by fresh medium with GM-CSF and IL-4 at day 3 and day 5.

extract_protocol: Total RNA was isolated from cells at indicated time point with Trizol.

treatment_protocol: DCs were matured by 300ng/ml LPS (0111:B4, Sigma) on day 5 and harvested on day 7 for mature DCs.

tag: in vitro culture

value: 5day in GMCSF/IL4 DC culture supplemented with DMSO


title: bone_het_rep1

status: Public on May 02 2014

type: RNA

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description:
SAMPLE 13
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using quantile normalisation with Illumina Genomestudio 2011.1

label: biotin

molecule: total RNA

organism: Mus musculus

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

tag: genotype/variation

value: heterozygote

tag: allele

value: Endra

tag: tissue

value: bone

tag: age

value: 117 days

tag: mouse id

tag: gender

value: male


title: LV linc-DC RNAi_rep2

city: Shanghai

country: China

organism: Homo sapiens

value: 5day in GMCSF/IL4 DC culture with linc-DC RNAi lentivirus infection at day0


title: bone_wt_rep4

description:
SAMPLE 12
replicate 4

value: wild type


title: bone_het_rep3

description:
SAMPLE 15
replicate 3


title: bone_wt_rep3

description:
SAMPLE 11
replicate 3


title: DMSO_rep1


title: bone_wt_rep2

description:
SAMPLE 10
replicate 2


title: Pancreatic islets from control mice 1

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

description: Gene expression data from pancreatic islets of control mice

hyb_protocol: Labeled ssDNA was hybridized to Mouse Gene 1.0 ST  Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were scanned with a Affymetrix GeneChip Scanner 3000 according to the Affimetrix protocol.

data_processing: Affymetrix® Expression Console™ Software for normalization, BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) and GeneSifter software (http://www.geospiza.com) for further analysis

source_name: Pancreatic islets isolated from control mice

label_protocol: The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

growth_protocol: Mice were housed under specific pathogen-free conditions at the animal facility of the University of Ulm and fed ad libitum.

extract_protocol: Total RNA was isolated from pancreatic islet with RNeasy mini kit (QIAGEN)

treatment_protocol: Mice were left untreated prior to islet isolation.

tag: cell type

value: Mouse pancreatic islets

value: C57BL/6 and NMRI (1:1)


title: bone_wt_rep1

description:
SAMPLE 9
replicate 1


title: STAT3 inhibition _rep1

value: 5day in GMCSF/IL4 DC culture supplemented with STAT3 inhibitor S3I-201(200uM)


title: iPS-derived neurons_uninfected 3

city: Pittsburgh

first: Leonardo

last: D'Aiuto

state: PA

address: 3811 O’Hara Street

country: USA

institute: UPMC

description: iPS-derived neurons

hyb_protocol: Labeled RNA was hybridized for 17 hr at 65C on Agilent gene expression array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8X60K array slides

data_processing: Agilent Feature Extraction v10.7.3.1 default parameters and further analyzed by  a cyclic loess algorithm authored in the R programming environment using the Bioconductor suite of tools, and only probes with Entrez gene IDs are selected for further analysis (in total 38804).

source_name: iPS-derived neurons_uninfected

label_protocol: Cy3-CTP  labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA.

extract_protocol: RNA was extracted using RNeasy kits (Qiagen)

treatment_protocol: Neuronal cultures were either infected with HSV-1 in triplicate or uninfected, with each individual sample harvested separately to provide biological replicates for expression analysis. Microarray analysis was performed on i) uninfected neurons; ii) neurons infected with HSV-1 at an MOI of 0.3 in the presence or absence of (E)-5-(2-bromovinyl)-2'-deoxyuridine along with interferon (IFN)-α; iii) neuron quiescent cultures treated with sodium butyrate (NaB, 5 mM);  iv) uninfected neurons treated with E)-5-(2-bromovinyl)-2'-deoxyuridine and interferon IFN-α; v) uninfected neurons treated with NaB

tag: tissue source

value: human skin biopsy samples

tag: cells

value: glutamatergic neurons

value: human iPS-derived neurons

value: female

tag: age (yrs)


title: MSKCC_LTS_208

city: New York

first: Naamit

middle: Kurshan

last: Gerber

state: NY

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: Affymetrix U133 2.0 microarray (Affymetrix) protocol.

data_processing: The raw CEL files of the 7 MSKCC LTS were imported into Partek without normalization or background correction. The TCGA level 1 data was imported from https://tcga-data.nci.nih.gov/docs/publications/gbm_2013/ (date of download 12/2014) without normalization or background correction. The two datasets were combined (they contained an equal number of probes) and quantile normalization was performed. The values in the matrix file are the normalized values for the MSKCC samples.

source_name: Glioblastoma, primary tumor

label_protocol: Expression analysis of tumors was performed using the Affymetrix U133 2.0 microarray (Affymetrix). Processing of the arrays was per the manufacturer’s protocol.

extract_protocol: RNeasy Lipid Tissue Mini Kit (Qiagen)

tag: who grade

value: IV glioma

tag: survival (months)

tag: subtype

value: Mesenchymal


title: MSKCC_LTS_209

scan_protocol: Affymetrix U133 2.0 microarray (Affymetrix) protocol.

value: Classical


title: STAT3 inhibition _rep2


title: MSKCC_LTS_207

value: Neural


title: heart_wt_rep4

description:
SAMPLE 8
replicate 4

value: Endra

value: heart


title: human_dendritic cells_7day in DC culture

value: 7day in GMCSF/IL4 DC culture


title: LV control_rep2

value: 5day in GMCSF/IL4 DC culture with control lentivirus infection at day0


title: heart_wt_rep3

description:
SAMPLE 7
replicate 3

value: 117 days

value: male


title: Ezh2_Delete_2day_1

city: San Francisco

first: William

last: Hwang

state: CA

address: Lim Lab - Box 0525, 35 Medical Center Way

department: Neurosurgery

institute: UCSF

description: replicate 1

scan_protocol: Standard Illumina scanning protocol

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

source_name: Differentiated NSCs

label_protocol: Biotinylated cRNA was generated from total RNA using an Ambion Illumina RNA amplification kit (Ambion)

growth_protocol: SVZ NSCs were passaged 5 times in proliferation medium(DMEM/F12/N2 – Invitrogen, 5% FCS - Hyclone, 20 ng ml-1 EGF, 20 ng ml-1 bFGF, 35 μg ml-1 bovine pituitary extract – Peprotech) before switching to differentiation media (same as proliferation media except with 2% FCS and no EGF or bFGF) for the specified time.

extract_protocol: Total RNA was isolated by Trizol (Life Technologies), purified using the RNeasy Plus Mini Kit (Qiagen) and quantified using the NanoDrop spectrophotometer. Samples were checked for quality using an Agilent TapeStation

treatment_protocol: Ezh2 was acutely deleted by the addition of 4-hydroxytamoxifen (4OHT) to SVZ NSC cultures generated from UBC-CreERT2;Ezh2F/F from P3-4

value: SVZ


title: human_cells_1day in DC culture

value: 1day in GMCSF/IL4 DC culture


title: human_cells_5day in DC culture

value: 5day in GMCSF/IL4 DC culture


title: MSKCC_LTS_205

value: Proneural


title: LV control_rep1


title: LV linc-DC RNAi_rep1

value: 5day in GMCSF/IL4 DC culture with linc-DC RNAi lentivirus infection at day0


title: MSKCC_LTS_203


title: human_cells_2day in DC culture

value: 2day in GMCSF/IL4 DC culture


title: human_monocytes_0day in DC culture

value: 0day in GMCSF/IL4 DC culture


title: human_cells_3day in DC culture

value: 3day in GMCSF/IL4 DC culture


title: MSKCC_LTS_202

value: IV glioma


title: heart_wt_rep2

description:
SAMPLE 6
replicate 2

value: wild type


title: heart_wt_rep1

description:
SAMPLE 5
replicate 1


title: heart_het_rep3

description:
SAMPLE 3
replicate 3

value: heterozygote


title: MSKCC_LTS_201

value: Neural


title: heart_het_rep4

description:
SAMPLE 4
replicate 4

value: Endra

value: heart


title: Mantle_19°C pH7.5_rep1

city: Beijing

first: Shiguo

last: Li

state: Beijing

address: Tsinghua University

department: School of Life Sciences

institute: Tsinghua University

description: Gene expression after 19°C, pH7.5,72hr in mantle

hyb_protocol: Each Slide was hybridized with 1.65  g Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer's instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5  m, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Significant analysis of the microarray was employed to compare differentially expressed genes with an FDR <5%. Differentiallyexpressed genes between treatment groups and control group were also identified by both t-test and the fold-change criteria of the microarray and the genes with p<0.05 and fold change>2 were considered to be up- or down-regulated in compared with control. To determine the relationship between the different treatments, the total hierarchical clustering analysis was performed on the most significant genes (p<0.05; fold change>2) by cluster3.0 (de Hoon et al., 2004 [67]) and java treeview software (Saldanha, 2004[68]) using hierarchical and average linkage algorithm as long as one treatment representing significant difference. Expression trends analysis were carried out on all the most significant genes at different levels of temperature (Control, 25  C and 31  C) and acidity (Control, pH7.8 and pH7.5) treatment by used of MeV4.6 software (Saeed et al., 2006 [69]). Venn diagrams were produced using Venny program (Olivers, 2007 [70]) in order to compare and list the same and different expression trend genes in different treatment conditions. The differentially expressed genes between each treatment group and control were further analyzed by hierarchical clustering analysis and expression analysis respectively.

organism: Pinctada fucata

source_name: Mantle, 19°C, pH7.5, replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer's instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The adult pearl oysters, P.fucata, were purchased from the Marine Biology Research Station at Leizhou Bay, Guangdong Ocean University, Zhanjiang, China. Animals were pre-cultured  one week in glass aquaria as performed by Fang et al (Sude Instant Sea Salt, 33±1‰ , pH8.1±0.05, at 19±1 °C) (2012).

extract_protocol: For microarray analysis, total RNA of mantle tissues from the two acute temperature treatments (25°C and 31°C), two acute acidity treatments (pH7.8 and pH7.5) samples at 72h and control (19°C and pH8.1) were extracted using TRIZOL Reagent (Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions.

treatment_protocol: After acclimation period, oysters were randomly assigned in 50-L tanks and incubated in the following acute and gradual treatment conditions. For acute temperature and acidity stress treatment, oysters were added into the tanks immediately with the maintaining conditions of temperature 25±1 °C and 31±1 °C, acidity pH7.8±0.05 and pH7.5±0.05, salinity 33±1‰ in recirculating seawater. The temperatures and pH values in the studies were near future levels and predicted for 2100 and 2300

value: Mantle

tag: temperature

tag: ph


title: Mantle_19°C pH7.8_rep3

description: Gene expression after 19°C, pH7.8,72hr in mantle

source_name: Mantle, 19°C, pH7.8, replicate 3


title: heart_het_rep1

description:
SAMPLE 1
replicate 1

value: 117 days


title: Mantle_19°C pH7.8_rep1

source_name: Mantle, 19°C, pH7.8, replicate 1


title: heart_het_rep2

description:
SAMPLE 2
replicate 2

value: male


title: Mantle_31°C pH8.1_rep2

description: Gene expression after 31°C, pH8.1,72hr in mantle

source_name: Mantle, 31°C, pH8.1, replicate 2


title: Mantle_31°C pH8.1_rep1

source_name: Mantle, 31°C, pH8.1, replicate 1


title: Mantle_31°C pH8.1_rep3

source_name: Mantle, 31°C, pH8.1, replicate 3


title: Mantle_19°C pH7.5_rep3

source_name: Mantle, 19°C, pH7.5, replicate 3


title: Mantle_19°C pH7.5_rep2

source_name: Mantle, 19°C, pH7.5, replicate 2


title: kidney_het rep4

description:
SAMPLE 24
replicate 4

source_name: kidney

tag: genotype

tag: mutation

value: 18.5 weeks


title: Mantle_19°C pH7.8_rep2

source_name: Mantle, 19°C, pH7.8, replicate 2


title: Mantle_25°C pH8.1_rep3

description: Gene expression after 25°C, pH8.1,72hr in mantle

source_name: Mantle, 25°C, pH8.1, replicate 3


title: kidney_het rep2

description:
SAMPLE 22
replicate 2

tag: strain


title: Mantle_25°C pH8.1_rep1

source_name: Mantle, 25°C, pH8.1, replicate 1


title: Mantle_25°C pH8.1_rep2

source_name: Mantle, 25°C, pH8.1, replicate 2


title: kidney_wt rep3

description:
SAMPLE 20
replicate 3


title: Mantle_19°C pH8.1_rep3

description: Gene expression after 19°C, pH8.1,72hr in mantle

source_name: Mantle, 19°C, pH8.1, replicate 3


title: kidney_het rep3

description:
SAMPLE 23
replicate 3


title: Mantle_19°C pH8.1_rep2

source_name: Mantle, 19°C, pH8.1, replicate 2


title: 344SQ with PIK3CA shRNA, replicate 2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: PI3K shRNA

hyb_protocol: According to Affymetrix protocol.

scan_protocol: According to Affymetrix protocol.

data_processing: Gene expression values were processed by Asuragen (Austin, TX) and subjected to quantile normalization.

source_name: 344SQ with PIK3CA shRNA

label_protocol: According to Affymetrix protocol.

growth_protocol: Murine lung cancer cells (344SQ) were cultured in RPMI 1640 (Mediatech) with 10% FBS (Sigma-Aldrich).

extract_protocol: According to Affymetrix protocol.

treatment_protocol: Vectors expressing mouse PIK3CA shRNA were purchased from OriGene. Cells were transfected using Lipofectamine-PlusTM (Invitrogen).

tag: cell line

value: 344SQ lung cancer cell line

value: PIK3CA knockdown


title: kidney_het rep1

description:
SAMPLE 18
replicate 1


title: 344SQ with PIK3CA shRNA, replicate 3

description: PI3K shRNA


title: kidney_wt rep4

description:
SAMPLE 21
replicate 4


title: 344SQ with PIK3CA shRNA, replicate 1

description: PI3K shRNA


title: 344SQ with control shRNA, replicate 2

description: control

source_name: 344SQ with control shRNA

value: control


title: 344SQ with control shRNA, replicate 1

description: control


title: 344SQ with control shRNA, replicate 3

description: control


title: heart_het rep3

description:
SAMPLE 15
replicate 3

source_name: heart


title: heart_wt rep4

description:
SAMPLE 13
replicate 4


title: kidney_wt rep1

description:
SAMPLE 17
replicate 1


title: heart_wt rep2

description:
SAMPLE 11
replicate 2


title: Mantle_19°C pH8.1_rep1

source_name: Mantle, 19°C, pH8.1, replicate 1

tag: tissue


title: heart_het rep4

description:
SAMPLE 16
replicate 4

tag: age


title: heart_het rep2

description:
SAMPLE 14
replicate 2

tag: mouse id


title: heart_het rep1

description:
SAMPLE 10
replicate 1


title: MB-231_Control2 (exon-level)

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: PLIER expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Standard Affymetrix WT protocol

scan_protocol: Standard Affymetrix rotocol for GCS30007G scanner

data_processing: CHP files generated at both gene- and exon-level with Affymetrix Expression Console using Core probeset

source_name: control

label_protocol: Standard Affymetrix WT protocol starting with 1ug total RNA and incuding riboreduction

growth_protocol: MDA-MB-231 cells with stable expression of either control shRNA or α3-targeting shRNA were maintained at 37 degrees C, 5% CO2, on standard tissue culture plates.  Cells were grown in DMEM supplemented with 10% FBS 100 units/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Total cellular RNA was isolated from cells using the RNeasy Plus isolation kit (Qiagen, Valencia, CA), and quality was confirmed on an Agilent Bioanalyzer.

tag: genotype/variation

value: control shRNA


title: MB-231_a3kd2 (exon-level)

source_name: alpha3 knockdown

value: alpha3-targeting shRNA


title: brain_het rep4

description:
SAMPLE 8
replicate 4

source_name: brain


title: Normal GIST-64

type: genomic

city: Boston

first: Jonathan

middle: A

last: Fletcher

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital and Harvard Medical School

hyb_protocol: DNA was digested with Nsp1, and linkers were ligated to the restriction fragments to permit PCR amplification. The PCR products were purified and fragmented by treatment with DNase I, then biotin-labeled and hybridized to microarray chips, according to the manufacturer's instructions.

scan_protocol: Hybridized chip arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G system, accroding to the manufacturer's protocol.

data_processing: The positions and intensities of the fluorescence emissions were analyzed using dChip software. Array intensity was normalized to the array with median intensity. 7 normal tissues corresponding to 7 patients were included as controls. Median  smoothing was used to infer copy number.

label: Biotin

molecule: genomic DNA

source_name: Normal frozen tissue

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to previously published standard conditions at the Fletcher Laboratory. Snap-frozen tumor biopsies and matched normal tissue samples were collected with institutional review board approval.

extract_protocol: High molecular weight genomic DNA was isolated using QIAamp DNA Mini Kit (QIAGEN) and analyzed by Affymetrix 250K SNP array. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

tag: gender

value: Female

tag: tumor type

value: Normal tissue

tag: primary/metastasis


title: heart_wt rep1

description:
SAMPLE 9
replicate 1


title: Metastatic LMS-121

source_name: Leiomyosarcoma cell line

value: Male

value: Leiomyosarcoma

value: Metastasis


title: Normal GIST-31


title: brain_het rep3

description:
SAMPLE 7
replicate 3

value: heterozygote


title: Metastatic LMS-120


title: Metastatic LMS-118

source_name: Leiomyosarcoma frozen tissue


title: Normal GIST-33


title: MB-231_a3kd1 (exon-level)


title: Normal GIST-51


title: MB-231_a3kd1 (gene-level)

description: PLIER expression value derived from Expression Console software; core-gene analysis


title: brain_het rep2

description:
SAMPLE 6
replicate 2


title: MB-231_a3kd2 (gene-level)


title: MB-231_Control1 (exon-level)


title: brain_wt rep4

description:
SAMPLE 5
replicate 4

value: wild type


title: Metastatic LMS-116-5


title: MB-231_Control1 (gene-level)


title: Normal GIST-62


title: MB-231_Control2 (gene-level)


title: brain_wt rep3

description:
SAMPLE 4
replicate 3


title: Normal GIST-61


title: brain_wt rep2

description:
SAMPLE 3
replicate 2


title: Metastatic LMS-116-4


title: brain_het rep1

description:
SAMPLE 2
replicate 1


title: Metastatic LMS-114


title: kidney_wt rep2

description:
SAMPLE 19
replicate 2

source_name: kidney


title: brain_wt rep1

description:
SAMPLE 1
replicate 1


title: Metastatic eRMS-83

source_name: Rhabdomyosarcoma cell line

value: Embryonal rhabdomyosarcoma


title: Primary LMS-109

value: Primary


title: Adipocyte+Rosi 48h, replicate 2

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Mouse Gene 1.1 ST Array Plates (#901418, Affymetrix) were used for microarray hybridization, wash, stain and scan with GeneTitan hyb-wash-stain kits (#901622, Affymetrix) and a GeneTitan instrument.

scan_protocol: GeneTitan scanner data were collected with default parameters.

data_processing: Scanned data were further analyzed using Partek Genomics Suite. Data were normalized using default RMA method.

source_name: Mature 3T3-L1 adipocyte

label_protocol: RNA samples (150 ng) with RNA integrity number >7 were used for target amplification and labeling via the Ambion WT Expression kit (#4411974) and Affymetrix WT Terminal Labeling kit (#900671) following manufacturer’s protocol.

growth_protocol: 3T3-L1 cells were obtained from American Type Culture Collection and grown in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Tissue Culture Biologics), 100 U/ml penicillin and 100 μg/ml treptomycin (Invitrogen). Two days post-confluence differentiation media was added, consisting of growth media with 1 μM dexamethasone, 10 μg/ml human insulin, and 0.5 mM 3-isobutyl-1-methylxanthine (Invitrogen). Cells were differentiated as described previously, by growth in differentiation media for 2 days, followed by growth media with insulin for 2 days, followed by growth media only.

extract_protocol: RNA was isolated from cells using TRIzol (Invitrogen), followed by the RNeasy Mini Kit (Qiagen)

treatment_protocol: Mature 3T3-L1 adipocytes were treated with 1μM rosiglitazone (Biomol) dissolved in DMSO.

tag: treatment

value: Rosi

tag: time point


title: Primary eRMS-72


title: Adipocyte+Rosi 48h, replicate 3


title: Adipocyte+Rosi 36h, replicate 3


title: lung_mut_chall_rep3

description:
SAMPLE 14
replicate 3

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

source_name: lung

tag: genotype/treatment

value: homozygote

tag: treatment protocol

value: OVA challenge

value: 22 weeks

value: lung


title: Adipocyte+Rosi 48h, replicate 1


title: lung_mut_chall_rep2

description:
SAMPLE 13
replicate 2


title: lung_mut_chall_rep1

description:
SAMPLE 12
replicate 1


title: lung_mut_chall_rep4

description:
SAMPLE 15
replicate 4


title: Metastatic GIST-64

source_name: GIST frozen tissue

value: Gastrointestinal stromal tumor


title: lung_wt_chall_rep4

description:
SAMPLE 11
replicate 4


title: heart_wt rep3

description:
SAMPLE 12
replicate 3

value: 18.5 weeks


title: Adipocyte+Rosi 24h, replicate 3


title: Adipocyte+Rosi 36h, replicate 1


title: Metastatic GIST-61-10


title: Metastatic GIST-59


title: Metastatic eRMS-80

source_name: Rhabdomyosarcoma frozen tissue


title: Metastatic eRMS-84


title: Normal GIST-36


title: Metastatic GIST-58


title: Adipocyte+Rosi 36h, replicate 2


title: Metastatic GIST-62


title: Adipocyte+Rosi 24h, replicate 2


title: lung_wt_chall_rep3

description:
SAMPLE 10
replicate 3


title: Adipocyte+Rosi 24h, replicate 1


title: Metastatic GIST-57


title: Adipocyte+Rosi 12h, replicate 3


title: Metastatic GIST-55


title: lung_mut_rep2

description:
SAMPLE 6
replicate 2

value: control


title: Metastatic GIST-54

value: Female


title: Metastatic GIST-56

source_name: GIST cell line


title: Metastatic GIST-52


title: lung_wt_chall_rep2

description:
SAMPLE 9
replicate 2


title: Adipocyte+Rosi 12h, replicate 2


title: lung_mut_rep1

description:
SAMPLE 5
replicate 1


title: Adipocyte+Rosi 6h, replicate 2


title: Metastatic GIST-51


title: Adipocyte+Rosi 6h, replicate 3


title: TgNmBr1-mero-c52-2

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

hyb_protocol: Standard Affymetrix protocol with 5.5 ug labeled cRNA.

scan_protocol: Standard Affymetrix protocol.

data_processing: Arrays from GSE32427 and those hybridized for this study were combined and analyzed as a set.  Microarray data were loaded into R using the “affy” library and processed using Robust Multi-array Average (RMA) and quantile normalization.

organism: Toxoplasma gondii

source_name: merozoite

label_protocol: Ambion MessageAmp Premier RNA Amplification Kit (Life Technologies) using 500 ng total RNA.

growth_protocol: Parasites were harvested from felid small intestine

extract_protocol: RNA was extracted using the Qiagen RNeasy kit (b-mercaptoethanol and DNase I treatment).

treatment_protocol: Standard harvesting techniques were used: needle passing, filtering and centrifugation.

tag: develpomental stage

value: merozoite


title: Metastatic GIST-48


title: lung_wt_rep2

description:
SAMPLE 2
replicate 2


title: Adipocyte+Rosi 6h, replicate 1


title: lung_mut_rep3

description:
SAMPLE 7
replicate 3


title: lung_wt_rep3

description:
SAMPLE 3
replicate 3


title: Adipocyte+Rosi 2h, replicate 3


title: lung_wt_rep1

description:
SAMPLE 1
replicate 1


title: Adipocyte+Rosi 12h, replicate 1


title: lung_wt_chall_rep1

description:
SAMPLE 8
replicate 1


title: lung_wt_rep4

description:
SAMPLE 4
replicate 4


title: TgNmBr1-mero-c52-1


title: Adipocyte+Rosi 2h, replicate 2


title: Metastatic GIST-47


title: Metastatic GIST-45

value: Male


title: Adipocyte+Rosi 2h, replicate 1


title: TgNmBr1-mero-c50


title: Adipocyte+Rosi 1h, replicate 2


title: Adipocyte+Rosi 1h, replicate 3


title: Metastatic GIST-44


title: Metastatic GIST-43


title: Metastatic GIST-40


title: Metastatic GIST-42


title: Adipocyte+Rosi 1h, replicate 1


title: Adipocyte+Rosi 30min, replicate 1


title: Adipocyte, replicate 3

value: No treatment


title: TgNmBr1-mero-c48


title: TgNmBr1-tachy-2

source_name: tachyzoite

value: tachyzoite


title: Adipocyte+Rosi 30min, replicate 2


title: Primary GIST-36


title: Muscle21_22

city: Saint-Jean-sur-Richelieu

first: Javad

last: Nadaf

state: Quebec

address: 84 Richelieu Street

country: Canada

institute: INRA,RI,DNALandmarks

description: comparing 2 genotypes on each array

hyb_protocol: The samples were labelled either CY3 or CY5 using either CY3 or CY5 monreactive dyes (General Electric) as appropriate . The samples were hybridised as a two dye experiment  with equimolar amounts of Cy3 and CY5 labelled samples.

scan_protocol: The slides were scanned using an Axon 4200 AL scanner set at 5 micron scanning.

data_processing: Global loess normalization was used to adjust the expression differences for intensity dependencies.Mixed model was used to correct the data for dye (fixed effect) and array (random effect). using SAS mixed model process

organism: Gallus gallus

label_protocol: The labelling protocol was the Ambion Message amp UTP Kit,(Life technologies) where in the cRNA production the UTP is replaced with a biotin UTP.

extract_protocol: Total RNA was extracted from 250 mg of pectorlis major muscle tissue of 12 qq and 12 QQ using 3mls of Ultraspec II reagent (AMS Biotechnology, Abingdon, UK) using a Polytron homogenizer 7mm (Kinematica AG, Luzern, Switzerland).

value: QQ

value: qq


title: TgNmBr1-tachy-1


title: Adipocyte+Rosi 30min, replicate 3


title: Adipocyte, replicate 2


title: Muscle23_24

description: comparing 2 genotypes on each array


title: Metastatic GIST-39

value: Metastasis


title: Primary GIST-35

value: Primary


title: Adipocyte, replicate 1


title: Muscle19_20

description: comparing 2 genotypes on each array


title: Muscle17_18

description: comparing 2 genotypes on each array


title: Primary GIST-31-1


title: uninfected Neural progenitor cells 3

hyb_protocol: After purification aliquots of each sample were hybridized to Illumina platform HumanHT-12 v4 Expression.

scan_protocol: After hybridization, each array was sequentially washed, stained with CY3, and scanned on the Illumina HiScan

data_processing: For array readout we used Illumina Feature Extraction Software (Genome Studio 11.0)

source_name: uninfected Neural progenitor cells

label_protocol: The cDNA was used as a template to generate biotin-labeled cRNA that was used for hybridization accordung to Illumina standard protocol

growth_protocol: NPCs were cultured in NP expansion medium (DMEM/F12 medium supplemented with 1% N2, bFGF (20 ng ml-1), 1 mM L-glutamine, 1% nonessential amino acids, 50 U ml_1 penicillin, 50 mg ml-1 streptomycin and 0.1 mM 2-mercaptoethanol).

extract_protocol: RNA was extracted using and RNeasy kit (Qiagen). RNA quantity was determined by OD measurement using the Nanodrop 1000 at 260 nm and RNA integrity by. The integrity of the RNA was determined using the Agilent 2100 Bioanalyzer to calculate the RNA integrity Number (RIN).

treatment_protocol: NPCs were infected with HSV-1 at MOI 0.1

value: male

tag: cell type

value: Neural progenitor cells


title: Muscle11_12

description: comparing 2 genotypes on each array

tag: genotype


title: Muscle15_16

description: comparing 2 genotypes on each array


title: Primary GIST-33


title: Primary GIST-34


title: Metastatic GIST-31-2


title: Primary GIST-28


title: uninfected Neural progenitor cells 2


title: Muscle13_14

description: comparing 2 genotypes on each array


title: Primary GIST-16


title: HSV-1-infected Neural progenitor cells 2

source_name: HSV-1-infected Neural progenitor cells


title: Muscle3_4

description: comparing 2 genotypes on each array


title: HSV-1-infected Neural progenitor cells 3


title: uninfected Neural progenitor cells 1


title: Wild type plants (control) biological replicate 3

city: Montreal

first: Fathey

last: Sarhan

address: CP 8888, Succursale Centre-Ville

department: Biology

institute: University of Quebec at Montreal

hyb_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin

scan_protocol: Arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

data_processing: Cel files obtained from chip images were imported in Flexarray (http://gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=ehttp://genomequebec.mcgill.ca/Flexarray); the data were normalized and corrected for background in R2.5.1 environment with the robust multi-array (RMA) method. To identify the probe-sets differentially regulated between two conditions, analysis of variance (ANOVA) was performed on the expression of three biological replicates for each condition.

organism: Triticum monococcum

source_name: whole aerial part

label_protocol: Synthesized cDNAs were transcribed to cRNAs with the 3’IVT labelling kit (Santa Clara, CA, USA)

growth_protocol: The einkorn wheat (Triticum monococcum 2n = 2x = 14, AmAm) mutant, maintained vegetative phase (mvp) is induced by nitrogen ion-beam treatment (Shitsukawa et al., 2007) Genes Genet. Syst. 82 p. 167-170. Wild type and the homozygous mvp mutant plants (selected from heterozygous parent seeds, see below) of spring einkorn wheat were grown in a controlled growth chamber (Conviron) at 20oC under long day (LD: 16 hours at 175 μmol m-2 s-1 and 8 hours dark) for three weeks. Plants were then acclimated at 4° for 7 days under LD conditions.

extract_protocol: The different biological samples of einkorn spring wheat leaves were ground in dry ice to fine powder and total RNA was extracted with trizol (Invitrogen, Burlington, ON, CA). Total RNA was cleaned using RNeasy plant mini kit (Qiagen) and integrity was determined on agarose gel and on a bioanalyser (Agilent 2100)

treatment_protocol: The homozygous mvp mutant plants were identified within the progeny of heterozygous parents by the absence of VRN1 expression and confirmed by their inability to transit from vegetative to reproductive phase. Each replicate (R1, R2 and R3) was obtained  from three wild type plants (control) or from five mvp plants (mutant) harvested randomly. Total RNA was extracted from whole aerial parts. Potential mvp mutant and wild type plants at the same age (three weeks old plants) were acclimated for one week at 4oC under LD conditions. The experimental design consisted of three biological replicates for each of the two conditions, 1: wild type plants (control) and 2: mvp plants (mutant).

value: Einkorn

value: leaf


title: Muscle9_10

description: comparing 2 genotypes on each array


title: Muscle1_2

description: comparing 2 genotypes on each array


title: Muscle5_6

description: comparing 2 genotypes on each array


title: mvp plants (mutant) biological replicate 3

value: Einkorn mvp


title: SM14_R3

status: Public on May 01 2014

city: College Station

first: Luis

middle: Humberto

last: Reyes

state: Texas

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

hyb_protocol: Samples were for hybridization by adding lyophilized 10X Blocking Agent (supplied with Agilent Oligo aCGH Hybridization Kit), following manufacture's protocol.  The samples were hybridazed in a Agilent's s. Cerevisia Gene Expression Microarray, 8x15K G4813A

scan_protocol: The arrays were scanned using the GenePix 4100A Microarray Scanner

data_processing: The image analysis performed using GenePix Pro 6.0 Software (Molecular Devices).

organism: Saccharomyces cerevisiae

source_name: liquid culture

label_protocol: 5 µg of cDNA was labeled using Cy3- and Cy5- mono-Reactive Dye Pack (GE Healthcare)

growth_protocol: The cells were grown in YPD media (20 g/L glucose), incubated at 30C for 24 hours in order to reach late exponential phase

extract_protocol: Total RNA extracted using ZR Fungal/Bacterial RNA MiniPrep™ (Zymo) kit

value: Adaptive Mutant SM14

value: Reference Ancestral Strain


title: SM14_R2


title: SM13_R3

value: Adaptive Mutant SM13


title: SM22_R1

value: Adaptive Mutant SM22


title: SM12_R2

value: Adaptive Mutant SM12


title: mvp plants (mutant) biological replicate 2


title: Primary GIST-15

value: Female

value: Gastrointestinal stromal tumor


title: Wild type plants (control) biological replicate 1


title: SM14_R1


title: mvp plants (mutant) biological replicate 1


title: SM22_R2


title: SM12_R3


title: SM22_R3


title: SM13_R1


title: Metastatic GIST-50

value: Male


title: Muscle7_8

description: comparing 2 genotypes on each array

value: QQ


title: SM13_R2


title: Wild type plants (control) biological replicate 2


title: HSV-1-infected Neural progenitor cells 1


title: SM12_R1


title: 2d CSC triple negative cells (minus CD44, CD133 and EpCAM expression)

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

hyb_protocol: hybridization was done according to manufacturer's instructions

scan_protocol: Arrays were scanned using the Illumina iScan instrument

data_processing: Data were exported from Illumina’s GenomeStudio software after performing the needed quality control checks and background subtraction. Data were quantile normalized using the 'qn' function in the SRMA package in R. The data were then Log base 2 transformation and quantile normalization was done to the raw probe-level intensity measurements for each assay to ensure that the distributions of intensity values were the same for all arrays.

source_name: pancreatic cancer cell line MiaPaCa-2

label_protocol: cy3 labeling was done according to manufacturer's instructions

growth_protocol: Human pancreatic cancer cell line MiaPaCa-2 cells

extract_protocol: Total RNA was extracted from cell pellets (~1x10x6 cells) using Qiagen EZ1 magnetic bead technology

treatment_protocol: MiaPaCa-2 and triple negative cells were cultured in 5% FBS DMEM medium, triple positive cells were cultured in serum-free sphere formation medium to maintain undifferentiated state of stem cell like cancer cells


title: 2a CSC triple negative cells (minus CD44, CD133 and EpCAM expression)


title: 3d CSC triple positive cells (positive for CD44, CD133 and EpCAM expression)


title: 3a CSC triple positive cells (positive for CD44, CD133 and EpCAM expression)


title: WB_99_KIL_100524

city: London

last: Levin

address: South Kensington Campus

department: Paediatrics

country: United Kingdom

institute: Imperial College London

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using Genome Studio, with background subtracted and quantile normalised.

source_name: Whole Blood from patient with other disease

label_protocol: Standard Illumina TotalPrep RNA Amplification kits (Applied Biosystems).

extract_protocol: Standard PAXgene® blood RNA extraction kit protocol (Qiagen).

tag: illness

value: other disease (IGRA +)

tag: hiv status

value: HIV negative

tag: geographical region

value: Kenya


title: WB_30_KIL_800980

source_name: Whole Blood from patient with Active TB

value: active tuberculosis (culture negative)

value: HIV positive


title: 1a MiaPaCa-2 cells unsorted

tag: cell line

value: MiaPaCa-2 cells unsorted


title: SM12_R4


title: 1b MiaPaCa-2 cells unsorted


title: 3b CSC triple positive cells (positive for CD44, CD133 and EpCAM expression)


title: WB_99_KIL_800771


title: 2b CSC triple negative cells (minus CD44, CD133 and EpCAM expression)


title: 1c MiaPaCa-2 cells unsorted


title: WB_99_KIL_100623


title: WB_99_KIL_100654


title: WB_99_KIL_100567


title: 2c CSC triple negative cells (minus CD44, CD133 and EpCAM expression)


title: WB_30_KIL_800696


title: WB_99_KIL_100472


title: WB_99_KIL_100310


title: WB_30_KIL_800828


title: WB_30_KIL_800911


title: WB_30_KIL_500583


title: 3c CSC triple positive cells (positive for CD44, CD133 and EpCAM expression)


title: WB_99_KIL_100337


title: WB_99_KIL_100513


title: 1d MiaPaCa-2 cells unsorted


title: WB_30_KIL_800874


title: WB_30_KIL_500553


title: WB_30_KIL_500279


title: WB_30_KIL_500077


title: WB_30_KIL_500130


title: WB_30_KIL_500029


title: WB_30_KIL_500113


title: WB_30_KIL_500208


title: WB_30_KIL_100565


title: WB_30_KIL_500169


title: WB_30_KIL_100528


title: WB_30_KIL_500122


title: WB_30_KIL_500056


title: WB_30_KIL_100521


title: WB_30_KIL_100427


title: WB_30_KIL_100258


title: WB_30_KIL_500190


title: WB_30_KIL_100436


title: WB_30_KIL_100297


title: WB_30_KIL_100421


title: WB_30_KIL_100446


title: WB_30_KIL_100291


title: WB_30_KIL_100220


title: WB_30_KIL_100376


title: WB_30_KIL_100219


title: WB_30_KIL_100261


title: WB_30_KIL_100424


title: WB_30_KIL_100437


title: WB_30_KIL_100211


title: WB_30_KIL_100115


title: WB_24_KIL_800862

source_name: Whole Blood from patient with LTBI

value: latent TB infection


title: WB_24_KIL_800755


title: WB_30_KIL_100032


title: WB_30_KIL_100183


title: WB_30_KIL_100088


title: WB_30_KIL_100151


title: WB_24_KIL_800787


title: WB_24_KIL_800718


title: WB_30_KIL_100100


title: WB_24_KIL_800679


title: WB_24_KIL_100644


title: WB_24_KIL_100304


title: WB_24_KIL_800695


title: WB_23_KIL_800856

value: other disease


title: WB_23_KIL_800837


title: WB_24_KIL_100564


title: WB_23_KIL_800685


title: WB_23_KIL_800716


title: WB_23_KIL_800682


title: WB_24_KIL_100656


title: WB_24_KIL_800681


title: WB_24_KIL_100631


title: WB_23_KIL_800804


title: WB_30_KIL_500191


title: WB_23_KIL_500556


title: WB_23_KIL_100594


title: WB_23_KIL_100615


title: WB_23_KIL_100514


title: WB_23_KIL_500170


title: WB_23_KIL_100611


title: WB_23_KIL_100516


title: WB_23_KIL_100438


title: WB_23_KIL_100458


title: WB_23_KIL_100410


title: WB_22_KIL_800665

value: active tuberculosis (culture confirmed)


title: WB_23_KIL_100255


title: WB_23_KIL_100325


title: WB_23_KIL_100182


title: WB_22_KIL_800743


title: WB_23_KIL_100394


title: WB_23_KIL_100193


title: WB_30_KIL_500089


title: WB_23_KIL_100448


title: WB_23_KIL_100393


title: WB_22_KIL_800864


title: WB_23_KIL_100430


title: WB_30_KIL_500009


title: WB_30_KIL_500088


title: WB_22_KIL_800958


title: WB_23_KIL_100299


title: WB_23_KIL_100200


title: WB_24_KIL_800715


title: WB_22_KIL_800932


title: WB_22_KIL_500570


title: WB_22_KIL_800725


title: WB_22_KIL_500562


title: WB_22_KIL_500656


title: WB_22_KIL_500530


title: WB_22_KIL_500504


title: WB_22_KIL_500525


title: WB_24_KIL_800819


title: WB_22_KIL_100597


title: WB_22_KIL_500380


title: WB_22_KIL_100198


title: WB_21_KIL_800667


title: WB_22_KIL_100106


title: WB_21_KIL_800772


title: WB_22_KIL_500109


title: WB_21_KIL_100655


title: WB_22_KIL_500485


title: WB_21_KIL_100651


title: WB_22_KIL_500121


title: WB_22_KIL_100150


title: WB_21_KIL_800733


title: WB_21_KIL_500613


title: WB_21_KIL_500236


title: WB_21_KIL_100598


title: WB_22_KIL_500249


title: WB_21_KIL_800768


title: WB_21_KIL_500342


title: WB_21_KIL_800669


title: WB_21_KIL_100630


title: WB_22_KIL_500288


title: WB_22_KIL_100166


title: WB_21_KIL_800760


title: WB_21_KIL_100569


title: WB_21_KIL_100556


title: WB_22_KIL_500043


title: WB_21_KIL_500053


title: WB_22_KIL_500435


title: WB_21_KIL_100487


title: WB_21_KIL_100372


title: WB_21_KIL_100226


title: WB_21_KIL_100460


title: WB_21_KIL_100205


title: WB_20_KIL_500544


title: WB_21_KIL_100485


title: WB_21_KIL_100484


title: WB_20_KIL_100406


title: WB_21_KIL_100269


title: WB_20_KIL_500119


title: WB_21_KIL_100218


title: WB_20_KIL_500318


title: WB_21_KIL_100267


title: WB_20_KIL_500591


title: WB_20_KIL_800849


title: 46

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: SAMPLE 46

data_processing: The data were quantile normalised using lumi library in R (v.3.0.1).

source_name: FAP_pouch mucosa

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was isolated from mucosal biopsies using the RNeasy Plus Mini Kit (Qiagen, Germany) followed by on-column DNase I digestion. The quality of RNA samples was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA); all samples used for microarray analysis displayed distinct peaks corresponding to intact 28S and 18S ribosomal RNA

tag: condition

value: familial adenomatous polyposis (FAP)

tag: inflammation status

value: inflamed


title: 37

description: SAMPLE 37

value: uninflamed


title: WB_20_KIL_100360


title: 45

description: SAMPLE 45


title: WB_20_KIL_500086


title: WB_21_KIL_100191


title: 22

description: SAMPLE 22


title: WB_20_KIL_100398


title: WB_20_KIL_100091


title: WB_21_KIL_100204


title: WB_21_KIL_100120


title: 19

description: SAMPLE 19


title: 7

description: SAMPLE 7

source_name: UC_pouch mucosa

value: ulcerative colitis (UC)


title: 49

description: SAMPLE 49


title: 14

description: SAMPLE 14


title: 41

description: SAMPLE 41


title: 42

description: SAMPLE 42


title: 13

description: SAMPLE 13


title: 24

description: SAMPLE 24


title: 26

description: SAMPLE 26


title: 35

description: SAMPLE 35


title: 11

description: SAMPLE 11


title: 43

description: SAMPLE 43


title: 23

description: SAMPLE 23


title: 10

description: SAMPLE 10


title: 4

description: SAMPLE 4


title: 29

description: SAMPLE 29


title: 36

description: SAMPLE 36


title: 32

description: SAMPLE 32


title: 5

description: SAMPLE 5


title: 17

description: SAMPLE 17


title: 40

description: SAMPLE 40


title: 38

description: SAMPLE 38


title: 18

description: SAMPLE 18


title: 31

description: SAMPLE 31


title: 25

description: SAMPLE 25


title: 15

description: SAMPLE 15


title: ID 9, visit 4, FO

city: OSLO

first: Mari

last: Myhrstad

address: Postboks 4, St. Olavs plass

department: Department of health

country: Norway

institute: Oslo and Akershus University College

hyb_protocol: Standard Illumina hybridization protocol.

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

source_name: PBMC, visit 4, FO

label_protocol: Labelled extracts were prepared using Illumina TotalPrep RNA Amplification Kit (Illumina Inc, CA 92122, USA).

extract_protocol: Total RNA was isolated from all PBMC samples using RNeasy mini kit (Qiagen) with lysis buffer added beta-mercaptoethanol according to the manufacturer's instructions, and stored at -80C. Quality control was performed with Agilent Bioanalyser.

value: peripheral blood mononuclear cells (PBMCs)

value: fish oil

value: wk 7

tag: disease status

value: healthy

tag: individual id


title: ID 78, visit 2, FO

source_name: PBMC, visit 2, FO

value: wk 0


title: ID 9, visit 2, FO


title: ID 9, visit 3, FO

source_name: PBMC, visit 3, FO

value: wk 3


title: 21

description: SAMPLE 21

hyb_protocol: Standard Illumina hybridization protocol


title: 12

description: SAMPLE 12


title: ID 89, visit 3, FO


title: ID 70, visit 3, FO


title: ID 8, visit 4, FO


title: 16

description: SAMPLE 16


title: ID 78, visit 3, FO


title: ID 88, visit 4, FO


title: 8

description: SAMPLE 8


title: ID 8, visit 3, FO


title: ID 88, visit 2, FO


title: ID 89, visit 4, FO


title: ID 88, visit 3, FO


title: ID 70, visit 2, FO


title: ID 7, visit 3, FO


title: ID 70, visit 4, FO


title: ID 78, visit 4, FO


title: ID 7, visit 4, FO


title: ID 8, visit 2, FO


title: ID 89, visit 2, FO


title: ID 7, visit 2, FO


title: 3

description: SAMPLE 3


title: 44

description: SAMPLE 44


title: ID 58, visit 4, FO


title: ID 56, visit 3, FO


title: ID 56, visit 4, FO


title: ID 56, visit 2, FO


title: ID 67, visit 4, FO


title: ID 67, visit 2, FO


title: ID 49, visit 4, FO


title: ID 6, visit 4, FO


title: ID 6, visit 3, FO


title: ID 6, visit 2, FO


title: ID 58, visit 2, FO


title: ID 67, visit 3, FO


title: ID 33, visit 3, FO


title: ID 58, visit 3, FO


title: ID 31, visit 3, FO


title: ID 30, visit 3, FO


title: ID 31, visit 4, FO


title: ID 36, visit 4, FO


title: ID 25, visit 4, FO


title: ID 33, visit 4, FO


title: ID 25, visit 3, FO


title: ID 49, visit 2, FO


title: ID 36, visit 3, FO


title: ID 31, visit 2, FO


title: ID 33, visit 2, FO


title: ID 49, visit 3, FO


title: ID 30, visit 2, FO


title: ID 30, visit 4, FO


title: ID 36, visit 2, FO


title: ID 25, visit 2, FO


title: ID 72, visit 3, HOSO

source_name: PBMC, visit 3, HOSO

value: high oleic sunflower oil


title: ID 69, visit 4, HOSO

source_name: PBMC, visit 4, HOSO


title: ID 77, visit 3, HOSO


title: ID 72, visit 4, HOSO


title: ID 68, visit 4, HOSO


title: ID 59, visit 4, HOSO


title: ID 77, visit 4, HOSO


title: ID 72, visit 2, HOSO

source_name: PBMC, visit 2, HOSO


title: ID 77, visit 2, HOSO


title: ID 59, visit 3, HOSO


title: ID 53, visit 4, HOSO


title: ID 69, visit 2, HOSO


title: ID 64, visit 3, HOSO


title: ID 68, visit 2, HOSO


title: ID 64, visit 2, HOSO


title: ID 46, visit 3, HOSO


title: ID 68, visit 3, HOSO


title: ID 64, visit 4, HOSO


title: ID 53, visit 3, HOSO


title: ID 52, visit 2, HOSO


title: ID 44, visit 4, HOSO


title: ID 46, visit 4, HOSO


title: ID 52, visit 3, HOSO


title: ID 53, visit 2, HOSO


title: ID 59, visit 2, HOSO


title: ID 46, visit 2, HOSO


title: ID 52, visit 4, HOSO


title: ID 45, visit 2, HOSO


title: ID 45, visit 3, HOSO


title: ID 21, visit 2, HOSO


title: ID 18, visit 3, HOSO


title: ID 16, visit 2, HOSO


title: ID 18, visit 2, HOSO


title: ID 32, visit 4, HOSO


title: ID 17, visit 2, HOSO


title: ID 17, visit 4, HOSO


title: ID 32, visit 2, HOSO


title: ID 17, visit 3, HOSO


title: ID 16, visit 4, HOSO


title: ID 44, visit 2, HOSO


title: ID 12, visit 3, HOSO


title: ID 12, visit 4, HOSO


title: ID 21, visit 3, HOSO


title: ID 12, visit 2, HOSO


title: ID 32, visit 3, HOSO


title: ID 16, visit 3, HOSO


title: ID 18, visit 4, HOSO


title: ID 21, visit 4, HOSO


title: ID 11, visit 2, HOSO


title: ID 11, visit 4, HOSO


title: ID 1, visit 3, HOSO


title: ID 1, visit 2, HOSO


title: ID 11, visit 3, HOSO


title: UC17

first: Tiewei

last: Cheng

state: United States

address: 7777 Knight Rd.

institute: UT MD Anderson Cancer Center

description: SAMPLE 30

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: urothelial cancer cell line

label_protocol: Biotinylated cRNA were prepared with Illumina RNA amplification kit

growth_protocol: Cell lines were cultured in 10% FBS modified Eagle's MEM with standard supplements at 37 °C in 5% CO2 incubator

extract_protocol: Total RNA was extracted by mirVANA miRNA Isolation Kit. Quality control was performed by NanoDrop ND-1000 and Agilent Bioanalyzer.

value: urothelial cancer cell line UC17


title: JPB

description: SAMPLE 29

value: urothelial cancer cell line JPB


title: ID 44, visit 3, HOSO


title: ID 1, visit 4, HOSO


title: TCCSUPB

description: SAMPLE 28

value: urothelial cancer cell line TCCSUPB


title: SW780

description: SAMPLE 27

value: urothelial cancer cell line SW780


title: UM-UC7

description: SAMPLE 19

value: urothelial cancer cell line UM-UC7


title: UM-UC16

description: SAMPLE 21

value: urothelial cancer cell line UM-UC16


title: HT1197

description: SAMPLE 12

value: urothelial cancer cell line HT1197


title: Um-UC15

description: SAMPLE 10

value: urothelial cancer cell line Um-UC15


title: UM-UC5

description: SAMPLE 18

value: urothelial cancer cell line UM-UC5


title: UM-UC14

description: SAMPLE 23

value: urothelial cancer cell line UM-UC14


title: RT4

description: SAMPLE 24

value: urothelial cancer cell line RT4


title: SCABER

description: SAMPLE 14

value: urothelial cancer cell line SCABER


title: RT112

description: SAMPLE 26

value: urothelial cancer cell line RT112


title: UM-UC18

description: SAMPLE 1

value: urothelial cancer cell line UM-UC18


title: X5637

description: SAMPLE 16

value: urothelial cancer cell line X5637


title: UM-UC6

description: SAMPLE 7

value: urothelial cancer cell line UM-UC6


title: UM-UC4

description: SAMPLE 17

value: urothelial cancer cell line UM-UC4


title: IA6

description: SAMPLE 11

value: urothelial cancer cell line IA6


title: HT1376

description: SAMPLE 13

value: urothelial cancer cell line HT1376


title: PBMC stimulated with RPMI.24h, rep35

first: Aylwin

last: Ng

address: 185 Cambridge Street

institute: CCIB, MGH

description: Replicate 35

scan_protocol: Standard Illumina scanning protocol using the Illumina iScan.

source_name: PBMCs, RPMI, 24h

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: peripheral blood mononuclear cells (PBMCs)

value: healthy

value: RPMI medium

tag: treatment duration


title: PBMC stimulated with RPMI.24h, rep34

description: Replicate 34


title: UM-UC9

description: SAMPLE 20

value: urothelial cancer cell line UM-UC9


title: UM-UC1

description: SAMPLE 22

value: urothelial cancer cell line UM-UC1


title: RT4V6

description: SAMPLE 25

value: urothelial cancer cell line RT4V6


title: Um-UC11

description: SAMPLE 3

value: urothelial cancer cell line Um-UC11


title: UM-UC3

description: SAMPLE 6

value: urothelial cancer cell line UM-UC3


title: BV

description: SAMPLE 4

value: urothelial cancer cell line BV


title: J82

description: SAMPLE 15

value: urothelial cancer cell line J82


title: Um-UC12

description: SAMPLE 8

value: urothelial cancer cell line Um-UC12


title: UM-UC10

description: SAMPLE 2

value: urothelial cancer cell line UM-UC10


title: UM-UC13

description: SAMPLE 9

value: urothelial cancer cell line UM-UC13


title: ID 45, visit 4, HOSO

value: high oleic sunflower oil

value: wk 7


title: PBMC stimulated with RPMI.24h, rep26

description: Replicate 26


title: T24

description: SAMPLE 5

value: urothelial cancer cell line T24


title: PBMC stimulated with RPMI.24h, rep32

description: Replicate 32


title: PBMC stimulated with RPMI.24h, rep28

description: Replicate 28


title: PBMC stimulated with RPMI.24h, rep30

description: Replicate 30


title: PBMC stimulated with RPMI.24h, rep29

description: Replicate 29


title: PBMC stimulated with RPMI.24h, rep33

description: Replicate 33


title: PBMC stimulated with RPMI.24h, rep21

description: Replicate 21


title: PBMC stimulated with RPMI.24h, rep20

description: Replicate 20


title: PBMC stimulated with RPMI.24h, rep23

description: Replicate 23


title: PBMC stimulated with RPMI.24h, rep27

description: Replicate 27


title: PBMC stimulated with RPMI.24h, rep25

description: Replicate 25


title: PBMC stimulated with RPMI.24h, rep16

description: Replicate 16


title: PBMC stimulated with RPMI.24h, rep22

description: Replicate 22


title: PBMC stimulated with RPMI.24h, rep24

description: Replicate 24


title: PBMC stimulated with RPMI.24h, rep15

description: Replicate 15


title: PBMC stimulated with RPMI.24h, rep17

description: Replicate 17


title: PBMC stimulated with RPMI.24h, rep11

description: Replicate 11


title: PBMC stimulated with RPMI.24h, rep31

description: Replicate 31


title: PBMC stimulated with RPMI.24h, rep10

description: Replicate 10


title: PBMC stimulated with RPMI.24h, rep8

description: Replicate 8


title: PBMC stimulated with RPMI.24h, rep12

description: Replicate 12


title: PBMC stimulated with RPMI.24h, rep19

description: Replicate 19


title: PBMC stimulated with RPMI.24h, rep18

description: Replicate 18


title: PBMC stimulated with RPMI.24h, rep6

description: Replicate 6


title: PBMC stimulated with RPMI.24h, rep14

description: Replicate 14


title: PBMC stimulated with RPMI.24h, rep13

description: Replicate 13


title: PBMC stimulated with RPMI.24h, rep9

description: Replicate 9


title: PBMC stimulated with RPMI.24h, rep7

description: Replicate 7


title: PBMC stimulated with RPMI.24h, rep1

description: Replicate 1


title: PBMC stimulated with RPMI.24h, rep4

description: Replicate 4


title: PBMC stimulated with RPMI.4h, rep30

description: Replicate 30

source_name: PBMCs, RPMI, 4h


title: PBMC stimulated with RPMI.24h, rep3

description: Replicate 3


title: PBMC stimulated with RPMI.4h, rep29

description: Replicate 29


title: PBMC stimulated with RPMI.4h, rep27

description: Replicate 27


title: PBMC stimulated with RPMI.4h, rep26

description: Replicate 26


title: PBMC stimulated with RPMI.4h, rep25

description: Replicate 25


title: PBMC stimulated with RPMI.24h, rep5

description: Replicate 5


title: PBMC stimulated with RPMI.4h, rep24

description: Replicate 24


title: PBMC stimulated with RPMI.24h, rep2

description: Replicate 2


title: PBMC stimulated with RPMI.4h, rep28

description: Replicate 28


title: PBMC stimulated with RPMI.4h, rep22

description: Replicate 22


title: PBMC stimulated with RPMI.4h, rep21

description: Replicate 21


title: PBMC stimulated with RPMI.4h, rep23

description: Replicate 23


title: PBMC stimulated with RPMI.4h, rep20

description: Replicate 20


title: PBMC stimulated with RPMI.4h, rep17

description: Replicate 17


title: PBMC stimulated with RPMI.4h, rep18

description: Replicate 18


title: PBMC stimulated with RPMI.4h, rep16

description: Replicate 16


title: PBMC stimulated with RPMI.4h, rep9

description: Replicate 9


title: PBMC stimulated with RPMI.4h, rep13

description: Replicate 13


title: PBMC stimulated with RPMI.4h, rep14

description: Replicate 14


title: PBMC stimulated with RPMI.4h, rep12

description: Replicate 12


title: PBMC stimulated with RPMI.4h, rep15

description: Replicate 15


title: PBMC stimulated with RPMI.4h, rep10

description: Replicate 10


title: PBMC stimulated with RPMI.4h, rep8

description: Replicate 8


title: PBMC stimulated with RPMI.4h, rep19

description: Replicate 19


title: PBMC stimulated with RPMI.4h, rep6

description: Replicate 6


title: PBMC stimulated with RPMI.4h, rep11

description: Replicate 11


title: PBMC stimulated with RPMI.4h, rep5

description: Replicate 5


title: PBMC stimulated with RPMI.4h, rep2

description: Replicate 2


title: PBMC stimulated with MTB.24h, rep32

description: Replicate 32

source_name: PBMCs, Mycobacterium, 24h

value: Mycobacterium tuberculosis (MTB)


title: PBMC stimulated with RPMI.4h, rep7

description: Replicate 7

value: peripheral blood mononuclear cells (PBMCs)


title: PBMC stimulated with RPMI.4h, rep4

description: Replicate 4

value: healthy


title: PBMC stimulated with MTB.24h, rep35

description: Replicate 35


title: PBMC stimulated with MTB.24h, rep36

description: Replicate 36


title: PBMC stimulated with MTB.24h, rep34

description: Replicate 34


title: PBMC stimulated with RPMI.4h, rep1

description: Replicate 1

value: RPMI medium


title: PBMC stimulated with MTB.24h, rep31

description: Replicate 31


title: PBMC stimulated with MTB.24h, rep30

description: Replicate 30


title: PBMC stimulated with MTB.24h, rep28

description: Replicate 28


title: PBMC stimulated with MTB.24h, rep33

description: Replicate 33


title: PBMC stimulated with MTB.24h, rep19

description: Replicate 19


title: PBMC stimulated with MTB.24h, rep18

description: Replicate 18


title: PBMC stimulated with MTB.24h, rep17

description: Replicate 17


title: PBMC stimulated with MTB.24h, rep29

description: Replicate 29


title: PBMC stimulated with MTB.24h, rep27

description: Replicate 27


title: PBMC stimulated with MTB.24h, rep16

description: Replicate 16


title: PBMC stimulated with MTB.24h, rep26

description: Replicate 26


title: PBMC stimulated with MTB.24h, rep15

description: Replicate 15


title: PBMC stimulated with MTB.24h, rep21

description: Replicate 21


title: PBMC stimulated with MTB.24h, rep14

description: Replicate 14


title: PBMC stimulated with MTB.24h, rep23

description: Replicate 23


title: PBMC stimulated with MTB.24h, rep24

description: Replicate 24


title: PBMC stimulated with MTB.24h, rep20

description: Replicate 20


title: PBMC stimulated with MTB.24h, rep25

description: Replicate 25


title: PBMC stimulated with MTB.24h, rep13

description: Replicate 13


title: PBMC stimulated with MTB.24h, rep11

description: Replicate 11


title: PBMC stimulated with MTB.24h, rep12

description: Replicate 12


title: PBMC stimulated with MTB.24h, rep10

description: Replicate 10


title: PBMC stimulated with MTB.24h, rep22

description: Replicate 22


title: PBMC stimulated with MTB.24h, rep8

description: Replicate 8


title: PBMC stimulated with MTB.24h, rep5

description: Replicate 5


title: PBMC stimulated with MTB.24h, rep4

description: Replicate 4


title: PBMC stimulated with MTB.24h, rep6

description: Replicate 6


title: PBMC stimulated with MTB.24h, rep1

description: Replicate 1


title: PBMC stimulated with MTB.24h, rep7

description: Replicate 7


title: PBMC stimulated with MTB.24h, rep9

description: Replicate 9


title: PBMC stimulated with MTB.24h, rep3

description: Replicate 3


title: PBMC stimulated with MTB.4h, rep23

description: Replicate 23

source_name: PBMCs, Mycobacterium, 4h


title: PBMC stimulated with MTB.4h, rep21

description: Replicate 21


title: PBMC stimulated with MTB.4h, rep22

description: Replicate 22


title: PBMC stimulated with MTB.4h, rep18

description: Replicate 18


title: PBMC stimulated with MTB.4h, rep20

description: Replicate 20


title: PBMC stimulated with MTB.4h, rep10

description: Replicate 10


title: PBMC stimulated with MTB.24h, rep2

description: Replicate 2


title: PBMC stimulated with MTB.4h, rep16

description: Replicate 16


title: PBMC stimulated with MTB.4h, rep19

description: Replicate 19


title: PBMC stimulated with MTB.4h, rep12

description: Replicate 12


title: PBMC stimulated with MTB.4h, rep14

description: Replicate 14


title: PBMC stimulated with MTB.4h, rep15

description: Replicate 15


title: PBMC stimulated with MTB.4h, rep13

description: Replicate 13


title: PBMC stimulated with MTB.4h, rep17

description: Replicate 17


title: PBMC stimulated with MTB.4h, rep9

description: Replicate 9


title: PBMC stimulated with MTB.4h, rep6

description: Replicate 6


title: PBMC stimulated with MTB.4h, rep4

description: Replicate 4


title: PBMC stimulated with MTB.4h, rep7

description: Replicate 7


title: PBMC stimulated with LPS.24h, rep21

description: Replicate 21

source_name: PBMCs, LPS, 24h

value: lipopolysaccharide (LPS)


title: PBMC stimulated with LPS.24h, rep24

description: Replicate 24


title: PBMC stimulated with MTB.4h, rep3

description: Replicate 3


title: PBMC stimulated with MTB.4h, rep5

description: Replicate 5


title: PBMC stimulated with LPS.24h, rep19

description: Replicate 19


title: PBMC stimulated with LPS.24h, rep14

description: Replicate 14


title: PBMC stimulated with LPS.24h, rep17

description: Replicate 17


title: PBMC stimulated with LPS.24h, rep20

description: Replicate 20


title: PBMC stimulated with MTB.4h, rep1

description: Replicate 1


title: PBMC stimulated with LPS.24h, rep11

description: Replicate 11


title: PBMC stimulated with LPS.24h, rep16

description: Replicate 16


title: PBMC stimulated with LPS.24h, rep23

description: Replicate 23


title: PBMC stimulated with MTB.4h, rep11

description: Replicate 11


title: PBMC stimulated with LPS.24h, rep15

description: Replicate 15


title: PBMC stimulated with LPS.24h, rep12

description: Replicate 12


title: PBMC stimulated with LPS.24h, rep13

description: Replicate 13


title: PBMC stimulated with LPS.24h, rep18

description: Replicate 18


title: PBMC stimulated with LPS.24h, rep8

description: Replicate 8


title: PBMC stimulated with LPS.24h, rep9

description: Replicate 9


title: PBMC stimulated with MTB.4h, rep2

description: Replicate 2


title: PBMC stimulated with RPMI.4h, rep3

description: Replicate 3


title: PBMC stimulated with LPS.24h, rep22

description: Replicate 22


title: PBMC stimulated with LPS.24h, rep10

description: Replicate 10


title: PBMC stimulated with LPS.24h, rep5

description: Replicate 5


title: PBMC stimulated with LPS.24h, rep6

description: Replicate 6


title: PBMC stimulated with LPS.24h, rep7

description: Replicate 7


title: PBMC stimulated with MTB.4h, rep8

description: Replicate 8


title: PBMC stimulated with LPS.24h, rep3

description: Replicate 3


title: PBMC stimulated with LPS.4h, rep24

description: Replicate 24

source_name: PBMCs, LPS, 4h


title: PBMC stimulated with LPS.24h, rep2

description: Replicate 2


title: PBMC stimulated with LPS.24h, rep4

description: Replicate 4


title: PBMC stimulated with LPS.4h, rep14

description: Replicate 14


title: PBMC stimulated with LPS.4h, rep25

description: Replicate 25


title: PBMC stimulated with LPS.24h, rep1

description: Replicate 1


title: PBMC stimulated with LPS.4h, rep9

description: Replicate 9


title: PBMC stimulated with LPS.4h, rep10

description: Replicate 10


title: PBMC stimulated with LPS.4h, rep18

description: Replicate 18


title: PBMC stimulated with LPS.4h, rep17

description: Replicate 17


title: PBMC stimulated with LPS.4h, rep21

description: Replicate 21


title: PBMC stimulated with LPS.4h, rep11

description: Replicate 11


title: PBMC stimulated with LPS.4h, rep16

description: Replicate 16


title: PBMC stimulated with LPS.4h, rep26

description: Replicate 26


title: PBMC stimulated with LPS.4h, rep22

description: Replicate 22


title: PBMC stimulated with LPS.4h, rep8

description: Replicate 8


title: PBMC stimulated with LPS.4h, rep19

description: Replicate 19


title: PBMC stimulated with LPS.4h, rep5

description: Replicate 5


title: PBMC stimulated with LPS.4h, rep6

description: Replicate 6


title: PBMC stimulated with LPS.4h, rep23

description: Replicate 23


title: PBMC stimulated with LPS.4h, rep20

description: Replicate 20


title: PBMC stimulated with LPS.4h, rep7

description: Replicate 7


title: PBMC stimulated with LPS.4h, rep15

description: Replicate 15


title: PBMC stimulated with LPS.4h, rep12

description: Replicate 12


title: PBMC stimulated with LPS.4h, rep13

description: Replicate 13


title: PBMC stimulated with LPS.4h, rep3

description: Replicate 3


title: PBMC stimulated with LPS.4h, rep1

description: Replicate 1


title: PBMC stimulated with Candida.24h, rep32

description: Replicate 32

source_name: PBMCs, Candida, 24h

value: Candida albicans


title: PBMC stimulated with Candida.24h, rep33

description: Replicate 33


title: PBMC stimulated with Candida.24h, rep27

description: Replicate 27


title: PBMC stimulated with LPS.4h, rep2

description: Replicate 2


title: PBMC stimulated with Candida.24h, rep29

description: Replicate 29


title: PBMC stimulated with Candida.24h, rep31

description: Replicate 31


title: PBMC stimulated with Candida.24h, rep26

description: Replicate 26


title: PBMC stimulated with Candida.24h, rep30

description: Replicate 30


title: PBMC stimulated with Candida.24h, rep24

description: Replicate 24


title: PBMC stimulated with LPS.4h, rep4

description: Replicate 4


title: PBMC stimulated with Candida.24h, rep34

description: Replicate 34


title: PBMC stimulated with Candida.24h, rep28

description: Replicate 28


title: PBMC stimulated with Candida.24h, rep17

description: Replicate 17


title: PBMC stimulated with Candida.24h, rep22

description: Replicate 22


title: PBMC stimulated with Candida.24h, rep23

description: Replicate 23


title: PBMC stimulated with Candida.24h, rep11

description: Replicate 11


title: PBMC stimulated with Candida.24h, rep13

description: Replicate 13


title: PBMC stimulated with Candida.24h, rep18

description: Replicate 18


title: PBMC stimulated with Candida.24h, rep19

description: Replicate 19


title: PBMC stimulated with Candida.24h, rep10

description: Replicate 10


title: PBMC stimulated with Candida.24h, rep14

description: Replicate 14


title: PBMC stimulated with Candida.24h, rep21

description: Replicate 21


title: PBMC stimulated with Candida.24h, rep12

description: Replicate 12


title: PBMC stimulated with Candida.24h, rep9

description: Replicate 9


title: PBMC stimulated with Candida.24h, rep16

description: Replicate 16


title: PBMC stimulated with Candida.24h, rep15

description: Replicate 15


title: PBMC stimulated with Candida.24h, rep25

description: Replicate 25


title: PBMC stimulated with Candida.24h, rep20

description: Replicate 20


title: PBMC stimulated with Candida.24h, rep8

description: Replicate 8


title: PBMC stimulated with Candida.4h, rep23

description: Replicate 23

source_name: PBMCs, Candida, 4h


title: PBMC stimulated with Candida.24h, rep6

description: Replicate 6


title: PBMC stimulated with Candida.4h, rep21

description: Replicate 21


title: PBMC stimulated with Candida.24h, rep7

description: Replicate 7


title: PBMC stimulated with Candida.24h, rep2

description: Replicate 2


title: PBMC stimulated with Candida.24h, rep5

description: Replicate 5


title: PBMC stimulated with Candida.24h, rep4

description: Replicate 4


title: PBMC stimulated with Candida.4h, rep22

description: Replicate 22


title: PBMC stimulated with Candida.24h, rep1

description: Replicate 1


title: PBMC stimulated with Candida.24h, rep3

description: Replicate 3


title: PBMC stimulated with Candida.4h, rep20

description: Replicate 20


title: PBMC stimulated with Candida.4h, rep24

description: Replicate 24


title: PBMC stimulated with Candida.4h, rep18

description: Replicate 18


title: PBMC stimulated with Candida.4h, rep11

description: Replicate 11


title: PBMC stimulated with Candida.4h, rep15

description: Replicate 15


title: PBMC stimulated with Candida.4h, rep3

description: Replicate 3


title: PBMC stimulated with Candida.4h, rep19

description: Replicate 19


title: PBMC stimulated with Candida.4h, rep4

description: Replicate 4


title: PBMC stimulated with Candida.4h, rep12

description: Replicate 12


title: PBMC stimulated with Candida.4h, rep14

description: Replicate 14


title: PBMC stimulated with Candida.4h, rep2

description: Replicate 2


title: PBMC stimulated with Candida.4h, rep8

description: Replicate 8


title: PBMC stimulated with Candida.4h, rep7

description: Replicate 7


title: PBMC stimulated with Candida.4h, rep6

description: Replicate 6


title: PBMC stimulated with Candida.4h, rep9

description: Replicate 9


title: PBMC stimulated with Candida.4h, rep5

description: Replicate 5


title: PBMC stimulated with Candida.4h, rep16

description: Replicate 16


title: PBMC stimulated with Candida.4h, rep10

description: Replicate 10


title: PBMC stimulated with Candida.4h, rep13

description: Replicate 13


title: PBMC stimulated with Candida.4h, rep17

description: Replicate 17


title: PBMC stimulated with Borrelia 24h, rep35

description: Replicate 35

source_name: PBMCs, Borrelia, 24h

value: Borrelia burgdorferi


title: PBMC stimulated with Borrelia 24h, rep28

description: Replicate 28


title: PBMC stimulated with Candida.4h, rep1

description: Replicate 1


title: PBMC stimulated with Borrelia 24h, rep33

description: Replicate 33


title: PBMC stimulated with Borrelia 24h, rep36

description: Replicate 36


title: PBMC stimulated with Borrelia 24h, rep29

description: Replicate 29


title: PBMC stimulated with Borrelia 24h, rep27

description: Replicate 27


title: PBMC stimulated with Borrelia 24h, rep32

description: Replicate 32


title: PBMC stimulated with Borrelia 24h, rep26

description: Replicate 26


title: PBMC stimulated with Borrelia 24h, rep25

description: Replicate 25


title: PBMC stimulated with Borrelia 24h, rep22

description: Replicate 22


title: PBMC stimulated with Borrelia 24h, rep24

description: Replicate 24


title: PBMC stimulated with Borrelia 24h, rep30

description: Replicate 30


title: PBMC stimulated with Borrelia 24h, rep23

description: Replicate 23


title: PBMC stimulated with Borrelia 24h, rep31

description: Replicate 31


title: PBMC stimulated with Borrelia 24h, rep19

description: Replicate 19


title: PBMC stimulated with Borrelia 24h, rep15

description: Replicate 15


title: PBMC stimulated with Borrelia 24h, rep21

description: Replicate 21


title: PBMC stimulated with Borrelia 24h, rep18

description: Replicate 18


title: PBMC stimulated with Borrelia 24h, rep9

description: Replicate 9


title: PBMC stimulated with Borrelia 24h, rep20

description: Replicate 20


title: PBMC stimulated with Borrelia 24h, rep10

description: Replicate 10


title: PBMC stimulated with Borrelia 24h, rep17

description: Replicate 17


title: PBMC stimulated with Borrelia 24h, rep11

description: Replicate 11


title: PBMC stimulated with Borrelia 24h, rep16

description: Replicate 16


title: PBMC stimulated with Borrelia 24h, rep14

description: Replicate 14


title: PBMC stimulated with Borrelia 24h, rep13

description: Replicate 13


title: PBMC stimulated with Borrelia 24h, rep1

description: Replicate 1


title: PBMC stimulated with Borrelia 24h, rep5

description: Replicate 5


title: PBMC stimulated with Borrelia 24h, rep12

description: Replicate 12


title: PBMC stimulated with Borrelia 4h, rep19

description: Replicate 19

source_name: PBMCs, Borrelia, 4h


title: PBMC stimulated with Borrelia 4h, rep25

description: Replicate 25


title: PBMC stimulated with Borrelia 24h, rep6

description: Replicate 6


title: PBMC stimulated with Borrelia 4h, rep27

description: Replicate 27


title: PBMC stimulated with Borrelia 24h, rep8

description: Replicate 8


title: PBMC stimulated with Borrelia 24h, rep4

description: Replicate 4


title: PBMC stimulated with Borrelia 4h, rep24

description: Replicate 24


title: PBMC stimulated with Borrelia 24h, rep7

description: Replicate 7


title: PBMC stimulated with Borrelia 4h, rep28

description: Replicate 28


title: PBMC stimulated with Borrelia 24h, rep34

description: Replicate 34


title: PBMC stimulated with Borrelia 24h, rep3

description: Replicate 3


title: PBMC stimulated with Borrelia 4h, rep26

description: Replicate 26


title: PBMC stimulated with Borrelia 4h, rep31

description: Replicate 31


title: PBMC stimulated with Borrelia 4h, rep30

description: Replicate 30


title: PBMC stimulated with Borrelia 4h, rep14

description: Replicate 14


title: PBMC stimulated with Borrelia 24h, rep2

description: Replicate 2


title: PBMC stimulated with Borrelia 4h, rep17

description: Replicate 17


title: PBMC stimulated with Borrelia 4h, rep23

description: Replicate 23


title: PBMC stimulated with Borrelia 4h, rep20

description: Replicate 20


title: PBMC stimulated with Borrelia 4h, rep29

description: Replicate 29


title: PBMC stimulated with Borrelia 4h, rep21

description: Replicate 21


title: PBMC stimulated with Borrelia 4h, rep22

description: Replicate 22


title: PBMC stimulated with Borrelia 4h, rep16

description: Replicate 16


title: PBMC stimulated with Borrelia 4h, rep12

description: Replicate 12


title: PBMC stimulated with Borrelia 4h, rep2

description: Replicate 2


title: PBMC stimulated with Borrelia 4h, rep15

description: Replicate 15


title: PBMC stimulated with Borrelia 4h, rep7

description: Replicate 7


title: PBMC stimulated with Borrelia 4h, rep9

description: Replicate 9


title: PBMC stimulated with Borrelia 4h, rep8

description: Replicate 8


title: PBMC stimulated with Borrelia 4h, rep1

description: Replicate 1


title: PBMC stimulated with Borrelia 4h, rep10

description: Replicate 10


title: PBMC stimulated with Borrelia 4h, rep3

description: Replicate 3


title: PBMC stimulated with Borrelia 4h, rep6

description: Replicate 6


title: PBMC stimulated with Borrelia 4h, rep5

description: Replicate 5


title: PBMC stimulated with Borrelia 4h, rep13

description: Replicate 13


title: PBMC stimulated with Borrelia 4h, rep11

description: Replicate 11


title: WB_23_M_40211

source_name: Whole Blood from patient with other disease

value: other disease

value: HIV positive

value: Malawi

tag: barcode


title: WB_23_M_40171


title: WB_23_SA_10329

value: South Africa


title: WB_23_SA_10321


title: PBMC stimulated with Borrelia 4h, rep4

description: Replicate 4

tag: treatment


title: WB_23_SA_10401


title: WB_23_SA_10302


title: WB_23_M_40181


title: WB_23_SA_10344


title: WB_23_SA_10630


title: WB_23_SA_10357


title: WB_23_SA_10404


title: WB_23_SA_10734


title: WB_23_SA_10320


title: WB_23_SA_10607


title: WB_23_SA_10228


title: WB_23_SA_10192


title: WB_23_SA_10233


title: WB_23_SA_10172


title: WB_23_SA_10285


title: WB_23_SA_10153


title: WB_23_SA_10190


title: WB_23_SA_10266


title: WB_23_SA_10284


title: WB_23_SA_10201


title: WB_23_SA_10123


title: WB_23_SA_10265


title: WB_23_SA_10115


title: WB_23_M_40451


title: WB_23_SA_10087


title: WB_23_M_40583


title: WB_23_SA_10050


title: WB_23_SA_10093


title: WB_23_SA_10040


title: WB_23_M_40325


title: WB_23_M_40339


title: WB_23_M_40499


title: WB_23_M_40475


title: WB_23_SA_10102


title: WB_23_SA_10092


title: WB_23_M_40327


title: WB_23_M_40338


title: WB_23_M_40248


title: WB_23_M_40207


title: WB_23_M_40450


title: WB_23_M_40469


title: WB_23_M_40523


title: WB_23_M_40477


title: WB_23_M_40458


title: WB_23_M_40443


title: WB_23_M_40472


title: WB_23_M_40286


title: WB_23_M_40271


title: WB_23_M_40456


title: WB_23_M_40199


title: WB_23_M_40295


title: PBMC stimulated with Borrelia 4h, rep18

description: Replicate 18


title: WB_23_M_40380


title: WB_23_M_40347


title: WB_23_M_40114


title: WB_21_SA_10641

value: HIV negative


title: WB_21_SA_10656


title: WB_23_M_40068


title: WB_23_M_40190


title: WB_21_SA_10700


title: WB_23_M_40193


title: WB_21_SA_10341


title: WB_23_M_40189


title: WB_21_SA_10315


title: WB_23_M_40034


title: WB_21_SA_10612


title: WB_21_SA_10349


title: WB_21_SA_10307


title: WB_21_SA_10625


title: WB_23_M_40082


title: WB_21_SA_10665


title: WB_23_M_40065


title: WB_21_SA_10608


title: WB_21_SA_10438


title: WB_23_M_40149


title: WB_21_SA_10299


title: WB_21_SA_10644


title: WB_21_SA_10279


title: WB_21_SA_10273


title: WB_21_SA_10234


title: WB_21_SA_10263


title: WB_21_SA_10231


title: WB_21_SA_10232


title: WB_21_SA_10260


title: WB_21_SA_10312


title: WB_21_SA_10240


title: WB_21_SA_10261


title: WB_21_SA_10241


title: WB_21_SA_10229


title: WB_21_SA_10225


title: WB_21_SA_10216


title: WB_21_SA_10237


title: WB_21_SA_10206


title: WB_21_SA_10227


title: WB_21_SA_10223


title: WB_21_SA_10178


title: WB_21_SA_10193


title: WB_21_SA_10199


title: WB_21_SA_10131


title: WB_21_SA_10219


title: WB_21_SA_10207


title: WB_21_SA_10146


title: WB_21_SA_10168


title: WB_21_SA_10161


title: WB_21_SA_10162


title: WB_21_SA_10098


title: WB_21_SA_10080


title: WB_21_SA_10155


title: WB_21_SA_10134


title: WB_21_M_40394


title: WB_21_M_40632


title: WB_21_M_40197


title: WB_21_M_40204


title: WB_21_SA_10029


title: WB_21_M_40200


title: WB_21_SA_10001


title: WB_21_M_40540


title: WB_21_M_40202


title: WB_21_M_40398


title: WB_21_M_40457


title: WB_21_M_40166


title: WB_21_M_40318


title: WB_21_SA_10126


title: WB_21_M_40273


title: WB_21_M_40289


title: WB_21_M_40348


title: WB_21_M_40188


title: WB_21_M_40214


title: WB_21_M_40165


title: WB_21_M_40156


title: WB_21_M_40326


title: WB_21_M_40183


title: WB_21_M_40198


title: WB_21_SA_10274


title: WB_21_M_40138


title: WB_21_M_40050


title: WB_21_M_40158


title: WB_21_M_40488


title: WB_21_M_40474


title: WB_21_M_40511


title: WB_21_M_40157


title: WB_21_M_40105


title: WB_21_M_40510


title: WB_21_M_40483


title: WB_21_M_40447


title: WB_21_M_40345


title: WB_21_M_40396


title: WB_21_M_40466


title: WB_21_M_40399


title: WB_21_M_40139


title: WB_21_M_40573


title: WB_21_M_40187


title: WB_21_M_40280


title: WB_21_M_40208


title: WB_21_M_40266


title: WB_21_M_40441


title: WB_21_M_40442


title: WB_21_M_40401


title: WB_21_M_40206


title: WB_21_M_40292


title: WB_21_M_40400


title: WB_21_M_40377


title: WB_21_M_40179


title: WB_24_SA_10509

source_name: Whole Blood from patient with LTBI

value: latent TB infection


title: WB_24_M_40604


title: WB_24_M_40617


title: WB_21_M_40137


title: WB_21_M_40097


title: WB_24_M_40640


title: WB_24_M_40582


title: WB_24_M_40581


title: WB_21_M_40080


title: WB_24_M_40486


title: WB_24_M_40496


title: WB_24_M_40536


title: WB_24_M_40515


title: WB_24_SA_10421


title: WB_24_M_40576


title: WB_24_SA_10333


title: WB_24_M_40453


title: WB_24_SA_10270


title: WB_24_M_40498


title: WB_24_M_40566


title: WB_24_M_40574


title: WB_24_M_40543


title: WB_24_M_40567


title: WB_24_M_40415


title: WB_24_M_40425


title: WB_24_M_40530


title: WB_24_M_40414


title: WB_24_M_40487


title: WB_24_M_40462


title: WB_24_M_40333


title: WB_24_M_40354


title: WB_24_M_40243


title: WB_24_M_40355


title: WB_24_M_40309


title: WB_24_M_40240


title: WB_24_M_40406


title: WB_24_M_40390


title: WB_24_M_40352


title: WB_24_M_40381


title: WB_24_M_40334


title: WB_24_M_40308


title: WB_24_M_40365


title: WB_20_SA_10674

source_name: Whole Blood from patient with Active TB

value: active tuberculosis


title: WB_24_M_40069


title: WB_24_M_40077


title: WB_24_M_40100


title: WB_24_M_40372


title: WB_24_M_40192


title: WB_24_M_40021


title: WB_24_M_40144


title: WB_24_M_40242


title: WB_20_SA_12010


title: WB_24_M_40096


title: WB_24_M_40029


title: WB_24_M_40070


title: WB_24_M_40049


title: WB_24_M_40220


title: WB_24_M_40107


title: WB_20_SA_10374


title: WB_20_SA_10552


title: WB_20_SA_10386


title: WB_20_SA_10214


title: WB_20_SA_10355


title: WB_20_SA_10464


title: WB_20_M_40611


title: WB_20_SA_10493


title: WB_20_SA_10423


title: WB_20_SA_10280


title: WB_20_SA_10291


title: WB_20_M_40502


title: WB_20_M_40701


title: WB_20_SA_10578


title: WB_20_SA_10114


title: WB_20_M_40560


title: WB_20_SA_10244


title: WB_20_SA_10336


title: WB_20_SA_10377


title: WB_20_M_40520


title: WB_20_SA_10024


title: WB_20_SA_10332


title: WB_20_M_40685


title: WB_20_M_40660


title: WB_20_SA_10366


title: WB_20_SA_10058


title: WB_20_SA_10129


title: WB_24_M_40670


title: WB_20_SA_10124


title: WB_20_M_40521


title: WB_20_M_40263


title: WB_22_SA_10731


title: WB_20_M_40397


title: WB_20_M_40384


title: WB_20_M_40182


title: WB_20_M_40385


title: WB_20_M_40445


title: WB_22_SA_10716


title: WB_22_SA_10719


title: WB_22_SA_10742


title: WB_22_SA_10479


title: WB_20_M_40422


title: WB_22_SA_10677


title: WB_20_M_40476


title: WB_22_SA_10737


title: WB_22_SA_10637


title: WB_22_SA_10496


title: WB_22_SA_10486


title: WB_22_SA_10722


title: WB_22_SA_10658


title: WB_20_M_40376


title: WB_22_SA_10474


title: WB_20_M_40012


title: WB_22_SA_10654


title: WB_22_SA_10733


title: WB_22_SA_10505


title: WB_22_SA_10465


title: WB_22_SA_10494


title: WB_22_SA_10483


title: WB_22_SA_10434


title: WB_22_SA_10428


title: WB_22_SA_10396


title: WB_22_SA_10422


title: WB_22_SA_10290


title: WB_22_SA_10393


title: WB_22_SA_10347


title: WB_22_SA_10392


title: WB_22_SA_10245


title: WB_22_SA_10258


title: WB_22_SA_10090


title: WB_22_SA_10189


title: WB_22_SA_10015


title: WB_22_SA_10294


title: WB_22_SA_10021


title: WB_22_SA_10150


title: WB_22_SA_10144


title: WB_22_SA_10182


title: WB_22_SA_10025


title: WB_22_SA_10187


title: WB_22_SA_10224


title: WB_22_SA_10133


title: WB_22_SA_10088


title: WB_22_SA_10143


title: WB_22_SA_10176


title: WB_22_SA_10322


title: WB_22_SA_10012


title: WB_22_SA_10148


title: WB_22_M_40699


title: WB_22_SA_10002


title: WB_22_M_40594


title: WB_22_M_40695


title: WB_22_M_40444


title: WB_22_M_40578


title: WB_22_M_40539


title: WB_22_M_40541


title: WB_22_M_40588


title: WB_22_M_40421


title: WB_22_M_40378


title: WB_22_SA_10697


title: WB_22_M_40335


title: WB_22_M_40007


title: WB_22_M_40332


title: WB_22_M_40362


title: WB_22_M_40121


title: Huh7.5 cells carrying pcDNA3.1 c_myc His vector_80% confluent_Total RNA_2

city: HYDERABAD

first: KRISHNAN

middle: HARINIVAS

last: HARSHAN

address: HABSIGUDA

country: India

institute: CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scannedusing  Agilent Technologies G2505C scanner

data_processing: Images were quantified using Feature Extraction Software (Version-10.7, Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version 12.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

source_name: Human hepatoma celline 7.5

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: HCV NS5A (Full Length) expressing and control Huh7.5 cells were cultured in complete DMEM supplemented with 10% FBS, 1X Non essential Amino acids, 1X Penicillin Streptomycin solution at 37°C with 5% CO2

extract_protocol: For total RNA preparartion, Qiagen Rneasy Kit was used and total RNA was extracted and quantified. For Polysomal RNA preparation, cells were lysed and normalized volumes containing 175 ug of corresponding RNA were separated on Sucrose gradient (10%-50%), samples were then  fractionated into mRNP, monosomal and polysomal fractions. Polysomal fractions   were pooled based on their profilies and RNA was prepared by initial ethanol precipitation followed by lithium chloride extraction and subsequent purification by RNeasy columns. Enriched polysomal RNA was used for microarray analysis.

treatment_protocol: 80% confluent pcDNA3.1 c_myc/His carrying and HCV NS5A (Full Length) expressing cells were trypsinised with 0.05% Trypsin EDTA. Cell were then washed with 1X PBS containing Cycloheximide (100µg/ml). For total RNA preparartion, Qiagen Rneasy Kit was used and total RNA was extracted and quantified. For Polysomal RNA preparation, Cells were lysed with Lysis buffer containing 20mM Tris pH-8.0, 140mM KCl, 1.5mM MgCl2, 1% Triton-X-100, 0.5mM DTT, 100 µg/ml Cycloheximide, 1X Protease Inhibitor cocktail, 1mg/ml Heparin and 100U of Ribolock and 175 ug of corresponding RNA from crude lysate was loaded onto Sucrose gradient (10%-50%). Samples were then centrifuged at 35000 rpm for 4 hrs at 4°C using Beckmann SW41 rotor. Resolved sucrose gradient samples were fractionated using Density gradient fractionator. Polysomal fractions were pooled based on their profilies and RNA was prepared by initial ethanol precipitation followed by Lithium chloride extraction. Enriched polysomal RNA was used for microarray analysis.

value: pcDNA3.1 c_myc His carrying Huh7.5

tag: rna fraction

value: total RNA


title: WB_22_M_40160


title: Huh7.5 expressing HCV NS5A (Full length)_80% confluent_polysome fractions_1

value: HCV NS5A (Full length) expressing huh7.5

value: polysome fraction


title: WB_22_M_40417


title: WB_22_M_40124


title: Huh7.5 expressing HCV NS5A (Full length)_80% confluent_Total RNA_2


title: WB_22_M_40264


title: WB_22_M_40321


title: Huh7.5 expressing HCV NS5A (Full length)_80% confluent_polysome fractions_2


title: Huh7.5 expressing HCV NS5A (Full length)_80% confluent_Total RNA_1


title: Huh7.5 cells carrying pcDNA3.1 c_myc His vector_80% confluent_ polysome fraction_1


title: 449245_A09

city: MEXICO, D.F.

first: JORGE

last: FERNANDEZ-RETANA

address: AV. SAN FERNANDO No22 COL SECCION XVI

department: INVESTIGACION BASICA

country: Mexico

institute: INSTITUTO NACIONAL DE CANCEROLOGIA

description: SAMPLE 57

hyb_protocol: Hybridization was performed by NimbleGen Systems (Nimblegen Roche, Mannheim, Germany), following their standard operating protocol. See www.nimblegen.com. After standard washes, arrays were scanned.

scan_protocol: Scanning was performed byNimblegen MS200 microarray scanner. Nimblegen Roche, Mannheim, Germany, following their standard operating protocol. Scanned images were gridded by using the NimbleScan v2.6 Software (Nimblegen Roche, Mannheim, Germany).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Cervical tissue

label_protocol: Labeling was performed by NimbleGen Systems One Color Llabeling kit (Nimblegen Roche, Mannheim, Germany), following their standard operating protocol. See www.nimblegen.com. (Nimblegen Roche, Mannheim, Germany).

growth_protocol: Biopsies were frozen in liquid nitrogen until nucleic acid extractionThe population under study included 89 patients prospectively enrolled into the National Cancer Institute of Mexico. All patients included signed informed consent; the protocol was approved by institutional ethics and scientific committees. Immediately after surgical excision, tumor biopsies were analyzed for pathological confirmation and frozen in liquid nitrogen until nucleic acid extraction.

extract_protocol: Total RNA was extracted using the MagNAPure Compact Instrument following manufacturer recommendations (Roche Diagnostics GmbH Roche Applied Science Mannheim, Germany). RNA quality was determined by by means of 18S:28S ratio.  Hybridization targets were prepared from 250 ng of total RNA and amplified with whole transcriptome amplification kit 2 (Sigma Aldrich, St Louis, MO)

tag: disease state

value: Locally advanced cervical cancer

tag: carcinoma type

value: Squamous cell carcinomas

tag: Stage

value: IIB


title: Huh7.5 cells carrying pcDNA3.1 c_myc His vector_80% confluent_Total RNA_1


title: 445087_A11

description: SAMPLE 47


title: 449245_A02

description: SAMPLE 50


title: 449245_A11

description: SAMPLE 59


title: WB_22_SA_10433


title: 445087_A08

description: SAMPLE 44


title: 449245_A10

description: SAMPLE 58


title: 449245_A07

description: SAMPLE 55


title: 445087_A12

description: SAMPLE 48


title: 449245_A03

description: SAMPLE 51

value: IIIB


title: 449245_A12

description: SAMPLE 60


title: 449245_A04

description: SAMPLE 52

value: Adenocarcinoma


title: 445087_A09

description: SAMPLE 45


title: 445087_A05

description: SAMPLE 41


title: 445087_A06

description: SAMPLE 42


title: 449245_A08

description: SAMPLE 56


title: 445087_A07

description: SAMPLE 43


title: 445087_A03

description: SAMPLE 39


title: 449245_A01

description: SAMPLE 49


title: 449245_A06

description: SAMPLE 54


title: 445087_A10

description: SAMPLE 46


title: 445087_A04

description: SAMPLE 40


title: 449245_A05

description: SAMPLE 53


title: 445087_A02

description: SAMPLE 38


title: H9_HEPs_DLL4+

city: Granada

first: Veronica

last: Ayllon

address: Av Ilustracion, 114

country: Spain

institute: GENYO. Centre for Genomics and Oncological Research

description: Gene expression in HEPs with high surface expression of DLL4

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent  Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.  Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).

source_name: H9-derived DLL4high HEPs

label_protocol: For the linear T7-based amplification step, 70 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000  Spectrophotometer (NanoDrop Technologies).

growth_protocol: Undifferentiated hESCs at confluence were treated with collagenase IV and scraped off of the Matrigel attachments. To allow human embryoid body (hEB) formation, hESC clumps were transferred to low-attachment plates (Corning) and incubated overnight in differentiation medium [DM; Knock-out-Dulbecco’s modified Eagle’s medium (KO-DMEM) supplemented with 20% non-heat-inactivated fetal bovine serum (FBS), 1% nonessential amino acids (NEAA), 1 mmol/L l-glutamine, and 0.1 mM β-mercaptoethanol]. The medium was changed the next day (day 1) with the same DM supplemented with hematopoietic cytokines: 300 ng/mL stem cell factor (SCF), 300 ng/mL Flt3L, 10 ng/mL interleukin (IL)-3, 10 ng/mL IL-6, 50 ng/mL granulocyte-colony stimulating factor (G-CSF) and 25 ng/mL bone morphogenetic protein 4 (BMP-4)19, 54. hEBs were dissociated using collagenase B (Roche Diagnostic) for 2 h at 37ºC followed by 10min incubation at 37ºC with enzyme-free Cell Dissociation Buffer (Invitrogen). A single-cell suspension was obtained by gentle pipetting and passage through a 70-µm cell strainer. The dissociated cells were stained with anti-CD34-PE-Cy7(BD Biosciences), anti-CD31-PE, anti-CD45-APC or -FITC and DLL4-APC or -PE antibodies (all from Miltenyi) and 7-actinomycinD (7-AAD, BD Biosciences). CD31+CD34+CD45-DLL4high and CD31+CD34+CD45-DLL4low/- HEPs were isolated using a FACSAria sorter (Becton Dickinson).

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin® RNA II). The RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies)

tag: cell type

value: hESC-derived HEPs


title: AND1_HEPs_DLL4-

description: Gene expression in HEPs with low/negative surface expression of DLL4

source_name: AND1-derived DLL4low/- HEPs


title: H9_HEPs_DLL4-

source_name: H9-derived DLL4low/- HEPs


title: AND1_HEPs_DLL4+

source_name: AND1-derived DLL4high HEPs


title: Stra8-cre total 24h RA-3

city: Pullman

last: Griswold

state: WA

address: 100 Dairy Rd.

department: School of Molecular Biosciences

institute: Washington State University

hyb_protocol: Fragmented, biotin labeled cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene ST 1.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Array output was normalized using the RMA algorithm, and data analysis was conducted using GeneSpring (Version 12.6 GX; Agilent Technologies).

source_name: Stra8_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 24h

label_protocol: Approximately 100 ng total RNA from each sample was used to generate cDNA using the Ovation RNA Amplification System V2 (NuGEN, San Carlos, CA) according to the manufacturer's instructions.  3.75ug of the cDNA was then fragmented and labelled using the Encore Biotin Module (NuGEN, San Carlos, CA) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using the Rneasy kit from Qiagen according to the manufacturer's protocol.

treatment_protocol: Animals were treated with WIN,18446 (BDAD) for 9 consecutive days then either euthanized or injectioned with RA

tag: strain

value: FVB/N

tag: fraction

value: Total RNA


title: 442761_A10

description: SAMPLE 34

value: IVA


title: 445087_A01

description: SAMPLE 37


title: Stra8-cre total 12h RA-1

source_name: Stra8_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 12h


title: 442761_A07

description: SAMPLE 31


title: Stra8-creIP 4h RA-1

source_name: Stra8_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 4h

value: polysome associated RNA


title: 442761_A12

description: SAMPLE 36


title: Stra8-cre total 24h RA-1


title: Stra8-cre total 4h RA-3

source_name: Stra8_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 4h


title: Stra8-cre IP 24h RA-1

source_name: Stra8_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 24h


title: Stra8-cre total 24h RA-2


title: Stra8-cre IP 12h RA-2

source_name: Stra8_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 12h


title: 442761_A04

description: SAMPLE 28


title: 442761_A06

description: SAMPLE 30


title: 442761_A11

description: SAMPLE 35


title: 442761_A05

description: SAMPLE 29


title: 442761_A08

description: SAMPLE 32


title: 442761_A01

description: SAMPLE 25


title: 442761_A03

description: SAMPLE 27


title: Stra8-creIP 4h RA-2


title: 442761_A09

description: SAMPLE 33


title: Stra8-cre total 24h RA-4


title: Stra8-cre total 12h RA-2


title: 442723_A12

description: SAMPLE 24


title: Huh7.5 cells carrying pcDNA3.1 c_myc His vector_80% confluent_ polysome fraction_2


title: Stra8-cre total 4h RA-1


title: Stra8-cre total 4h RA-2


title: 442761_A02

description: SAMPLE 26


title: Stra8-cre IP 12h RA-1