title: CytD_exp|uninfected_5min_w/o_CytD|experiment_2|replicate_1

description: CytochalasinD experiment

tag: cell line

tag: infectious agent


title: P49

status: Public on Dec 31 2014

type: RNA

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

hyb_protocol: According to manufacturer (Illumina) specifications.

data_processing: Data was back+B51ground-corrected using the Illumina BeadStudio median background substraction algorithm, a constant 11 was added to every expression value, genes with missing values in >10% of samples were excluded; otherwise missing values were imputed using k-nearest neighbors implemented in the impute R package. Quantile normalization was performed using the preprocessCore R package and values were log2 transformed. Each gene was median centered across the 49 primary data sets. Subtyping was performed on the normalized expression matrix using the genefu R package and the published gene lists PAM50, Sorlie and Hu.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary breast tumor

extract_protocol: QIAGEN AllPrep

tag: tissue

value: primary breast tumor

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

value: Basal

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

tag: erbb2 status

value: Negative

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_3|replicate_1

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: CytochalasinD experiment

hyb_protocol: After precipitation, purification and quantification the labeled samples were hybridized according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 5µm resolution, 16 bit and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA ( Agilent Technologies)

label_protocol: Total RNA labeling was performed with the one color Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: 1. Wash twice cryopreserved THP-1 cells* (one vial contains 5 x 10^6 cells) with complete medium - cRPMI (RPMI-1640 medium supplemented with 1% L-glutamine, 1% Hepes, 0.1% 2ME and fetal bovine serum to a final concentration of 10%). Use 50 ml Flacon tubes and 20 ml medium to wash, spin down for 5 min at 1500 rpm (400xg, Heraeus Megafuge), 4°C.    2. Seed cells in 6 well plates/ T75 flask and expand cell numbers by sub culturing in T75 flasks in 10 ml cRPMI and later in T150 flasks in 50 ml cRPMI.  Sub-cultures are established by centrifugation with subsequent re-suspension at 2-5 x 10^5 viable cells/ml, every 2-3 day. Cells reach density of 8 x 10^5 cells/ml within this period of time. For proper viability and fitness of the cells do not exceed before sub-culturing 1x10^6 cells/ml. Use T150 flasks and maximum volume of 80 ml cRPMI per flask to generate large cell numbers (eg 15 x T150 flasks to get 5 x 10^8 cells). Incubate cell cultures at 37°C and 5% CO2.  3. Differentiation to macrophages** is triggered by addition of PMA (50 ng/ml) and overnight incubation. This is followed by 2 washes (cRPMI)*** and addition of complete media over 48 h post differentiation. This protocol elicits a uniform population of resting macrophages prior infection experiments. For T150 flasks use 2x10^7 cells/20 ml cRPMI (30 flasks per time-point for MS platforms), for 6 well plate use 10^6 cells/well/3 ml cRPMI (triplicates per time-point).  Transfer differentiated THP-1 cells to the BSL3 lab.

extract_protocol: 1. Preparation of Mtb infected THP-1 macrophages for RNA extraction/isolation: At different time-points following infection wash once the macrophage monolayer with RT PBS (Invitrogen, # 20012-043). Add 1 ml cold 4M GITC solution (Invitrogen, # 15577-018) per well and gently scrape the cells. Collect solution in 1 ml screw cap. Centrifuge at 12,000 × g for 10 min. at 4°C. Add 3 Vol. Trizol LS (Invitrogen, # 10296-010) to supernatant and homogenize (eukaryotic fraction). Store homogenate of eukaryotic fraction at -80°C freezer until further processed. Resuspend pellet by pipetting up and down in residual GITC. Add 1 ml Trizol (Invitrogen, # 15596-018) containing 20 g/ml linear acrylamide to the pellet (prokaryotic fraction). Use pipette to homogenate in Trizol. Store homogenate of prokaryotic pellet at -80°C freezer until further processed.  2. Isolation of total eukaryotic host RNA: Note:  process only 1ml from total homogenate, store remaining volume at –80°C for future processing. Thaw Trizol homogenate of eukaryotic fraction and incubate for 5 min. at RT (15 to 30°C). Add 0.2 ml of chloroform per 0.75 ml of Trizol LS for phase separation. Shake tubes vigorously by hand for 15 sec. and incubate them at RT for 5 min. Centrifuge at 12,000 × g for 15 min.at 4°C. Transfer the colorless aqueous (upper) phase to a clean tube (typical volume will be ~500 µl, assure not to carry over anything from the white interphase or the red phenol phase)

treatment_protocol: Mtb infection stocks will be freshly prepared by cultivation of WSL* (working seed lot – 10^8 bacteria per vial, cryopreserved in 7H9+glycerol 50%) in 9 ml 7H9+ADC at 37°C under shaking with 90 rpm for 5 days. When bacterial growth is visible (day 5-7) inoculate 45 ml 7H9 with 5 ml bacterial suspension.      1. Grow infection stock in 7H9+ADC 0,05% Tween 80 for about 5 days to OD 0.3-0.6.    2. Spin down bacteria: 20 min at 4.000 rpm, 4°C  3. Wash once with equal amount of cold PBS and discard clumps by filtration using 40 μm pore size filters (BD).   4. Determine bacteria number: OD580 0.1 >>>> 5 x 10^7 bacteria/ml  5. Dilute PBS washed infection stock with cRPMI and infect cells – MOI 5 for up to day 3 and MOI 1 for longer time-points  6. Wash away non-internalized bacteria 4h after infection (use room temperature PBS 20 ml per flask, twice) and place cells back in cRPMI  7. For infection of macrophages in plates, change the culture media to media containing Mtb and spin down to obtain a uniform infectivity, 2 min, 700 rpm  8. For infection of macrophages in flasks, add 1ml of media containing Mtb to the 25 ml of cRPMI per flask


title: rep1-control

city: Singapore

first: Wei

last: Zhou

address: 8 College Road

department: Signature Program in Cardiovascular and Metabolic Disorders

country: Singapore

institute: DUKE-NUS Graduate Medical School

description:
82A
Sample 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: Biotin

label_protocol: Biotin-labelled cRNA were prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) from 500ng of total RNA

growth_protocol: Multiple myeloma (MM) cells RPMI8266 were maintained on RPMI1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Hyclone) to the exponential growth stage.

extract_protocol: Cells were spun down 200 × g for 5 min. Total RNA were extracted using RNeasy Kit (Qiagen), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit Quality and quantity of RNA was determined by Agilent Bioanalyzer.

treatment_protocol: Cells were treated with Guanabenz (GBZ) 50µM, Sal003 20µM or no treatment for 24 hr

tag: cell type

value: Multiple myeloma (MM) cells

tag: treated with

value: none (untreated control)


title: P46-replicate

scan_protocol: According to manufacturer (Illumina) specifications.


title: P45

label_protocol: According to manufacturer (Illumina) specifications.

value: LumA


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_1|replicate_1

description: CytochalasinD experiment

tag: cell line


title: CHC1154T

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw data were obtained by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Santa Clara, USA). Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm.

source_name: Hepatocellular Carcinoma

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix)

extract_protocol: RNA samples were extracted from frozen tissues, in accordance with standard procedures, as previously described [Rebouissou et al. J Biol Chem 2007]

value: Hepatocellular Carcinoma

tag: disease state

value: Solid Tumor

tag: gender

value: Male

tag: age

tag: metavir

tag: edmonson

value: I-II

tag: etiology

value: HBV


title: sample114

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..

treatment_protocol: stored at -20 degree

tag: disease

value: Wilms Tumor


title: uninfected_5d|experiment_3|replicate_3

description: late time point

tag: infectious agent


title: uninfected_5d|experiment_2|replicate_3

description: late time point


title: CHC884T

tag: tissue

value: III-IV

value: Al


title: uninfected_5d|experiment_1|replicate_3

description: late time point


title: fresh frozen metastatic tumor_1

type: genomic

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

country: USA

institute: Karmanos Cancer Institute & Wayne State University

hyb_protocol: Genome-wide copy number variation was measured by a 2-color microarray approach using Agilent SurePrint G3 ISCA Human Cancer CGH+SNP 180K x 4 arrays

scan_protocol: CytoCGH_0205_Oct12 protocol and Agilent G4900DA SureScan Microarray Scanner System

data_processing: Raw data files were acquired using software: Agilent Feature Extraction for Cytogenomics 2.5.1.0. Sample Tables contain the log10 Cy5/Cy3 from the Feature Extraction File.  Log2 ratios for genome (hg19) coordinates and genes showing copy number variation (CNV) were acquired using Agilent CytoGenomics Edition 2.5.8.1 using the CGH_v2 default, the ADM2 threshold set at 6 and an 8 probe minimum. An additional absolute log2 ratio threshold was set at 0.4 for analysis of reoccurring lesions or 0.8 to study high amplitude copy number aberrations. The sample supplementary files named "IntervalBasedReport*.txt" contain the genomic coordinates and genes displaying CNV.

molecule: genomic DNA

label_protocol: Cancer and reference DNA (500ng each) were labeled with fluorescent dyes, Cy5 and Cy3 respectively, using the SureTag Complete DNA Labeling Kit (Agilent Technologies) or Universal Linkage System labeling kit for DNA from FFPE specimens

extract_protocol: DNA was isolated using the EZ1 Advanced XL magnetic bead technology, the EZ1 DNA de-paraffinization method (where appropriate) and the EZ1 DNA Tissue kit (Qiagen, Valencia, CA). DNA was analyzed for quantity by nanodrop 3000 () and quality using the TapeStation (Agilent Technologies, Santa Clara, CA).

treatment_protocol: tumor specimens were either FFPE or fresh frozen as indicated in the sample list

value: breast cancer metastasis brain tumor

source_name: Female Reference DNA

tag: reference tissue

value: Agilent Female European DNA


title: CHC879T


title: P44

value: primary breast tumor

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

tag: pgr status

tag: erbb2 status

tag: kmt2c mutations

tag: pik3ca mutations

tag: pten mutations

tag: tp53 mutations


title: uninfected_5d|experiment_3|replicate_2

description: late time point

tag: cell line


title: P46

value: Basal

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: sample113

tag: disease

value: lung cancer


title: sample112


title: sample111


title: sample110

value: melanoma


title: CHC469T

tag: tissue

tag: disease state

tag: gender

value: Female

tag: age

tag: metavir

tag: edmonson

tag: etiology

value: w/o ETIOLOGY


title: P43

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Negative

tag: pgr status

tag: erbb2 status


title: P41

value: LumB

value: Normal

value: LumA

value: Positive

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: pik3ca mutations


title: P41-replicate

tag: tissue

tag: tp53 mutations


title: uninfected_5d|experiment_2|replicate_2

description: late time point

tag: cell line

tag: infectious agent


title: uninfected_5d|experiment_1|replicate_2

description: late time point


title: CHC152T

value: Hepatocellular Carcinoma

tag: disease state

value: Solid Tumor

tag: gender

value: Male

tag: age

tag: metavir

tag: edmonson

value: I-II

tag: etiology

value: HBV


title: P40

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

tag: erbb2 mutations


title: uninfected_5d|experiment_3|replicate_1

description: late time point


title: P42

tag: tissue

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: cdh1 mutations

tag: map3k1 mutations


title: CHC059T

tag: disease state

tag: gender

tag: age

tag: metavir

tag: edmonson

value: III-IV

tag: etiology

value: Al


title: sample107

tag: disease


title: sample108


title: uninfected_5d|experiment_2|replicate_1

description: late time point

tag: cell line

tag: infectious agent


title: sample106


title: CHC028T

tag: tissue

value: HCV


title: infected_5d|experiment_2|replicate_1|MOI5

description: late time point

value: Mycobacterium tuberculosis (Mtb)


title: uninfected_5d|experiment_1|replicate_1

description: late time point


title: infected_5d|experiment_2|replicate_3|MOI1

description: late time point


title: CHC1040T


title: P39

value: primary breast tumor

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

tag: pgr status

tag: apc mutations

tag: tp53 mutations


title: CHC1035T

tag: disease state

tag: gender

tag: age

tag: metavir

value: Al. HBV


title: CHC912T

tag: edmonson

tag: etiology

value: Al. HCV


title: P38

tag: tissue

tag: erbb2 status

value: Negative

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: infected_5d|experiment_2|replicate_2|MOI1

description: late time point

tag: cell line

tag: infectious agent


title: P36

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

tag: pik3ca mutations


title: CHC1159T

tag: disease state

tag: gender

tag: age

tag: metavir

tag: edmonson

value: w/o ETIOLOGY


title: P37

tag: tissue

value: Normal

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: sf3b1 mutations


title: sample105

tag: disease

value: others


title: sample104


title: sample102


title: sample101

value: ductal adenocarcinoma


title: infected_5d|experiment_2|replicate_1|MOI1

description: late time point

tag: cell line

tag: infectious agent


title: CHC703T

value: Hepatocellular Carcinoma

tag: etiology

value: Al. HM


title: infected_5d|experiment_3|replicate_1|MOI5

description: late time point


title: P34

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: lymphocyte content (1


title: CHC798T

tag: tissue

tag: disease state

value: Solid Tumor

tag: gender

value: Male

tag: age

tag: metavir

tag: edmonson

value: I-II


title: sample100

tag: disease


title: sample99


title: CHC789T

value: HM


title: CHC898T

value: III-IV


title: infected_5d|experiment_3|replicate_2|MOI5

description: late time point

tag: cell line

tag: infectious agent

value: Mycobacterium tuberculosis (Mtb)


title: sample103


title: infected_5d|experiment_3|replicate_3|MOI5

description: late time point


title: CHC613T

tag: etiology

value: Al


title: infected_5d|experiment_3|replicate_2|MOI1

description: late time point


title: CHC614T

value: METAB


title: infected_5d|experiment_3|replicate_3|MOI1

description: late time point


title: CHC609T

value: Al. HBV METAB


title: infected_5d|experiment_1|replicate_3|MOI5

description: late time point


title: P29

value: primary breast tumor

tag: ht12 subtype pam50

value: Basal

tag: ht12 subtype sorlie

value: Negative

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: nf1 mutations

tag: tp53 mutations


title: P33

tag: tissue

value: LumB

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Amplified

tag: lymphocyte content (1

tag: sf3b1 mutations


title: P35


title: P32

tag: pik3ca mutations


title: P30

tag: ht12 subtype pam50


title: P31

tag: ht12 subtype sorlie

tag: kmt2c mutations


title: sample98

tag: disease

value: ductal adenocarcinoma


title: CHC445T

value: Hepatocellular Carcinoma

tag: disease state

tag: gender

tag: age

tag: metavir

tag: edmonson

tag: etiology

value: Al. HCV


title: infected_5d|experiment_3|replicate_1|MOI1

description: late time point

tag: cell line

tag: infectious agent


title: P28

tag: tissue

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

value: Positive

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: tp53 mutations


title: sample97

tag: disease


title: sample96


title: sample95

value: others


title: CHC303T

tag: disease state

value: Solid Tumor

tag: gender

value: Male

tag: age


title: sample92


title: sample93

value: pancreatitis


title: infected_5d|experiment_1|replicate_2|MOI1

description: late time point

value: Mycobacterium tuberculosis (Mtb)


title: P27

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

tag: er status

tag: lymphocyte content (1

tag: pik3ca mutations


title: CHC302T

tag: tissue

tag: metavir

tag: edmonson

value: I-II

tag: etiology

value: HCV


title: infected_5d|experiment_1|replicate_2|MOI5

description: late time point

tag: cell line

tag: infectious agent


title: P26

value: primary breast tumor

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1


title: sample91

tag: disease


title: CHC317T

tag: disease state

tag: gender

value: Female

tag: age

value: III-IV


title: infected_5d|experiment_1|replicate_1|MOI5

description: late time point


title: CHC258T

tag: tissue

tag: metavir

value: METAB


title: infected_5d|experiment_1|replicate_1|MOI1

description: late time point


title: P24

tag: ht12 subtype pam50

value: LumB

tag: ht12 subtype sorlie

tag: er status

value: Amplified

tag: lymphocyte content (1


title: sample90


title: infected_5d|experiment_2|replicate_2|MOI5

description: late time point

tag: cell line

tag: infectious agent


title: infected_3d|experiment_3|replicate_3

description: mid time point


title: P25

value: Basal

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

value: Negative

tag: kmt2c mutations

tag: tp53 mutations


title: infected_5d|experiment_1|replicate_3|MOI1

description: late time point


title: P23

value: Positive

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1


title: infected_5d|experiment_2|replicate_3|MOI5

description: late time point


title: P22

tag: tissue

tag: nf1 mutations


title: CHC097T

value: Hepatocellular Carcinoma

tag: disease state

tag: gender

tag: age

tag: metavir

tag: edmonson

tag: etiology


title: CHC031T

value: Solid Tumor

value: Al


title: CHC051T


title: P23-replicate

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: er status

tag: lymphocyte content (1


title: CHC1201T

value: Male

value: Al. METAB


title: P24-replicate

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: pgr status

tag: erbb2 status

tag: kmt2c mutations


title: sample94

tag: disease

value: ductal adenocarcinoma


title: sample89

value: lung cancer


title: sample88


title: sample87


title: sample86


title: infected_3d|experiment_1|replicate_3

description: mid time point

tag: cell line

tag: infectious agent

value: Mycobacterium tuberculosis (Mtb)


title: P21

tag: tissue

value: primary breast tumor

tag: nottingham grade

tag: tumor cell content (1

tag: tp53 mutations


title: sample109

value: melanoma


title: CHC1061T

tag: disease state

tag: gender

value: Female

tag: age

tag: metavir

tag: edmonson

value: I-II

tag: etiology

value: w/o ETIOLOGY


title: CHC1162T


title: sample85


title: P20

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

value: Normal

tag: rna-seq subtype hu

tag: er status

tag: lymphocyte content (1


title: CHC1190T

tag: tissue

value: Al. HCV


title: P19

value: LumB

value: Positive

tag: pgr status

value: Negative

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1


title: sample84

tag: disease


title: CHC1060T

value: Hepatocellular Carcinoma

tag: disease state

value: Solid Tumor

tag: gender

tag: age

tag: metavir

value: III-IV

value: METAB


title: P18

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: pik3ca mutations

tag: runx1 mutations


title: infected_3d|experiment_2|replicate_2

description: mid time point

tag: cell line

tag: infectious agent


title: infected_3d|experiment_2|replicate_3

description: mid time point


title: CHC983T

value: Male

tag: edmonson

tag: etiology

value: Al


title: P17

tag: tissue

value: primary breast tumor

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

tag: pgr status

tag: lymphocyte content (1

tag: arid1a mutations


title: CHC1052T

tag: disease state

tag: gender

tag: age

tag: metavir


title: P15

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: map3k1 mutations

tag: pik3ca mutations


title: sample82

tag: disease

value: lung cancer


title: infected_3d|experiment_3|replicate_1

description: mid time point

tag: cell line

tag: infectious agent

value: Mycobacterium tuberculosis (Mtb)


title: P14

tag: tissue

value: Basal

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

tag: pgr status

tag: atm mutations

tag: tbl1xr1 mutations


title: infected_3d|experiment_2|replicate_1

description: mid time point


title: CHC918T

tag: disease state

tag: gender

tag: age

tag: metavir

tag: edmonson

value: I-II

tag: etiology


title: CHC896T

value: Al. METAB


title: infected_3d|experiment_1|replicate_2

description: mid time point

tag: cell line


title: sample80

tag: disease


title: P16

tag: tissue

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

value: Normal

value: LumA

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: pik3ca mutations

tag: tp53 mutations


title: infected_3d|experiment_1|replicate_1

description: mid time point

tag: infectious agent


title: sample83


title: sample81


title: sample79


title: sample78

value: sarcoidosis


title: CHC892T

tag: disease state

tag: gender

value: Female

value: w/o ETIOLOGY


title: infected_2d|experiment_3|replicate_3

description: mid time point


title: sample77


title: CHC805T

value: Hepatocellular Carcinoma

tag: age

tag: metavir


title: P13

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

value: Negative


title: infected_2d|experiment_2|replicate_3

description: mid time point

tag: cell line


title: CHC799T

tag: tissue

value: Solid Tumor

tag: edmonson

tag: etiology


title: CHC734T

value: Male

value: III-IV


title: infected_2d|experiment_1|replicate_3

description: mid time point


title: P10

value: primary breast tumor

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: infected_2d|experiment_3|replicate_2

description: mid time point

tag: infectious agent


title: sample76

tag: disease


title: infected_2d|experiment_2|replicate_2

description: mid time point


title: sample75


title: P9

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: tp53 mutations


title: sample74


title: P11

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

tag: pik3ca mutations


title: CHC715T

tag: tissue

tag: disease state

tag: gender

tag: age

tag: metavir

tag: edmonson

value: NASH


title: P12

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: rb1 mutations


title: P8

value: LumB

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: lymphocyte content (1


title: infected_2d|experiment_3|replicate_1

description: mid time point

tag: cell line

tag: infectious agent

value: Mycobacterium tuberculosis (Mtb)


title: infected_2d|experiment_1|replicate_2

description: mid time point


title: CHC307T

tag: tissue

tag: disease state

tag: gender

tag: etiology

value: Al


title: P7

tag: ht12 subtype pam50

tag: rna-seq subtype hu

tag: er status


title: P6-replicate

value: Basal

tag: ht12 subtype sorlie

tag: pgr status

tag: erbb2 status


title: CHC306T

tag: age

tag: metavir

tag: edmonson

value: I-II

value: HCV


title: infected_2d|experiment_2|replicate_1

description: mid time point


title: CHC220T


title: sample71

tag: disease

value: lung cancer


title: sample73

value: others


title: sample70


title: P6

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: chek2 mutations

tag: nf1 mutations


title: infected_1d|experiment_3|replicate_3

description: mid time point

tag: cell line

tag: infectious agent


title: sample69


title: P5-replicate

tag: tissue

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

value: LumA

tag: rna-seq subtype hu

tag: er status

tag: tp53 mutations


title: infected_2d|experiment_1|replicate_1

description: mid time point


title: infected_1d|experiment_2|replicate_3

description: mid time point


title: CHC210T

value: Hepatocellular Carcinoma

tag: disease state

tag: gender

tag: age

tag: metavir

tag: edmonson

tag: etiology


title: infected_1d|experiment_1|replicate_3

description: mid time point


title: P4

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: sample67

tag: disease


title: P5

tag: tissue

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: setd2 mutations


title: sample68


title: sample72

value: tumor of stomach


title: CHC196T

tag: disease state

value: Solid Tumor

tag: gender

tag: age

tag: metavir

tag: edmonson

value: w/o ETIOLOGY


title: sample66


title: infected_1d|experiment_3|replicate_2

description: mid time point

tag: cell line

tag: infectious agent


title: P3

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: pgr status

value: Negative

tag: erbb2 status

tag: nottingham grade

tag: erbb2 mutations


title: CHC037T

tag: tissue

value: Male

tag: etiology


title: CHC1196T

value: III-IV

value: HBV


title: CHC173T

value: HM


title: infected_1d|experiment_3|replicate_1

description: mid time point

value: Mycobacterium tuberculosis (Mtb)


title: infected_1d|experiment_2|replicate_2

description: mid time point


title: CHC1199T


title: CHC1055T

value: Al


title: sample65

tag: disease

value: long-lived individuals


title: infected_3d|experiment_3|replicate_2

description: mid time point


title: CHC882T

tag: disease state


title: infected_1d|experiment_1|replicate_2

description: mid time point


title: sample64


title: sample63

value: pancreatitis


title: P2

value: primary breast tumor

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

value: Normal

tag: rna-seq subtype hu

tag: er status

tag: tumor cell content (1

tag: lymphocyte content (1

tag: map3k1 mutations

tag: pik3ca mutations

tag: smad4 mutations


title: sample62

value: lung cancer


title: infected_1d|experiment_2|replicate_1

description: mid time point

tag: cell line

tag: infectious agent


title: sample61


title: CHC794T

value: Hepatocellular Carcinoma

tag: gender

tag: age

tag: metavir

tag: edmonson


title: infected_1d|experiment_1|replicate_1

description: mid time point


title: sample59

tag: disease

value: others


title: G13D_3_9965581010_L.mean

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description:
Gene expression data from human mammary epithelial cells
SAMPLE 12

hyb_protocol: Subsequent steps include array hybridization, washing, blocking, and streptavidin-Cy3 staining as recommended by the manufacturer (Illumina).

scan_protocol: Scanning was performed on an iScan Scanner as recommended by the manufacturer using default settings. The software used was the GenomeStudio software.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: MCF10A cell line

label_protocol: A standard assay protocol was used for sample preparation and labeling [first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides] (Illumina).

growth_protocol: The MCF10A cell line was obtained from the American Type Culture Collection (CRL-10317) and maintained at 37°C with 5% CO2. Cells were grown in DMEM/F12 (Invitrogen) supplemented with 5% horse serum (Invitrogen), 20 ng/ml EGF (Peprotech), 0.5 mg/ml hydrocortisone (Sigma), 100 ng/ml cholera toxin (Sigma), 10 µg/ml insulin (Gibco), and 1x penicillin/streptomycin (PAA Laboratories). Cells were fed twice a week and grown to 70% confluency before subculturing. Briefly, cells were washed once with PBS (Biochrom) and incubated with trypsin (Invitrogen) for 15-20 minutes. Completely detached cells were resuspended in complete medium and centrifuged at 1,500 rpm for 3 minutes. Cell pellets were diluted 1:5.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen).

treatment_protocol: The KRAS cDNA in the pDONR221 vector (Invitrogen) was generated, and sequence variants (KRAS-G12D and -G13D) were generated using the Quik Change XL Site-Directed Mutagenesis Kit (Stratagene), and mutations were confirmed by direct sequencing. cDNAs were cloned into the pLenti6.2/V5-DEST lentiviral vector (Invitrogen). Generation of lentiviral particles and lentiviral transduction of MCF10A cells were performed, and infected cells were selected with 10 µg/ml blasticidin (Invitrogen). For the generation of clones, stably transduced MCF10A cells were diluted and seeded in 96-well plates, and wells containing only one cell were marked. Cell lines that grew out from single cells were further investigated.

tag: transduction


title: G12D_3_9965581010_I.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 9


title: G13D_1_9965581010_J.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 10


title: sample60


title: uninfected_3d|experiment_3|replicate_3

description: mid time point


title: uninfected_3d|experiment_2|replicate_3

description: mid time point


title: P1

tag: tissue

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype hu

value: LumB

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

value: Positive

tag: pgr status

tag: erbb2 status

tag: nottingham grade


title: uninfected_3d|experiment_1|replicate_3

description: mid time point


title: CHC909T

tag: disease state

value: Solid Tumor

tag: etiology

value: w/o ETIOLOGY


title: CHC793T

value: Male

value: III-IV


title: CHC736T


title: G12D_1_9965581010_G.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 7


title: sample58

value: ductal adenocarcinoma


title: G13D_2_9965581010_K.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 11


title: G12D_2_9965581010_H.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 8


title: uninfected_3d|experiment_3|replicate_2

description: mid time point

tag: cell line

tag: infectious agent


title: sample57


title: CHC046T

tag: gender

value: Female

tag: age

value: HBV


title: CHC254T

tag: metavir

tag: edmonson

value: HBV HCV


title: sample55

tag: disease

value: normal


title: CHC451T

tag: tissue

value: I-II

value: Al. HCV


title: CHC211T

value: Al


title: WT_2_9965581010_E.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 5

tag: transduction

value: wild type KRAS


title: uninfected_3d|experiment_2|replicate_2

description: mid time point


title: uninfected_3d|experiment_1|replicate_2

description: mid time point


title: WT_3_9965581010_F.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 6


title: sample54


title: WT_1_9965581010_D.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 4


title: EV_3_9965581010_C.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 3

value: empty vector


title: sample53

value: others


title: Caco2-siRNA-control2-rep2

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

description:
101263-11
replicate 2

hyb_protocol: 50 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4 as per manufacturer's instructions.

scan_protocol: The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.

data_processing: Data were processed using R/Bioconductor (the lumi package), Raw data were transformed using a Variance Stabilizing Transformation, and normalized with the quantile normalization algorithm. Probes were selected which fulfilled the criteria of Illumina probe detection p-value of <0.01.

source_name: Caco-2 Control siRNA 2

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate Biotin labeled (biotin-16-UTP), amplified cRNA starting from 200ng total RNA.

growth_protocol: Human epithelial colonic adenocarcinoma, Caco-2, cells were grown in Dulbeco’s Modified Eagle medium, containing 10% (v/v) fetal calf serum; 60 μg/ml gentamycin and 1% (v/v) non essential amino acids (Sigma).

extract_protocol: Total RNA isolated using Pure Link RNAmini kit [Ambion] following manufacturer’s protocol, RNA integrity checked using Agilent Bioanalyzer.

treatment_protocol: Cells were transfected with oligonucleotides using lipofectamine RNAiMAX

tag: sirna

value: Dhamracon negative siGENOME Non-Targeting siRNA


title: sample56

value: pancreatitis


title: CHC961T

value: Hepatocellular Carcinoma

value: Solid Tumor


title: Caco2-siRNA-control2-rep3

description:
101263-12
replicate 3

value: Human epithelial colonic adenocarcinoma, Caco-2


title: CHC1053T

value: Male

value: III-IV


title: uninfected_3d|experiment_3|replicate_1

description: mid time point


title: CHC1192T


title: uninfected_3d|experiment_2|replicate_1

description: mid time point


title: uninfected_3d|experiment_1|replicate_1

description: mid time point


title: CHC889T

value: HM METAB


title: uninfected_2d|experiment_3|replicate_3

description: mid time point


title: EV_2_9965581010_B.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 2


title: EV_1_9965581010_A.mean

description:
Gene expression data from human mammary epithelial cells
SAMPLE 1


title: sample52


title: sample51

value: ductal adenocarcinoma


title: CHC1062T

value: HM


title: uninfected_2d|experiment_2|replicate_3

description: mid time point


title: Caco2-siRNA-control2-rep1

description:
101263-10
replicate 1


title: sample50


title: sample49


title: sample47

value: normal


title: uninfected_2d|experiment_1|replicate_3

description: mid time point


title: sample46


title: sample48


title: CHC339T

value: Female

value: I-II

value: HBV


title: uninfected_2d|experiment_3|replicate_2

description: mid time point


title: Caco2-siRNA2-rep2

description:
101263-08
replicate 2

source_name: Caco-2 ZNF658 siRNA 2

value: siRNA2 (Dhamacon)


title: Caco2-siRNA-control1-rep3

description:
101263-06
replicate 3

source_name: Caco-2 Control siRNA 1

value: Sense Control siRNA (Ambion)


title: CHC398T


title: sample45


title: uninfected_2d|experiment_2|replicate_2

description: mid time point


title: CHC080T

value: Al. HBV HCV


title: Caco2-siRNA2-rep3

description:
101263-09
replicate 3


title: uninfected_2d|experiment_1|replicate_2

description: mid time point


title: CHC203T

value: Al


title: uninfected_2d|experiment_3|replicate_1

description: mid time point


title: uninfected_2d|experiment_2|replicate_1

description: mid time point


title: uninfected_2d|experiment_1|replicate_1

description: mid time point


title: CHC725T


title: CHC239T


title: Caco2-siRNA-control1-rep2

description:
101263-05
replicate 2


title: Caco2-siRNA2-rep1

description:
101263-07
replicate 1


title: CHC050T


title: Caco2-siRNA1-rep3

description:
101263-03
replicate 3

source_name: Caco-2 ZNF658 siRNA 1

value: siRNA1 (Ambion)


title: sample44


title: uninfected_1d|experiment_2|replicate_3

description: mid time point


title: sample42


title: Caco2-siRNA1-rep2

description:
101263-02
replicate 2


title: sample41


title: uninfected_1d|experiment_3|replicate_3

description: mid time point


title: CHC1185T

value: Hepatocellular Carcinoma

value: Al. HBV


title: CHC1010T

value: Solid Tumor


title: sample40


title: Caco2-siRNA-control1-rep1

description:
101263-04
replicate 1

value: Human epithelial colonic adenocarcinoma, Caco-2


title: uninfected_1d|experiment_3|replicate_2

description: mid time point


title: Caco2-siRNA1-rep1

description:
101263-01
replicate 1


title: CHC891T

value: III-IV

value: w/o ETIOLOGY


title: uninfected_1d|experiment_1|replicate_3

description: mid time point


title: sample39

value: multiple sclerosis


title: uninfected_1d|experiment_2|replicate_2

description: mid time point


title: sample43


title: uninfected_1d|experiment_3|replicate_1

description: mid time point


title: Pre_Ab_only-Pass8-B

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ.

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset. After filtering probes, quantile normalization was applied across all arrays. Mixed-effects ANOVA was performed on the normalized log2 expression estimates to test for mRNA expression differences, with cell culture passage number used as the random effect. A p-value of 0.05 was used for the statistical significance cutoff, after adjusting for the familywize error rate (FWER) using Benjamini-Hochberg method to account for multiple testing. Statistical analysis was performed using JMP/Genomics software version 6.0.

source_name: Primary lung fibroblasts (ATCC CCL-75), TNF/IL17, anti-Ra2 Ab, no stimulation

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion), 300 nanograms total RNA input.

growth_protocol: Lung fibroblasts were grown in DMEM supplemented with 10% heat inactivated fetal bovine serum and subcultured as per ATCC recommendation. For the experiment, cells were seeded in 12 well plates and rested overnight before further treatment.

extract_protocol: RNA was purified by Qiagen RNeasy kit.

treatment_protocol: Lung fibroblasts were first incubated with TNF/IL-17 for 72 hours to induce high IL-13Ra2 expression and some wells were treated with a highly selective neutralizing anti-human IL-13Ra2 monoclonal antibody during the last 1 hour. Subsequently, the wells were washed with media, and treated with IL-13 for 20 hours.

tag: gts biosample_id

value: CCL-75 (ATCC)

tag: cell type

value: lung fibroblast cell line

tag: cell culture passage

tag: stimulation

tag: pre-treatment-cytokine

tag: pre-treatment-antibody

value: anti-Ra2 Ab

tag: technical replicate

value: B


title: CHC434T

tag: disease state

value: Female

tag: etiology


title: Pre_Ab_only-Pass8-A

tag: cell line

value: A


title: uninfected_1d|experiment_1|replicate_2

description: mid time point

tag: infectious agent


title: CHC1044T

tag: gender

value: Male

tag: age

tag: metavir


title: Pre_Ab_IL13-Pass8-A

source_name: Primary lung fibroblasts (ATCC CCL-75), TNF/IL17, anti-Ra2 Ab, IL13 stimulation


title: sample38

tag: disease


title: uninfected_1d|experiment_2|replicate_1

description: mid time point


title: CHC327T

tag: tissue

tag: edmonson

value: I-II

value: HCV


title: CHC250T

value: HBV HCV


title: CHC235T

value: Hepatocellular Carcinoma


title: Pre_Ab_IL13-Pass8-B

tag: gts biosample_id


title: sample35


title: sample34


title: CHC228T


title: Pre_IL13-Pass8-B

source_name: Primary lung fibroblasts (ATCC CCL-75), TNF/IL17, no Ab, IL13 stimulation

tag: cell type


title: sample33


title: sample36


title: sample32


title: sample31


title: Pre_only-Pass8-B

source_name: Primary lung fibroblasts (ATCC CCL-75), TNF/IL17, no Ab, no stimulation

tag: cell culture passage


title: uninfected_18h|experiment_3|replicate_2

description: intermediate time point


title: CHC934N.rep3

source_name: Non tumor liver

value: Non tumor liver


title: CHC934N.rep2


title: uninfected_18h|experiment_3|replicate_1

description: intermediate time point


title: uninfected_18h|experiment_3|replicate_3

description: intermediate time point


title: uninfected_1d|experiment_1|replicate_1

description: mid time point


title: CHC932N


title: CHC934N


title: CHC012T

value: Solid Tumor

value: HBV


title: Pre_IL13-Pass8-A

tag: stimulation


title: Control-Pass8-B

source_name: Primary lung fibroblasts (ATCC CCL-75), no cytokine, no Ab, no stimulation

tag: pre-treatment-cytokine


title: uninfected_6h|experiment_3|replicate_3

description: intermediate time point


title: IL13-Pass8-B

source_name: Primary lung fibroblasts (ATCC CCL-75), no cytokine, no Ab, IL13 stimulation

tag: pre-treatment-antibody


title: Control-Pass8-A

tag: technical replicate


title: Pre_Ab_only-Pass6-B


title: CHC932N.rep2

tag: disease state


title: uninfected_6h|experiment_3|replicate_1

description: intermediate time point


title: uninfected_6h|experiment_3|replicate_2

description: intermediate time point


title: IL13-Pass8-A


title: Pre_Ab_only-Pass6-A


title: uninfected_18h|experiment_2|replicate_3

description: intermediate time point


title: sample30


title: CHC591N.rep3


title: sample29


title: sample28


title: sample26


title: sample24


title: uninfected_18h|experiment_2|replicate_2

description: intermediate time point


title: CHC591N


title: CHC562N


title: Pre_Ab_IL13-Pass6-A


title: uninfected_18h|experiment_2|replicate_1

description: intermediate time point


title: Pre_IL13-Pass6-B


title: Pre_IL13-Pass6-A


title: CHC469N


title: Pre_Ab_IL13-Pass6-B


title: uninfected_6h|experiment_2|replicate_2

description: intermediate time point


title: uninfected_6h|experiment_2|replicate_3

description: intermediate time point


title: uninfected_6h|experiment_2|replicate_1

description: intermediate time point


title: uninfected_18h|experiment_1|replicate_2

description: intermediate time point


title: Control-Pass6-B


title: Pre_only-Pass6-B


title: CHC591N.rep2


title: TIG-3 iPSC #10-2

city: Hiroshima City

first: Akira

last: Shimamoto

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Department of Cellular and Molecular Biology

country: Japan

institute: Hiroshima University, Graduate School of Biomedical & Health Sciences

description: Gene expression data from normal human fibroblast-derived iPSCs

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

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

data_processing: The data were analyzed with GC-RMA (robust multiarray average) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Normal human fibroblast-derived iPSCs

label_protocol: Cy3-cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was prepared from WS fibroblasts, WS iPSCs, TIG-3 iPSCs (normal) and human ESCs using RNeasy spin columns (Qiagen) according to the manufacturer’s instructions.

value: Fibroblasts


title: Pre_only-Pass6-A


title: human ESCs KhES-2

description: Gene expression data from normal human embryonic stem cells

source_name: Normal human embryonic stem cells

value: Blastocyst


title: sample27

value: multiple sclerosis


title: uninfected_18h|experiment_1|replicate_3

description: intermediate time point


title: sample21


title: sample22


title: uninfected_18h|experiment_1|replicate_1

description: intermediate time point


title: Control-Pass6-A

value: CCL-75 (ATCC)


title: WS iPSC #34

description: Gene expression data from Werner syndrome patient-specific iPSCs

source_name: Werner syndrome patient-specific iPSCs


title: WS fibroblast A0031

description: Gene expression data from fibroblasts derived from Werner syndrome patient

source_name: Fibroblasts derived from Werner syndrome patient

value: Skin


title: sample23

source_name: RNA from blood


title: sample20


title: IL13-Pass6-B

value: lung fibroblast cell line


title: sample37


title: sample19


title: sample18


title: sample25


title: sample17

value: normal


title: sample16

value: lung cancer


title: IL13-Pass6-A

value: A


title: uninfected_6h|experiment_1|replicate_3

description: intermediate time point


title: PC3 culture Repeat 3

city: Rochester

first: Chao

last: Xie

state: NY

address: 601 Elmwood Ave. Box665

department: Orthopaedics

institute: University of Rochester

description: CXIE 4.3

hyb_protocol: A hybridization cocktail was prepared according to GeneChip® Hybridization that including the fragmented target, and probe array controls. It is then hybridized to the probe array during a 16-hour incubation. The detailed hybridization process used for this study is described in the sections of manufacture’s instructions.

scan_protocol: The GeneChip® Scanner 3000 7G was used following manufacture’s scan protocol.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
The 'full_data_matrix.txt' contains sample group average, fold-change, and t-test results.

source_name: pure PC3 cells

label_protocol: Synthesis of biotin-labeled cDNA fragments for target labeling assay were following manufacture’s instruction. Briefly, total RNA was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to GeneChip expression arrays.

growth_protocol: The base medium for renal cell carcinoma cells (786-O) and PC3 cells were cultured with ATCC-formulated RPMI1640 and F-12K culture medium, respectively. Primary myoblast were isolated from 5-day-old C57BL/6-Tg GFP neonate mice limbs that were digested using collagenase/dispase/CaCl2, and purified and enriched culture using F-10-based primary myoblast growth medium. All cancer cells or myoblast were in a 370C, 5% CO2 incubator with medium changes every 3 days. Myoblast were cultured in enriched media for up to 2 weeks with the F-10-based primary myoblast growth medium made with Ham’s F-10 nutrient mixture with 20% fetal bovine serum (FBS), 2.5μg/ml basic fibroblast growth factor (bFGF) and 100 U/ml penicillin/streptomycin.

extract_protocol: Qiagen RNeasy mini kit (Qiagen 74104) was used to extract total RNA according to the manufacturer's instructions, and RNA quality was checked on the Agilent 2100 Bioanalyzer. The RNA integrity number (RIN) was 10 (B.02.05) and the rRNA ratio (28s/18s) that checked at 260 and 280 nm were 1.9-2.1 in all samples.

treatment_protocol: Co-cultures were performed in transwell culture plates.  A total 3x104 cells of RCC or PC3 were pre-seeded into the bottom of the 12-well culture dish for 6 hours in their growth culture medium.  Then 1x104 myoblast cells were added to the top chamber, and the co-culture system was incubated at 370C, 5% CO2 for 12 hours prior to RNA extraction.

value: human prostate carcinoma cell

tag: co-cultured with


title: PC3 culture Repeat 2

description: CXIE 4.2

tag: cell line


title: uninfected_6h|experiment_1|replicate_2

description: intermediate time point

tag: infectious agent


title: sample14


title: PC3 culture Repeat 1

description: CXIE 4.1


title: Myoblast/PC3 co-culture Repeat 2

description: CXIE 3.2

source_name: 1:1 co-culture of myoblasts with PC

value: murine primary myoblast

tag: myoblast source

value: 5-day-old C57BL/6-Tg GFP neonatal mouse limbs


title: infected_18h|experiment_3|replicate_3

description: intermediate time point

value: Mycobacterium tuberculosis (Mtb)


title: infected_18h|experiment_3|replicate_1

description: intermediate time point


title: infected_18h|experiment_3|replicate_2

description: intermediate time point


title: infected_6h|experiment_3|replicate_3

description: intermediate time point


title: uninfected_6h|experiment_1|replicate_1

description: intermediate time point


title: Myoblast/PC3 co-culture Repeat 1

description: CXIE 3.1


title: D53 gamma

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

scan_protocol: BeadChips were scanned using Illumina HiScan.

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.3

source_name: SCLC cell line

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

growth_protocol: Cells were grown as suspension or partially attached monolayer culture in RPMI 1640 medium supplemented with 5-10% fetal bovine serum at 37 ˚C under humidified condition of 5% CO2 and 95% air.

extract_protocol: Total RNA was isolated using RNeasy kits (QIAGEN, Valencia, CA) according to manufacturer instructions.

treatment_protocol: Cells were seeded in 96-well plates at approximately 1-2 x 104 cells per well. After 48 hours, exponentially growing cells were treated by continuous exposure to vehicle, single agent or combinations of specific drugs of interest for 48-72 hours. The surviving cell population following drug exposure was detected using MTS [(3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium)/ phenazine methosulfate (PMS)] colorimetric assay, Promega (Madison, WI) according to the manufacturer’s protocol.

tag: treatment

value: 2 GY gamma-radiation

tag: cytotoxicity

value: YES


title: D114 gamma


title: D153 C+50

value: Cisplatin (4.7uM) +ABT888 (50uM)


title: 786-O culture Repeat 3

description: CXIE 2.3

source_name: pure 786-O cells

value: human renal carcinoma cell


title: 786-O culture Repeat 2

description: CXIE 2.2


title: Myoblast/PC3 co-culture Repeat 3

description: CXIE 3.3


title: D153 gamma


title: sample13

tag: disease


title: sample15


title: sample12


title: H526 gamma


title: infected_6h|experiment_3|replicate_2

description: intermediate time point


title: sample11


title: H209 gamma


title: infected_6h|experiment_3|replicate_1

description: intermediate time point


title: sample10


title: sample9


title: D153 C+5

value: Cisplatin (4.7uM) +ABT888 (5uM)


title: 786-O culture Repeat 1

description: CXIE 2.1


title: Myoblast/786-O co-culture Repeat 3

description: CXIE 1.3

source_name: 1:1 co-culture of myoblast with 786-O cells


title: Myoblast/786-O co-culture Repeat 2

description: CXIE 1.2


title: D153 C+0

value: Cisplatin (4.7uM)


title: H187 gamma


title: infected_18h|experiment_2|replicate_3

description: intermediate time point


title: infected_18h|experiment_2|replicate_1

description: intermediate time point


title: infected_18h|experiment_2|replicate_2

description: intermediate time point


title: sample8


title: sample7


title: H146 gamma


title: Myoblast/786-O co-culture Repeat 1

description: CXIE 1.1


title: D153 A50


title: infected_6h|experiment_2|replicate_2

description: intermediate time point


title: H128 gamma


title: sample6


title: sample5


title: infected_6h|experiment_2|replicate_1

description: intermediate time point


title: sample4


title: sample3


title: infected_18h|experiment_1|replicate_3

description: intermediate time point


title: D153 A5


title: H69 gamma


title: infected_6h|experiment_2|replicate_3

description: intermediate time point


title: Bechets_disease-CD14_cells-replicate_7

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

hyb_protocol: per Affymetrix instructions using their GeneChip® 450 fluidics station

scan_protocol: using the Affymetrix GeneChip® 3000 7G scanner

data_processing: Raw microarray data were processed using Affymetrix Expression Console version 1.1 (http://www.affymetrix.com/browse/level_seven software_products_only.jsp?productId =131414&categoryId=35623#) to extract gene level intensities using RMA method. The subsequent analysis was performed using the R statistical environment (http://www.R-project.org) and BioConductor packages [36]. Quality control of the data included a comparison of boxplots of gene expression level among the conditions, and hierarchical clustering of condition-specific gene expression profiles to identify potential outliers. The data were quantile normalized and deposited in GEO along with raw .CEL files. (All data conform with the Minimal Information About a Microarray Experiment (MIAME) guidelines.  Differentially expressed probes were identified by Significance Analysis of Microarrays (SAM) [37]. A fold change cutoff of 1.5 was imposed to filter out less differentially expressed probes, and the delta was adjusted to keep false discovery rate <10%. Owing to the fact that some probes may detect expression of different exons, probe lists were converted to gene lists keeping all gene names. Gene lists were analyzed by Ingenuity Pathway Analysis (IPA; Ingenuity® Systems, Redwood City, CA, http://www.ingenuity.com), a web-based bioinformatics tool.  Each gene list was tested against the full Affymetrix Human Gene 1.0 ST Array dataset to identify significantly overrepresented functions and canonical pathways as compared to the same number of randomly selected genes. The most significant functions and canonical pathways were selected and genes overrepresented in the functions and pathways were identified.

source_name: CD14, Bechet's disease

label_protocol: per Affymetrix instructions

growth_protocol: Nine patients with Behcet’s Disease followed in the multi-disciplinary Behcet’s Clinic of Marmara University Hospital and 9 healthy controls were studied in the first phase of the study for the microarray analysis of CD14+ monocyte and CD4+ T lymphocytes. In the second phase, when flow cytometric analysis of STAT3 and pSTAT3 levels were investigated, a larger group of patients with BD (n=26, 15 F/11 M, mean age: 35.3±9.1 years) and healthy controls (n=26, 19 F/7 M, mean age: 33.9 ±10.5 years) were recruited. All patients fulfilled the ISG Criteria for the classification of BD and had a mean disease duration of 6.9±4.6 years [35]. Oral ulcers were present in all patients, 96% (n=25) had cutaneous lesions, 81% (n=21) had genital ulcers, 31% (n=8) had musculoskeletal involvement and 50% (n=13) had pathergy positivity. Among major manifestations, 19% (n=5) of the patients had vascular, 12% (n=3) had ocular and 4% (n=1) had central-nervous system disease. Ten patients (38%) were under immunosuppressive treatment (prednisolone >10 mg/d and/or azathioprine). Patients studied for microarray analysis had similar characteristics to the whole group (9/9 patients with mucocutaneous, 3/9 with musculoskeletal, 2/9 with vascular and 1/9 with ocular manifestations). All patients had at least one active BD-associated disease manifestation at the time of blood sampling. The study was approved by the local Ethical Committee of Marmara University and informed consent was taken.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood samples using density gradient centrifugation (Amersham Biosciences, Uppsala, Sweden). Monocytes and T-helper cells were purified using magnetic bead separation from PBMCs (Miltenyi Biotec, Cologne, Germany). The purity of isolated cell populations was confirmed by flow cytometry analysis using fluorochrome-conjugated antibodies against CD4 for T-helper lymphocytes and CD14 for monocytes and was over 90% for both cell populations. Total RNA of purified cell populations was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) according to the protocol recommended by the manufacturer. Total RNA (>50 ng/ul (80-156)) from monocytes was available from all 9 patients and 9 controls, and from CD4+ T cells from all 9 patients and 3 controls. Total RNA was then hybridized to GeneChip Human Genome U133 Plus 2.0 microarrays (Affymetrix, Santa Clara, CA, USA) following manufacturer's protocols.

tag: disease status


title: sample2


title: Bechets_disease-CD14_cells-replicate_8


title: Bechets_disease-CD14_cells-replicate_6


title: Bechets_disease-CD14_cells-replicate_9


title: Bechets_disease-CD14_cells-replicate_5


title: sample1


title: infected_18h|experiment_1|replicate_2

description: intermediate time point


title: infected_18h|experiment_1|replicate_1

description: intermediate time point


title: Bechets_disease-CD14_cells-replicate_2


title: Bechets_disease-CD14_cells-replicate_4


title: infected_6h|experiment_1|replicate_3

description: intermediate time point


title: D153 Con

value: Vehicle

value: NO


title: D53 C+50

value: Cisplatin (12.5uM) +ABT888 (50uM)


title: Healthy-CD14_cells-replicate_9

source_name: CD14, healthy

value: healthy


title: sample1049

value: others


title: D53 C+5

value: Cisplatin (12.5uM) +ABT888 (5uM)


title: sample1048


title: infected_6h|experiment_1|replicate_1

description: intermediate time point


title: Bechets_disease-CD14_cells-replicate_1


title: infected_90min|experiment_5|replicate_3

description: early time point


title: Healthy-CD14_cells-replicate_8


title: D114 C+5

value: Cisplatin (8uM) +ABT888 (5uM)


title: sample1047


title: sample1046


title: D114 C+0

value: Cisplatin (8uM)


title: sample1045


title: infected_90min|experiment_4|replicate_3

description: early time point


title: infected_90min|experiment_3|replicate_3

description: early time point


title: sample1044


title: infected_90min|experiment_2|replicate_3

description: early time point


title: Healthy-CD14_cells-replicate_5


title: Healthy-CD14_cells-replicate_7


title: infected_90min|experiment_1|replicate_3

description: early time point


title: D53 C+0

value: Cisplatin (12.5uM)


title: sample1043

value: Wilms Tumor


title: infected_90min|experiment_4|replicate_2

description: early time point

value: Mycobacterium tuberculosis (Mtb)


title: infected_90min|experiment_5|replicate_2

description: early time point


title: Healthy-CD14_cells-replicate_6


title: sample1042

value: Renal cancer


title: D53 A50

value: YES


title: D114 A5


title: Healthy-CD14_cells-replicate_3


title: D114 A50


title: D53 A5


title: Healthy-CD14_cells-replicate_4


title: D114 Con


title: infected_6h|experiment_1|replicate_2

description: intermediate time point


title: infected_90min|experiment_2|replicate_2

description: early time point


title: infected_90min|experiment_3|replicate_2

description: early time point


title: Healthy-CD14_cells-replicate_1


title: sample1041


title: Healthy-CD14_cells-replicate_2


title: sample1040


title: sample1039


title: sample1038


title: sample1037


title: sample1036


title: H209 C+50

value: Cisplatin (14.2uM) +ABT888 (50uM)


title: D53 Con


title: infected_90min|experiment_5|replicate_1

description: early time point


title: H526 C+50

value: Cisplatin (0.4uM) +ABT888 (50uM)


title: Bechets_disease-CD4_cells-replicate_6

source_name: CD4, Bechet's disease


title: infected_90min|experiment_4|replicate_1

description: early time point


title: infected_90min|experiment_3|replicate_1

description: early time point


title: infected_90min|experiment_1|replicate_1

description: early time point


title: Bechets_disease-CD4_cells-replicate_8


title: H526 C+0

value: Cisplatin (0.4uM)


title: Bechets_disease-CD4_cells-replicate_7


title: Bechets_disease-CD4_cells-replicate_3


title: H526 A50


title: H526 C+5

value: Cisplatin (0.4uM) +ABT888 (5uM)


title: sample1034


title: Bechets_disease-CD4_cells-replicate_4


title: Bechets_disease-CD4_cells-replicate_5


title: infected_90min|experiment_2|replicate_1

description: early time point


title: H209 C+5

value: Cisplatin (14.2uM) +ABT888 (5uM)


title: infected_60min|experiment_5|replicate_3

description: early time point


title: Bechets_disease-CD4_cells-replicate_9


title: Bechets_disease-CD4_cells-replicate_2


title: infected_60min|experiment_4|replicate_3

description: early time point


title: sample1035


title: H209 C+0

value: Cisplatin (14.2uM)


title: H209 A50


title: sample1033


title: sample1032


title: sample1031


title: H526 A5


title: sample1029


title: infected_60min|experiment_3|replicate_3

description: early time point


title: sample1028


title: H526 Con

value: Vehicle

value: NO


title: Healthy-CD4_cells-replicate_3

source_name: CD4, healthy

value: healthy


title: H209 A5


title: infected_60min|experiment_1|replicate_3

description: early time point


title: H187 C+50

value: Cisplatin (1.7uM) +ABT888 (50uM)


title: Healthy-CD4_cells-replicate_2


title: infected_60min|experiment_2|replicate_3

description: early time point


title: Healthy-CD4_cells-replicate_1


title: H209 Con


title: D114 C+50

value: Cisplatin (8uM) +ABT888 (50uM)


title: sample1027


title: Bechets_disease-CD4_cells-replicate_1


title: infected_60min|experiment_5|replicate_2

description: early time point


title: infected_60min|experiment_4|replicate_2

description: early time point


title: sample1030


title: sample1026


title: Liv_GW_3

city: Los Angeles

first: Cynthia

last: Hong

state: CA

address: 675 Charles E Young Dr. S

institute: UCLA

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix Standard Protocol

data_processing: MAS 5.0

organism: Macaca fascicularis

source_name: Non human primate

label_protocol: Affymetrix Standard Protocol

extract_protocol: RNA was isolated from liver tissue RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: LXR

tag: tissue

value: Liver


title: infected_60min|experiment_3|replicate_2

description: early time point


title: H146 C+50

value: Cisplatin (5.2uM) +ABT888 (50uM)


title: H187 C+5

value: Cisplatin (1.7uM) +ABT888 (5uM)


title: Liv_GW_1


title: infected_60min|experiment_2|replicate_2

description: early time point

value: Mycobacterium tuberculosis (Mtb)


title: Liv_Veh_3

value: vehicle


title: Liv_GW_2


title: sample1025

value: Wilms Tumor


title: sample1024


title: sample1023

value: prostate cancer


title: H187 C+0

value: Cisplatin (1.7uM)

value: YES


title: sample1021


title: H146 C+0

value: Cisplatin (5.2uM)


title: infected_60min|experiment_1|replicate_2

description: early time point


title: infected_60min|experiment_4|replicate_1

description: early time point


title: sample1022


title: infected_60min|experiment_3|replicate_1

description: early time point


title: sample1019


title: sample1020

value: benign prostate hyperplasia


title: Liv_Veh_2


title: H146 A50


title: OCI-AML3-200 nM BC2059-8 hours

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1400 Holcombe Blvd., Unit 428

institute: MD Anderson Cancer Center

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning of the chip is conducted using an Affymetrix GeneChip® Scanner 3000 7G with autoloader.

data_processing: Data were analyzed using Affy Expression Console using MAS5 algorithm

source_name: AML cell line, treated BC2059, 8 hours

label_protocol: Cy3 labeled cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Roche High Pure RNA isolation kit with on-column DNAse I digestion. Elution in RNAse free water.

value: lymphocyte


title: H187 A50


title: OCI-AML3-untreated- 8 hours

source_name: AML cell line, untreated, 8 hours


title: infected_60min|experiment_2|replicate_1

description: early time point


title: H146 A5


title: infected_60min|experiment_5|replicate_1

description: early time point


title: Liv_Veh_1


title: infected_60min|experiment_1|replicate_1

description: early time point


title: H187 A5


title: infected_30min|experiment_5|replicate_3

description: early time point


title: Primary AML-untreated-8 hours

source_name: AML blast cell, untreated, 8 hours

value: primary AML


title: infected_30min|experiment_4|replicate_3

description: early time point


title: Primary AML-200 nM BC2059-8 hours

source_name: AML blast cell, treated BC2059, 8 hours


title: HH + 0.1% FBS

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: Sample 3

hyb_protocol: Quiagen single amplification protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: HH_0.1% FBS

label_protocol: Quiagen single amplification protocol

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol

value: HH

value: cutaneous T-cell lymphoma (CTCL) cell line

tag: culture condition

value: 0.1% FCS without IL-32g for 40h


title: HH + 0.1% FBS + IL-32g 5ng/ml

description: Sample 4

source_name: HH_0.1% FBS + IL-32g 5ng/ml

tag: cell type

value: 0.1% FCS with 5ng/ml IL-32g for 40h


title: H146 Con

value: Vehicle

value: NO


title: H187 Con


title: sample1016

source_name: RNA from blood

value: others


title: sample1015


title: sample1018


title: sample1013


title: sample1017


title: infected_30min|experiment_2|replicate_3

description: early time point

value: Mycobacterium tuberculosis (Mtb)


title: H128 C+50

value: Cisplatin (14.5uM) +ABT888 (50uM)


title: MyLa + 0.1% FBS + IL-32g 5ng/ml

description: Sample 2

source_name: MyLa_0.1% FBS + IL-32g 5ng/ml

value: MyLa

value: Mycosis Fungoides (MF) cell line


title: H146 C+5

value: Cisplatin (5.2uM) +ABT888 (5uM)


title: infected_30min|experiment_5|replicate_2

description: early time point


title: sample1012

value: Wilms Tumor


title: infected_30min|experiment_3|replicate_3

description: early time point


title: sample1014


title: infected_30min|experiment_3|replicate_2

description: early time point


title: infected_30min|experiment_1|replicate_3

description: early time point


title: infected_30min|experiment_4|replicate_2

description: early time point


title: H69 C+5

value: Cisplatin (4.3uM) +ABT888 (5uM)

value: YES


title: H69 C+50

value: Cisplatin (4.3uM) +ABT888 (50uM)


title: H69 C+0

value: Cisplatin (4.3uM)


title: H128 C+5

value: Cisplatin (14.5uM) +ABT888 (5uM)


title: sample1010


title: MyLa + 0.1% FBS

description: Sample 1

source_name: MyLa_0.1% FBS


title: infected_30min|experiment_2|replicate_2

description: early time point


title: infected_30min|experiment_1|replicate_2

description: early time point


title: sample1011


title: sample1009


title: H69 A50

source_name: SCLC cell line


title: infected_30min|experiment_5|replicate_1

description: early time point


title: H128 A50


title: infected_30min|experiment_4|replicate_1

description: early time point


title: H128 A5


title: sample1007

value: prostate cancer


title: sample1008


title: H128 C+0

value: Cisplatin (14.5uM)


title: infected_30min|experiment_3|replicate_1

description: early time point


title: sample1005

value: psoriasis


title: sample1006


title: sample1004


title: H128 Con

value: Vehicle


title: infected_30min|experiment_2|replicate_1

description: early time point


title: sample1003


title: H69 Con

value: NO


title: REC-1: PBS-control_rep3

city: Penzberg

first: Helmut

last: Burtscher

address: Nonnenwald 2

institute: Roche Pharma

description: gene expression data

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and scaling mean as normalization method.

source_name: REC-1: PBS-control

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip 3' IVT Express Kit, 2008, Affymetrix).

growth_protocol: Mantle cell lymphoma cell lines were cultured at 37°C (5% CO2 in RPMI1640, 2mM L-glutamine and 20% fetal bovine serum).

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: MCL cells were treated with either obinutuzumab or rituximab or a combination of both at concentrations of 10 µg/ml each.

value: mantle cell lymphoma


title: REC-1: PBS-control_rep2

description: gene expression data


title: infected_30min|experiment_1|replicate_1

description: early time point

scan_protocol: Scanning of microarrays was performed with 5µm resolution, 16 bit and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

label_protocol: Total RNA labeling was performed with the one color Quick Amp Labeling Kit (Agilent Technologies)

value: Mycobacterium tuberculosis (Mtb)


title: H69 A5


title: infected_5min|experiment_5|replicate_3

description: early time point


title: sample1002


title: sample1001


title: REC-1: PBS-control_rep1

description: gene expression data


title: infected_5min|experiment_2|replicate_3

description: early time point


title: siKLF9_T3_24h_REP2

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

description: replicate 2

scan_protocol: Standard Illumina scanning protocol

data_processing: Unmodified microarray data obtained from GenomeStudio (Illumina) was background-subtracted and quantile-normalized using the lumi package within R

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

growth_protocol: HepG2 cells stably expressing Flag tagged TRβ were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum.

extract_protocol: RNA was extracted and prepared using Aurum Total RNA kit (Bio-Rad) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser

treatment_protocol: Cells were plated in 6-well plates and transfected with KLF9 or scramble siRNA. After three days cells were treated with 100 nM T3 for 0, 8 or 24 h..

tag: overexpression

value: flag TRβ

tag: sirna

value: Triiodothytonine

tag: time point


title: infected_5min|experiment_3|replicate_3

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: early time point

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA ( Agilent Technologies)

extract_protocol: 1. Preparation of Mtb infected THP-1 macrophages for RNA extraction/isolation: At different time-points following infection wash once the macrophage monolayer with RT PBS (Invitrogen, # 20012-043). Add 1 ml cold 4M GITC solution (Invitrogen, # 15577-018) per well and gently scrape the cells. Collect solution in 1 ml screw cap. Centrifuge at 12,000 × g for 10 min. at 4°C. Add 3 Vol. Trizol LS (Invitrogen, # 10296-010) to supernatant and homogenize (eukaryotic fraction). Store homogenate of eukaryotic fraction at -80°C freezer until further processed. Resuspend pellet by pipetting up and down in residual GITC. Add 1 ml Trizol (Invitrogen, # 15596-018) containing 20 g/ml linear acrylamide to the pellet (prokaryotic fraction). Use pipette to homogenate in Trizol. Store homogenate of prokaryotic pellet at -80°C freezer until further processed.  2. Isolation of total eukaryotic host RNA: Note:  process only 1ml from total homogenate, store remaining volume at –80°C for future processing. Thaw Trizol homogenate of eukaryotic fraction and incubate for 5 min. at RT (15 to 30°C). Add 0.2 ml of chloroform per 0.75 ml of Trizol LS for phase separation. Shake tubes vigorously by hand for 15 sec. and incubate them at RT for 5 min. Centrifuge at 12,000 × g for 15 min.at 4°C. Transfer the colorless aqueous (upper) phase to a clean tube (typical volume will be ~500 µl, assure not to carry over anything from the white interphase or the red phenol phase)


title: sample1000


title: REC-1: Isotype-control_rep2

description: gene expression data

source_name: REC-1: Isotype-control


title: infected_5min|experiment_1|replicate_3

description: early time point


title: siKLF9_T3_24h_REP1

description: replicate 1


title: REC-1: Isotype-control_rep3

description: gene expression data


title: sample999


title: siKLF9_T3_8h_REP2

description: replicate 2

value: 8 h


title: siKLF9_T3_24h_REP3

description: replicate 3


title: infected_90min|experiment_1|replicate_2

description: early time point


title: infected_5min|experiment_5|replicate_2

description: early time point


title: REC-1: GA101+Rituximab_rep2

description: gene expression data

source_name: REC-1: GA101+Rituximab


title: sample998


title: REC-1: Isotype-control_rep1

description: gene expression data


title: siKLF9_T3_8h_REP3

description: replicate 3


title: sample997


title: infected_5min|experiment_4|replicate_2

description: early time point


title: siKLF9_ctrl_REP3

description: replicate 3

value: 0 h


title: REC-1: GA101+Rituximab_rep1

description: gene expression data


title: siKLF9_T3_8h_REP1

description: replicate 1


title: siKLF9_ctrl_REP1

description: replicate 1


title: siKLF9_ctrl_REP2

description: replicate 2


title: REC-1: GA101+Rituximab_rep3

description: gene expression data


title: sample996

value: others


title: infected_5min|experiment_1|replicate_2

description: early time point


title: REC-1: Rituximab_rep2

description: gene expression data

source_name: REC-1: Rituximab


title: REC-1: Rituximab_rep1

description: gene expression data


title: sample995


title: REC-1: Rituximab_rep3

description: gene expression data


title: sample994


title: T3_24h_REP3

description: replicate 3

value: scramble


title: T3_24h_REP2

description: replicate 2


title: infected_5min|experiment_2|replicate_2

description: early time point


title: infected_5min|experiment_3|replicate_2

description: early time point


title: sample993


title: infected_5min|experiment_4|replicate_1

description: early time point


title: sample992


title: infected_5min|experiment_5|replicate_1

description: early time point


title: T3_24h_REP1

description: replicate 1


title: sample991


title: REC-1: GA101_rep3

description: gene expression data


title: T3_8h_REP3

description: replicate 3


title: infected_5min|experiment_3|replicate_1

description: early time point


title: JEKO-1: PBS-control_rep3

description: gene expression data

source_name: JEKO-1: PBS-control


title: infected_5min|experiment_2|replicate_1

description: early time point


title: JEKO-1: PBS-control_rep1

description: gene expression data


title: T3_8h_REP2

description: replicate 2


title: sample989


title: REC-1: GA101_rep1

description: gene expression data


title: ctrl_REP3

description: replicate 3


title: JEKO-1: PBS-control_rep2

description: gene expression data


title: T3_8h_REP1

description: replicate 1


title: REC-1: GA101_rep2

description: gene expression data


title: sample990


title: JEKO-1: Isotype-control_rep3

description: gene expression data

source_name: JEKO-1: Isotype-control


title: sample987


title: ctrl_REP2

description: replicate 2


title: sample988


title: uninfected_0min|experiment_5|replicate_3

description: early time point


title: sample986


title: sample985


title: JEKO-1: Isotype-control_rep1

description: gene expression data


title: uninfected_0min|experiment_4|replicate_3

description: early time point


title: ctrl_REP1

description: replicate 1


title: uninfected_0min|experiment_3|replicate_3

description: early time point


title: sample984


title: uninfected_0min|experiment_2|replicate_3

description: early time point


title: sample983


title: JEKO-1: GA101+Rituximab_rep3

description: gene expression data

source_name: JEKO-1: GA101+Rituximab


title: siYAP1&TAZ_3

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: SK Hep1_siYAP&TAZ_3

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: SK Hep1_siYAP&TAZ

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: human hepatic adenocarcinoma cells

tag: transfected with

value: siRNA targeting YAP1 and TAZ


title: JEKO-1: Isotype-control_rep2

description: gene expression data


title: uninfected_0min|experiment_1|replicate_3

description: early time point


title: siYAP1&TAZ_2

description: SK Hep1_siYAP&TAZ_2


title: JEKO-1: GA101+Rituximab_rep1

description: gene expression data


title: siYAP1&TAZ_1

description: SK Hep1_siYAP&TAZ_1


title: JEKO-1: GA101+Rituximab_rep2

description: gene expression data


title: siCon_3

description: SK Hep1_siLuc_3

source_name: SK Hep1_siLuc

value: control siRNA


title: siCon_2

description: SK Hep1_siLuc_2


title: uninfected_0min|experiment_5|replicate_2

description: early time point


title: uninfected_0min|experiment_4|replicate_2

description: early time point


title: uninfected_0min|experiment_3|replicate_2

description: early time point


title: sample982


title: siCon_1

description: SK Hep1_siLuc_1


title: JEKO-1: Rituximab_rep3

description: gene expression data

source_name: JEKO-1: Rituximab


title: JEKO-1: Rituximab_rep2

description: gene expression data


title: JEKO-1: Rituximab_rep1

description: gene expression data


title: infected_5min|experiment_1|replicate_1

description: early time point


title: sample980


title: sample981


title: sample978


title: sample977


title: sample979


title: Aorta Normal No.5

city: Shanghai

first: Sun

last: Pan

address: Fenglin Road 180

department: Department of Cardiac Surgery

country: China

institute: Zhongshan Hospital, Fudan University

description: SAMPLE 12

scan_protocol: Standard Illumina scanning protocol.

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

source_name: Aorta normal

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 QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: ascending aorta

tag: gender

value: male

value: normal


title: uninfected_0min|experiment_5|replicate_1

description: early time point


title: sample976

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..

value: lung cancer


title: uninfected_0min|experiment_2|replicate_2

description: early time point


title: uninfected_0min|experiment_1|replicate_2

description: early time point


title: JEKO-1: GA101_rep3

description: gene expression data

source_name: JEKO-1: GA101


title: Aorta Normal No.4

description: SAMPLE 11

tag: disease state


title: infected_5min|experiment_4|replicate_3

description: early time point


title: sample975


title: uninfected_0min|experiment_4|replicate_1

description: early time point


title: uninfected_0min|experiment_2|replicate_1

description: early time point


title: uninfected_0min|experiment_1|replicate_1

description: early time point


title: uninfected_0min|experiment_3|replicate_1

description: early time point


title: JEKO-1: GA101_rep1

description: gene expression data


title: HBL-2: PBS-control_rep1

description: gene expression data

source_name: HBL-2: PBS-control


title: Aorta Normal No.3

description: SAMPLE 7


title: Aorta Dissected No.7

description: SAMPLE 10

source_name: Aorta dissected

value: acute Stanford type A aortic dissection


title: Aorta Dissected No.6

description: SAMPLE 9


title: JEKO-1: GA101_rep2

description: gene expression data


title: Aorta Normal No.2

description: SAMPLE 6


title: Aorta Dissected No.5

description: SAMPLE 8

value: female


title: sample974

source_name: RNA from blood


title: sample973


title: sample972


title: sample971


title: HBL-2: Isotype-control_rep3

description: gene expression data

source_name: HBL-2: Isotype-control

value: mantle cell lymphoma


title: HBL-2: Isotype-control_rep1

description: gene expression data


title: Aorta Dissected No.4

description: SAMPLE 4


title: Aorta Normal No.1

description: SAMPLE 5


title: Aorta Dissected No.2

description: SAMPLE 2


city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

country: Canada

institute: CHU-Q, Centre de recherche-HDQ

description:
Sample 3
Gene expression comparison of siRNA-mediated TG+FIIB knockdown HeLa clone  vs control siRNA-transfected HeLa clone_3

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: control siRNA transfected HeLa cells

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: HeLa cells in DMEM medium with 5% fetal calf serum

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells (0.5.106) are electroporated with 1 microgram of siRNA. Next cells are plated  and grown for 70 hours before harvesting for RNA isolation

value: human cervical carcinoma cell line HeLa

tag: genotype/variation

value: control

source_name: TFIIB siRNA transfected HeLa cells

value: TFIIB knockdown


title: sample969


title: HBL-2: Isotype-control_rep2

description: gene expression data

tag: cell line


description:
Sample 2
Gene expression comparison of siRNA-mediated TG+FIIB knockdown HeLa clone  vs control siRNA-transfected HeLa clone_2


title: HBL-2: GA101+Rituximab_rep3

description: gene expression data

source_name: HBL-2: GA101+Rituximab


title: sample970


title: Aorta Dissected No.3

description: SAMPLE 3


title: HBL-2: PBS-control_rep2

description: gene expression data


title: HBL-2: GA101+Rituximab_rep2

description: gene expression data


title: Aorta Dissected No.1

description: SAMPLE 1


description:
Sample 4
Gene expression comparison of siRNA-mediated TG+FIIB knockdown HeLa clone  vs control siRNA-transfected HeLa clone_4


description:
Sample 1
Gene expression comparison of siRNA-mediated TG+FIIB knockdown HeLa clone  vs control siRNA-transfected HeLa clone_1


title: sample966


title: sample967


title: HBL-2: Rituximab_rep3

description: gene expression data

source_name: HBL-2: Rituximab


title: IOR/OS14 transfected with LSAMP open reading frame, clone 21

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

data_processing: The data was quantile normalisation in GenomeStudio

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

growth_protocol: The cells were grown in DMEM (Lonza) supplemented with 10 % FBS (Fisher Scientific, Waltham, MA, USA), GlutaMAX (Invitrogen, CA, USA) and Geneticin (Invitrogen) , at 37 °C in a humidified atmosphere with 5 % CO2.

extract_protocol: RNA was isolated using miRNeasy mini kit (Qiagen), according to the manufacturers’ instructions.

value: Male


title: HBL-2: GA101+Rituximab_rep1

description: gene expression data


title: sample964

value: chronic obstructive pulmonary disease (COPD)


title: HBL-2: PBS-control_rep3

description: gene expression data


title: HBL-2: Rituximab_rep2

description: gene expression data


title: HBL-2: GA101_rep3

description: gene expression data


title: Experiment 2

city: New Delhi

first: Pradeep

last: Sharma

email: praddybiotech@gmail.com, ravipathak@aol.in, raghuram98@hotmail.com, rvarshney@rediffmail.com, dwarakanathdrbs@gmail.com

state: Delhi

address: Lucknow Road, Timarpur

department: Division of radiation biosciences

country: India

institute: Institute of Nuclear medicine and allied sciences (INMAS, DRDO)

description: 2 Gy irradiated Head and neck squamous carcinoma_cultured cells after 24 hours, Biological replicate 1 of 3. VS. Pooled sample of 3 Biological replicates of combination (2-DG + 6-AN) treated irradiated (2 Gy) head and neck squamous carcinoma_cultured cells after 24hours

hyb_protocol: 825ng of cy3 labeled  samples and 825ng of cy5 labeled samples were pooled, fragmented and hybridized and data from these channels were used for comparison to test hybridizations of respective channels.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

data_processing: Data extraction done using Agilent Feature extraction software v 9.5.

label_protocol: The samples for Gene expression were labeled using Agilent Low RNA Input Linear amplification Kit (Part number:5184-3523).  Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 42°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dyes Cy3 CTP(Agilent) for control samples and Cy5 CTP(Agilent) for test samples were incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: KB (PE = 0.68) derived from head and neck squamous carcinoma was maintained as monolayer cultures at 37 ºC in a humidified CO2 incubator (5 % CO2, 95 % air). KB cells were maintained in high glucose DMEM supplemented with 10 % fetal bovine serum (FBS), HEPES (10 mM) and antibiotics (30 mg ml-1 penicillin G, 50 mg ml-1streptomycin and 2 mg ml-1 nystatin).

extract_protocol: RNA was extracted using Qiagen’s RNeasy minikit.

treatment_protocol: Monolayer KB, (1.0 × 106 cells were seeded in duplicate in 90 mm Petri dishes, each containing 8 ml of growth media) was grown for 24 h (exponential growth phase) in high glucose DMEM containing 10 % FBS. After 24 h of seeding,  6-AN (5 µM) and 2-DG (5 mM), obtained from SIGMA chemicals, were added to liquid-holding media (Hanks balanced salt solution, HBSS) just before irradiation (2 Gy) and removed after 4 h of incubation and fresh growth media was added to Petri dishes.

value: Head and neck squamous carcinoma


title: IOR/OS14 transfected with LSAMP open reading frame, clone 17

hyb_protocol: Standard Illumina hybridization protocol


title: IOR/OS14 transfected with LSAMP open reading frame, clone 16


title: sample965

value: prostate cancer


title: HBL-2: GA101_rep1

description: gene expression data


title: HBL-2: GA101_rep2

description: gene expression data


title: IOR/OS14 transfected with LSAMP open reading frame, clone 9


title: IOR/OS14 transfected with LSAMP open reading frame, clone 11


title: C175 CML BM CD34+ cells

city: Beijing

first: Lisheng

last: Wang

address: 27 Taiping Road

department: Experimental Hematology

institute: Beijing Institute of Radation Medicine

hyb_protocol: Microarray analysis of miRNA was performed using the G4470B human miRNA microarray 8x15K version 2.

scan_protocol: standard Agilent protocol

data_processing: The miRNA expression was log2 transformed after quantile normalization. The differential expression for miRNA and mRNA between PBSC and CML samples was identified by two–sample t-test using the LIMMA package in R and Bioconductor. Multiple-testing was adjusted for by calculating false discovery rate (FDR).

source_name: Bone Marrow

label_protocol: standard Agilent protocol

extract_protocol: Mononuclear cells of CML bone marrow and mobilized peripheral blood were prepared by Ficoll-Hypaquegradient centrifugation. CD34+ cells were isolated using the microbead kit from Miltenyi Biotec. Total RNAs including miRNAs were extracted from cells using the miRNeasy Mini Kit. The integrity of RNA samples were analyzed using an Agilent bioanalyzer.

value: chronic myelogenous leukemia from bone marrow


title: C174 PB CD34+ cells

source_name: Blood

value: peripheral blood from healthy donor


title: Experiment 3

source_name: Pooled sample of 3 Biological replicates of combination (2-DG + 6-AN) treated irradiated (2 Gy) head and neck squamous carcinoma_cultured cells after 24hours

source_name: 2 Gy irradiated Head and neck squamous carcinoma_cultured cells after 24 hours, Biological replicate 1 of 3.


title: C425 CML BM CD34+ cells


title: C421 PB CD34+ cells


title: C419 PB CD34+ cells


title: sample963

city: Homburg

hyb_protocol: according to manufacturers instruction (febit biomed)

value: others


title: HBL-2: Rituximab_rep1

description: gene expression data


title: sample962


title: C424 CML BM CD34+ cells


title: GRANTA-519: PBS-control_rep3

description: gene expression data

source_name: GRANTA-519: PBS-control


title: sample961


title: C423 CML BM CD34+ cells


title: C420 PB CD34+ cells


title: sample959


title: C422 CML BM CD34+ cells


title: C418 PB CD34+ cells


title: sample958


title: GRANTA-519: PBS-control_rep2

description: gene expression data


title: sample960


title: GRANTA-519: Isotype-control_rep3

description: gene expression data

source_name: GRANTA-519: Isotype-control


title: GRANTA-519: PBS-control_rep1

description: gene expression data


title: Fish oil emulsion rep 4

city: Perth

first: Sam

last: Buckberry

state: WA

address: 35 Stirling Highway, Crawley

country: Australia

institute: The University of Western Australia

description:
Fish oil emulsion rep 4
D4

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay.

scan_protocol: Illumina iScan Scanner.

data_processing: Data pre-processed and quantile normalized using the beadarray package in R.

source_name: HTR8/SVneo cells

label_protocol: Illumina TotalPrep RNA Amplification Kit.

growth_protocol: 200,000 HTR8/SVneo cells per well were seeded in SRM in a 6-well plate and incubated for 24 hours at 37ºC in 20% oxygen and 5% CO2.

extract_protocol: Standard Trizol extraction.

treatment_protocol: After 24 hours, 2ml of either SRM (N), SRM containing 50μM Soy Oil emulsion (S), or SRM containing 50μM Fish Oil emulsion (D) were added to each well.

value: Fish oil emulsion

tag: rep


title: sample956

value: psoriasis


title: sample957


title: sample968


title: Fish oil emulsion rep 3

description:
Fish oil emulsion rep 3
D3


title: IOR/OS14 transfected with LSAMP open reading frame, clone 18