title: 41 Tg islets, biological replicate 1

city: Rehovot

first: MIchael

middle: D

last: Walker

address: POB 26

institute: Weizmann Institute of Science

hyb_protocol: 2ug ss cDNA in 80 ul total volume were hybridized to a Mouse Gene 2.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: The analysis was carried out using Partek Genomic Suite software (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA. Probesets not assigned genes excluded

label_protocol: 250ng Total RNA were used for labeling. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit

growth_protocol: We isolated pancreatic islets of 5-6 month old C57BL/6 WT or 41 Tg mice. Islets were incubated in RPMI medium and total RNA was purified.

extract_protocol: Total RNA was isolated by Tri-Reagent (Molecular Research Center, Cincinnati, OH, USA) followed by Direct-zol RNA MiniPrep (Zymo Re- search, Irvine, CA, USA) according to manufacturer instructions.

treatment_protocol: comparison of WT to 41 Tg

value: Pancreatic islets


title: 10

status: Public on Aug 17 2016

type: RNA

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: PDAC

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U219 arrays, followed by staining and washing in a GeneChip Fluidics Station 450 (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the xps package of Bioconductor. Expression values are represented on a log2-scale.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: head of pancreas

label_protocol: RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the NuGEN Ovation Pico WTA System, an amount of 2 ng of total RNA was amplified and converted to cDNA. An amount of 5 ug of cDNA was fragmented and labeled with biotin using the NuGEN Encore Biotin Module.

growth_protocol: Snap-frozen tissue samples were stored in liquid nitrogen and/or at -80C in RNALater (Qiagen) until further use.

extract_protocol: total RNA was extracted using the RNeasy Mini kit (Qiagen) according the manufacturer's instructions. Only samples with an RNA integrity number (RIN) of >7.0 were used.

tag: tissue

value: pancreatic tumor

tag: Stage

tag: grouped stage

value: Early


title: 146

description: PDAC

source_name: body/tail of pancreas


title: WT islets, biological replicate 2

country: Israel

organism: Mus musculus


title: KO mLIF 6 hours Replicate 1

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: IDAT files from BeadStudio were read into the limma package for R using the read.idat function with Illumina manifest file MouseWG-6_V2_0_R3_11278593_A.bgx. Raw intensities were neqc background corrected with offset 16, quantile normalized then log2-transformed.

source_name: Primary calvarial osteoblasts

label_protocol: not provided.

growth_protocol: Cells were grown in osteoblast differentiation media (alpha-minimal essesential media containing 15% heat inactivated fetal bovine serum and 50ng/ml ascorbate) for 17 days.

extract_protocol: RNA was isolated with Trizol

treatment_protocol: Cells with treated with 10ng/ml of human OSM (R&D), mouse OSM (R&D) or human LIF (Chemicon).

tag: background strain

tag: cell type

value: osteocyte

tag: genotype

value: Osmr KO

tag: treatment

value: mLIF

tag: treatment time

value: 6 hours

tag: replicate

tag: date cells were defrosted

tag: beadchip barcode

tag: beadchip section

value: A


title: KO mLIF 1 hour Replicate 1

value: 1 hour

value: F


title: WT mLIF 1 hour Replicate 1

value: Osmr WT

value: C


title: KO mOSM 6 hours Replicate 1

value: mOSM


title: 41 Tg islets, biological replicate 2


title: WT control 1 hour Replicate 1

value: control

value: E


title: WT islets, biological replicate 1


title: 9

description: PDAC


title: WT hOSM 1 hour Replicate 1

value: hOSM

value: D


title: 126

description: PDAC

value: Advanced


title: 8

description: PDAC

value: pancreatic tumor


title: 11

description: PDAC

value: LNM


title: KO hOSM 6 hours Replicate 1

value: osteocyte

value: B


title: KO control 6 hours Replicate 1

value: Osmr KO


title: 12

description: PDAC


title: KO control 1 hour Replicate 1


title: 6

description: PDAC

value: Early


title: KO hOSM 1 hour Replicate 1


title: 4

description: PDAC


title: 7

description: PDAC


title: Hela_microRNA-26a mimics_rep1

city: Xi'an

first: Xiang

last: Zhang

address: Changle west road #169

country: China

institute: the Fourth Military Medical University

description: Gene expression after microRNA-26a mimics transfected Hela cells

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours 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), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Hela, miR-26a, replicate 1

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

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: cell line

value: HeLa

tag: gender

value: female

value: cervical cancer


title: 123

description: PDAC


title: KO mOSM 1 hour Replicate 1

value: 1 hour


title: 1

description: PDAC


title: Hela_negative control mimics_rep1

description: Gene expression after netative control mimics transfected Hela cells

source_name: Hela, negative control, replicate 1


title: 103

description: PDAC


title: 3

description: PDAC


title: 111

description: Control

source_name: Control sample

value: non-tumoral pancreatic tissue


title: Dox_1

city: Chicago

first: Jonna

last: Frasor

state: IL

address: 835 S. Wolcott MC901

department: Physiology and Biophysics

country: USA

institute: University of Illinois at Chicago

hyb_protocol: The GeneChip® Hybridization, Wash, and Stain Kit was used as per manufacturer’s protocols. The GeneChip® Fluidics Station 450 was used for washing and staining using fluidics script FS450_0002.

scan_protocol: Microarray chips were read on the GeneChip® Scanner 3000 7G with AGCC version 4.0.0.1567.

data_processing: RMA in Partek Genomics Suite 6.6

source_name: Dox, constitutively active IKK β-MCF-7 cells

label_protocol: Samples were labeled using the Affymetrix GeneChip® 3' IVT PLUS Reagent Kit as per manufacturer's protocols.

growth_protocol:
Cells were routinely maintained in Roswell Park Memorial Institute medium (RPMI) 1640 with phenol red (Life Technologies) supplemented with 10% tetracycline approved fetal bovine serum, 1% penicillin-streptomycin antibiotics,
1% non-essential amino acids, 2 mM L-glutamine and 6 ng/mL insulin and the selection markers Geneticin (100μg/mL) and Puromycin (1μg/mL)

extract_protocol: RNA was extracted, using Trizol followed by the RNeasy RNA Extraction Kit (Qiagen, Valencia, CA, USA) using on-column DNase I digestion.

treatment_protocol:
Before treatment, cells were cultured in phenol red-free RPMI 1640 medium supplemented with 5% charcoal-dextran-stripped tetracycline approved FBS, 1% penicillin-streptomycin antibiotics, 1% non-essential amino acids, 2 mM L-glutamine,
Geneticin (100μg/mL) and Puromycin (1μg/mL) for 48 hrs. Cells were then treated with E2, Dox or E2+Dox for 72 hrs.

value: constitutively active IKK β-MCF-7 cells

value: Dox


title: 7730

description: PDAC


title: E2_3

source_name: E2, constitutively active IKK β-MCF-7 cells


title: 2

description: PDAC


title: Dox_2


title: E2+Dox_1

source_name: E2+Dox, constitutively active IKK β-MCF-7 cells


title: Dox_3


title: E2_2


title: E2+Dox_3


title: E2+Dox_2


title: Vehicle_3

source_name: Vehicle, constitutively active IKK β-MCF-7 cells

value: Vehicle


title: E2_1


title: Vehicle_1


title: Vehicle_2


title: WT mOSM 1 hour Replicate 1

value: Osmr WT

value: mOSM


title: KLSF-INV16 transduced-rep 3

status: Public on Aug 16 2016

city: Birmingham

first: Chris

middle: Alan

last: Klug

state: AL

address: 1825 University Blvd

department: Microbiology

institute: University of Alabama at Birmingham

hyb_protocol: Biotinylated cRNA was fragmented by metal-induced hydrolysis and cRNA hybridized to arrays at 45C for 16 hours using Affymetrix hybridization kit reagents

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

molecule: polyA RNA

source_name: KSLF cells - INV16 retrovirus

label_protocol: cDNA was synthesized from purified poly-A RNA using Affymetrix 2 cycle cDNA amplifcation kit, which was used as template for synthesizing biotinylated cRNA using T7 polymerase-mediated RNA transcription in vitro with Affymetrix's GeneChip IVT Labeling Kit.

growth_protocol: Cells were cultured at 37 C in DMEM supplemented with 10% FBS, 50 ng/ml SCF, 5 ng/ml IL-6.

extract_protocol: RNA was isolated from sorted, GFP-positive cells by Trizol extraction followed by isopropanol precipitation and column purification using Qiagen RNAeasy microkit.

treatment_protocol: FACS sorted cells were cultured for 24 hr before transduction with retrovirus by incubation with retroviral supernatants in the presence of polybrene for 4 hr. Cells were cultured an additional 20 hr in fresh media before extraction of RNA.

tag: sorted cell population surface phenotype

value: lineage-negative, c-kit+, sca-1+, FLT3-negative

tag: transduced virus

value: INV16 retrovirus


title: KLSF-INV16 transduced-rep 1


title: KLSF-INV16 transduced-rep 4


title: KLSF-MIB control transduced-rep 4

source_name: KSLF cells - MIB control retrovirus

value: MIB control retrovirus


title: KLSF-MIB control transduced-rep 6


title: KLSF-INV16 transduced-rep 2


title: KLSF-MIB control transduced-rep 7


title: KLSF-MIB control transduced-rep 3


title: KLSF-INV16 ACD mutant transduced-rep 2

source_name: KSLF cells - INV16 ACD mutant retrovirus

value: INV16 ACD mutant retrovirus


title: KLSF-MIB control transduced-rep 5


title: KLSF-INV16 ACD mutant transduced-rep 3


title: E15.5-epithelium-Yy1_KO-rep1

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Rd

department: Genetics

institute: Rutgers University

description: Gene expression from mouse embryonic small intestinal epithelium at E15.5(Yy1ko)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: data were processed using R Bioconductor with gcrma normalization and limma package.

source_name: Mouse embryonic small intestinal epithelium at E15.5(Yy1ko)

label_protocol: total RNA was processed and hybridized according to Affymetrix instructions

growth_protocol: Mouse embryonic Epcam positive epithelium cells were isolated from E15.5 small intestine (proximal stomach to distal caecum) using magnetic selection.

extract_protocol: Cells were then dissolved in Trizol and RNA prepared by ethanol precipitation using 10ug LPA

treatment_protocol: Littermate controls were used to have similar treatment conditions for both YY1f/f and Yy1f/f; Shh-Cre embryos.

value: Yy1f/f; Shh-Cre

tag: age


title: MH

city: Beijing

first: Jugao

last: Fang

address: No. 1 Dongjiao Min Xiang, Dongcheng District

institute: Capital University of Medical Sciences attaches to Beijing Tongr

description: replicate 19

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: quantile normalized

source_name: HSCC tissue

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

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

tag: chemosensitivity

value: non-sensitive


title: E15.5-epithelium-WT-rep-2

description: Gene expression from mouse embryonic small intestinal epithelium at E15.5

source_name: Mouse embryonic small intestinal epithelium at E15.5

tag: tissue


title: E15.5-epithelium-Yy1_KO-rep2

value: Mouse embryonic small intestinal epithelium


title: E15.5-epithelium-WT-rep-1


title: HYW

description: replicate 18


title: LGZ

description: replicate 13


title: WZM

description: replicate 16


title: NSS

description: replicate 17


title: LFL

description: replicate 11

value: sensitive


title: SB

description: replicate 9


title: DXX

description: replicate 12


title: ZSY

description: replicate 10


title: YYT

description: replicate 14


title: LXJ

description: replicate 6


title: GBM

description: replicate 7


title: FKY

description: replicate 15


title: LPL

description: replicate 5


title: OCC-hiPS-27 [all]

city: Okayama

first: Akimasa

last: Seno

state: Okayama

address: 1-1, Tsushima-Naka, 1-chome, Kita-Ku

department: Applied Chemistry and Biotechnology

country: Japan

institute: Okayama University

description:
Gene expression of induced cancer stem cell induced from human iPS cell by Lu99B cell culture medium
OCC-hiPS-27

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized for 17 hours at 65°C with Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies) using parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity by Agilp in series supplementary file.

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of Lu99B, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: Using the RNeasy column purification (QIAGEN) total RNA was prepared.

treatment_protocol: Human iPS cells kept undifferentiated were cultured in induction medium to allow differentiation. During the induction of differentiation, half of the medium was exchanged every day and the cells were passaged once or twice every two weeks. The period of induction of differentiation was at least 28 days, and at most two months. The cells were cultured at 37 °C under the atmosphere of 2% CO2.

value: Female


title: LF

description: replicate 4


title: ZJH

description: replicate 8


title: OCC-hiPS-20 [all]

description:
Gene expression of induced cancer stem cell induced from human iPS cell by MOLT4 cell culture medium
OCC-hiPS-20

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of MOLT4, replicate 1


title: OCC-hiPS-19 [all]

description:
Gene expression of induced cancer stem cell induced from human iPS cell by MY cell culture medium
OCC-hiPS-19

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of MY, replicate 1


title: OCC-hiPS-17 [all]

description:
Gene expression of induced cancer stem cell induced from human iPS cell by CW-2 cell culture medium
OCC-hiPS-17

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of CW-2, replicate 1


title: OCC-hiPS-25 [all]

description:
Gene expression of induced cancer stem cell induced from human iPS cell by Li-7 cell culture medium
OCC-hiPS-25

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of Li-7, replicate 1


title: FYY

description: replicate 1


title: YZL

description: replicate 2


title: XZP

description: replicate 3


title: FWY

description: replicate 20


title: OCC-hiPS-16 [all]

description:
Gene expression of induced cancer stem cell induced from human iPS cell by ECC4 cell culture medium
OCC-hiPS-16

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of ECC4, replicate 1


title: OCC-hiPS-10 [all]

description:
Gene expression of induced cancer stem cell induced from human iPS cell by HT-29 cell culture medium
OCC-hiPS-10

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of HT-29, replicate 1


title: KLSF-INV16 ACD mutant transduced-rep 1


title: OCC-hiPS-6 [all]

description:
Gene expression of induced cancer stem cell induced from human iPS cell by ZR-75-1 cell culture medium
OCC-hiPS-6

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of ZR-75-1, replicate 1


title: OCC-hiPS-12 [all]

description:
Gene expression of induced cancer stem cell induced from human iPS cell by SKOV3 cell culture medium
OCC-hiPS-12

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of SKOV3, replicate 1


title: Liver_ treated_4day_WT_biological_rep 4

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

hyb_protocol: Standard Affymetrix Procedures

scan_protocol: Standard Affymetrix Procedures

data_processing:
Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's oligo-package
Robust Multichip Average preprocessing methodolgy allowing background subtraction, quantile normalization and summarization (via median-polish)
The text files associated with each sample contain processed data with the following columns: PROBE (probe set ID), INTENSITY (sample probe set normalized intensity), LOG10RATIO (INTENSITY - COMP_INTENSITY), COMP_INTENSITY (the average normalized probe set intensity of the four untreated control replicates of the same genotype, KO or WT).

label: Biotin

source_name: Liver_ treated_4day_WT

label_protocol: Standard Affymetrix Procedures

extract_protocol: Liver RNA was isolated using a modified guanidinium isothiocyanate method (TRIzol®, Invitrogen) and was further purified using silica membrane spin columns (RNeasy®, Qiagen, Valencia, CA).  RNA integrity was assessed by the RNA 6000 LabChip® kit using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

value: Wildtype

tag: strain

tag: Sex

value: Male

tag: chemical

value: Oltipraz

tag: vehicle

value: Corn Oil

tag: dose

value: 75 mg/kg/day

tag: route

value: Oral gavage

tag: number of doses

value: Liver


title: Liver_ treated_4day_WT_biological_rep 3

tag: genotype


title: Liver_ treated_4day_KO_biological_rep 4

source_name: Liver_ treated_4day_Nrf2-null_KO


title: Liver_ vehicle control_4day_WT_biological_rep 4

source_name: Liver_ vehicle control_4day_WT

value: 0 mg/kg/day


title: Liver_ treated_4day_WT_biological_rep 2


title: Liver_ vehicle control_4day_KO_biological_rep 1


title: Liver_ vehicle control_4day_WT_biological_rep 1


title: Liver_ treated_4day_KO_biological_rep 2


title: Liver_ vehicle control_4day_WT_biological_rep 3


title: Liver_ treated_4day_KO_biological_rep 1


title: Liver_ treated_4day_KO_biological_rep 3


title: Repeat-ChIp Input 2

type: genomic

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

hyb_protocol: Roche-Nimblegen, proprietary

scan_protocol: Roche-Nimblegen, proprietary

data_processing: Signalmap

molecule: genomic DNA

source_name: K562 cancer cell line

label_protocol: Roche-Nimblegen, proprietary

extract_protocol: cells growing asynchronously were crosslinked (10 min , 1 % formaldehyde, 23˚C) quenched for 10 min by 200 mM glycine, washed three times with PBS, and then resuspended in chromatin buffer containing 150 mM NaCl, 1% Triton X100, 0.1% SDS, 20 mM Tris HCl pH8.0, and 2 mM EDTA. DNA was sheared using Covaris S220, so that most fragments were in the 300-500 bp range. Chromatin was precipitated overnight with magnetic beads (DiaMag, Diagenode, Inc.) loaded with anti-CTCF or anti-BORIS antibodies. The precipitate was washed, crosslinks reversed, protein component was digested with proteinase K, and DNA was extracted using phenol/chloroform/isoamyl alcohol. DNA concentration was measured by Qubit (Life Technologies) and/or Nanodrop (Thermo Scientific) fluorimeters. The immunoprecipitated DNA was amplified using the Phi29 strand-displacement procedure (GE Bioscience) following the concatemerization of precipitated DNA fragments via ligation to double strand adaptors containing BamHI overhangs and internal SapI sites. Both amplified and nonamplified samples showed essentially the same relative enrichment for known sites of CTCF and BORIS binding. Following the amplification, adapters were removed by SapI digestion and agarose gel purification. Input DNA was used as a hybridization reference for the hybridization of amplified ChIP DNA

tag: antibody


title: BWS

description: replicate 1


title: Repeat-ChIp IP 6

value: anti-BORIS


title: Repeat-ChIp IP 2

value: anti-CTCF


title: Liver_ vehicle control_4day_KO_biological_rep 2


title: Liver_ vehicle control_4day_KO_biological_rep 3


title: Liver_ treated_4day_WT_biological_rep 1


title: Liver_ vehicle control_4day_KO_biological_rep 4


title: Repeat-ChIp IP 5


title: Repeat-ChIp IP 4


title: Repeat-ChIp Input 5


title: Repeat-ChIp IP 3


title: Repeat-ChIp Input 3


title: Repeat-ChIp Input 6


title: Repeat-ChIp IP 1


title: Liver_ vehicle control_4day_WT_biological_rep 2


title: Repeat-ChIp Input 1


title: Repeat-ChIp Input 4


title: Tibetan_McLeod_Ganj_sample_06

city: Salt Lake City

first: Lynn

last: Jorde

state: UT

department: Human Genetics

institute: University of Utah

description: Hybridized to GenomeWideSNP_6

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software. Contrast quality-control (QC) measurements, which measure how well homozygote and heterozygote genotype calls can be differentiated on the genotyping chip, were performed on each sample array using the Affymetrix. Genotypes were called using the Birdseed-v2 algorithm in the Affymetrix Genotyping Console Software.

source_name: Whole blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from whole blood using the Qiagen DNA Blood Mini Kit. Quantity was assessed using a Nanodrop Spectrophotometer.

tag: population

value: Tibetan McLeod Ganj


title: Tibetan_McLeod_Ganj_sample_05

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_51

description: Hybridized to GenomeWideSNP_6

value: Kashmiri Tibetan


title: Kashmiri_Tibetan_sample_23

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_47

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_24

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_48

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_03

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_02

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_12

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_07

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_08

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_25

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_18

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_25

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_27

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_19

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_30

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_01

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_24

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_21

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_52

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_17

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_Tibetan_sample_19

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_20

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_16

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_17

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_14

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_09

description: Hybridized to GenomeWideSNP_6


title: QT_94_TS

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

source_name: Luminal

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: Large Intestine

tag: region

value: TS


title: QT_94_CB

source_name: Center

value: CB


title: Tibetan_McLeod_Ganj_sample_12

description: Hybridized to GenomeWideSNP_6


title: QT_94_IF

source_name: Front

value: IF


title: QT_9_TS


title: QT_85_TS


title: QT_85_IF


title: QT_9_IF


title: QT_76_TS


title: Kashmiri_sample_26

description: Hybridized to GenomeWideSNP_6

value: Kashmiri


title: Tibetan_McLeod_Ganj_sample_08

description: Hybridized to GenomeWideSNP_6


title: Tibetan_McLeod_Ganj_sample_03

description: Hybridized to GenomeWideSNP_6


title: QT_9_CB


title: QT_76_IF


title: QT_85_CB


title: Kashmiri_sample_15

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_sample_25

description: Hybridized to GenomeWideSNP_6


title: QT_76_CB


title: Kashmiri_sample_21

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_sample_06

description: Hybridized to GenomeWideSNP_6


title: QT_63_TS


title: Kashmiri_sample_17

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_sample_02

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_sample_14

description: Hybridized to GenomeWideSNP_6


title: QT_63_CB


title: QT_47_IF


title: Kashmiri_sample_30

description: Hybridized to GenomeWideSNP_6


title: QT_47_CB


title: Kashmiri_sample_20

description: Hybridized to GenomeWideSNP_6


title: Kashmiri_sample_01

description: Hybridized to GenomeWideSNP_6


title: QT_31_CB


title: QT_173_TS


title: QT_31_IF


title: Kashmiri_sample_13

description: Hybridized to GenomeWideSNP_6


title: QT_47_TS


title: QT_162_IF


title: QT_173_IF


title: QT_173_CB


title: QT_162_CB


title: QT_31_TS


title: QT_147_IF


title: QT_147_TS


title: QT_139_IF


title: QT_162_TS


title: QT_139_TS


title: QT_147_CB


title: QT_134_TS


title: QT_134_CB


title: QT_13_IF


title: QT_13_CB


title: QT_124_CB


title: QT_139_CB


title: QT_13_TS


title: QT_124_TS


title: QT_124_IF


title: QT_117_IF


title: QT_117_CB


title: QT_63_IF


title: QT_107_TS


title: Col_08_CB

description: Large Intestine


title: QT_10_TS


title: Col_08_TS

description: Large Intestine

value: DTS


title: QT_10_IF


title: Col_05_TS

description: Large Intestine


title: Col_08_IF

description: Large Intestine


title: QT_117_TS


title: QT_10_CB


title: Col_05_CB

description: Large Intestine


title: QT_107_IF


title: Col_04_CB

description: Large Intestine


title: QT_107_CB


title: Col_05_IF

description: Large Intestine


title: Kashmiri_sample_11

description: Hybridized to GenomeWideSNP_6


title: QT_134_IF


title: Kashmiri_sample_22

description: Hybridized to GenomeWideSNP_6


title: Col_04_IF

description: Large Intestine


title: Col_03_IF

description: Large Intestine


title: Kashmiri_sample_27

description: Hybridized to GenomeWideSNP_6


title: Col_04_TS

description: Large Intestine


title: Col_91_RD

description: Large Intestine


title: Col_03_CB

description: Large Intestine


title: Col_91_MD

description: Large Intestine


title: Col_90_RD

description: Large Intestine


title: Col_03_TS

description: Large Intestine


title: Col_89_RD

description: Large Intestine


title: Col_88_MD

description: Large Intestine


title: Col_88_RD

description: Large Intestine


title: Col_90_MD

description: Large Intestine


title: Col_86_MD

description: Large Intestine


title: Col_90_FD

description: Large Intestine


title: Col_85_RD

description: Large Intestine


title: Col_84_MD

description: Large Intestine


title: Col_86_RD

description: Large Intestine


title: Col_86_FD

description: Large Intestine


title: Col_88_FD

description: Large Intestine


title: Col_84_RD

description: Large Intestine


title: Col_89_FD

description: Large Intestine


title: Col_84_FD

description: Large Intestine


title: Col_85_FD

description: Large Intestine


title: Col_91_FD

description: Large Intestine


title: Col_83_MD

description: Large Intestine


title: Col_85_MD

description: Large Intestine


title: Col_83_RD

description: Large Intestine


title: Col_89_MD

description: Large Intestine


title: Col_81_FD

description: Large Intestine


title: Col_82_FD

description: Large Intestine


title: Col_82_MD

description: Large Intestine


title: Col_81_RD

description: Large Intestine


title: Col_82_RD

description: Large Intestine


title: Col_81_MD

description: Large Intestine


title: Col_83_FD

description: Large Intestine


title: Col_80_RD

description: Large Intestine


title: Col_79_MD

description: Large Intestine


title: Col_79_FD

description: Large Intestine


title: Col_80_FD

description: Large Intestine


title: Col_80_MD

description: Large Intestine


title: Col_78_RD

description: Large Intestine


title: Col_76_RD

description: Large Intestine


title: Col_77_FD

description: Large Intestine


title: Col_77_RD

description: Large Intestine


title: Col_78_FD

description: Large Intestine


title: Col_76_MD

description: Large Intestine


title: Col_76_FD

description: Large Intestine


title: Col_71_RD

description: Large Intestine


title: Col_71_FD

description: Large Intestine


title: Col_79_RD

description: Large Intestine


title: Col_71_MD

description: Large Intestine


title: Col_68_MD

description: Large Intestine


title: Col_78_MD

description: Large Intestine


title: Col_66_RD

description: Large Intestine


title: Col_69_RD

description: Large Intestine


title: Col_70_RD

description: Large Intestine


title: Col_69_MD

description: Large Intestine


title: Col_70_FD

description: Large Intestine


title: Col_68_RD

description: Large Intestine


title: Col_69_FD

description: Large Intestine


title: Col_68_FD

description: Large Intestine


title: Col_67_MD

description: Large Intestine


title: Col_70_MD

description: Large Intestine


title: Col_77_MD

description: Large Intestine


title: Col_67_RD

description: Large Intestine


title: Col_66_MD

description: Large Intestine


title: Col_66_FD

description: Large Intestine


title: Col_65_FD

description: Large Intestine


title: Col_63_FD

description: Large Intestine


title: Col_64_RD

description: Large Intestine


title: Col_63_MD

description: Large Intestine


title: Col_65_RD

description: Large Intestine


title: Col_65_MD

description: Large Intestine


title: Col_63_RD

description: Large Intestine


title: Col_62_FD

description: Large Intestine


title: Col_64_FD

description: Large Intestine


title: Col_62_RD

description: Large Intestine


title: Col_64_MD

description: Large Intestine


title: Col_61_RD

description: Large Intestine


title: Col_61_FD

description: Large Intestine


title: Col_58_MD

description: Large Intestine


title: Col_59_RD

description: Large Intestine


title: Col_59_MD

description: Large Intestine


title: Col_57_MD

description: Large Intestine


title: Col_59_FD

description: Large Intestine


title: Col_56_MD

description: Large Intestine


title: Col_62_MD

description: Large Intestine


title: Col_57_FD

description: Large Intestine


title: Col_58_RD

description: Large Intestine


title: Col_57_RD

description: Large Intestine


title: Col_56_FD

description: Large Intestine


title: Col_67_FD

description: Large Intestine


title: Col_54_FD

description: Large Intestine


title: Col_55_FD

description: Large Intestine


title: Col_55_RD

description: Large Intestine


title: Col_55_MD

description: Large Intestine


title: Col_56_RD

description: Large Intestine


title: Col_54_MD

description: Large Intestine


title: Col_54_RD

description: Large Intestine


title: Col_52_RD

description: Large Intestine


title: Col_51_FD

description: Large Intestine


title: Col_51_RD

description: Large Intestine


title: Col_51_MD

description: Large Intestine


title: Col_61_MD

description: Large Intestine


title: Col_48_MD

description: Large Intestine


title: Col_46_RD

description: Large Intestine


title: Col_47_RD

description: Large Intestine


title: Col_50_FD

description: Large Intestine


title: Col_52_MD

description: Large Intestine


title: Col_52_FD

description: Large Intestine


title: Col_46_FD

description: Large Intestine


title: Col_48_FD

description: Large Intestine


title: Col_50_RD

description: Large Intestine


title: Col_45_RD

description: Large Intestine


title: Col_47_MD

description: Large Intestine


title: Col_46_MD

description: Large Intestine


title: Col_50_MD

description: Large Intestine


title: Col_44_MD

description: Large Intestine


title: Col_44_RD

description: Large Intestine


title: Col_45_FD

description: Large Intestine


title: Col_44_FD

description: Large Intestine


title: Col_58_FD

description: Large Intestine


title: Col_45_MD

description: Large Intestine


title: Col_45_S

description: Large Intestine

source_name: Metastasis


title: Col_47_FD

description: Large Intestine


title: exosomes derived from lung cancer cell A549

city: Nanjing

first: Jifeng

last: Feng

address: No.42, Baiziting

institute: Jiangsu Cancer Hospital

description: miRNA expression of exosomes derived from A549 cells

hyb_protocol: Dry  the labeled RNA with vacuum concentrator. Assemble Hybridization mixture with Hyb Spike-In according to the manufacturer's instructions  (#5190-0456, Agilent). Hybridization mixture hybridized to Agilent microRNA array (G4872A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with Wash Buffer 1 (Agilent) and Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 046064_D_F_20121223) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: exosomes from DDP sensitive A549 lung cancer cells

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 30μl concentrated exosomal RNA using the Agilent miRNA Complete Labeling and Hyb Kit (#5190-0456, Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was isolated using the Total RNA Purification Kit  (Norgen, Cat. 17200) according to the manufacturer's instructions from 200 μL of frozen exosome in PBS. The volume of the obtained RNA solution was 30 μL.

treatment_protocol: Exosome-depleted FBS was used to avoid the impact of exosomes. FBS was depleted of exosomes by ultracentrifugation at 1×106g at 4°C for 16h (Beckman Coulter Avanti J-30I, USA). After being incubated for 48-72h, the culture medium was harvested and isolated by ultracentrifugation. Briefly, cell culture medium was sequentially centrifuged at 300g for 10min, 2,000g for 15min, and 12,000g for 30min to remove floating cells and cellular debris. These were then passed through a 0.22μm filter. The supernatant was further ultracentrifuged at 1×106 g for 2h at 4°C, washed in phosphate-buffered saline (PBS), and submitted to a second ultracentrifugation in the same conditions. The final exosome pellets were used immediately or resuspended in 100μl of PBS and stored at −80°C for further analysis.

tag: phenotype

value: cancer cells sensitive to DDP


title: exosomes derived from cisplatin (DDP) resistant A549/DDP lung cancer cells

description: miRNA expression of exosomes derived from A549/DDP cells

source_name: exosomes from DDP resistant A549 lung cancer cells

value: cancer cells resistant to DDP


title: cisplatin(DDP) resistant A549 lung cancer cells

description: miRNA expression of A549/DDP cells

source_name: DDP resistant A549 lung cancer cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Agilent miRNA Complete Labeling and Hyb Kit (#5190-2305, Agilent) according to the manufacturer's instructions.

growth_protocol: Cells were growth in RPMI-1640 medium containing 10% fetal bovine serum. The cells were incubated at 37°C and 5% CO2 in a humidified atmosphere.The A549/DDP was successfully established from A549 in our laboratory, by exposing A549 to gradually increasing DDP concentrations, until the final concentration at 1μg/ml. To avoid the influence of drug to the A549/DDP cells, they were cultured in a drug-free medium for at least two weeks before subsequent experiments.

extract_protocol: RNA was isolated using the TRIzol Reagent  (Invitrogen) according to the manufacturer's instructions from A549 cells. The volume of the obtained RNA solution was 30 μL. The RNA quality passed the criteria OD260/280>1.8, OD260/238>1.8, and RIN> 8.

treatment_protocol: When cells grow close to full in the culture dish, cells were digested with trypsin. Cells were then collected to extract RNA.

value: resistant to DDP


title: lung cancer cell A549

description: miRNA expression of A549 cells

source_name: DDP sensitive A549 lung cancer cells

value: sensitive to DDP


title: Col_43_RD

description: Large Intestine


title: Col_43_MD

description: Large Intestine


title: Col_43_FD

description: Large Intestine


title: Col_42_RD

description: Large Intestine


title: Col_40_MD

description: Large Intestine


title: Col_42_MD

description: Large Intestine


title: Col_41_FD

description: Large Intestine


title: Col_48_RD

description: Large Intestine


title: Col_41_RD

description: Large Intestine


title: Col_40_RD

description: Large Intestine


title: Col_38_RD

description: Large Intestine


title: Col_38_MD

description: Large Intestine


title: Col_39_RD

description: Large Intestine


title: Col_39_MD

description: Large Intestine


title: Col_37_S

description: Large Intestine


title: Col_38_FD

description: Large Intestine


title: Col_37_RD

description: Large Intestine


title: Col_41_MD

description: Large Intestine


title: Col_37_FD

description: Large Intestine


title: Col_39_S

description: Large Intestine


title: Col_37_MD

description: Large Intestine


title: Col_40_FD

description: Large Intestine


title: Col_35_RD

description: Large Intestine


title: Col_36_FD

description: Large Intestine


title: Col_36_RD

description: Large Intestine


title: Col_36_S

description: Large Intestine


title: Col_34_RD

description: Large Intestine


title: Col_36_MD

description: Large Intestine


title: Col_35_MD

description: Large Intestine


title: Col_39_FD

description: Large Intestine


title: Col_33_RD

description: Large Intestine


title: Col_33_S

description: Large Intestine


title: Col_34_S

description: Large Intestine


title: Col_34_MD

description: Large Intestine


title: Col_33_MD

description: Large Intestine


title: Col_35_FD

description: Large Intestine


title: Col_33_FD

description: Large Intestine


title: Col_35_S

description: Large Intestine


title: Col_34_FD

description: Large Intestine


title: Col_32_FD

description: Large Intestine


title: Col_32_MD

description: Large Intestine


title: DAR95_CWI_POST

city: Collegeville

first: Johannes

middle: M

last: Freudenberg

state: Pennsylvania

address: 1250 S Collegeville Rd

institute: GlaxoSmithKline

description: DNA methylation data from vastus lateralis muscle tissue collected after 10 week training (CWI study arm)

hyb_protocol: DNA samples were amplified, labeled, hybridized to Illumina HumanMethylation450 BeadChips, and scanned using standard protocols (Expression Analysis, Inc., Durham, North Carolina, U.S.A.).

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting (Expression Analysis, Inc., Durham, North Carolina, U.S.A.).

data_processing: Data was processed using the using the minfi R/Bioconductor package.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Muscle tissue samples (~20mg) were collected under local anaethesia from the vastus lateralis muscle midway between the patella and iliac crest using the microbiopsy technique.

extract_protocol: Genomic DNA was extracted from muscle samples using standard protocols.

treatment_protocol: Participants were required to attend the laboratory on 24 occasions across a period of ≤12 weeks.  Visits 1-2 were performed a minimum of 72 h prior to visit 3, and were used to train and familiarise participants in three separate weight-lifting techniques.  Muscle tissue samples were collected from participants in visits 3 and 24 for analysis of epigenetic modification and gene expression.  In visits 4, 10, 17 and 23, participants were assessed for their 5 repetition maximum (RM) in the three weight-lifting techniques.  The remaining visits (5-9, 11-16 and 18-22) were strength training sessions, during which participants followed a lower limb strength training programme.  All visits took place a minimum of 48 h apart, with no more than 2 visits occurring in any 7 d period.  This programming allowed for a 10 week (2 sessions per week) training programme, with familiarisation included in the 2 weeks prior to this training period.  Immediately-post each strength training or assessment visit, the treatment group completed a CWI exposure, while the placebo group participants consumed a sham recovery drink.  Throughout the study period, participants were instructed to refrain from any strength-training outside of the prescribed programme and to continue their normal cycling training and dietary routines respectively.

value: vastus lateralis

tag: group

value: Cold-water Immersion

tag: time

value: Post

tag: participant

tag: batch


title: DAR85_PLA_PRE

description: DNA methylation data from vastus lateralis muscle tissue collected before 10 week training

tag: tissue

value: Placebo

value: Pre


title: Col_31_MD

description: Large Intestine


title: DAR81_CWI_POST

source_name: vastus lateralis muscle tissue collected after 10 week training (CWI study arm)


title: Col_31_FD

description: Large Intestine


title: Col_30_RD

description: Large Intestine


title: Col_31_S

description: Large Intestine


title: Col_31_RD

description: Large Intestine


title: DAR72_PLA_POST

description: DNA methylation data from vastus lateralis muscle tissue collected after 10 week training (Placebo study arm)


title: Col_32_RD

description: Large Intestine


title: Col_42_FD

description: Large Intestine


title: DAR85_PLA_POST

source_name: vastus lateralis muscle tissue collected after 10 week training (Placebo study arm)


title: Col_29_S

description: Large Intestine


title: DAR81_CWI_PRE

source_name: vastus lateralis muscle tissue collected before 10 week training


title: Col_30_S

description: Large Intestine


title: Col_30_FD

description: Large Intestine


title: DAR21_PLA_POST


title: Col_29_RD

description: Large Intestine


title: DAR32_PLA_POST


title: DAR21_PLA_PRE


title: Col_29_FD

description: Large Intestine


title: Differentially expressed genes by knocking down of FOXQ1-2 in PANC-1

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

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

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell line

tag: cell type

value: pancreatic cancer

tag: transfection

value: no transfection

source_name: si-FOXQ1-2 transfected cell line


title: DAR26_PLA_PRE

source_name: vastus lateralis muscle tissue collected before 10 week training (Placebo study arm)


title: DAR7_PLA_POST


title: DAR32_PLA_PRE


title: DAR57_CWI_PRE


title: Col_30_MD

description: Large Intestine

value: Large Intestine


title: Col_28_RD

description: Large Intestine


title: DAR26_PLA_POST


title: Col_28_FD

description: Large Intestine


title: Col_28_N

description: Large Intestine

source_name: Normal


title: Col_26_RD

description: Large Intestine


title: Col_26_MD

description: Large Intestine


title: DAR64_PLA_POST


title: DAR64_PLA_PRE


title: Col_28_MD

description: Large Intestine


title: Col_27_N

description: Large Intestine


title: Col_26_N

description: Large Intestine


title: DAR7_PLA_PRE


title: DAR95_CWI_PRE


title: DAR6_CWI_POST


title: Col_26_FD

description: Large Intestine


title: DAR72_PLA_PRE


title: Col_26_S

description: Large Intestine


title: Differentially expressed genes by knocking down of FOXQ1-1 in PANC-1

source_name: si-FOXQ1-1 transfected cell line


title: Identification of miR-99a-3p target genes in PC3

value: prostate cancer

source_name: miR-99a-3p transfected cell line


title: Identification of miR-100-3p target genes in PC3

source_name: miR-100-3p transfected cell line


title: Identification of miR-150-3p target genes in PC3

source_name: miR-150-3p transfected cell line


title: Col_28_S

description: Large Intestine


title: Col_25_S

description: Large Intestine


title: Identification of miR-99a-5p target genes in FaDu

value: FaDu

value: hypopharyngeal squamous cell carcinoma

source_name: miR-99a-5p transfected cell line


title: Identification of miR-150-5p target genes in PC3

source_name: miR-150-5p transfected cell line


title: Col_25_RD

description: Large Intestine

source_name: Center

value: CB


title: Identification of miR-99a-3p target genes in FaDu


title: Ler-0_1

city: Münster

first: Maik

last: Boehmer

state: Deutschland

address: Schlossplatz 7

department: IBBP

country: Germany

institute: Westfälische Wilhelms Universität

hyb_protocol: standard Nottingham Arabidopsis Stock Center (NASC) hybridization protocol

scan_protocol: standard Nottingham Arabidopsis Stock Center (NASC) scanning protocol

data_processing: The data were analyzed using Bioconductor

organism: Arabidopsis thaliana

source_name: wildtype seeds

label_protocol: standard Nottingham Arabidopsis Stock Center (NASC) labeling protocol

extract_protocol: RNA-hot-borate extraction protocol (Wan, C.Y., and Wilkins, T.A. (1994). Analytical Biochemistry 223, 7-12.)

treatment_protocol: 10 mg dry seeds were incubated in liquid 0.5 MS media with 2 µM ABA for 4 days

value: wildtype


title: wrky43-1_2

source_name: wrky43-1 seeds


title: Ler-0_2


title: wrky43-1_1


title: DAR57_CWI_POST


title: DAR6_CWI_PRE


title: iPS-GC1-5 [all]

description:
Gene expression of induced cancer stem cells established from human gastric cancer tissue-derived cells
iPS-GC1-5

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 250 ml of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61×21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent Technologies) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity by Agilp in series supplementary file.

source_name: Cancer stem cell, induced from human gastric cancer tissue of patient GC1, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA, USA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Using the AllPrep DNA/RNA Mini kit (Qiagen), total RNA was prepared from each clone that was cultured on the MEFs (5 X 10^4 cells/cm^2) with mTeSR1 (StemCell Technologies) medium in gelatin-coated 100-mm dishes before long-term serial passage. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The isolated clones were subcultured in each well of gelatin-coated 24-well plates. After an expansion culture, each clone was further cultured to each well of gelatin-coated 6-well plates and finally cultured in a gelatin-coated 100-mm dish. The expanded clones were treated with a dissociation solution (0.25% trypsin–EDTA [Gibco] and 1% collagenase [Invitrogen]) or 0.25% trypsin–EDTA and passaged in mTeSR1 supplemented with 10–20 μM Y-27632 (Calbiochem and Wako) to avoid cell death. Those clones were cultured with the MEFs (5 X 10^4 cells/cm^2) mainly in mTeSR1 medium and occasionally in Primate ESC medium (ReproCell) on gelatin-coated dishes. Total RNA was prepared from each 100-mm dish and subjected to microarray analysis.

tag: gender

value: Male

tag: age


title: Col_29_MD

description: Large Intestine

source_name: Luminal

value: DTS


title: DAR41_CWI_POST

source_name: vastus lateralis muscle tissue collected after 10 week training (CWI study arm)


title: iPS-GC1-7 [all]

description:
Gene expression of induced cancer stem cells established from human gastric cancer tissue-derived cells
iPS-GC1-7

source_name: Cancer stem cell, induced from human gastric cancer tissue of patient GC1, replicate 5


title: DAR1_CWI_PRE

source_name: vastus lateralis muscle tissue collected before 10 week training


title: DAR1_CWI_POST


title: iPS-GC1-3 [all]

description:
Gene expression of induced cancer stem cells established from human gastric cancer tissue-derived cells
iPS-GC1-3

source_name: Cancer stem cell, induced from human gastric cancer tissue of patient GC1, replicate 3


title: HSF1-CM-2

city: Los Angeles

first: Heather

last: Christofk

state: California

address: 615 Charles E Young Drive South

department: Molecular and Medical Pharmacology/ Biological Chemistry

institute: University of California, Los Angeles

description: HSF1 feeder-free hESCs treated with MEF-conditioned medium, biological replicate 2

hyb_protocol: Performed by UCLA Clinical Microarray Core on Affymetrix Human Genome U133 Plus 2.0 Array

data_processing: Date were processed using Bioconductor package in R, normalized using the RMA method

label_protocol: Performed by UCLA Clinical Microarray Core using Ambion Labeling Kit

extract_protocol: Total RNA was isolated by using the Absolutely RNA kit (Stratagene)

tag: treatment

value: MEF-conditioned medium

tag: treatment duration

value: 5 days

tag: culture system

value: feeder-free


title: iPS-GC1-8 [all]

description:
Gene expression of induced cancer stem cells established from human gastric cancer tissue-derived cells
iPS-GC1-8

source_name: Cancer stem cell, induced from human gastric cancer tissue of patient GC1, replicate 6


title: iPS-GC1-1 [all]

description:
Gene expression of induced cancer stem cells established from human gastric cancer tissue-derived cells
iPS-GC1-1

source_name: Cancer stem cell, induced from human gastric cancer tissue of patient GC1, replicate 1


title: Col_25_FD

description: Large Intestine

source_name: Front

value: IF


title: Col_25_MD

description: Large Intestine


title: HSF1-CM-1

description: HSF1 feeder-free hESCs treated with MEF-conditioned medium, biological replicate 1

scan_protocol: Performed by UCLA Clinical Microarray Core


title: DAR41_CWI_PRE

value: vastus lateralis

value: Cold-water Immersion


title: Col_24_MD

description: Large Intestine


title: Col_23_RD

description: Large Intestine


title: Col_24_S

description: Large Intestine

source_name: Metastasis


title: iPS-CC1-18 [all]

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-18

source_name: Cancer stem cell, induced from human colon cancer tissue of patient CC1, replicate 5


title: HSF1-FF-3

description: HSF1 feeder-free hESCs, biological replicate 3

value: unconditioned medium

value: control


title: iPS-GC1-2 [all]

description:
Gene expression of induced cancer stem cells established from human gastric cancer tissue-derived cells
iPS-GC1-2

source_name: Cancer stem cell, induced from human gastric cancer tissue of patient GC1, replicate 2


title: iPS-CC1-17 [all]

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-17

source_name: Cancer stem cell, induced from human colon cancer tissue of patient CC1, replicate 4


title: Col_24_FD

description: Large Intestine


title: iPS-CC1-11 [all]

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-11

source_name: Cancer stem cell, induced from human colon cancer tissue of patient CC1, replicate 3


title: Col_23_MD

description: Large Intestine


title: Col_23_N

description: Large Intestine

source_name: Normal


title: Col_24_RD

description: Large Intestine

source_name: Center


title: iPS-CC1-10 [all]

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-10

source_name: Cancer stem cell, induced from human colon cancer tissue of patient CC1, replicate 2


title: Col_23_FD

description: Large Intestine


title: Col_22_RD

description: Large Intestine


title: iPS-CC1-4 [all]

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-4

source_name: Cancer stem cell, induced from human colon cancer tissue of patient CC1, replicate 1


title: HSF1-FF-2

description: HSF1 feeder-free hESCs, biological replicate 2


title: iPS-CC1-25 [all]

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-25

source_name: Cancer stem cell, induced from human colon cancer tissue of patient CC1, replicate 6


title: Col_23_S

description: Large Intestine


title: CSC_humanGC1_rep6

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 250 ml of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity by Agilp in series supplementary file.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA, USA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cancer tissue-derived cells were seeded on collagen-coated dishes with DMEM supplemented with 10% fetal bovine serum. One day later, the cells at approximately 5-10% confluency were incubated with the pantropic retrovirus vector solution (OCT3/4, KLF4, and SOX2) at 37°C for one day. The pantropic retrovirus vector solution was prepared. Mitomycin C-treated mouse embryonic fibroblasts were seeded following the infection. The culture was replaced with confluency. The confluent culture was further refreshed with mTeSR1 medium every day from day 15. Each clone was isolated.

value: Cancer stem cell, induced from human gastric cancer tissue of patient GC1


title: CSC_humanGC1_rep5


title: HSF1-FF-1

description: HSF1 feeder-free hESCs, biological replicate 1


title: HSF1-CM-3

description: HSF1 feeder-free hESCs treated with MEF-conditioned medium, biological replicate 3


title: Col_22_S

description: Large Intestine

value: Large Intestine


title: CSC_humanGC1_rep3


title: H9-CM-1

description: H9 feeder-free hESCs treated with MEF-conditioned medium, biological replicate 1


title: CSC_humanGC1_rep4

description:
Gene expression of induced cancer stem cells established from human gastric cancer tissue-derived cells
iPS-GC1-5

source_name: Cancer stem cell, induced from human gastric cancer tissue of patient GC1, replicate 4


title: H9-FF-3

description: H9 feeder-free hESCs, biological replicate 3


title: H9-CM-2

description: H9 feeder-free hESCs treated with MEF-conditioned medium, biological replicate 2


title: H9-CM-3

description: H9 feeder-free hESCs treated with MEF-conditioned medium, biological replicate 3


title: CSC_humanGC1_rep2


title: HSF1-FF-MCTli

description: HSF1 feeder-free hESCs treated with 250nM MCT1 inhibitor

value: 250nM MCT1 inhibitor


title: H9-FF-2

description: H9 feeder-free hESCs, biological replicate 2


title: H9-FF-1

description: H9 feeder-free hESCs, biological replicate 1


title: Col_22_FD

description: Large Intestine


title: CSC_humanCC1_rep6

growth_protocol: The cancer tissue-derived cells were seeded on collagen-coated dishes with DMEM supplemented with 10% fetal bovine serum. One day later, the cells at approximately 5-10% confluency were incubated with the pantropic retrovirus vector solution (OCT3/4, KLF4, and SOX2) at 37°C for one day. The pantropic retrovirus vector solution was prepared. Mitomycin C-treated mouse embryonic fibroblasts were seeded following the infection. The culture was replaced with confluency. The confluent culture was further refreshed with mTeSR1 medium every day from day 22. Each clone was isolated.

extract_protocol: Using the AllPrep DNA/RNA Mini kit (Qiagen), total RNA was prepared from each clone that was cultured on the MEFs (5 X 10^4 cells/cm^2) with mTeSR1 (StemCell Technologies) medium in gelatin-coated 100-mm dishes before long-term serial passage. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

value: Cancer stem cell, induced from human colon cancer tissue of patient CC1


title: HSF1-FF-DMSO

description: HSF1 feeder-free hESCs treated with DMSO

value: DMSO


title: Col_21_MD

description: Large Intestine

source_name: Luminal


title: CSC_humanGC1_rep1

description:
Gene expression of induced cancer stem cells established from human gastric cancer tissue-derived cells
iPS-GC1-1


title: Col_22_MD

description: Large Intestine


title: Col_22_N

description: Large Intestine


title: CSC_humanCC1_rep5

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-18


title: HSF1-FS-DMSO

description: HSF1 feeder-supported hESCs treated with DMSO

value: feeder-supported


title: HSF1-FS-MCTli

description: HSF1 feeder-supported hESCs treated with 250nM MCT1 inhibitor


title: Col_21_FD

description: Large Intestine


title: CSC_humanCC1_rep3

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-11


title: CSC_humanCC1_rep2

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-10


title: Col_21_RD

description: Large Intestine

value: CB


title: CSC_humanCC1_rep4

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-17

value: Male


title: H9-FF-MCTli

description: H9 feeder-free hESCs treated with 250nM MCT1 inhibitor


title: Col_18_FD

description: Large Intestine


title: H9-FF-DMSO

description: H9 feeder-free hESCs treated with DMSO


title: H9-FS-DMSO

description: H9 feeder-supported hESCs treated with DMSO


title: H1-FF-MCTli

description: H1 feeder-free hESCs treated with 250nM MCT1 inhibitor


title: Col_20_FD

description: Large Intestine


title: Col_18_MD

description: Large Intestine

value: DTS


title: CSC_humanCC1_rep1

description:
Gene expression of induced cancer stem cells established from human colon cancer tissue-derived cells
iPS-CC1-4


title: WT proB and preB cells, biological replicate 4

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from WT proB and preB cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

source_name: WT PROB AND PREB 4

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

growth_protocol: Animals were housed in conventional facility and they have been exposed to common pathogens.

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

treatment_protocol: Not applicable

value: Bone marrow ProB and PreB cells


title: Col_19_RD

description: Large Intestine


title: WT proB and preB cells, biological replicate 2

source_name: WT PROB AND PREB 2


title: H1-FS-MCTli

description: H1 feeder-supported hESCs treated with 250nM MCT1 inhibitor

value: 5 days


title: H9-FS-MCTli

description: H9 feeder-supported hESCs treated with 250nM MCT1 inhibitor


title: WT proB and preB cells, biological replicate 3

source_name: WT PROB AND PREB 3


title: Col_20_RD

description: Large Intestine


title: H1-FF-DMSO

description: H1 feeder-free hESCs treated with DMSO

value: feeder-free


title: Salivary tissue from trans-heterzygous dTCTP[EY09182]/dTCTP[h59] mutants, biological rep2

city: Daejeon

first: Kwang-wook

last: Choi

address: KAIST 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description: Gene expression data from salivary glands tissue of 3rd instar larvae. Trans-Heterozygous dTCTP[EY09182]/dTCTP[h59] mutation

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the Affymetrix GeneChip® Drosophila 2.0 arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained using SAPE (Streptavidin Phycoerythrin) and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix). the image data was extracted through Affymetrix Commnad Console software1.1.

data_processing: The raw .cel file generated through above procedure meant expression intensity data and was used for the next step.  Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

organism: Drosophila melanogaster

source_name: salivary gland tissues from mid-3rd instar larvae

label_protocol: Per RNA sample, 300 ng were used as input into the Affymetrix procedure as recommended by protocol (http://www.affymetrix.com). Briefly, 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA (cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: 3rd instar larvae are incubated at 25C. Day and night cycle are 12:12 hour.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, USA). RNA quality was assessed by Agilent 2100 bioanalyser (Agilent Technologies, USA), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: mid-3rd instar larvae are collected and dissected to obtain salivary glands tissues. Dissection was performed in ice-cold M3+BPYE media without serum to reduce possible tissue damages. 50 pairs of salivary glands were collected for each genotype and frozen in liquid nitrogen.

value: salivary glands

tag: genotype

value: mid-third instar larvae


title: WT proB and preB cells, biological replicate 1

source_name: WT PROB AND PREB 1


title: Salivary tissue from trans-heterzygous dTCTP[EY09182]/dTCTP[h59] mutants, biological rep3


title: Col_17_RD

description: Large Intestine


title: Sca1-BCR/ABLp190 proB and preB cells, biological replicate 3

description: Gene expression data from Sca1-BCR/ABLp190 proB and preB cells

source_name: BCRABL PROB AND PREB 3


title: Salivary tissue from trans-heterzygous dTCTP[EY09182]/dTCTP[h59] mutants, biological rep1


title: Col_16_RD

description: Large Intestine


title: Salivary tissue from heterzygous dTCTP[h59] null mutants, biological rep3

description: Gene expression data from salivary glands tissue of 3rd instar larvae. Heterozygous +/dTCTP[h59] mutation


title: Col_17_N

description: Large Intestine


title: Col_19_FD

description: Large Intestine

source_name: Front

value: IF


title: H1-FS-DMSO

description: H1 feeder-supported hESCs treated with DMSO


title: Sca1-BCR/ABLp190 proB and preB cells, biological replicate 2

source_name: BCRABL PROB AND PREB 2


title: Sca1-BCR/ABLp190+Pax5+/- proB and preB cells, biological replicate 3

description: Gene expression data from Sca1-BCR/ABLp190+Pax5+/- proB and preB cells

source_name: BCRABL_PAX5 PROB AND PREB 3


title: Sca1-BCR/ABLp190 proB and preB cells, biological replicate 1

source_name: BCRABL PROB AND PREB 1


title: Col_19_MD

description: Large Intestine


title: Col_16_FD

description: Large Intestine


title: Salivary tissue from heterzygous dTCTP[h59] null mutants, biological rep1


title: Col_17_FD

description: Large Intestine


title: Sca1-BCR/ABLp190+Pax5+/- proB and preB cells, biological replicate 1

source_name: BCRABL_PAX5 PROB AND PREB 1


title: Salivary tissues from wildtype control, biological rep2

description: Gene expression data from salivary glands tissue of 3rd instar larvae. Widetype control


title: B220+ bone marrow B cells, biological replicate 5

description: Gene expression data from B220+ bone marrow B cells

source_name: WT Bcells 5

value: Bone marrow B220 cells


title: Col_16_MD

description: Large Intestine


title: Col_15_FD

description: Large Intestine


title: Salivary tissues from wildtype control, biological rep1


title: Col_15_N

description: Large Intestine

source_name: Normal


title: Salivary tissue from heterzygous dTCTP[h59] null mutants, biological rep2


title: Salivary tissues from wildtype control, biological rep3


title: Col_15_MD

description: Large Intestine


title: B220+ bone marrow B cells, biological replicate 3

source_name: WT Bcells 3


title: B220+ bone marrow B cells, biological replicate 4

source_name: WT Bcells 4


title: Col_20_MD

description: Large Intestine


title: Col_18_RD

description: Large Intestine

source_name: Center


title: Col_14_RD

description: Large Intestine


title: Col_14_MD

description: Large Intestine

source_name: Luminal


title: Col_14_N

description: Large Intestine


title: B220+ bone marrow B cells, biological replicate 1

source_name: WT Bcells 1


title: Col_14_FD

description: Large Intestine


title: Sca1-BCR/ABLp190 bone marrow cells, biological replicate 2

description: Gene expression data from Sca1-BCR/ABLp190 bone marrow cells

source_name: BCRABL 2

value: Bone marrow


title: Sca1-BCR/ABLp190 bone marrow cells, biological replicate 1

source_name: BCRABL 1


title: Col_13_MD

description: Large Intestine


title: Sca1-BCR/ABLp190+Pax5+/- bone marrow cells, biological replicate 7

description: Gene expression data from Sca1-BCR/ABLp190+Pax5+/- bone marrow cells

source_name: BCRABL_Pax5 7


title: B220+ bone marrow B cells, biological replicate 2

source_name: WT Bcells 2


title: Sca1-BCR/ABLp190+Pax5+/- bone marrow cells, biological replicate 6

source_name: BCRABL_Pax5 6


title: DAR95_CWI_PRE

description: Gene expression data from vastus lateralis muscle tissue collected before 10 week training

hyb_protocol: RNA samples were amplified, labeled, hybridized to Affymetrix HG-U133 plus 2.0 GeneChip® microarrays, and scanned using standard protocols (Expression Analysis, Inc., Durham, North Carolina, U.S.A.) to generate raw data files (CEL files).

data_processing: Raw data files (CEL files) were analyzed using a battery of data quality checks and samples failing these checks were removed from subsequent analyses.  Raw data was then pre-processed using the RMA (Robust Multi-chip Average) pipeline  in combination with the most current re-annotated probeset definitions.

extract_protocol: Muscle sample preservation and stabilization was assured by the immediate addition of 500 µL of RNALater® solution (ThermoFisher Scientific Inc, Massachusettes, USA).  As per manufacturer’s instructions, the vial containing the muscle sample was then left at room temperature for 24 h to allow the RNALater® solution to fully permeate the sample, before being stored at -80°C for later analysis.

value: vastus lateralis

value: Cold-water Immersion

value: Pre


title: Sca1-BCR/ABLp190+Pax5+/- proB and preB cells, biological replicate 2

source_name: BCRABL_PAX5 PROB AND PREB 2


title: DAR95_CWI_POST

description: Gene expression data from vastus lateralis muscle tissue collected after 10 week training (CWI study arm)

scan_protocol: RNA samples were amplified, labeled, hybridized to Affymetrix HG-U133 plus 2.0 GeneChip® microarrays, and scanned using standard protocols (Expression Analysis, Inc., Durham, North Carolina, U.S.A.) to generate raw data files (CEL files).

value: Post


title: Sca1-BCR/ABLp190+Pax5+/- bone marrow cells, biological replicate 5

source_name: BCRABL_Pax5 5


title: Col_17_MD

description: Large Intestine

value: Large Intestine


title: Col_12_MD

description: Large Intestine


title: DAR85_PLA_POST

description: Gene expression data from vastus lateralis muscle tissue collected after 10 week training (Placebo study arm)

label_protocol: RNA samples were amplified, labeled, hybridized to Affymetrix HG-U133 plus 2.0 GeneChip® microarrays, and scanned using standard protocols (Expression Analysis, Inc., Durham, North Carolina, U.S.A.) to generate raw data files (CEL files).

value: Placebo


title: Col_12_S

description: Large Intestine

source_name: Metastasis


title: Col_15_RD

description: Large Intestine

value: CB


title: Sca1-BCR/ABLp190+Pax5+/- bone marrow cells, biological replicate 4

source_name: BCRABL_Pax5 4


title: DAR81_CWI_POST

source_name: vastus lateralis muscle tissue collected after 10 week training (CWI study arm)


title: DAR85_PLA_PRE

source_name: vastus lateralis muscle tissue collected before 10 week training


title: Sca1-BCR/ABLp190+Pax5+/- bone marrow cells, biological replicate 3

source_name: BCRABL_Pax5 3


title: Sca1-BCR/ABLp190+Pax5+/- bone marrow cells, biological replicate 2

source_name: BCRABL_Pax5 2


title: Col_12_FD

description: Large Intestine

source_name: Front


title: DAR81_CWI_PRE


title: Sca1-BCR/ABLp190+Pax5+/- bone marrow cells, biological replicate 1

source_name: BCRABL_Pax5 1


title: Col_09_MD

description: Large Intestine

source_name: Luminal


title: Col_09_S

description: Large Intestine


title: DAR72_PLA_POST

source_name: vastus lateralis muscle tissue collected after 10 week training (Placebo study arm)


title: Col_13_RD

description: Large Intestine

source_name: Center


title: GQY

description: replicate 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: LSCC tissue

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

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

tag: chemosensitivity

value: sensitive


title: Col_12_RD

description: Large Intestine

tag: region


title: Col_09_RD

description: Large Intestine


title: Col_08_RD

description: Large Intestine


title: Col_13_FD

description: Large Intestine


title: Col_09_FD

description: Large Intestine


title: DAR21_PLA_POST


title: Col_08_MD

description: Large Intestine

value: DTS


title: DAR21_PLA_PRE


title: GZY

description: replicate 9


title: DAR72_PLA_PRE


title: Col_07_S

description: Large Intestine


title: PXL

description: replicate 7


title: XBC

description: replicate 8

value: non-sensitive


title: Col_08_S

description: Large Intestine


title: DAR32_PLA_POST


title: WMX

description: replicate 6


title: DAR32_PLA_PRE


title: Col_07_RD

description: Large Intestine


title: DAR7_PLA_POST


title: WHPTD

description: replicate 5


title: Col_08_FD

description: Large Intestine


title: WH

description: replicate 4


title: Col_59_CB

hyb_protocol: DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol


title: Col_59_TS


title: DAR57_CWI_POST


title: LDS

description: replicate 3


title: DAR7_PLA_PRE


title: Col_59_IF


title: DAR57_CWI_PRE


title: Col_06_S

description: Large Intestine


title: Col_52_TS


title: DYZ

description: replicate 2


title: Col_06_RD

description: Large Intestine


title: ZLL

description: replicate 1


title: Col_52_IF


title: Col_06_FD

description: Large Intestine


title: Col_45_CB


title: Col_07_MD

description: Large Intestine


title: Col_06_MD

description: Large Intestine


title: DAR26_PLA_PRE


title: Col_07_FD

description: Large Intestine


title: Col_52_CB


title: DAR64_PLA_POST


title: WZ

description: replicate 1


title: DAR64_PLA_PRE


title: Col_05_RD

description: Large Intestine


title: Col_45_TS


title: Col_05_MD

description: Large Intestine


title: Col_45_IF


title: DAR6_CWI_POST


title: DAR26_PLA_POST


title: DAR6_CWI_PRE


title: DAR1_CWI_POST


title: DAR1_CWI_PRE


title: Col_38_CB


title: Col_38_IF


title: Col_04_RD

description: Large Intestine


title: Col_34_TS


title: Col_38_TS


title: DAR41_CWI_POST


title: Col_05_FD

description: Large Intestine


title: DAR41_CWI_PRE


title: Col_03_MD

description: Large Intestine


title: Col_33_TS


title: Col_34_CB


title: Col_04_MD

description: Large Intestine


title: Col_04_FD

description: Large Intestine


title: Col_34_IF


title: Col_03_S

description: Large Intestine


title: Col_03_FD

description: Large Intestine


title: HOC313-LM whole cell gene expression 1

status: Public on Aug 15 2016

city: Tokyo

first: Tomoki

last: Muramatsu

address: 1-5-45 Yushima Bunkyo-ku

department: Medical research institute

institute: Tokyo Medical and Dental University

description: Dish culture

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107; normalized algorithm: percentile shift) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HOC313-LM whole cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HOC313-P and -LM were maintained in appropriate media, D-MEM medium supplemented with 10% fetal bovine serum or 10% exosome depleted FBS .

extract_protocol: RNA fractions from whole cell were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. The protocol includes clean up step after TURBO DNA-free™ Kit (Ambion, Austin, TX) digestion. RNAs were quantified using a NanoDrop-1000 spectrophotometer and Agilent 2100 bioanalyzer . Also, total RNA from exosomes was extracted using Total Exosome RNA and Protein Isolation Kit (Thermo Fisher Scientific) according to manufacturer’s instructions.(rna frm exosome by kit)

treatment_protocol: For gene expression array, HOC313-Parent (HOC313-P) cells were transfected with NT, miR-342-3p and-1246 for 72hrs.

value: Oral squamous cell carcinoma

tag: cell subtype

value: high-metastatic subline

tag: sample type

value: whole cell


title: HOC313-LM whole cell gene expression 2

description: Dish culture


title: Col_01_RD

description: Large Intestine


title: HOC313-P overexpressed with miR-1246 gene expression 1

description: Dish culture

source_name: HOC313-P overexpressed with miR-1246

value: low-metastatic subline

tag: transfected with

value: miR-1246 for 72 hrs


title: Col_01_S

description: Large Intestine


title: Col_33_CB


title: HOC313-P Negative control gene expression 1

description: Dish culture

source_name: HOC313-P Negative control

value: negative control for 72hrs


title: HOC313-P Negative control gene expression 2

description: Dish culture


title: Col_03_RD

description: Large Intestine


title: Col_01_MD

description: Large Intestine


title: AMC09_RV1

city: Chuncheon

first: Bong-seok

last: Jo

address: Kangwon university street 1

institute: Kangwon national university

description: Cardiomyocyte, Right vnetricle

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each humanHT-12 expression v.4 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3(Gene Expression Module v3.3.8).

data_processing: Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was normalized by quantile method.

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was extracted from cells using  the RNeasy mini kit/RNeasy mini spin columns (Qiagen Inc.)

value: Male

value: RV(Right vnetricle)


title: Col_16_TS


title: HOC313-P overexpressed with miR-342-3p gene expression 2

description: Dish culture

source_name: HOC313-P overexpressed with miR-342-3p

value: miR-342-3p for 72 hrs


title: SMC02_RV1

description: Cardiomyocyte, Right vnetricle


title: SMC01_RV1

description: Cardiomyocyte, Right vnetricle

value: Female


title: SMC07_RV1

description: Cardiomyocyte, Right vnetricle


title: SNU02_LV1

description: Cardiomyocyte, Left ventricle

value: LV(Left ventricle)


title: SNU02_RV1

description: Cardiomyocyte, Right vnetricle


title: AMC09_LV1

description: Cardiomyocyte, Left ventricle


title: HOC313-P overexpressed with miR-1246 gene expression 2

description: Dish culture


title: SMC08_RV1

description: Cardiomyocyte, Right vnetricle


title: HOC313-P overexpressed with miR-342-3p gene expression 1

description: Dish culture


title: SMC08_LV1

description: Cardiomyocyte, Left ventricle


title: SNU03_LV1-1

description: Cardiomyocyte, Left ventricle, replicate


title: SNU03_RV1

description: Cardiomyocyte, Right vnetricle


title: AMC07_LV1

description: Cardiomyocyte, Left ventricle


title: AMC08_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: Col_16_CB

value: Large Intestine


title: Col_12_TS


title: SMC07_LV1

description: Cardiomyocyte, Left ventricle


title: Col_12_CB


title: SNU05_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: Col_12_IF

value: IF


title: SNU05_LV1

description: Cardiomyocyte, Left ventricle


title: SNU02_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: Col_16_IF


title: SMC05_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: SNU03_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: BelTatar_92

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress-24 v1.0 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

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

source_name: Belarusian Lipka Tatars_blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

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

tag: population

value: Belarusian Lipka Tatars

value: Belarus

value: blood


title: AMC02_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: AMC07_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: SMC07_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: AMC06_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: AMC09_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: AMC05_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: AMC03_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: SMC08_LV2

description: Cardiomyocyte, Left ventricle(apex)


title: cultured PBMCs_100 ug/ml YM treatment_rep1

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

institute: Biodonostia Institute

description: cultured human PBMCs stimulated with 0.5% PHA during 72h with 100 ug/ml yerba mate treatment

hyb_protocol: GeneChip Hybridization, Wash and Stain kit was used for hybridization in a GeneChip Hybridization oven 640 and in a GeneChip Fluidics Station 450 using the protocol FS450_0001, as explained in the protocol provided by Affymetrix.

scan_protocol: Arrays were scanned in a GeneChip 7G scanner and analysed in Affymetrix GeneChip Command Console Scan Control v4.0.0.1567.

data_processing: Quality control, normalization and summarization of the data were performed in Expression Console software build 1.4.0.38 (Affymetrix).

source_name: PHA-stimulated PBMCs 100 ug/ml YM

label_protocol: Total RNA was labeled using GeneChip® WT PLUS Reagent Kit

growth_protocol: PBMCs were isolated from whole blood and were cultured with RPMI medium supplemented with 5% FBS and antibiotics in a P96 plate (100.000cells/well) for 72h.

extract_protocol: miRNeasy mini kit (Qiagen)

treatment_protocol: To induce PBMC activation,  Phytohemagglutinin (PHA) (ThermoFisher) (0.5%) was used.

value: PBMCs

value: male


title: BelTatar_65


title: cultured PBMCs_100 ug/ml YM treatment_rep2


title: Col_08_IF

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures


title: BelTatar_78


title: Day3 Mtb

city: New Delhi

first: Kuldeep

middle: Singh

last: Attri

state: Delhi

address: Sukhdev Vihar

department: Systems Biology

country: India

institute: CSIR-IGIB

description: Poly-A controls were added to input RNA.

hyb_protocol: Labeled fragments were hybridized to Affymetrix WT Mouse ST2.0 gene array for 16hr at 45°C with 60rpm in Affymetrix Hybridization oven 645.

scan_protocol: Hybridized microarrays were washed and stained in Affymetrix fluidic station 450 and scanned in Affymetrix G3000 Gene Array Scanner.

data_processing: Image analysis of microarray chips was carried out by Affymetrix Genechip command console software which uses MAS5 algorithm. Affymetrix Expression Console was used to analyze ,CEL files to generate normalized signal intensities form raw signal intensities using RMA algorithm.

source_name: Primary murine cells

label_protocol: 300ng RNA was taken as input RNA and was processed with Ambion WT Expression Kit.cDNAS were fragmented and labeled with Affymetrix terminal labeling kit.

growth_protocol: Murine bone marrow derived macrophage precursors were initially grown in presence of MCSF while post Mtb treatment cells were cultured with MCSF and RANKL growth factors.

extract_protocol: Total RNA from uninfected and Mtb infected cells was isolated by TRIzol RNA isolation method and later purified by RNAeasy column purification.

treatment_protocol: Mtb infections were carried out by infecting primary cells with Mtb at MOI of 1:5 for 4hours.

tag: strain

value: Balb/c

value: Macrophage-Osteoclast


title: cultured PBMCs_no YM treatment_rep1

description: cultured human PBMCs stimulated with 0.5% PHA during 72h

source_name: PHA-stimulated PBMCs

tag: tissue


title: Day2 Mtb


title: Col_33_IF

data_processing: Genome Studio V2011.2


title: HOC313-LM exosomes miRNA expression 1

description: Dish culture

source_name: HOC313-LM exosomes

tag: cell line

value: Oral squamous cell carcinoma

value: high-metastatic subline

value: exosomes


title: HOC313-LM exosomes miRNA expression 2

description: Dish culture

tag: cell type


title: HOC313-P exosomes miRNA expression 1

description: Dish culture

source_name: HOC313-P exosomes

value: low-metastatic subline


title: HOC313-P exosomes miRNA expression 2

description: Dish culture


title: Day0 Mtb


title: HOC313-LM whole cell miRNA expression 1

description: Dish culture

value: whole cell


title: Day 2 Control


title: HOC313-LM whole cell miRNA expression 2

description: Dish culture


title: Col_01_FD

description: Large Intestine

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol


title: Day 4 Control


title: SNU04_RV1

description: Cardiomyocyte, Right vnetricle

value: Male

value: RV(Right vnetricle)


title: Day4 Mtb


title: HOC313-P whole cell miRNA expression 1

description: Dish culture

source_name: HOC313-P whole cell


title: HOC313-P whole cell miRNA expression 2

description: Dish culture