title: Female Control-2

city: Lucknow

first: Neetu

last: Singh

address: Chowk

department: Center for Advance Research

institute: King George's Medical University

description: Normal Blood Sample

hyb_protocol: Briefly, the 75 ng DNA/sample were hybridized to MIP probe for 17 hours followed by gap filling with AT/GC. After removing the un-ligated (non gap-filled, linear) probes through exonuclease treatment, the cleavage enzyme was added to linearize the gap-filled circular MIP Probes. This was followed by amplification and enrichment of the gap-filled, linearized MIP probe through 1st and 2nd PCR. The enriched product was digested by HaeIII enzyme and hybridized to the OncoScan™ Array for 17 hours at 49 degree C at 60rpm.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner, Affymetrix

data_processing: The .cel file generated after scanning, was converted to OSCHP files through Oncoscan Console Software (Biodiscovery, Inc., CA USA). Further the OSCHP file was analyzed through tumor Scan (TuScan) and BioDiscovery’s SNP-FASST2 algorithm using the Nexus Express for Oncoscan software version 3.0 and 7.5 (Biodiscovery, Inc., CA USA). The TuScan algorithm creates segmentation to differentiate between adjacent clusters of probes and determines the copy number changes. The BioDiscovery’s SNP-FASST2 algorithm, a proprietary variation of a hidden Markov model (HMM) is used to identify the allelic event calls.

source_name: Blood

label_protocol: Biotin labelled fragmented DNA were prepared according to the standard OncoScan™ Array protocol  (Affymetrix).

extract_protocol: Genomic DNA was extracted from fresh tumor tissue using a QIAamp DNA mini kit (Qiagen, Germany) according to the manufacturer's instructions.

treatment_protocol: All patients were commenced to Imatinib treatment alone or in combination with Hydrea/Hydroxyurea. Importantly, in some cases when patients failed to achieve time dependent molecular targets we switched to nilotinib or high dose Imatinib. Clinical outcomes included molecular response on the basis of BCR-ABL1

tag: sample id

value: Female Control-2

tag: chronic phase

value: Normal Blood


title: Female Control-1

status: Public on Feb 06 2016

type: genomic

country: India

description: Normal Blood Sample

label: biotin

molecule: genomic DNA

organism: Homo sapiens

value: Female Control-1


title: Male-Control

description: Normal Blood Sample

value: Male-Control

value: Normal Blood Sample


title: Negative Control

description: Supplied by kit

value: Negative Control

value: Supplied by kit


title: CML-8

description: Blast-Under Treatment-8-Imatinib for 8 months; 24 years Male

value: CML- 8

tag: age

value: 24 years

tag: gender

value: Male


title: Positive Control

description: Supplied by kit

value: Positive Control


title: CML-47

description: Blast-New-47; 48 years Male

value: 48 years


title: Heliothis virescens  Rest of body-C4

type: RNA

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

country: Germany

institute: Max Planck Institute for Chemical Ecology

description: pooled from 5 individuals

hyb_protocol: The Cy3 labeled cRNA was hybridized to H. virescens (4x 180 K) microarray slides for 17 h at 65 °C in a hybridization oven. The microarray slides were washed in GE Wash Buffers according to the manufacturer´s instructions (Agilent Technologies). Slides were treated in Stabilization and Drying Solution and scanned.

scan_protocol: As per manufacturers instruction, using an Agilent Microarray Scanner

data_processing: Data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Feature extracted data were analyzed using GeneSpring GX version 12.5 (Agilent Technologies) software. The data points were normalized between arrays to the median intensity and log base 2-transformation of the normalized data was performed.

molecule: total RNA

organism: Heliothis virescens

source_name: Heliothis virescens  Rest of body-C4

label_protocol: Agilent Technologies spike-in RNA was added to 100 ng of total RNA and labeled following the One-color Microarray-Based Gene Expression Analyisis (Low Input Quick Amp Labeling kit) protocol (Agilent Technologies). Labeled amplified cRNA samples were purified using Qiagen RNeasy Minikit columns and analyzed on a Nanodrop ND-1000 spectrophotometer using the microarray function. Amplified cRNA samples were used for microarray hybridisation only if the yield was >1600 ng and the specific activity >6.0 pmol Cy3 per ug cRNA.

growth_protocol: H. virescens larvae were provided by North Carolina State University and had been originally collected in Clayton, North Carolina, USA, in 1988 (JEN strain). H. virescens larvae were reared on pinto bean diet (Joyner and Gould, 1985) under laboratory conditions (26 °C, 55% relative humidity, 16:8 h light:dark photoperiod) in Jena, Germany. For feeding assays pinto bean diet was used.  Newly molted 5th instar H. virescens  larvae were reared for 3 days on artificial control diet and diet supplemented with gossypol, respectively, with following concentrations: 0.32% (w/v) and  0% (w/v) of gossypol. Larvae were kept at 27 °C during treatment. After weighing, larvae were anesthetized on ice and dissected into gut and rest of the body. Tissues were pooled according to their biological replicates (5 larvae and 5 guts, respectively, are one replicate, four biological replicates were prepared), snap frozen in liquid nitrogen and stored at -80 °C until RNA isolation.

extract_protocol: For RNA isolation, tissues were ground to fine powder under liquid nitrogen. Total RNA was extracted by using the innuPREP RNA Mini Kit (Analytik Jena). RNA quality and integrity was assessed using RNA Nano chips on an Agilent 2100 Bioanalyzer (Agilent Technologies). The RNA quantity was determined using the NanoDrop ND-1000 spectrophotometer (Peqlab).

tag: tissue

value: rest of body

tag: treatment

value: Control


title: Heliothis virescens  Rest of body-G032-2

description: pooled from 5 individuals

source_name: Heliothis virescens  Rest of body-G032-2


title: peripheral blood T-cells newly diagnosed ITP3

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

country: USA

institute: University of Arkansas for Medical Sciences

description: gene expression data from subcutaneous adipose tissue

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

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

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

label: Biotin

source_name: peripheral blood T-cell

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

extract_protocol: Total RNA was prepared using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Tissues were snap frozen in liquid nitrogen

tag: group

value: New ITP


title: peripheral blood T-cells newly diagnosed ITP1


title: CML-34

description: Blast-NEW-34; 24 year Male


title: CML-37

description: Accelerated Phase-Under Treatment-37-Imatinib 8 months; 27 years Female

value: 27 years

value: Female


title: CML-22

description: Accelerated Phase-Under Treatment-22-Hydab and Imatinib for 5.2 years; 40 years Male

value: 40 years


title: peripheral blood T-cells newly diagnosed ITP4


title: peripheral blood T-cells newly diagnosed ITP2


title: Heliothis virescens  Rest of body-C2

description: pooled from 5 individuals

source_name: Heliothis virescens  Rest of body-C2


title: CML-38

description: Accelerated Phase-Under Treatment-38-Imatinib 1.5 years; 60 years Male

value: 60 years


title: Heliothis virescens  Gut-C3

description: pooled from 5 individuals

source_name: Heliothis virescens  Gut-C3

value: gut


title: CML-01

description: Accelerated Phase-Under Treatment-1- Imatinib for 1.8 years 35 years Male

value: 35 years


title: Heliothis virescens  Rest of body-C1

description: pooled from 5 individuals

source_name: Heliothis virescens  Rest of body-C1


title: CML-32

description: Accelerated Phase-Under Treatment-32-Initially treated with Myeleron, Hydab irocos, Zyloric since may 2005 on Imatinib treated for 15 years; 27 years Female


title: Heliothis virescens  Rest of body-C3

description: pooled from 5 individuals

source_name: Heliothis virescens  Rest of body-C3


title: CML-49

description: Blast-Under Treatment-49-Imatinib for 1.4 years; 15 years Male

value: 15 years


title: CML-51

description: Accelerated Phase-Under Treatment-51-Initially treated with Myeleron, Hydab irocos, Zyloric since may 2005 on Imatinib for 25 years; 60 years Male


title: peripheral blood T-cells newly diagnosed ITP6


title: CML-48

description: Chronic Phase-Under Treatment-48-Initially Hydroxyurea and since December 2004 Imatinib for 10.4 years; 33 years Male

value: 33 years


title: Heliothis virescens  Gut-G032-4

description: pooled from 5 individuals

source_name: Heliothis virescens  Gut-G032-4


title: CML-11

description: Blast-NEW-11; 20 year Male

value: 20 years


title: CML-07

description: Chronic Phase-Under Treatment-7-Imatinib for 7.2 years; 41 years Male

value: 41 years


title: (ITESM) PC3 P4

city: Monterrey

first: Roberto

last: Portillo Lara

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur Col. Tecnológico

department: División de Biotecnología y Alimentos

country: Mexico

institute: Tecnológico de monterrey

description: Sample 56

hyb_protocol: Three different nCounter Gene Expression CodeSets were used for the analysis: the GX Human Cancer Reference Kit consisting of 230 genes, the Stem Cell virtual panel consisting of 193 genes, and the custom-made ITESM CodeSet consisting of 14 genes related to PCa (NanoString Technologies). Hybridization was carried out at 65oC for 16 hours.

scan_protocol: Detection of mRNA transcripts was carried out in multiplexed hybridization reactions using the NanoString nCounter Analysis System according to instructions from the manufacturer.

data_processing: Data acquisition and normalization was carried out using the nSolver Analysis software version 2.0 (NanoString Technologies). The relative fold changes of each gene were calculated and ranked using Microsoft Excel. Genes with a fold change larger than 1.5 were selected for further analysis.

label: not provided

source_name: Prostate carcinoma

label_protocol: The cells were fluorescently labeled using Anti-Human CD133/2 (293C3)-PE (Miltenyi Biotec), and CD133+ cells were isolated via MACS using the Anti-PE MultiSort Kit (Miltenyi) according to instructions from the manufacturer.

growth_protocol: monolayer cultures in DMEM-F12 (Gibco) supplemented with 5% fetal bovine serum (FBS, Invitrogen) and 100 U/100 μg/ml penicillin-streptomycin (Gibco). Monolayer cultures were maintained at a maximum confluence level of 80% and the culture medium was replaced every 48 hours. Cultures were propagated for 12 days at 37oC at 95% relative humidity in a 5% CO2 and 95% air atmosphere.

extract_protocol: Total RNA was extracted and purified from CD133+ cells isolated from prostaspheres and monolayers using the RNeasy Micro and Mini Kits (Qiagen) according to instructions from the manufacturer. The integrity of the purified RNA samples was evaluated using a NanoDrop ND-1000 spectrophotometer at 260/280 nm.

treatment_protocol: Prostasphere cultures in EpiGRO human Prostate Complete Media Kit (Millipore), supplemented with 20 ng/μl hEGF (Gibco) and 20 ng/μl bFGF (Gibco). Prostasphere cultures were seeded at a density of 2x104 cells/ml and were passaged every 96 hours on days 4 and 8. Cultures were propagated for 12 days at 37oC at 95% relative humidity in a 5% CO2 and 95% air atmosphere.

tag: cell type

value: Prostate cancer cell line

tag: cell line

tag: time point

value: day 12


title: Heliothis virescens  Gut-G032-3

description: pooled from 5 individuals

source_name: Heliothis virescens  Gut-G032-3


title: (ITESM) PC3 P3

description: Sample 55

value: day 8


title: FFPE specimen of NP, biological rep4 [gene-level]

city: suzhou

first: weikang

last: xing

address: 188 shizi street

country: China

institute: The First Affiliated Hospital of Soochow University

description: Gene expression data from FFPE specimen

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 640 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded by Genesrping software (version 13.0; Agilent Technologies) and Transcriptome Analysis Console (version2.0, Affymetrix) separately.

source_name: obtained from autopsy without PA

label_protocol: Total RNA were amplified, labeled and purified by using WT Terminal Labeling and Controls Kit (Cat#901524, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

value: female

value: pituitary

value: 28 years old


title: (ITESM) PC3 P2

description: Sample 54

value: day 4


title: FFPE specimen of NP, biological rep2 [gene-level]

description: Gene expression data from FFPE specimen

value: 55 years old


title: Heliothis virescens  Gut-G032-1

description: pooled from 5 individuals

source_name: Heliothis virescens  Gut-G032-1


title: Heliothis virescens  Gut-C2

description: pooled from 5 individuals

source_name: Heliothis virescens  Gut-C2

value: Control


title: Heliothis virescens  Gut-C4

description: pooled from 5 individuals

source_name: Heliothis virescens  Gut-C4


title: Heliothis virescens  Gut-C1

description: pooled from 5 individuals

source_name: Heliothis virescens  Gut-C1


title: Heliothis virescens  Gut-G032-2

description: pooled from 5 individuals

source_name: Heliothis virescens  Gut-G032-2


title: FFPE specimen of NFPA, biological rep5 [gene-level]

description: Gene expression data from FFPE specimen

source_name: obtained from archived tissue samples derived from patients with NFPA

value: 60 years old


title: FFPE specimen of NP, biological rep5 [gene-level]

description: Gene expression data from FFPE specimen

value: 30 years old


title: (ITESM) PC3 P1

description: Sample 53

value: day 0


title: CML-04

description: Chronic Phase-Under Treatment-4-Imatinib 10 months; 14 years Male

source_name: Blood

value: 14 years

value: Male


title: FFPE specimen of NP, biological rep3 [gene-level]

description: Gene expression data from FFPE specimen

value: male


title: FFPE specimen of NFPA, biological rep4 [gene-level]

description: Gene expression data from FFPE specimen

value: 48 years old


title: FFPE specimen of NFPA, biological rep3 [gene-level]

description: Gene expression data from FFPE specimen

value: 58 years old


title: FFPE specimen of NFPA, biological rep1 [gene-level]

description: Gene expression data from FFPE specimen

value: 49 years old


title: FFPE specimen of NFPA, biological rep2 [gene-level]

description: Gene expression data from FFPE specimen

value: 36 years old


title: FFPE specimen of NP, biological rep1 [gene-level]

description: Gene expression data from FFPE specimen

value: 33 years old


title: CML-43

description: Chronic Phase-Under Treatment-43-Initially Hydroxyurea and Imatinib treated for 7 years; 27 yeras Male

value: 27 years


title: CML-02

description: Chronic Phase-Under Treatment-2-Droxygel (Antacid), Unidrea and Imatinib treated; 50 years Male

value: 50 years


title: (ITESM) DU145 P1

description: Sample 25

value: Prostate cancer cell line


title: (ITESM) DU145 P3

description: Sample 27

value: day 8


title: (ITESM) LNCaP P4

description: Sample 42

value: LNCaP

value: day 12


title: (ITESM) LNCaP P1

description: Sample 39


title: (ITESM) LNCaP P3

description: Sample 41


title: CML-36

description: Chronic Phase-Under Treatment-36-Hydab and Imatinib treated for 6.10 years; 23 years Male

value: 23 years


title: CML-24

description: Chronic Phase-Under Treatment-24-Initially treated with Myeleron, Hydab irocos, Zyloric since may 2005 on Imatinib treated for 8.5 years; 26 years Male

value: 26 years


title: (ITESM) LNCaP P2

description: Sample 40

value: day 4


title: CML-35

description: Accelerated Phase-Under Treatment-35-Imatinib 6.3 years-28 yeras Female

value: 28 years

value: Female


title: (ITESM) DU145 P4

description: Sample 28


title: (ITESM) 22Rv1 P3

description: Sample 13


title: (ITESM) 22Rv1 P2

description: Sample 12


title: (ITESM) 22Rv1 P4

description: Sample 14


title: CML-30

description: Chronic Phase-New-30

value: Chronic Phase-New-30

value: male


title: (ITESM) 22Rv1 P1

description: Sample 11

value: day 0


title: CML-29

description: Blast-Under Treatment-29-Imatinib one month; 35 years female

value: 35 years


title: (ITESM) DU145 P2

description: Sample 26


title: (CancerReference) PC3 P1_2

description: Sample 44

value: Day 0


title: (CancerReference) PC3 P3

description: Sample 47

value: Day 8


title: (CancerReference) PC3 P2

description: Sample 46

value: Day 4


title: (CancerReference) PC3 P1_3

description: Sample 45


title: (CancerReference) PC3 P1_1

description: Sample 43


title: CML-26

description: Chronic Phase-Under Treatment-26-Imatinib 2.1 years


title: (CancerReference) PC3 P4

description: Sample 48

value: Day 12


title: (CancerReference) LNCaP P3

description: Sample 33

value: Prostate cancer cell line


title: (CancerReference) LNCaP P4

description: Sample 34


title: CML-21

description: Chronic Phase-Under Treatment-21-Droxygel (Antacid), Unidrea and Imatinib treated for 3.8 years; 60 year Male

value: 60 year

value: Male


title: (CancerReference) LNCaP P2

description: Sample 32

value: LNCaP


title: CML-13

description: Chronic Phase-Under Treatment-13-Droxygel (Antacid), Unidrea and Imatinib treated for 7.1 years; 50 years Male

value: 50 years


title: CML-33

description: Accelerated Phase-Under Treatment-33-Imatinib for 2 years; 20 years Male

value: 20 years


title: (CancerReference) LNCaP P1_3

description: Sample 31


title: CML-59

description: Chronic Phase-Under Treatment-59-Hydroxyurea , Zyloric and Imatinib treated 3months; 15 years Female

value: 15 years


title: CML-58

description: Chronic Phase-Under Treatment-58-Hydroxyurea , Zyloric and  Imatinib treated nine months; 32 years Female

value: 32 years


title: (CancerReference) DU145 P3

description: Sample 19


title: (CancerReference) LNCaP P1_1

description: Sample 29


title: (CancerReference) DU145 P4

description: Sample 20


title: (CancerReference) DU145 P2

description: Sample 18


title: (CancerReference) LNCaP P1_2

description: Sample 30


title: CML-57

description: Chronic Phase-Under Treatment-57-Hydroxyurea , Zyloric and  Imatinib treated; 42 years Male

value: 42 years


title: (CancerReference) DU145 P1_3

description: Sample 17


title: CML-23

description: Chronic Phase-Under Treatment-23-Unidrea and Imatinib, Nilotinib treated for 2.4 years; 40 years Male

value: 40 years


title: (CancerReference) DU145 P1_2

description: Sample 16


title: CML-55

description: Chronic Phase-Under Treatment-55-Imatinib treated for 3 months; 60 years Male

value: 60 years


title: (CancerReference) DU145 P1_1

description: Sample 15


title: CML-14

description: Chronic Phase-NEW-14; 35 years Female

value: Chronic Phase-NEW-14

value: Female


title: (CancerReference) 22Rv1 P4

description: Sample 6


title: (CancerReference) 22Rv1 P1_2

description: Sample 2

value: Day 0


title: (CancerReference) 22Rv1 P3

description: Sample 5

value: Day 8


title: (CancerReference) 22Rv1 P1_1

description: Sample 1


title: (CancerReference) 22Rv1 P2

description: Sample 4

value: Day 4


title: (CancerReference) 22Rv1 P1_3

description: Sample 3


title: CML-10

description: Chronic Phase-NEW-10; 46 year Male

value: Chronic Phase-NEW-10

value: 46 years


title: CML-09

description: Chronic Phase-NEW-9; 46 years Male

value: Chronic Phase-NEW-9


title: CML-56

description: Chronic Phase-Under Treatment-56-Hydroxyurea , Zyloric and  Imatinib treated one year; 43 years Female

value: 43 years


title: (STEM) PC3 P4

description: Sample 52

value: Prostate cancer cell line

value: day 12


title: (STEM) PC3 P3

description: Sample 51

value: day 8


title: (STEM) PC3 P2

description: Sample 50

value: day 4


title: (STEM) PC3 P1

description: Sample 49

value: day 0


title: (STEM) LNCaP P2

description: Sample 36

value: LNCaP


title: KO Adrenal biological replicate 2

city: Aubiere

first: Pierre

last: Val

address: 24 avenue des Landais

country: France

institute: CNRS

description: gene expression

hyb_protocol: Following fragmentation, CDNA were hybridized for 17h at 45C on GenChip MouseGene2.0 from Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: RMA normalisation was performed with R and the BioConductor package

organism: Mus musculus

source_name: Prkar1a conditional KO Mouse adrenal

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500 ng of total RNA (Following the GeneChip® WT PLUS Reagent Kit Affymetrix)

extract_protocol: Total RNA were extracted from whole adrenal glands using RNA II nucleotide extraction kit from Macherey Nagel. RNA quality was assessed by Agilent bioanalyzer chips.

value: Whole adrenal gland

tag: genotype

value: sf1:Cre; Prkar1a Fl/Fl


title: KO Adrenal biological replicate 4

description: gene expression


title: Helicoverpa armigera Rest of body-G016-2

description: pooled from 5 individuals

hyb_protocol: The Cy3 labeled cRNA was hybridized to H. armigera (4x 44 K)  microarray slides for 17 h at 65 °C in a hybridization oven. The microarray slides were washed in GE Wash Buffers according to the manufacturer´s instructions (Agilent Technologies). Slides were treated in Stabilization and Drying Solution and scanned.

organism: Helicoverpa armigera

label_protocol: Agilent Technologies spike-in RNA was added to 100 ng of total RNA and labeled following the One-color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling kit) protocol (Agilent Technologies). Labeled amplified cRNA samples were purified using Qiagen RNeasy Minikit columns and analyzed on a Nanodrop ND-1000 spectrophotometer using the microarray function. Amplified cRNA samples were used for microarray hybridisation only if the yield was >1600 ng and the specific activity >6.0 pmol Cy3 per ug cRNA.

growth_protocol: H. armigera larvae were collected from Toowoomba, Queensland, Australia, in 2003. H. armigera larvae were reared on artificial diet (BioServ, F9772, Frenchtown, NJ, USA and Pintobean diet) under laboratory conditions (26°C, 55% RH, 16:8 hr =L:D) in Jena, Germany. For feeding assays pinto bean diet was used.  Newly molted 5th instar H. armigera larvae were reared for 3 days on artificial control diet and diet supplemented with gossypol, respectively, with following concentrations: 0.016% (w/v) and  0.16% (w/v) of gossypol. Larvae were kept at 27 °C during treatment. After weighing, larvae were anesthetized on ice and dissected into gut and rest of the body. Tissues were pooled according to their biological replicates (5 larvae and 5 guts, respectively, are one replicate, four biological replicates were prepared), snap frozen in liquid nitrogen and stored at -80 °C until RNA isolation.

value: rest of body


title: (STEM) LNCaP P4

description: Sample 38


title: (STEM) LNCaP P1

description: Sample 35


title: Helicoverpa armigera Rest of body-G016-4

description: pooled from 5 individuals


title: Helicoverpa armigera Rest of body-G016-3

description: pooled from 5 individuals


title: KO Adrenal biological replicate 1

description: gene expression


title: Helicoverpa armigera Rest of body-G0016-4

description: pooled from 5 individuals


title: WT Adrenal biological replicate 2

description: gene expression

source_name: WT Mouse adrenal

value: WT


title: (STEM) LNCaP P3

description: Sample 37


title: WT Adrenal biological replicate 3

description: gene expression


title: WT Adrenal biological replicate 4

description: gene expression


title: KO Adrenal biological replicate 3

description: gene expression


title: Helicoverpa armigera Rest of body-G0016-2

description: pooled from 5 individuals


title: (STEM) DU145 P4

description: Sample 24


title: WT Adrenal biological replicate 1

description: gene expression


title: Helicoverpa armigera Rest of body-G016-1

description: pooled from 5 individuals


title: Helicoverpa armigera Rest of body-G0016-3

description: pooled from 5 individuals


title: Helicoverpa armigera Rest of body-C3

description: pooled from 5 individuals

source_name: Helicoverpa armigera Rest of body-C3

value: Control


title: (STEM) DU145 P3

description: Sample 23


title: (STEM) DU145 P2

description: Sample 22


title: Helicoverpa armigera Rest of body-C4

description: pooled from 5 individuals

source_name: Helicoverpa armigera Rest of body-C4


title: Helicoverpa armigera Rest of body-G0016-1

description: pooled from 5 individuals


title: Helicoverpa armigera Rest of body-C2

description: pooled from 5 individuals

source_name: Helicoverpa armigera Rest of body-C2


title: Helicoverpa armigera Rest of body-C1

description: pooled from 5 individuals

source_name: Helicoverpa armigera Rest of body-C1


title: (STEM) DU145 P1

description: Sample 21


title: (STEM) 22Rv1 P4

description: Sample 10


title: Helicoverpa armigera Gut-G016-3

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-G016-3

value: gut


title: Helicoverpa armigera Gut-G0016-4

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-G0016-4


title: Helicoverpa armigera Gut-G0016-2

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-G0016-2


title: Helicoverpa armigera Gut-G016-1

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-G016-1


title: (STEM) 22Rv1 P2

description: Sample 8

source_name: Prostate carcinoma


title: Helicoverpa armigera Gut-G016-2

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-G016-2


title: (STEM) 22Rv1 P1

description: Sample 7


title: Helicoverpa armigera Gut-C4

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-C4


title: Helicoverpa armigera Gut-G016-4

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-G016-4


title: TIARΔRRM2-FLAG-associated mRNAs LPS- Replica 2

status: Public on Feb 05 2016

city: Barcelona

first: Yacine

last: Kharraz

state: Catalunya

address: 88 calle Aiguader

department: DCEXS

country: Spain

institute: University Pompeu Fabra

description: Sample were hybridized to MEEBO arrays (70mer oligonucleotide probes)

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 5xSSC, SDS 0.1%, HEPES 24mM, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Cyanine-labeled cRNA samples were mixed with 30 µg of mouse cot-1, incubated for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, slides were washed twice for 2 min at 60°C with 2xSSC, 0.03% SDS, once 2 min at 60°C with 2xSSC, and finally briefly washed in 0.2xSSC at room temperature. They were dried by centrifugation at 800 rpm for 13 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and expression levels were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing: A non-linear Lowess (locally weighted scatter plot) normalization method was carried out. The values corresponding to the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2 are provided.

source_name: RNAs co-immunoprecipitated with TIARΔRRM2-FLAG without LPS

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30min in 50% DMSO at room temperature in a dark environment

growth_protocol: RAW 264.7 cell clones were cultured in Glutamax Dubelcco Modified Eagle Medium (Gibco-BRL®) complemented with 5% fetal bovine serum, 1mM Na pyruvate and 1% penicillin-streptomycin.

extract_protocol: RAW 264.7 cells expressing TIAR-FLAG or TIARΔRRM2-FLAG were lysed in polysome lysis buffer containing 10 mM HEPES pH 7.0, 100 mM KCl, 25 mM EDTA, 2 mM DTT, 5 mM MgCl2, 0.5% NP40 and 2 μl RNAse OUT™ (Invitrogen®). TIAR-FLAG or TIARΔRRM2-FLAG were then immunoprecipitated overnight with anti-FLAG M2 agarose beads (Sigma®) according to the manufacturer’s instructions and then eluted in a buffer containing 50 mM Tris pH 7.4, 150 mM NaCl, 1 mM MgCl2, 2μl de RNase OUT™ (Invitrogen®) and the FLAG peptide (Sigma®) at a final concentration of 250 µg/ml. mRNAs where then isolated by Trizol (Invitrogen®) extraction according to the manufacturer’s protocol.

treatment_protocol: Cells were either left untreated or treated for 2 hours with 100 ng/ml LPS from E. coli (0127:B8; Sigma®)

value: RAW 264.7 cells

source_name: Total RNA from TIARΔRRM2-FLAG expressing RAW 264.7 cells without treatment


title: TIARΔRRM2-FLAG-associated mRNAs LPS+ Replica 2

source_name: RNAs co-immunoprecipitated with TIARΔRRM2-FLAG after LPS treatment

source_name: Total RNA from TIARΔRRM2-FLAG expressing RAW 264.7 cells after LPS treatment


title: Helicoverpa armigera Gut-C2

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-C2


title: TIARΔRRM2-FLAG-associated mRNAs LPS+ Replica 1


title: TIAR-FLAG-associated mRNAs LPS- Replica 2

source_name: RNAs co-immunoprecipitated with TIAR-FLAG without LPS

source_name: Total RNA from TIAR-FLAG expressing RAW 264.7 cells without treatment


title: TIARΔRRM2-FLAG-associated mRNAs LPS- Replica 1


title: Helicoverpa armigera Gut-G0016-3

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-G0016-3


title: TIAR-FLAG-associated mRNAs LPS- Replica 1


title: Helicoverpa armigera Gut-C3

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-C3


title: (STEM) 22Rv1 P3

description: Sample 9


title: R. hominis 28d-AC, rep3

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip NuGO Mouse Array (NuGO_Mm1a520177). GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. The moderated t-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when P<0.05 using the Benjamini and Hochberg false discovery method.

source_name: Mouse ascending colon, 28d after colonization, R. hominis

label_protocol: Fragmented and biotin-labelled cRNA was synthesized from 8 ug purified RNA using the One-Cycle Target Labeling Kit (Affymetrix) according to the manufacturer's protocol.

growth_protocol: C3H/HeN mice were bred at the INRA facilities in Jouy-en-Josas. Germ-free (GF) mice were maintained in plastic isolators and fed ad libitum on a commercial diet (R03-40; UAR) sterilized by γ-irradiation (40 kGy).

extract_protocol: Ileal and ascending colon tissue was excised, processed in ice-cold PBS, transferred to RNAlater (Ambion) and stored at -20 °C. Tissue was removed from RNAlater, lyzed in Trizol (Invitrogen), and RNA was extracted using chloroform/isopropanol steps. Total RNA was further treated with the RNeasy kit (Qiagen) according to the manufacturer’s instructions, including an RNase-free DNase I (Qiagen) digestion step.

treatment_protocol: GF male mice were gavaged at 0d with 100 uL of  R. hominis culture. All mice were sacrificed on 14d and 28d post-colonization in parallel to age-matched GF controls.

tag: strain

value: male

value: ascending colon

tag: condition

value: Roseburia hominis colonization

tag: time

value: 28 days post-colonization


title: R. hominis 28d-AC, rep5


title: R. hominis 28d-AC, rep4


title: TIAR-FLAG-associated mRNAs LPS+ Replica 1

source_name: RNAs co-immunoprecipitated with TIAR-FLAG after LPS treatment

source_name: Total RNA from TIAR-FLAG expressing RAW 264.7 cells after LPS treatment


title: TIAR-FLAG-associated mRNAs LPS+ Replica 2


title: FFPE specimen of NP, biological rep4 [exon-level]

description: Gene expression data from FFPE specimen

source_name: obtained from autopsy without PA

value: female

value: pituitary

value: 28 years old


title: Helicoverpa armigera Gut-G0016-1

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-G0016-1


title: R. hominis 28d-AC, rep1


title: R. hominis 28d-AC, rep2


title: R. hominis 14d-AC, rep5

source_name: Mouse ascending colon, 14d after colonization, R. hominis

value: 14 days post-colonization


title: R. hominis 14d-AC, rep2


title: R. hominis 14d-AC, rep3


title: R. hominis 14d-AC, rep4


title: Germfree 28d-AC, rep4

source_name: Mouse ascending colon, 28d, germfree control

value: germ-free


title: Helicoverpa armigera Gut-C1

description: pooled from 5 individuals

source_name: Helicoverpa armigera Gut-C1


title: Germfree 28d-AC, rep2


title: R. hominis 14d-AC, rep1


title: FFPE specimen of NP, biological rep5 [exon-level]

description: Gene expression data from FFPE specimen

value: 30 years old


title: Germfree 28d-AC, rep3


title: Germfree 28d-AC, rep1


title: FFPE specimen of NP, biological rep3 [exon-level]

description: Gene expression data from FFPE specimen

value: 60 years old


title: Germfree 14d-AC, rep3

source_name: Mouse ascending colon, 14d, germfree control


title: Germfree 14d-AC, rep4


title: FFPE specimen of NFPA, biological rep5 [exon-level]

description: Gene expression data from FFPE specimen

source_name: obtained from archived tissue samples derived from patients with NFPA


title: FFPE specimen of NFPA, biological rep4 [exon-level]

description: Gene expression data from FFPE specimen

value: 48 years old


title: FFPE specimen of NP, biological rep1 [exon-level]

description: Gene expression data from FFPE specimen

value: 33 years old


title: Germfree 14d-AC, rep2


title: Germfree 14d-AC, rep1


title: FFPE specimen of NFPA, biological rep1 [exon-level]

description: Gene expression data from FFPE specimen

value: 49 years old


title: R. hominis 28d-IL, rep5

source_name: Mouse ileum, 28d after colonization, R. hominis

value: ileum


title: R. hominis 28d-IL, rep2


title: FFPE specimen of NP, biological rep2 [exon-level]

description: Gene expression data from FFPE specimen

value: 55 years old


title: FFPE specimen of NFPA, biological rep2 [exon-level]

description: Gene expression data from FFPE specimen

value: 36 years old


title: R. hominis 14d-IL, rep3

source_name: Mouse ileum, 14d after colonization, R. hominis

value: male


title: R. hominis 28d-IL, rep3


title: R. hominis 28d-IL, rep4


title: FFPE specimen of NFPA, biological rep3 [exon-level]

description: Gene expression data from FFPE specimen

value: 58 years old


title: R. hominis 14d-IL, rep4

value: Roseburia hominis colonization


title: R. hominis 28d-IL, rep1

value: 28 days post-colonization


title: R. hominis 14d-IL, rep5


title: Germfree 28d-IL, rep4

source_name: Mouse ileum, 28d, germfree control


title: R. hominis 14d-IL, rep1


title: Germfree 28d-IL, rep2


title: Germfree 14d-IL, rep3

source_name: Mouse ileum, 14d, germfree control


title: Germfree 28d-IL, rep1


title: Germfree 14d-IL, rep4


title: Germfree 14d-IL, rep2


title: Germfree 14d-IL, rep1


title: Germfree 28d-IL, rep3


title: R. hominis 14d-IL, rep2


title: Rat cardiomyocyte celecoxib reference concentration 1/25 24h replicate 3

city: Jinju

first: Dong-hoon

last: Lee

state: Gyeongnam

address: 15 Jinju-daero 816 Beon-gil

department: Convergence Medical Science

country: South Korea

institute: Gyeongsang National University

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: GenePix Pro 6.0 software (Axon Instruments, Union City, CA)

data_processing: Agilent's GeneSpring GX 7.3 software

organism: Rattus norvegicus

source_name: cardiomyocyte

label_protocol: Agilent Low RNA Input Linear Amplification kit PLUS

growth_protocol: Primary cultures were established using neonatal rat heart tissues collected after anesthetizing the rats, cultures were left to grow for one day on DMEM media then were treated as follow

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Variables of treatment included two time points (6h or 24h) and three reference concentrations (1, 1/5 and 1/25).

value: Heart

tag: developmental stage

value: Neonate

value: celecoxib

tag: concentration


title: Rat cardiomyocyte celecoxib reference concentration 1/25 24h replicate 1


title: Rat cardiomyocyte celecoxib reference concentration 1/5 24h replicate 2


title: Rat cardiomyocyte celecoxib reference concentration 1/5 24h replicate 3


title: Rat cardiomyocyte celecoxib reference concentration 1/25 24h replicate 2


title: Rat cardiomyocyte celecoxib reference concentration 1 24h replicate 3


title: Rat cardiomyocyte celecoxib reference concentration 1 24h replicate 2


title: Rat cardiomyocyte celecoxib reference concentration 1/5 24h replicate 1


title: Rat cardiomyocyte celecoxib reference concentration 1 24h replicate 1


title: Rat cardiomyocyte celecoxib reference concentration 1/25 6h replicate 3


title: RA patient with active disease versus OA patient (REP3 of 3)

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

hyb_protocol: Labeled samples were hybridized onto human miRCURY LNA™ microRNA Array Kit, v.11.0 (Exiqon)

scan_protocol: Slides were scanned at 5 um resolution in an Axon 4000B scanner and spots quantified with GenePix 5.0 software

data_processing: Raw intensity values were background-substracted by normexp (offset 50), normalized by loess and quantile adjusted. Functions from bioconductor's limma and affy packages were used

source_name: macrophages from synovial membrane of OA patient

label_protocol: One microgram of total RNA from each sample was subjected to specific labeling of miRNAs using miRCURY LNA™ microRNA Hy3/Hy5 Power labeling kit (Exiqon) following manufacturer’s instructions.

growth_protocol: Synovial macrophages were obtained by centrifugation on Ficoll of synovial fluid (SF) from RA patients, or by collagenase I digestion of the synovial membrane of OA patients who had undergone knee joint replacement surgery; both procedures were followed by magnetic separation of CD14+ cells.  SF was obtained from patients with active knee arthritis; only those with high cellularity were used.

extract_protocol: Total RNA was extracted from purified macrophages with TRI Reagent (Sigma-Aldrich) and further cleaned using RNeasy (Qiagen).  RNA was determined to be of sufficient quality by electropherogram analyis (Agilent Bioanalyzer).

tag: disease state

value: osteoarthritis

value: macrophage

source_name: macrophages from synovia of RA patient with active disease

value: rheumatoid arthritis


title: RA patient with active disease versus OA patient (REP2 of 3)


title: RA patient with active disease versus OA patient (REP1 of 3)


title: Dermis_Old_donor4

city: Shanghai

first: Leihong

last: Xiang

address: 12 Wulumuqi Zhong Road

institute: Huashan Hospital, Shanghai Medical College, Fudan University

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US)

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US)

source_name: Human dermis, old

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section

extract_protocol: Total RNA of dermal tissue or dermal fibroblasts was extracted using mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer’s instructions

treatment_protocol: Normal human skin tissue (8x5x3mm) from sun-protected part of body was obtained. Adipose tissue and epidermis was carefully removed by forceps. The remained dermal tissue was stored in the liquid nitrogen at -196℃.

value: dermis

value: above 60yrs


title: Dermis_Old_donor3


title: Dermis_Old_donor1


title: Rat cardiomyocyte celecoxib reference concentration 1 6h replicate 3


title: Rat cardiomyocyte celecoxib reference concentration 1/5 6h replicate 2


title: Rat cardiomyocyte celecoxib reference concentration 1 6h replicate 2


title: Dermis_Young_donor6

source_name: Human dermis, young

value: below 10yrs


title: Rat cardiomyocyte celecoxib reference concentration 1/25 6h replicate 1


title: Rat cardiomyocyte celecoxib reference concentration 1/5 6h replicate 1


title: Rat cardiomyocyte celecoxib reference concentration 1/5 6h replicate 3


title: Dermis_Old_donor6


title: Rat cardiomyocyte non-treated replicate 1

value: untreated


title: Rat cardiomyocyte non-treated replicate 2


title: Rat cardiomyocyte celecoxib reference concentration 1/25 6h replicate 2


title: Rat cardiomyocyte celecoxib reference concentration 1 6h replicate 1


title: Dermis_Old_donor5


title: Dermis_Young_donor5


title: Dermis_Young_donor2


title: Dermis_Young_donor1


title: Dermis_Young_donor3


title: MLN4924

city: Richmond

first: Steven

last: Grant

address: 401 College Street

institute: VCU

description: MLN 16 hours

data_processing:
The microarray data was analyzed via QIAGEN online service RT2 Profiler PCR Array Data Analysis Version 3.5.
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
For normalization, the average of five housekeeping genes was used as follows: B2M, HPRT1 , RPLP0, GAPDH, and ACTB.
Target gene signals were normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green ROXTM

source_name: human AML cell line U937

label_protocol: Microarray was carried out using the Human DNA Damage Signaling Pathway PCR Array kit (PAHS-029Z ) from QIAGEN.

growth_protocol: U937 cells were cultured in RPMI-1640 medium containing 10% heat-inactivated FBS.

extract_protocol: Total RNAs were extracted from U937 cells for untreeated control and each treatment condition using the RNeasy Plus MINI kit (Cat. No. 74134) from QIAGEN.

treatment_protocol: 4^10e5 U937 cells were treated with either MLN4924 (100 nM) or PXD-101 (belinostat, 300 nM) alone or in combination for 16 hrs.

value: MLN 16 hours

value: Blood


title: UT

description: untreated control


title: MLN4924+PXD101

description: Cotreated with MLN and PXD16 hours

value: Cotreated with MLN and PXD16 hours


title: PXD101

description: PXD 16 hours

value: PXD 16 hours


title: Dermis_Old_donor2


title: Dermis_Young_donor4


title: Spneumoniae_ R6_Mox10_t30_rep_2

city: Majadahonda

first: Antonio

middle: J.

last: Martin-Galiano

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

institute: Instituto de Salud Carlos III

description:
RNA extracted from S. pneumoniae R6
Spn R6 Mox10 t30 R2

hyb_protocol: 250 ng of labelled cDNA were used for hybridization. Arrays were hybridized at 65ºC for 40 hours.

scan_protocol: Scanning was done on a Roche MS200 scanner

data_processing: Raw data were extracted and normalized using Agilent Feature extraction 11.5.1.1 software. The median expression of every probeset was obtained, scaled to log2 and normalized by quantile using Bioconductor.

organism: Streptococcus pneumoniae R6

source_name: Bacteria

label_protocol: 25 ng of RNA were used to obtain cDNA with WTA2 from Sigma. This cDNA was labelled with Cy3 with ULS kit following Agilent's instructions

growth_protocol: Bacteria were grown in AGCH + 0.5% yeast extract + 0.3% sucrose medium until OD620=0.4

extract_protocol: RNA was extracted with Mini Rneasy columns from Quiagen and treated with DNAse I

treatment_protocol: Moxifloxacin was added to the culture (1,25 µg/mL; 10 x MIC) and samples were taken at 0, 15 and 30 min

tag: growth phase

value: Exponential growth

tag: growth medium

tag: agent

value: moxifloxacin

value: 30 min


title: Spneumoniae_ R6_Mox10_t30_rep_1

description:
RNA extracted from S. pneumoniae R6
Spn R6 Mox10 t30 R1

value: AGCH + 0.5% yeast extract + 0.3% sucrose


title: Spneumoniae_ R6_Mox10_t15_rep_2

description:
RNA extracted from S. pneumoniae R6
Spn R6 Mox10t15 R2

value: 15 min


title: Spneumoniae_ R6_Mox10_t15_rep_1

description:
RNA extracted from S. pneumoniae R6
Spn R6 Mox10 t15 R1


title: ZR-751 treated with 10 ng/mL IL-6, day 5_rep1

status: Public on Feb 04 2016

city: Beerse

first: Tine

last: Casneuf

address: Turnhoutseweg 30

department: Oncology Translational Research

country: Belgium

institute: Janssen R&D

hyb_protocol: A total of 4.5 µg fragmented biotin-labeled aRNA was hybridized on a HT Human Genome (HG)U219 96-array plate (Affymetrix).

scan_protocol: The plate was washed, stained, and scanned with the GeneTitan Instrument (Affymetrix).

data_processing: The microarray data were normalized with robust multi-array analysis (RMA; as per Irizarry et al, 2003) and summarized with the HG-U219H Entrezg 15.0.0 chip definition files (CDF).

label_protocol: Biotin-labeled, amplified RNA (aRNA) was synthesized from 200 ng total RNA using the 3’IVT Express Kit (Affymetrix, Santa Clara, USA).  The aRNA was then purified using Agencourt RNAClean XP beads (Beckman Coulter Inc., Indianapolis, USA) on the BioMek Fx Workstation (Beckman Coulter Inc.).  Biotin-labeled aRNA was fragmented using the 3’IVT Express Kit (Affymetrix).

growth_protocol: Ten ERα-positive breast cancer cell lines, T47D, MDA-MB-134VI, BT474, BT-483, HCC1428, EFM-19, MCF-7, MDA-MB-175-VIIdsRed, MDA-MB-415 and ZR-751, were grown in TME-aligned 3D culture.

extract_protocol: After culturing, the media overlay was removed by aspiration and 150 μl Qiazol (Qiagen) immediately added to the cells plus BME to achieve lysis. This mixture was combined with an additional 600 μl Qiazol and stored at -80 °C until RNA isolation.  RNA isolation was performed using the miRNeasy 96 Kit (Qiagen). The RNA concentration of all the samples was determined on a Nanodrop-8000 UV-Vis Spectrophotometer (Thermo Scientific).

treatment_protocol: After establishment, the cells were grown in triplicate for 6 days in the absence or presence of 10 ng/ml IL-6, which was added on day 1. Sampling was performed on days 4, 5, and 6.  Five additional conditions were investigated in duplicate: (i) 10 ng/ml IL-6 added on day 0 + 50 μg/ml siltuximab added on day 1 (ii) 10 ng/ml IL-6 added on day 1 + 50 μg/ml siltuximab added on day 1 (iii) 50 μg/ml siltuximab added on day 0 (iv) human marrow stromal cell-conditioned media (hMSC-CM) (v) hMSC-CM + 50 μg/ml siltuximab.

value: ERα-positive breast cancer cell line

value: D1:10 ng/mL IL-6

tag: time point (day)


title: ZR-751 treated with 10 ng/mL IL-6, day 6_rep1_rep1


title: Spneumoniae_ R6_t0_rep_1

description:
RNA extracted from S. pneumoniae R6
Spn R6 t0 R1

value: control

value: 0 min


title: ZR-751 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3

source_name: ZR-751_hMSC-CM + 50 ug Siltuximab_day 4

value: hMSC-CM + 50 ug/mL Siltuximab


title: ZR-751 untreated, day 6_rep1

source_name: ZR-751 untreated_day 6


title: ZR-751 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1


title: ZR-751 treated with 10 ng/mL IL-6, day 6_rep2_rep1


title: Spneumoniae_ R6_t0_rep_2

description:
RNA extracted from S. pneumoniae R6
Spn R6 t0 R2


title: ZR-751 treated with 10 ng/mL IL-6, day 5_rep2


title: ZR-751 treated with hMSC-CM, day 4_rep3

source_name: ZR-751_hMSC-CM_day 4

value: hMSC-CM


title: ZR-751 treated with hMSC-CM, day 4_rep1


title: ZR-751 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2


title: ZR-751 untreated, day 5_rep2

source_name: ZR-751 untreated_day 5


title: ZR-751 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2

source_name: ZR-751_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4

value: D1:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: MDA-MB-453_sulforaphene_48h

city: Beijing,China

first: Wendi

last: Teng

address: North three ring,East road,15

institute: Beijing University of Chemical Technology

description: female,epithelial,breast carcinoma,48 years adult,Caucasian

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: Raw data were normalized by Expression Console

source_name: MDA-MB-453, sulforaphene

label_protocol: Labeled cRNA were prepared according to the manufacturer’s instructions from 200ng total RNA (Affymetrix  WT PLUS Reagent Kit).

growth_protocol: Volumes used in this protocol are for 25 cm2 flask; proportionally reduce or increase amount of dissociation medium for culture vessels of other sizes.  Remove and discard culture medium.  Briefly rinse the cell layer with 0.25% (w/v) Trypsin- 0.53 mM EDTA solution to remove all traces of serum that contains trypsin inhibitor.  Add 1.0 mL of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 1 minutes).  Note: To avoid clumping do not agitate the cells by hitting or shaking the flask while waiting for the cells to detach. Cells that are difficult to detach may be placed at 37°C to facilitate dispersal.  Add 3.0 to 4.0 mL of complete growth medium and aspirate cells by gently pipetting.  Add appropriate aliquots of the cell suspension to new culture vessels.  Cultures can be established between 2 x 103 and 1 x 104 viable cells/cm2. Do not exceed 7 x 104 cels/cm2.  Incubate cultures at 37°C.  Interval: Maintain cultures at a cell concentration between 6 X 103 and 6 X 104 cell/cm2.  Subcultivation Ratio: A subcultivation ratio of 1:3 to 1:8 is recommended  Medium Renewal: 2 to 3 times per week

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

treatment_protocol: 15µM sulforaphene was used for treatment in L15 medium. Total RNA were prepared after treatment 48h.

tag: gender

value: female

value: breast carcinoma

tag: age

value: 48 years adult

tag: ethnicity

value: Caucasian


title: ZR-751 treated with hMSC-CM, day 4_rep2

tag: cell type

tag: treatment


title: ZR-751 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1

tag: cell line


title: MDA-MB-453_NC_48h

source_name: MDA-MB-453, untreated


title: ZR-751 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3

source_name: ZR-751_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4

value: D0:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: ZR-751 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1


title: ZR-751 treated with 10 ng/mL IL-6, day 4_rep3


title: ZR-751 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3


title: ZR-751 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2


title: ZR-751 treated with 10 ng/mL IL-6, day 4_rep2


title: ZR-751 untreated, day 5_rep1

value: untreated


title: ZR-751 untreated, day 6_rep2


title: ZR-751 treated with 50 ug Siltuximab, day 4_rep3

source_name: ZR-751_50 ug Siltuximab_day 4

value: 50 ug/mL Siltuximab


title: ZR-751 treated with 50 ug Siltuximab, day 4_rep1


title: ZR-751 treated with 10 ng/mL IL-6, day 4_rep1


title: ZR-751 untreated, day 1_rep1

source_name: ZR-751 untreated_day 1


title: ZR-751 untreated, day 0_rep3

source_name: ZR-751 untreated_day 0


title: ZR-751 untreated, day 4_rep3

source_name: ZR-751 untreated_day 4


title: ZR-751 untreated, day 0_rep1


title: MDA-MB-415 untreated, day 6_rep2

source_name: MDA-MB-415 untreated_day 6


title: ZR-751 untreated, day 4_rep1


title: ZR-751 untreated, day 4_rep2


title: ZR-751 untreated, day 1_rep3


title: MDA-MB-415 treated with 10 ng/mL IL-6, day 6_rep2

source_name: MDA-MB-415_10 ng/mL IL-6_day 6


title: ZR-751 untreated, day 0_rep2


title: MDA-MB-415 treated with 10 ng/mL IL-6, day 5_rep2

source_name: MDA-MB-415_10 ng/mL IL-6_day 5


title: MDA-MB-415 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1

source_name: MDA-MB-415_hMSC-CM + 50 ug Siltuximab_day 4


title: ZR-751 untreated, day 1_rep2


title: MDA-MB-415 treated with hMSC-CM, day 4_rep2

source_name: MDA-MB-415_hMSC-CM_day 4


title: ZR-751 treated with 50 ug Siltuximab, day 4_rep2


title: MDA-MB-415 treated with 10 ng/mL IL-6, day 6_rep1


title: MDA-MB-415 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3

source_name: MDA-MB-415_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4


title: MDA-MB-415 treated with hMSC-CM, day 4_rep1


title: MDA-MB-415 untreated, day 6_rep1


title: MDA-MB-415 treated with hMSC-CM, day 4_rep3


title: MDA-MB-415 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2


title: MDA-MB-415 untreated, day 5_rep1

source_name: MDA-MB-415 untreated_day 5


title: MDA-MB-415 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3


title: MDA-MB-415 treated with 10 ng/mL IL-6, day 5_rep1


title: MDA-MB-415 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1


title: MDA-MB-415 untreated, day 5_rep2


title: MDA-MB-415 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2


title: MDA-MB-415 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2

source_name: MDA-MB-415_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4


title: MDA-MB-415 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3


title: MDA-MB-415 treated with 10 ng/mL IL-6, day 4_rep3

source_name: MDA-MB-415_10 ng/mL IL-6_day 4


title: MDA-MB-415 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1


title: MDA-MB-415 untreated, day 0_rep2

source_name: MDA-MB-415 untreated_day 0


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6, day 6_rep2

source_name: MDA-MB-175-VIIdsRed_10 ng/mL IL-6_day 6


title: MDA-MB-415 untreated, day 1_rep3

source_name: MDA-MB-415 untreated_day 1


title: MDA-MB-415 untreated, day 0_rep1


title: MDA-MB-415 treated with 50 ug Siltuximab, day 4_rep2

source_name: MDA-MB-415_50 ug Siltuximab_day 4


title: MDA-MB-415 treated with 50 ug Siltuximab, day 4_rep3


title: MDA-MB-415 untreated, day 1_rep2


title: MDA-MB-415 treated with 10 ng/mL IL-6, day 4_rep1


title: MDA-MB-415 treated with 10 ng/mL IL-6, day 4_rep2


title: MDA-MB-415 untreated, day 4_rep1

source_name: MDA-MB-415 untreated_day 4


title: MDA-MB-415 untreated, day 4_rep3


title: MDA-MB-175-VIIdsRed untreated, day 6_rep1

source_name: MDA-MB-175-VIIdsRed untreated_day 6


title: MDA-MB-415 treated with 50 ug Siltuximab, day 4_rep1


title: MDA-MB-415 untreated, day 0_rep3


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6, day 6_rep1


title: MDA-MB-415 untreated, day 1_rep1


title: MDA-MB-175-VIIdsRed untreated, day 5_rep1

source_name: MDA-MB-175-VIIdsRed untreated_day 5


title: MDA-MB-175-VIIdsRed treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2

source_name: MDA-MB-175-VIIdsRed_hMSC-CM + 50 ug Siltuximab_day 4


title: MDA-MB-175-VIIdsRed treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3


title: MDA-MB-175-VIIdsRed untreated, day 5_rep2


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6, day 5_rep2

source_name: MDA-MB-175-VIIdsRed_10 ng/mL IL-6_day 5


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6, day 5_rep1


title: MDA-MB-415 untreated, day 4_rep2


title: MDA-MB-175-VIIdsRed untreated, day 6_rep2


title: MDA-MB-175-VIIdsRed treated with hMSC-CM, day 4_rep2

source_name: MDA-MB-175-VIIdsRed_hMSC-CM_day 4


title: MDA-MB-175-VIIdsRed treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1


title: MDA-MB-175-VIIdsRed treated with hMSC-CM, day 4_rep3


title: MDA-MB-175-VIIdsRed treated with hMSC-CM, day 4_rep1


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3

source_name: MDA-MB-175-VIIdsRed_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6, day 4_rep2

source_name: MDA-MB-175-VIIdsRed_10 ng/mL IL-6_day 4


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2

source_name: MDA-MB-175-VIIdsRed_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6, day 4_rep1


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6, day 4_rep3


title: MDA-MB-175-VIIdsRed untreated, day 4_rep1

source_name: MDA-MB-175-VIIdsRed untreated_day 4


title: MDA-MB-175-VIIdsRed untreated, day 4_rep3


title: MDA-MB-175-VIIdsRed treated with 50 ug Siltuximab, day 4_rep1

source_name: MDA-MB-175-VIIdsRed_50 ug Siltuximab_day 4


title: MDA-MB-175-VIIdsRed untreated, day 4_rep2


title: MDA-MB-175-VIIdsRed treated with 50 ug Siltuximab, day 4_rep2


title: MDA-MB-175-VIIdsRed treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3


title: MDA-MB-175-VIIdsRed untreated, day 1_rep1

source_name: MDA-MB-175-VIIdsRed untreated_day 1


title: MDA-MB-175-VIIdsRed untreated, day 1_rep2


title: Liver AdMafG rep1

city: Los Angeles

first: Thomas

middle: A

last: Vallim

state: CA

address: 650 Charles E. Young Drive South, A2-237 CHS

institute: UCLA

hyb_protocol: Illumina  Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: Illumina iScan confocal scanner using standard direct Hyb settings

data_processing: Data was processed using Illumina GenomeSuite V2011.1, 1.9.0

source_name: whole liver

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrepTM-96 RNA Amplification Kit

extract_protocol: RNA was extracted with QIAzol reagent, using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Ad-MafG


title: MDA-MB-175-VIIdsRed treated with 50 ug Siltuximab, day 4_rep3


title: Liver control rep3

value: Ad-Control (Ad-CMV)


title: MDA-MB-175-VIIdsRed untreated, day 0_rep2

source_name: MDA-MB-175-VIIdsRed untreated_day 0


title: MCF-7 treated with 10 ng/mL IL-6, day 6_rep1

source_name: MCF-7_10 ng/mL IL-6_day 6


title: MDA-MB-175-VIIdsRed untreated, day 1_rep3


title: Liver control rep2


title: Liver AdMafG rep2


title: Liver AdMafG rep3


title: MDA-MB-175-VIIdsRed untreated, day 0_rep1


title: MCF-7 treated with 10 ng/mL IL-6, day 6_rep2


title: MDA-MB-175-VIIdsRed untreated, day 0_rep3


title: Liver control rep1


title: MCF-7 untreated, day 6_rep2

source_name: MCF-7 untreated_day 6


title: MCF-7 treated with 10 ng/mL IL-6, day 5_rep2

source_name: MCF-7_10 ng/mL IL-6_day 5


title: MCF-7 untreated, day 6_rep1


title: SNm1

city: beijing

first: zhao

last: mengxin

address: Haidian District Zhongguancun Street

institute: tsinghua university

description: replicate 1

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a scanner (MS 200 Microarray Scanner, NimbieGen) using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) the data were then logarithmically transformed and divided by the mean value of each slide.; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: uncultured bacterium

source_name: Soil microbes in three zonal agricultural soil types

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

treatment_protocol: In August-September 2011, soil samples were collected from all of the plots. Ten soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

tag: sample site

value: Hailun

tag: soil type

value: Ultisol

tag: landuse of bare fallow, maize cropping or npk fertilization

value: maize cropping


title: MCF-7 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2

source_name: MCF-7_hMSC-CM + 50 ug Siltuximab_day 4

value: ERα-positive breast cancer cell line


title: MCF-7 treated with hMSC-CM, day 4_rep1

source_name: MCF-7_hMSC-CM_day 4


title: MCF-7 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1


title: SNf3

description: replicate 3

value: fertilization


title: MCF-7 treated with hMSC-CM, day 4_rep2


title: MCF-7 treated with 10 ng/mL IL-6, day 5_rep1

value: D1:10 ng/mL IL-6


title: MCF-7 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3

source_name: MCF-7_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4


title: MCF-7 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3

value: hMSC-CM + 50 ug/mL Siltuximab


title: MCF-7 untreated, day 5_rep2

source_name: MCF-7 untreated_day 5


title: MCF-7 untreated, day 5_rep1


title: SNm2

description: replicate 2


title: MCF-7 treated with 10 ng/mL IL-6, day 4_rep3

source_name: MCF-7_10 ng/mL IL-6_day 4


title: MCF-7 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2


title: Sm3

description: replicate 3

value: Yingtan


title: MCF-7 treated with 10 ng/mL IL-6, day 4_rep2


title: SN1

description: replicate 1

value: bare soil


title: MCF-7 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1

source_name: MCF-7_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4

value: D1:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: MCF-7 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1


title: MCF-7 treated with hMSC-CM, day 4_rep3

value: hMSC-CM


title: MCF-7 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3


title: SN3

description: replicate 3


title: SNf1

description: replicate 1


title: SN2

description: replicate 2


title: SNf2

description: replicate 2


title: SNm3

description: replicate 3


title: Sm2

description: replicate 2


title: Vizaya3

city: Cambridge

first: Luca

last: Pagani

state: UK

address: Henry Wellcome Building, Fitzwilliam Street

department: Biological Anthropology

institute: University of Cambridge

hyb_protocol: Followed Illumina standard protocol

scan_protocol: Followed Illumina standard protocol

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: Saliva

label_protocol: Followed Illumina standard protocol

extract_protocol: Extraction of genomic DNA from saliva was performed using standard extraction protocols.

value: F

tag: population

value: Vizayan (Filipino)

tag: region

value: Philippines


title: MCF-7 treated with 10 ng/mL IL-6, day 4_rep1


title: Vizaya1


title: Vizaya2


title: MCF-7 treated with 50 ug Siltuximab, day 4_rep3

source_name: MCF-7_50 ug Siltuximab_day 4

value: 50 ug/mL Siltuximab


title: MCF-7 treated with 50 ug Siltuximab, day 4_rep2


title: Viet_9

value: M

value: Vietnamese

value: Vietnam


title: MCF-7 untreated, day 4_rep1

source_name: MCF-7 untreated_day 4

value: untreated


title: Sm1

description: replicate 1

value: Ultisol

value: maize cropping


title: Viet_8


title: MCF-7 untreated, day 1_rep1

source_name: MCF-7 untreated_day 1

value: ERα-positive breast cancer cell line


title: MCF-7 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2


title: Sf3

description: replicate 3

value: fertilization


title: Viet_6


title: MCF-7 untreated, day 1_rep3


title: Vizaya4


title: Viet_36


title: SCm1

description: replicate 1

value: Fengqiu


title: MCF-7 untreated, day 1_rep2


title: Viet_5


title: EFM-19 treated with 10 ng/mL IL-6, day 6_rep2

source_name: EFM-19_10 ng/mL IL-6_day 6

value: D1:10 ng/mL IL-6


title: Sf1

description: replicate 1

value: Yingtan


title: SCm2

description: replicate 2


title: EFM-19 treated with 10 ng/mL IL-6, day 6_rep1


title: MCF-7 untreated, day 0_rep3

source_name: MCF-7 untreated_day 0


title: Viet_35


title: MCF-7 untreated, day 4_rep3


title: MCF-7 treated with 50 ug Siltuximab, day 4_rep1


title: MCF-7 untreated, day 4_rep2


title: SCm3

description: replicate 3


title: MCF-7 untreated, day 0_rep1


title: Viet_34


title: MCF-7 untreated, day 0_rep2


title: EFM-19 untreated, day 6_rep1

source_name: EFM-19 untreated_day 6


title: EFM-19 untreated, day 6_rep2


title: Sf2

description: replicate 2


title: Viet_33


title: Viet_32


title: EFM-19 treated with 10 ng/mL IL-6, day 5_rep1

source_name: EFM-19_10 ng/mL IL-6_day 5


title: EFM-19 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3

source_name: EFM-19_hMSC-CM + 50 ug Siltuximab_day 4

value: hMSC-CM + 50 ug/mL Siltuximab


title: EFM-19 treated with 10 ng/mL IL-6, day 5_rep2


title: SCf3

description: replicate 3


title: SCf1

description: replicate 1


title: SC3

description: replicate 3

value: bare soil


title: EFM-19 untreated, day 5_rep2

source_name: EFM-19 untreated_day 5


title: EFM-19 untreated, day 5_rep1


title: Viet_30

value: F


title: EFM-19 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2


title: EFM-19 treated with hMSC-CM, day 4_rep3

source_name: EFM-19_hMSC-CM_day 4

value: hMSC-CM


title: SCf2

description: replicate 2

source_name: Soil microbes in three zonal agricultural soil types


title: Viet_29


title: EFM-19 treated with hMSC-CM, day 4_rep2


title: EFM-19 treated with hMSC-CM, day 4_rep1


title: Viet_28


title: S3

description: replicate 3


title: Viet_27


title: EFM-19 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3

source_name: EFM-19_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4

value: D0:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: EFM-19 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1

source_name: EFM-19_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4

value: D1:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: SC1

description: replicate 1


title: EFM-19 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2


title: Viet_26


title: S2

description: replicate 2


title: EFM-19 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1


title: EFM-19 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2


title: EFM-19 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1


title: EFM-19 treated with 10 ng/mL IL-6, day 4_rep3

source_name: EFM-19_10 ng/mL IL-6_day 4


title: EFM-19 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3


title: SC2

description: replicate 2


title: S1

description: replicate 1


title: Viet_12


title: EFM-19 treated with 10 ng/mL IL-6, day 4_rep2


title: Viet_24


title: Viet_11

value: M


title: Viet_10

value: Vietnamese


title: EFM-19 treated with 10 ng/mL IL-6, day 4_rep1


title: EFM-19 untreated, day 4_rep3

source_name: EFM-19 untreated_day 4


title: Murut8

value: Murut

value: Brunei


title: EFM-19 treated with 50 ug Siltuximab, day 4_rep2

source_name: EFM-19_50 ug Siltuximab_day 4

value: 50 ug/mL Siltuximab


title: NSm3

description: replicate 3

value: Mollisol

value: maize cropping


title: EFM-19 treated with 50 ug Siltuximab, day 4_rep3

value: ERα-positive breast cancer cell line


title: EFM-19 untreated, day 4_rep1

value: untreated


title: EFM-19 untreated, day 4_rep2


title: EFM-19 untreated, day 1_rep3

source_name: EFM-19 untreated_day 1


title: EFM-19 treated with 50 ug Siltuximab, day 4_rep1


title: Murut7

source_name: Saliva


title: NSf3

description: replicate 3

value: fertilization


title: Murut9


title: EFM-19 untreated, day 1_rep2


title: NSf1

description: replicate 1

value: Yingtan


title: NSf2

description: replicate 2


title: NS2

description: replicate 2


title: Murut6


title: EFM-19 untreated, day 1_rep1


title: HCC1428 treated with 10 ng/mL IL-6, day 6_rep2

source_name: HCC1428_10 ng/mL IL-6_day 6

value: D1:10 ng/mL IL-6


title: NSm1

description: replicate 1


title: NSm2

description: replicate 2


title: HCC1428 treated with 10 ng/mL IL-6, day 6_rep1


title: Murut4


title: Murut5


title: HCC1428 untreated, day 6_rep2

source_name: HCC1428 untreated_day 6


title: EFM-19 untreated, day 0_rep3

source_name: EFM-19 untreated_day 0


title: Nm3

description: replicate 3

value: Hailun


title: EFM-19 untreated, day 0_rep2


title: Murut22

description: Sample removed due to QC or inbreeding

value: F


title: HCC1428 treated with 10 ng/mL IL-6, day 5_rep2

source_name: HCC1428_10 ng/mL IL-6_day 5


title: Nm2

description: replicate 2


title: NS1

description: replicate 1

value: bare soil


title: EFM-19 untreated, day 0_rep1


title: Nm1

description: replicate 1


title: HCC1428 untreated, day 6_rep1


title: HCC1428 untreated, day 5_rep1

source_name: HCC1428 untreated_day 5


title: Murut23


title: Murut21

description: Sample removed due to QC or inbreeding


title: NS3

description: replicate 3


title: HCC1428 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2

source_name: HCC1428_hMSC-CM + 50 ug Siltuximab_day 4

value: hMSC-CM + 50 ug/mL Siltuximab


title: Murut3


title: HCC1428 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3


title: Murut20


title: Nf2

description: replicate 2


title: HCC1428 treated with hMSC-CM, day 4_rep1

source_name: HCC1428_hMSC-CM_day 4

value: hMSC-CM


title: Nf3

description: replicate 3


title: Nf1

description: replicate 1


title: HCC1428 treated with hMSC-CM, day 4_rep3


title: Murut2

description: Sample removed due to QC or inbreeding


title: HCC1428 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2

source_name: HCC1428_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4

value: D1:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: HCC1428 untreated, day 5_rep2


title: Murut18

value: M


title: HCC1428 treated with hMSC-CM, day 4_rep2


title: HCC1428 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1


title: HCC1428 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3

source_name: HCC1428_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4

value: D0:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: NCm2

description: replicate 2

source_name: Soil microbes in three zonal agricultural soil types

value: Fengqiu


title: HCC1428 treated with 10 ng/mL IL-6, day 4_rep3

source_name: HCC1428_10 ng/mL IL-6_day 4


title: HCC1428 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3


title: HCC1428 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2


title: HCC1428 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1


title: HCC1428 treated with 10 ng/mL IL-6, day 5_rep1


title: NCm1

description: replicate 1


title: Murut17

description: Sample removed due to QC or inbreeding

value: Murut

value: Brunei


title: HCC1428 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1


title: HCC1428 treated with 10 ng/mL IL-6, day 4_rep1


title: HCC1428 treated with 10 ng/mL IL-6, day 4_rep2


title: HCC1428 treated with 50 ug Siltuximab, day 4_rep3

source_name: HCC1428_50 ug Siltuximab_day 4

value: 50 ug/mL Siltuximab


title: NCf3

description: replicate 3

value: Mollisol


title: Murut19


title: HCC1428 treated with 50 ug Siltuximab, day 4_rep2

value: ERα-positive breast cancer cell line


title: Murut16


title: NCf2

description: replicate 2

value: fertilization


title: HCC1428 untreated, day 4_rep3

source_name: HCC1428 untreated_day 4

value: untreated


title: HCC1428 treated with 50 ug Siltuximab, day 4_rep1


title: NCf1

description: replicate 1


title: NC3

description: replicate 3


title: Murut15

description: Sample removed due to QC or inbreeding


title: Murut14


title: Murut13


title: HCC1428 untreated, day 4_rep1


title: Murut11


title: HCC1428 untreated, day 4_rep2


title: Murut10


title: HCC1428 untreated, day 1_rep1

source_name: HCC1428 untreated_day 1


title: NC2

description: replicate 2


title: HCC1428 untreated, day 1_rep2


title: HCC1428 untreated, day 1_rep3


title: BT-483 treated with 10 ng/mL IL-6, day 6_rep2

value: D1:10 ng/mL IL-6


title: BT-483 untreated, day 6_rep1

source_name: BT-483 untreated_day 6


title: BT-483 untreated, day 5_rep1

source_name: BT-483 untreated_day 5


title: NC1

description: replicate 1


title: BT-483 untreated, day 6_rep2


title: BT-483 treated with 10 ng/mL IL-6, day 6_rep1


title: Murut1

source_name: Saliva


title: Murut12


title: N1

description: replicate 1

value: Hailun


title: Malay8

value: F

value: Malay

value: Malaysia


title: BT-483 untreated, day 5_rep2


title: BT-483 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2

source_name: BT-483_hMSC-CM + 50 ug Siltuximab_day 4

value: hMSC-CM + 50 ug/mL Siltuximab


title: BT-483 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3


title: BT-483 treated with 10 ng/mL IL-6, day 5_rep1


title: CSm3

description: replicate 3

value: Yingtan

value: Inceptisol

value: maize cropping


title: BT-483 treated with hMSC-CM, day 4_rep3

source_name: BT-483_hMSC-CM_day 4

value: hMSC-CM


title: Malay7


title: BT-483 treated with hMSC-CM, day 4_rep2


title: BT-483 treated with hMSC-CM, day 4_rep1


title: BT-483 treated with 10 ng/mL IL-6, day 5_rep2


title: N3

description: replicate 3

value: bare soil


title: BT-483 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1


title: Malay5


title: CSm1

description: replicate 1


title: Malay3

value: M


title: BT-483 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3

source_name: BT-483_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4

value: D1:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: Malay25


title: CSf3

description: replicate 3


title: CSf2

description: replicate 2


title: BT-483 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2

source_name: BT-483_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4

value: D0:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: CSm2

description: replicate 2


title: BT-483 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3

value: ERα-positive breast cancer cell line


title: BT-483 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1


title: N2

description: replicate 2

value: Mollisol


title: BT-483 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2


title: Malay23


title: Malay24


title: BT-483 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1


title: Malay21


title: CSf1

description: replicate 1

value: fertilization


title: BT-483 treated with 10 ng/mL IL-6, day 4_rep2

value: D1:10 ng/mL IL-6


title: CS3

description: replicate 3


title: BT-483 treated with 10 ng/mL IL-6, day 4_rep3


title: Malay20


title: Malay2


title: Malay17


title: BT-483 treated with 50 ug Siltuximab, day 4_rep2

source_name: BT-483_50 ug Siltuximab_day 4

value: 50 ug/mL Siltuximab


title: Malay16

value: F


title: BT-483 treated with 10 ng/mL IL-6, day 4_rep1


title: BT-483 treated with 50 ug Siltuximab, day 4_rep4


title: BT-483 treated with 50 ug Siltuximab, day 4_rep1


title: BT-483 treated with 50 ug Siltuximab, day 4_rep3


title: BT-483 untreated, day 4_rep2

source_name: BT-483 untreated_day 4

value: untreated


title: Malay15

value: Malay

value: Malaysia


title: BT-483 untreated, day 4_rep1


title: CNm2

description: replicate 2

value: Hailun


title: CNm3

description: replicate 3

value: Inceptisol


title: CS1

description: replicate 1

value: Yingtan


title: BT-483 untreated, day 1_rep3

source_name: BT-483 untreated_day 1


title: CS2

description: replicate 2


title: NCm3

description: replicate 3

value: Fengqiu

value: maize cropping


title: Malay14


title: BT474 treated with 10 ng/mL IL-6, day 6_rep2

source_name: BT474_10 ng/mL IL-6_day 6


title: BT474 treated with 10 ng/mL IL-6, day 6_rep1


title: BT-483 untreated, day 1_rep1


title: BT474 untreated, day 6_rep1

source_name: BT474 untreated_day 6


title: BT-483 untreated, day 1_rep2


title: BT474 untreated, day 6_rep2


title: CNf3

description: replicate 3

source_name: Soil microbes in three zonal agricultural soil types


title: BT474 treated with 10 ng/mL IL-6, day 5_rep2

source_name: BT474_10 ng/mL IL-6_day 5


title: CNm1

description: replicate 1


title: CNf2

description: replicate 2


title: Malay13

value: M


title: BT474 untreated, day 5_rep2

source_name: BT474 untreated_day 5


title: CN3

description: replicate 3

value: bare soil


title: CNf1

description: replicate 1


title: Malay10


title: Malay1


title: Malay_9


title: BT474 untreated, day 5_rep1


title: BT474 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3

source_name: BT474_hMSC-CM + 50 ug Siltuximab_day 4

value: hMSC-CM + 50 ug/mL Siltuximab


title: BT474 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1

value: ERα-positive breast cancer cell line


title: CN1

description: replicate 1


title: BT474 treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2


title: BT474 treated with hMSC-CM, day 4_rep1

source_name: BT474_hMSC-CM_day 4

value: hMSC-CM


title: BT474 treated with 10 ng/mL IL-6, day 5_rep1


title: Malay_6


title: BT474 treated with hMSC-CM, day 4_rep3


title: Malay_4


title: Cm3

description: replicate 3


title: CN2

description: replicate 2


title: BT474 treated with hMSC-CM, day 4_rep2


title: BT474 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3

source_name: BT474_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4

value: D1:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: Cm2

description: replicate 2


title: Malay_22


title: Malay_19


title: Malay_18


title: Cm1

description: replicate 1


title: BT474 treated with 10 ng/mL IL-6, day 4_rep3

source_name: BT474_10 ng/mL IL-6_day 4

value: D1:10 ng/mL IL-6


title: BT474 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1

source_name: BT474_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4

value: D0:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: BT474 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2


title: Cf1

description: replicate 1

value: fertilization


title: BT474 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2


title: BT474 treated with 10 ng/mL IL-6, day 4_rep2


title: BT474 treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1


title: BT474 treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3


title: Malay_12

source_name: Saliva


title: Cf3

description: replicate 3


title: Malay_11


title: Luz_9

value: F

value: Luzon (Filipino)

value: Philippines


title: BT474 treated with 10 ng/mL IL-6, day 4_rep1


title: aCGH of KMBC_2

city: Kanazawa

first: Kazunori

last: Kawaguchi

address: 13-1 Takara-Machi

department: Gastroenterology

country: Japan

institute: Kanazawa University

description: cholangiocarcinoma

hyb_protocol: Labeled samples were hybridized onto slides at 37 °C overnight. The microarray technique was similar to the conventional method.

scan_protocol: A microarray scanner was used to calculate the intensity of each dye.

data_processing: The ratio of the green:red channel of each clone was calculated and all CGH ratios were converted to log base 2 (log2 ratios). The clones with log2 ratios that exceeded ± 0.25 were considered gain and loss of the copy number.  Note that the ID_REF is the Plate position in the raw data files and Plate No in the *Ratio.txt files.

source_name: cholangiocarcinoma

label_protocol: 0.5 micrograms of genomic DNA from tumor cells was labeled by Cy3-dUTP and the same amount of control genomic DNA from peripheral blood mononuclear cells of healthy volunteers was labeled by Cy5-dUTP.

growth_protocol: These cell lines were cultured in DMEM with 10% FBS and Penicillin-Streptomycin.

extract_protocol: Genomic DNA was treated by proteinase K in the presence of SDS and salt, following phenol-chloroform extraction and ethanol precipitation.

value: cholangiocarcinoma

value: KMBC

tag: sample type

value: reference

value: peripheral blood mononuclear cells

value: healthy


title: BT474 untreated, day 4_rep2

source_name: BT474 untreated_day 4

value: untreated


title: Cf2

description: replicate 2

value: Fengqiu

value: Inceptisol


title: aCGH of KMBC_1

description: cholangiocarcinoma

tag: disease state

source_name: peripheral blood mononuclear cells of healthy volunteers


title: Luz_8


title: BT474 untreated, day 4_rep3

value: ERα-positive breast cancer cell line


title: Luz_6


title: BT474 untreated, day 1_rep2

source_name: BT474 untreated_day 1


title: BT474 treated with 50 ug Siltuximab, day 4_rep1

source_name: BT474_50 ug Siltuximab_day 4

value: 50 ug/mL Siltuximab


title: BT474 untreated, day 1_rep3


title: BT474 treated with 50 ug Siltuximab, day 4_rep2


title: BT474 treated with 50 ug Siltuximab, day 4_rep3


title: Luz_5


title: aCGH of HeLa_2

description: cervical cancer

source_name: cervical cancer

value: cervical cancer

value: HeLa


title: aCGH of HeLa_1

description: cervical cancer


title: MDA-MB-134VI treated with 10 ng/mL IL-6, day 6_rep2

source_name: MDA-MB-134VI_10 ng/mL IL-6_day 6

value: D1:10 ng/mL IL-6


title: C2

description: replicate 2

value: bare soil


title: aCGH of Huh6_2

description: hepatoma

source_name: hepatoma

value: hepatoma


title: MDA-MB-134VI treated with 10 ng/mL IL-6, day 5_rep2

source_name: MDA-MB-134VI_10 ng/mL IL-6_day 5


title: C1

description: replicate 1

source_name: Soil microbes in three zonal agricultural soil types


title: MDA-MB-134VI treated with 10 ng/mL IL-6, day 5_rep1


title: BT474 untreated, day 4_rep1


title: MDA-MB-134VI untreated, day 6_rep2

source_name: MDA-MB-134VI untreated_day 6


title: BT474 untreated, day 1_rep1


title: MDA-MB-134VI untreated, day 5_rep2

source_name: MDA-MB-134VI untreated_day 5


title: Luz_4

value: F

value: Luzon (Filipino)


title: MDA-MB-134VI untreated, day 6_rep1


title: Luz_7

value: Philippines


title: MDA-MB-134VI treated with 10 ng/mL IL-6, day 6_rep1


title: aCGH of Huh6_1

description: hepatoma


title: Luz_3


title: Luz_2


title: Luz_12


title: aCGH of PLC/PRF/5_2

description: hepatoma


title: Luz_10


title: aCGH of PLC/PRF/5_1

description: hepatoma


title: Luz_11


title: MDA-MB-134VI treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3

source_name: MDA-MB-134VI_hMSC-CM + 50 ug Siltuximab_day 4

value: hMSC-CM + 50 ug/mL Siltuximab


title: aCGH of HLE_2

description: hepatoma

value: HLE

value: reference


title: aCGH of HLE_1

description: hepatoma

value: peripheral blood mononuclear cells

value: healthy


title: Luz_1


title: MDA-MB-134VI treated with hMSC-CM, day 4_rep3

source_name: MDA-MB-134VI_hMSC-CM_day 4

value: hMSC-CM


title: MDA-MB-134VI treated with hMSC-CM, day 4_rep1


title: MDA-MB-134VI treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3

source_name: MDA-MB-134VI_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4

value: D1:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: MDA-MB-134VI treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1

value: ERα-positive breast cancer cell line


title: MDA-MB-134VI treated with hMSC-CM, day 4_rep2


title: MDA-MB-134VI treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2


title: aCGH of SKHep1_1

description: hepatoma


title: MDA-MB-134VI treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2


title: aCGH of SKHep1_2

description: hepatoma


title: aCGH of HepG2_3

description: hepatoma


title: MDA-MB-134VI treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2

source_name: MDA-MB-134VI_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4

value: D0:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: MDA-MB-134VI treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1


title: MDA-MB-134VI treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3


title: MDA-MB-134VI treated with 10 ng/mL IL-6, day 4_rep3

source_name: MDA-MB-134VI_10 ng/mL IL-6_day 4


title: MDA-MB-134VI treated with 10 ng/mL IL-6, day 4_rep2


title: lebbo18

source_name: Saliva

value: M

value: Lebbo

value: Indonesia


title: aCGH of HepG2_2

description: hepatoma


title: lebbo 9


title: lebbo 8


title: lebbo 7

description: Sample removed due to QC or inbreeding


title: lebbo19


title: aCGH of HepG2_1

description: hepatoma


title: MDA-MB-134VI treated with 10 ng/mL IL-6, day 4_rep1

value: D1:10 ng/mL IL-6


title: MDA-MB-134VI treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1


title: MDA-MB-134VI treated with 50 ug Siltuximab, day 4_rep3

source_name: MDA-MB-134VI_50 ug Siltuximab_day 4

value: 50 ug/mL Siltuximab


title: lebbo 6


title: aCGH of Hep3B_1

description: hepatoma

value: hepatoma

source_name: peripheral blood mononuclear cells of healthy volunteers


title: MDA-MB-134VI untreated, day 5_rep1

value: untreated


title: MDA-MB-134VI treated with 50 ug Siltuximab, day 4_rep2


title: lebbo 5

value: F


title: MDA-MB-134VI untreated, day 4_rep3

source_name: MDA-MB-134VI untreated_day 4


title: MDA-MB-134VI untreated, day 4_rep1


title: lebbo 4

description: Sample removed due to QC or inbreeding


title: C3

description: replicate 3

value: Fengqiu

value: Inceptisol

value: bare soil


title: aCGH of Hep3B_2

description: hepatoma

value: reference

value: peripheral blood mononuclear cells


title: aCGH of Huh7_2

description: hepatoma

value: healthy


title: T47D untreated, day 6_rep2

source_name: T47D untreated_day 6


title: lebbo 3


title: MDA-MB-134VI untreated, day 4_rep2


title: aCGH of Huh7_3

description: hepatoma


title: T47D treated with 10 ng/mL IL-6, day 6_rep2

source_name: T47D_10 ng/mL IL-6_day 6


title: MDA-MB-134VI untreated, day 1_rep1

source_name: MDA-MB-134VI untreated_day 1


title: MDA-MB-134VI untreated, day 1_rep2


title: lebbo 17


title: MDA-MB-134VI untreated, day 1_rep3


title: MDA-MB-134VI treated with 50 ug Siltuximab, day 4_rep1


title: T47D untreated, day 6_rep1


title: T47D treated with 10 ng/mL IL-6, day 6_rep1


title: lebbo 16


title: aCGH of Huh7_1

description: hepatoma

source_name: hepatoma


title: T47D treated with 10 ng/mL IL-6, day 5_rep1

source_name: T47D_10 ng/mL IL-6_day 5


title: lebbo 15


title: Wild type cells, rep2

city: Gothenburg

first: Jeanette

middle: Annika

last: Nilsson

address: Medicinaregatan 9C

department: Chemistry and Molecular Biology

country: Sweden

institute: Gothenburg university

description: HC11 cell line a clone of the COMMA-1D mouse (Balb/c) mammary epithelial cell line

hyb_protocol: Done by the SCIBLU Micoarray Resourse Center (MARC), Lund University, Sweden

data_processing: RMA normalization, done by the SCIBLU Micoarray Resourse Center (MARC), Lund University, Sweden

source_name: Mammary epithelial HC11 cells

growth_protocol: The HC11 cells were grown at 37°C in a 5% CO2/95% air atmosphere in RPMI-1640 medium supplemented with 10% FCS, 1% PEST, 5 μg/ml insulin and 10ng/ml EGF.

value: Mammary epithelial


title: Wild type cells, rep1

scan_protocol: Done by the SCIBLU Micoarray Resourse Center (MARC), Lund University, Sweden


title: T47D untreated, day 5_rep2

source_name: T47D untreated_day 5

value: ERα-positive breast cancer cell line


title: Wild type cells, rep3

label_protocol: Done by the SCIBLU Micoarray Resourse Center (MARC), Lund University, Sweden


title: lebbo 14


title: T47D treated with hMSC-CM + 50 ug Siltuximab, day 4_rep3

source_name: T47D_hMSC-CM + 50 ug Siltuximab_day 4

value: hMSC-CM + 50 ug/mL Siltuximab


title: T47D treated with hMSC-CM + 50 ug Siltuximab, day 4_rep2


title: NFI-C2 transfected cells, rep 3

tag: transfected construct


title: T47D treated with hMSC-CM, day 4_rep2

source_name: T47D_hMSC-CM_day 4

value: hMSC-CM


title: T47D treated with 10 ng/mL IL-6, day 5_rep2


title: T47D treated with hMSC-CM + 50 ug Siltuximab, day 4_rep1


title: NFI-C2 transfected cells, rep 2


title: lebbo 12

value: M

value: Lebbo


title: T47D treated with hMSC-CM, day 4_rep1


title: NFI-C2 transfected cells, rep 1


title: lebbo 11

value: Indonesia


title: T47D treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep2

source_name: T47D_10 ng/mL IL-6 d1 + 50 ug Siltuximab d1_day 4

value: D1:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: T47D treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep3

source_name: T47D_10 ng/mL IL-6 d0 + 50 ug Siltuximab d1_day 4

value: D0:10 ng/mL IL-6 + D1:50 ug/mL Siltuximab


title: T47D treated with hMSC-CM, day 4_rep3


title: lebbo 10

description: Sample removed due to QC or inbreeding


title: lebbo 13


title: T47D treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep3


title: FoxF1 transfected cells, rep 2


title: T47D treated with 10 ng/mL IL-6, day 4_rep3

source_name: T47D_10 ng/mL IL-6_day 4

value: D1:10 ng/mL IL-6


title: T47D treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep1


title: lebbo 1


title: T47D treated with 10 ng/mL IL-6 d0 + 50 ug Siltuximab d1, day 4_rep2


title: FoxF1 transfected cells, rep 1


title: T47D treated with 10 ng/mL IL-6, day 4_rep1


title: FoxF1 transfected cells, rep 3


title: Igorot7

value: F

value: Kankanaey (Igorot)

value: Philippines


title: T47D treated with 10 ng/mL IL-6, day 4_rep2


title: Igorot6

description: Sample removed due to QC or inbreeding


title: Igorot5


title: T47D treated with 50 ug Siltuximab, day 4_rep1

source_name: T47D_50 ug Siltuximab_day 4

value: 50 ug/mL Siltuximab


title: Igorot4

source_name: Saliva


title: T47D treated with 50 ug Siltuximab, day 4_rep3


title: T47D untreated, day 4_rep3

source_name: T47D untreated_day 4

value: untreated


title: T47D treated with 50 ug Siltuximab, day 4_rep2


title: Igorot9


title: T47D untreated, day 1_rep3

source_name: T47D untreated_day 1


title: HD neurons iPSHD34 3m r1

city: Moscow

first: Evgeny

last: Nekrasov

address: gubkina, 3

country: Russia

institute: Vavilov Institute of General Genetics

description:
SAMPLE 11
replicate 1
9345344033_K_Grn.idat

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was normalised using Genome Studio.

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit.

extract_protocol: RNA was extracted with the Qiagen QIAamp RNA Blood Mini Kit, followed by DNase I treatment and ethanol precipitation. Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: HD

value: 3 months

tag: tissue

value: striatum-like

value: iPSCs derived GABA MS-like neurons


title: T47D untreated, day 4_rep1

value: ERα-positive breast cancer cell line

tag: time point (day)


title: 56559

hyb_protocol: Biotin-double-stranded cDNA (3.75 μg) was hybridized, washed, stained, and scanned with the Affymetrix GeneTitan Instrument on an Affymetrix Human Gene 1.1 ST array plate (Affymetrix).  For some samples 200 ng of total RNA or 25 µg senseRNA or 5 µg double-stranded cDNA was not available.  In that case, all the available material was used.

scan_protocol: standard Affymetrix protocol

data_processing:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.1.0/entrezg.download/HuGene11stv1_Hs_ENTREZG_15.1.0.zip
Raw Affymetrix gene expression data were pre-processed with RMA and summarized using the HU-gene11stv1hsentrezg 15.0.0.

source_name: FFPE tumor sample

label_protocol: A total of 25 μg SenseRNA was reverse transcribed and double-stranded cDNA was generated using the Biotin Labeling Kit for ST/Exon Arrays (Genisphere).  Using the same kit, 5 μg of double-stranded cDNA was fragmented and end-labeled with biotin.

extract_protocol: From each block four slices of 10 µm each were cut and transferred to a 1.5 ml Eppendorf tube.  Paraffin was removed using Deparaffinization Solution (Qiagen).  The tissue was then lyzed in proteinase K digestion (PKD) buffer (Qiagen).  RNA isolation was continued using the RNeasy FFPE kit (Qiagen) according to the manufacturer’s instructions.  The RNA concentration of all the samples was determined on a Nanodrop-8000 UV-Vis Spectrophotometer (Thermo Scientific).  For a selection of samples, the RNA quality was determined with the RNA 6000 Nano LabChip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions.  SenseRNA was generated from 200 ng of total RNA using the Sensation RNA Amplification Kit (Genisphere, Hatfield, PA, USA).

tag: tissue type

value: FFPE tumor sample

tag: panoptic il6


title: T47D untreated, day 1_rep2


title: WT neurons hESM01 3m r2

description:
SAMPLE 10
replicate 2
9345344033_J_Grn.idat

value: wildtype

tag: age


title: Igorot3

tag: gender


title: T47D untreated, day 1_rep1

tag: cell type

tag: treatment


title: 51563


title: 51558


title: 42862


title: HD neurons iPSHD34 3m r2

description:
SAMPLE 12
replicate 2
9345344033_L_Grn.idat


title: T47D untreated, day 4_rep2

tag: cell line


title: T47D treated with 10 ng/mL IL-6 d1 + 50 ug Siltuximab d1, day 4_rep1


title: HD neurons iPSHD22 2m r2

description:
SAMPLE 6
replicate 2
9345344033_F_Grn.idat

value: 2 months


title: HD neurons iPSHD22 3m r2

description:
SAMPLE 8
replicate 2
9345344033_H_Grn.idat


title: 41896


title: Igorot23

value: M


title: 51560


title: Igorot22


title: HD neurons iPSHD22 3m r1

description:
SAMPLE 7
replicate 1
9345344033_G_Grn.idat


title: Igorot20


title: 41623


title: Igorot2


title: 44589


title: Igorot19


title: 51257


title: 43774


title: 42891


title: 51306


title: Igorot21


title: 44642


title: 51559


title: 51264


title: 41389


title: WT neurons endo-iPS12 3m r2

description:
SAMPLE 4
replicate 2
9345344033_D_Grn.idat


title: 51556


title: WT neurons endo-iPS12 3m r1

description:
SAMPLE 3
replicate 1
9345344033_C_Grn.idat


title: Igorot17


title: WT neurons endo-iPS12 2m r1

description:
SAMPLE 1
replicate 1
9345344033_A_Grn.idat


title: Igorot18


title: Igorot16


title: 36427