title: altitude exposure at post7, biological rep 019


title: altitude exposure at post7, biological rep 011

status: Public on Oct 19 2017

type: genomic

city: Aurora

first: Robert

middle: C

last: Roach

state: CO

address: Campus Box F-524, 12469 E. 17th Place

department: Department of Pulmonology

country: USA

institute: University of Colorado

hyb_protocol: Genome-wide methylation was assessed using Illumina's Infinium HumanMethylation450 BeadChip

scan_protocol: Illumina HiScan was used with control software version 3.2.26.

data_processing: Data were normalized with the SWAN algorithm as implemented in the R/Bioconductor minfi package.

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: post7, PBMC

label_protocol: gDNA was quantitated with the NanoDrop spectrophotometer, bisulfite converted using the Zymo EZ DNA Methylation Kit, and labeled according to Illumina protocols.

growth_protocol: not applicable

extract_protocol: Peripheral blood samples were collected from an antecubital vein prior to exercise on the first, seventh, and sixteenth days of initial altitude exposure (ALT1, ALT7, and ALT16) and on the re-exposure days (POST7 and POST21), and placed into a BD Vacutainer Cell Preparation Tube containing sodium citrate and Ficoll Hypaque density fluid. PBMC (peripheral blood mononuclear cell) pellets were stored at -80C until analysis.  gDNA was purified using the Qiagen QIAEX II Kit.

treatment_protocol: exposure to altitude

tag: time point

tag: subject

tag: age

tag: Sex

value: F

tag: height (in.)

tag: weight (kg.)


title: altitude exposure at post7, biological rep 017


title: altitude exposure at post21, biological rep 006

source_name: post21, PBMC

value: M


title: altitude exposure at alt16, biological rep 022

source_name: alt16, PBMC


title: altitude exposure at post7, biological rep 025


title: altitude exposure at post7, biological rep 012


title: altitude exposure at alt16, biological rep 023


title: altitude exposure at post7, biological rep 010


title: altitude exposure at alt16, biological rep 019


title: altitude exposure at post7, biological rep 013


title: 143B_Cybrid C/143BRho0

type: RNA

city: Birmingham

first: Keshav

last: Singh

state: AL

address: 720 20th Street South Kaul 630

department: Genetics

institute: University of Alabama at Birmingham

hyb_protocol: The array and all of its hybridization, washing etc was conducted by a commercial company according to their in house protocols.

scan_protocol: The array scanning and image acquisition were conducted by a commercial company according to their in house protocols.

data_processing: Data were normalized using the non-linear regression method (LOWESS)

molecule: total RNA

source_name: 143B Osteosarcoma Parental Cells with depleted mitochondrial DNA fused with platelet cells from human origin

label_protocol: Labelling was done with the miRCURY LNA array power labeling kit. The protocol was conducted by a commerical company according to proprietary protocols.

extract_protocol: RNA was isolated using Trizol according to manufacturer's protocol.

tag: tissue


title: altitude exposure at alt16, biological rep 025


title: altitude exposure at alt16, biological rep 018


title: 143B_Cybrid M/143BRho0

value: 143B Osteosarcoma Parental Cells with depleted mitochondrial DNA fused with platelet cells from human origin


title: altitude exposure at alt16, biological rep 017


title: altitude exposure at alt16, biological rep 020


title: altitude exposure at alt16, biological rep 015


title: 143B/143BRho0

source_name: 143B Osteosarcoma Parental Cells

value: 143B Osteosarcoma Parental Cells

source_name: 143B Osteosarcoma Parental Cells with depleted mitochondrial DNA


title: altitude exposure at alt16, biological rep 012


title: altitude exposure at alt16, biological rep 014


title: miRNA_BreastCancer_rep50

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

country: Japan

institute: Japanese Foundation For Cancer Research

hyb_protocol: RNA was hybridized with Agilent miRNA Complete Hybri kit Arrays following manufactuer's instruction.

scan_protocol: Array was scanned using the Agilent DNA Microarray scanner.

data_processing: Data was processed with excel using 90% tile shift.

label: Agilent miRNA Complete Labeling and Hybri kit

source_name: Breast Cancer tissue

label_protocol: Cy3 labelled RNA was prepared with Agilent miRNA Complete Labeling kit according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN　miRNeasy mini kit following manufacturer's　instruction.

value: breast cancer

tag: gender


title: altitude exposure at alt16, biological rep 021


title: altitude exposure at alt16, biological rep 011


title: altitude exposure at alt16, biological rep 006


title: miRNA_BreastCancer_rep49


title: altitude exposure at alt16, biological rep 010


title: altitude exposure at alt16, biological rep 007


title: altitude exposure at alt16, biological rep 002


title: altitude exposure at alt7, biological rep 015

source_name: alt7, PBMC


title: miRNA_BreastCancer_rep48


title: miRNA_BreastCancer_rep47


title: altitude exposure at alt7, biological rep 023


title: altitude exposure at alt16, biological rep 005


title: miRNA_BreastCancer_rep46


title: altitude exposure at alt7, biological rep 022


title: altitude exposure at alt16, biological rep 001


title: altitude exposure at alt7, biological rep 014


title: altitude exposure at alt7, biological rep 019


title: miRNA_BreastCancer_rep45


title: altitude exposure at alt7, biological rep 013


title: miRNA_BreastCancer_rep44


title: altitude exposure at alt16, biological rep 013


title: altitude exposure at alt7, biological rep 018


title: altitude exposure at alt7, biological rep 025


title: altitude exposure at alt7, biological rep 017


title: miRNA_BreastCancer_rep42


title: altitude exposure at alt7, biological rep 021


title: altitude exposure at alt7, biological rep 006


title: altitude exposure at alt7, biological rep 012


title: altitude exposure at alt7, biological rep 001


title: miRNA_BreastCancer_rep40


title: miRNA_BreastCancer_rep41


title: miRNA_BreastCancer_rep43


title: altitude exposure at alt7, biological rep 002


title: miRNA_BreastCancer_rep39


title: altitude exposure at alt1pm, biological rep 021

source_name: alt1pm, PBMC


title: altitude exposure at alt7, biological rep 007


title: altitude exposure at alt7, biological rep 010


title: altitude exposure at alt1pm, biological rep 019


title: altitude exposure at alt7, biological rep 011


title: altitude exposure at alt1pm, biological rep 025


title: altitude exposure at alt1pm, biological rep 012


title: miRNA_BreastCancer_rep37


title: miRNA_BreastCancer_rep36


title: altitude exposure at alt1pm, biological rep 015


title: altitude exposure at alt1pm, biological rep 023


title: altitude exposure at alt1pm, biological rep 018


title: altitude exposure at alt1pm, biological rep 022


title: altitude exposure at alt1pm, biological rep 011


title: miRNA_BreastCancer_rep35


title: altitude exposure at alt7, biological rep 005


title: altitude exposure at alt1pm, biological rep 013


title: miRNA_BreastCancer_rep32


title: altitude exposure at alt1pm, biological rep 014


title: altitude exposure at alt1noon, biological rep 025

source_name: alt1noon, PBMC


title: miRNA_BreastCancer_rep34


title: altitude exposure at alt1pm, biological rep 007


title: miRNA_BreastCancer_rep38


title: altitude exposure at alt1pm, biological rep 017


title: altitude exposure at alt1noon, biological rep 019


title: altitude exposure at alt1noon, biological rep 023


title: altitude exposure at alt1pm, biological rep 010


title: altitude exposure at alt1noon, biological rep 018


title: altitude exposure at alt1noon, biological rep 021


title: altitude exposure at alt1noon, biological rep 010


title: altitude exposure at alt1noon, biological rep 022


title: altitude exposure at alt1noon, biological rep 012


title: altitude exposure at alt1noon, biological rep 017


title: altitude exposure at alt1noon, biological rep 013


title: miRNA_BreastCancer_rep29


title: miRNA_BreastCancer_rep31


title: miRNA_BreastCancer_rep28


title: miRNA_BreastCancer_rep30


title: miRNA_BreastCancer_rep27


title: miRNA_BreastCancer_rep26

value: unknown


title: miRNA_BreastCancer_rep33


title: altitude exposure at alt1noon, biological rep 001


title: miRNA_BreastCancer_rep24


title: baseline condition at sea level, biological rep 025

source_name: sea level, PBMC

value: baseline (sea level)


title: miRNA_BreastCancer_rep25


title: miRNA_BreastCancer_rep23


title: altitude exposure at alt1noon, biological rep 015


title: altitude exposure at alt1noon, biological rep 002


title: altitude exposure at alt1noon, biological rep 020


title: altitude exposure at alt1noon, biological rep 011


title: miRNA_BreastCancer_rep22


title: miRNA_BreastCancer_rep21


title: baseline condition at sea level, biological rep 018


title: baseline condition at sea level, biological rep 017


title: baseline condition at sea level, biological rep 020


title: baseline condition at sea level, biological rep 022


title: miRNA_BreastCancer_rep19


title: baseline condition at sea level, biological rep 021


title: miRNA_BreastCancer_rep17


title: miRNA_BreastCancer_rep18


title: baseline condition at sea level, biological rep 023


title: miRNA_BreastCancer_rep20


title: baseline condition at sea level, biological rep 015


title: altitude exposure at alt1noon, biological rep 014


title: altitude exposure at alt1noon, biological rep 006


title: altitude exposure at alt1noon, biological rep 005


title: baseline condition at sea level, biological rep 019


title: baseline condition at sea level, biological rep 005


title: baseline condition at sea level, biological rep 012


title: miRNA_BreastCancer_rep13


title: baseline condition at sea level, biological rep 013


title: miRNA_BreastCancer_rep14


title: miRNA_BreastCancer_rep12


title: miRNA_BreastCancer_rep11


title: miRNA_BreastCancer_rep10


title: baseline condition at sea level, biological rep 011


title: baseline condition at sea level, biological rep 014


title: baseline condition at sea level, biological rep 006


title: baseline condition at sea level, biological rep 002


title: miRNA_BreastCancer_rep15


title: miRNA_BreastCancer_rep9


title: miRNA_BreastCancer_rep16


title: miRNA_BreastCancer_rep8


title: baseline condition at sea level, biological rep 007


title: miRNA_BreastCancer_rep6


title: baseline condition at sea level, biological rep 010


title: miRNA_BreastCancer_rep7


title: miRNA_BreastCancer_rep4


title: miRNA_BreastCancer_rep5


title: miRNA_BreastCancer_rep3


title: miRNA_BreastCancer_rep2


title: miRNA_BreastCancer_rep1


title: IPSRG4S_p25

city: Moscow

first: Rinat

middle: I

last: Sultanov

address: Malaya Pirogovskaya, 1a

country: Russia

institute: FRCC of Physical Chemical Medicine of the FMBA of the Russian Federation

description: iPSC derived from healthy fibroblasts with Sendai virus

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: BeadStudio software

label: Cy5 and Cy3

source_name: fibroblasts

label_protocol: Standard Illumina Protocol

extract_protocol: DNA from the cells was isolated by phenol–chloroform extraction.

tag: sample type

value: iPSC

tag: disease state

value: normal

tag: reprogramming type

value: Sendai virus


title: IPSPDL2.9S

description: iPSC derived from fibroblasts with mutation in PARK8 with Sendai virus

value: Parkinson's disease


title: vessel at T7, biological rep2

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from mouse vessel Angiotensin II treated for 7days

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip  Affymetrix Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

organism: Mus musculus

source_name: Mouse vessel  Angiotensin II treated for 7days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Eight to ten-week-old C57BL/6 male mice were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: All mice were euthanized by an overdose of pentobarbital on days 1, 3 and 7 of Ang II treatment. Total RNA was isolated with TRIzol (Invitrogen) from  vessels at each time point according to manufacturer's instructions.

treatment_protocol: Mice were implanted with osmotic pumps (Alzet Model 1007D; Cupertino, CA,USA) and infused with Angiotensin II at 1500ng/kg/min in Ringer's solution (0.01mmol/L acetic acid in saline) for 1, 3, and 7 days . Systolic blood pressure was measured by the tail-cuff method before starting treatment and again every day after Angiotensin II infusion.

value: vessel

tag: agent

value: Angiotensin II

value: 7 days

tag: stain


title: vessel at T7, biological rep3


title: vessel at T0, biological rep3

description: Gene expression data from mouse vessel with no Angiotensin II  treatmeant

source_name: Mouse vessel with no Angiotensin II  treatmeant


title: N31+W20_72hr_rep2

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

institute: Kyoto Univ.

description: W20-expressing NPCs 72 hr after initiation of cell reprogramming

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K G4122F for 17 hours at 65°C in a rotating 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides.

data_processing: The array data were analyzed using GeneSpring software (Agilent). Gene expression values were normalized by excluding low-signal intensity data and percentile shifts.

source_name: mouse ESC-derived neural progenitor cells

label_protocol: Microarray experiments were performed according to the manufacturer’s instruction. Twenty hundred nanograms of total RNA was labelled with cyanine 3-CTP and hybridized in Whole Mouse Genome Microarray 4x44K G4122F (Agilent Technologies).

growth_protocol: Cells cells were maintained on a gelatin-coated culture plate in an NPC medium, RHB basal (StemCells, Inc) containing the epidermal growth factor (EGF) containing 40 ng/ml Dox for 48 hr followed by GMEM supplemented with 10% KSR, 1 μM ACTH, 1 mM sodium pyruvate, 1× nonessential amino acids, 100 μM 2-mercaptoethanol and 1000 U/ml of LIF 40 ng/ml Dox for 24 hr (Peprotech) at 10 ng/ml and the human basic fibroblast growth factor (bFGF) (Peprotech) at 10 ng/ml.

extract_protocol: Total RNA was extracted using the RNeasy Kit (QIAGEN) and was assessed by Agilent 2100 Bioanalyzer and the RNA 6000 LabChip Kit (Agilent Technologies).

tag: treatment


title: N31+W20_72hr_rep1

value: W20-expressing NPCs 72 hr after initiation of cell reprogramming


title: N31+EGFP_72hr_rep1

description: control NPC cells 72 hr after initiation of cell reprogramming


title: vessel at T1, biological rep1

description: Gene expression data from mouse vessel Angiotensin II treated for 1days

source_name: Mouse vessel  Angiotensin II treated for 1days

value: 1 day


title: vessel at T3, biological rep2

description: Gene expression data from mouse vessel Angiotensin II treated for 3days

source_name: Mouse vessel  Angiotensin II treated for 3days

value: 3 days


title: vessel at T1, biological rep2


title: vessel at T3, biological rep3


title: vessel at T1, biological rep3


title: N31+EGFP_72hr_rep2

value: control NPC cells 72 hr after initiation of cell reprogramming


title: vessel at T0, biological rep2


title: vessel at T7, biological rep1


title: vessel at T3, biological rep1


title: IPSRG10S_p10


title: IPSPDL2.15L

description: iPSC derived from fibroblasts with mutation in PARK8 gene with lentiviral transduction

value: lentiviral


title: Small intestinal mucosa_4th-infection_rep1

status: Public on Oct 18 2017

city: Sapporo

first: Hirokazu

last: Kouguchi

address: N19, W12, Kita-ku

institute: Hokkaido Institute of Public Health

description: Gene expression in small intestinal mucosa of 4th-infection group after 6days infection.

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

scan_protocol: Microarray slides were scanned in an Agilent DNA Sure Scan G4900DA at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Canis lupus familiaris

source_name: Small intestinal mucosa, 4th-infection group,  6days after infection, replicate1

label_protocol: Agilent one-color Low Input Quick Amp Labeling Kit labeling protocol

extract_protocol: Tissue samples from infected-dogs were carefully thawed in RNA later at room temprature. Frozen tissue from normal dogs were treated with RNAlater-ICE according to the manufacture’s instruction. Small intestinal mucosa was scraped with micro spatula on a plastic culture dishes and total RNA was extracted from tissue sample with RNeasy Mini Kit (Qiagen) according to the manufacture’s instruction. Concentration and purity of total RNA samples were checked by Nanodrop 1000 optical photometer. In each group, equal amount of purified total RNA from four dogs were pooled and then used for microarray analysis.

treatment_protocol: For the control group, dogs were euthanized and necropsies were performed. The small intestine was cut out, the central part (approximately 15 cm) was washed with cold saline, then quickly frozen with liquid nitrogen. This samples were preserved in liquid nitrogen until use. For the first-infection group, 100,000 protoscoleces were orally administrated to infect E. multilocularis. For the repeated-infection group (n=4), 500,000 protoscoleces was administrated orally at 1st, 2nd and 3rd infection. At the repeated infection, the infection was terminated 35 days postinfection (dpi) by administrating 100 mg of praziquantel (2 tablets of Droncit®, Bayer-Animal Health). At the final infection, 100,000 protoscoleces was administrated by identical method. After six days of infection, the central part of small intestine from dogs infected with E. multilocularis was cut out as above mentioned method and the samples were treated with RNA later according to the manufacture’s instruction. The sample were preserved at -70°C until use.

value: small intestinal mucosa (including submucosa and muscularis externa)

value: female

value: 8 month old


title: IPSPDL2.15L_DN

description: Neurons differentiated from IPSPDL2.15

value: Neurons differentiated from iPSC


title: baseline condition at sea level, biological rep 001

value: baseline (sea level)

value: M


title: IPSRG4S_p11

value: iPSC

value: normal


title: IPSRG2L_p10

description: iPSC derived from healthy fibroblasts with lentiviral transduction


title: IPSRG6L_p27


title: IPSPDL1.6L_DN

description: Neurons differentiated from IPSPDL1.6L

value: Parkinson's disease


title: Small intestinal mucosa_1st-infection_rep1

description: Gene expression in small intestinal mucosa of 1st-infection group after 6days infection.

source_name: Small intestinal mucosa, 1st-infection group, 6days after infection, replicate0


title: female gonad_NF56_rep1

city: Krakow

first: Rafal

middle: P.

last: Piprek

address: Gronostajowa 9

department: Department of Comparative Anatomy

country: Poland

institute: Jagiellonian University

hyb_protocol: Fluorescently labeled cRNA samples were fragmented, combined with Agilent Hi-RPM Hybridization Buffer, and hybridized at 65oC for 17 hours, then was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; at RT) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; room temperature) for 1 minute each, and finally dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing: TIF files from microarray scanner processed using Agilent Feature Extraction software version 10.5.1.1. Control features and non-uniform features were removed, and remaining values for each unique probe sequence were averaged, then log (base 2) transformed. Log base 2 intensities were median centered between arrays.

organism: Xenopus laevis

source_name: female gonad at stage NF56, replicate 1

label_protocol: Agilent One-Color Quick Amp Labeling Protocol

extract_protocol: All tadpoles were genotyped to identify genetic sex using primers for DM-W gene. The tadpoles were dissected and gonads were placed in RNAlater. Total RNA was extracted using TRIzol reagent according to ZymoResearch protocol.

tag: developmental stage

value: gonad


title: Small intestinal mucosa_normal_rep1

description: Gene expression in small intestinal mucosa of normal dog group

source_name: Small intestinal mucosa, normal, replicate1

value: 9 month old


title: IPSRG2L_p26


title: male gonad_NF56_rep1

source_name: male gonad at stage NF56, replicate 1

value: male


title: female gonad_NF62_rep3

source_name: female gonad at stage NF62, replicate 3


title: male gonad_NF62_rep3

source_name: male gonad at stage NF62, replicate 3


title: IPSRG6L_p15


title: IPSRG2L_DN

description: Neurons differentiated from IPSRG2L


title: male gonad_NF50_rep3

source_name: male gonad at stage NF50, replicate 3


title: female gonad_NF62_rep1

source_name: female gonad at stage NF62, replicate 1


title: female gonad_NF56_rep2

source_name: female gonad at stage NF56, replicate 2


title: male gonad_NF53_rep2

source_name: male gonad at stage NF53, replicate 2


title: female gonad_NF53_rep3

source_name: female gonad at stage NF53, replicate 3


title: male gonad_NF62_rep1

source_name: male gonad at stage NF62, replicate 1


title: female gonad_NF56_rep3

source_name: female gonad at stage NF56, replicate 3


title: male gonad_NF56_rep3

source_name: male gonad at stage NF56, replicate 3


title: male gonad_NF50_rep1

source_name: male gonad at stage NF50, replicate 1


title: male gonad_NF56_rep2

source_name: male gonad at stage NF56, replicate 2


title: male gonad_NF50_rep2

source_name: male gonad at stage NF50, replicate 2


title: female gonad_NF50_rep3

source_name: female gonad at stage NF50, replicate 3


title: female gonad_NF50_rep1

source_name: female gonad at stage NF50, replicate 1


title: female gonad_NF50_rep2

source_name: female gonad at stage NF50, replicate 2


title: male gonad_NF53_rep1

source_name: male gonad at stage NF53, replicate 1


title: female gonad_NF53_rep2

source_name: female gonad at stage NF53, replicate 2


title: female gonad_NF53_rep1

source_name: female gonad at stage NF53, replicate 1


title: male gonad_NF53_rep3

source_name: male gonad at stage NF53, replicate 3


title: male gonad_NF62_rep2

source_name: male gonad at stage NF62, replicate 2


title: female gonad_NF62_rep2

source_name: female gonad at stage NF62, replicate 2


title: vessel at T0, biological rep1

source_name: Mouse vessel with no Angiotensin II  treatmeant

value: vessel


title: non-stress_D_vulgaris_evolved_ES9-11_rep3

type: mixed

city: Norman

first: Aifen

last: Zhou

state: OK

address: 101 David L. Boren Blvd

department: Microbiology & Plant Biology

institute: University of Oklahoma

description: ES9-11 grown in non-stress condition, biological replicate 3 of 3.

hyb_protocol: Cy3-labeled cDNA and Cy5-labeled gDNA (aliquot from pooled Cy5-labeled gDNA, equivalent to 1/12 of each labeling reaction) was co-hybridized to each array for 16 h at 42oC.

scan_protocol: The arrays were scanned with a NimbleGen MS200 microarray scanner (RocheNimbleGen, Madison, WI, USA) at a laser power of 100% and 100% PMT (photomultiplier tube).

data_processing: The raw signal intensities were obtained by follwoing instruction in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.). The transcript abundance was calculated as a ratio of the signal intensities of Cy3 / Cy5. The Log(Cy3/Cy5) values are shown in the matrix. Cutoff for true hybridization was signal to noise ratios (SNR) ≥ 2.0. Genes with detected signals in at least two out of three biological replicates were kept for detrended correspondence analysis (DCA).

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: mid-log phase cell culture

label_protocol: Total RNA (2 µg per sample) was labeled with fluorescence dye Cy3 through reverse transcription and genomic DNA (gDNA) was labeled with fluorescence dye Cy5 (1.5 µg gDNA per labeling reaction) (Chhabra SR et al.,2006. J. Bacteriol. 188:1817-1828)

growth_protocol: Desulfovibrio vulgaris Hildenborough strains including ancestor and evolved strains 5000g-ES10-5 and 1200g-ES9-11 were grown to mid-log phase (O.D.600nm about 0.4) anerobically at 37°C in standard defined medium LS4D  (Mukhopadhyay A et al. J. Bacteriol. 2006. 188: 4068-4078).

extract_protocol: Total RNA was isolated from the cell pellets with NucleoSpin RNA II and DNA was removed by on-column DNase digestion (Cat: 740955, Clontech).  RNA quality and concentration was determined by nanodrop and running agarose.

treatment_protocol: Desulfovibrio vulgaris Hildenborough  including ancestor and evolved strains 5000g-ES10-5 and 1200g-ES9-11 were  grown to mid-log phase (O.D.600nm about 0.4 for 5000g-ES10-5, about 0.3 for 1200g-ES9-11, about 0.15 for ancestor) anerobically at 37°C in high salinity medium LS4D+300 mM NaCl.

tag: strain

value: evolved DvH strain ES9-11

tag: growth condition

value: non-stress

source_name: late-log phase cell culture

value: ancestor DvH


title: stress_D_vulgaris_evolved_ES10-5_rep3

description: ES10-5 grown in high salinity condition (LS4D+300 mM NaCl), biological replicate 3 of 3.

value: evolved DvH strain ES10-5

value: high salinity (LS4D+300 mM NaCl)


title: stress_D_vulgaris_evolved_ES9-11_rep1

description: ES9-11 grown in high salinity condition (LS4D+300 mM NaCl), biological replicate 1 of 3.


title: stress_D_vulgaris_evolved_ES10-5_rep1

description: ES10-5 grown in high salinity condition (LS4D+300 mM NaCl), biological replicate 1 of 3.


title: stress_D_vulgaris_evolved_ES9-11_rep3

description: ES9-11 grown in high salinity condition (LS4D+300 mM NaCl), biological replicate 3 of 3.


title: non-stress_D_vulgaris_evolved_ES10-5_rep1

description: ES10-5 grown in non-stress condition, biological replicate 1 of 3.


title: non-stress_D_vulgaris_evolved_ES10-5_rep2

description: ES10-5 grown in non-stress condition, biological replicate 2 of 3.


title: non-stress_D_vulgaris_evolved_ES10-5_rep3

description: ES10-5 grown in non-stress condition, biological replicate 3 of 3.


title: stress_D_vulgaris_evolved_ES9-11_rep2

description: ES9-11 grown in high salinity condition (LS4D+300 mM NaCl), biological replicate 2 of 3.


title: stress_D_vulgaris_evolved_ES10-5_rep2

description: ES10-5 grown in high salinity condition (LS4D+300 mM NaCl), biological replicate 2 of 3.


title: stress_D_vulgaris_ancestor_rep2

description: ancestor grown in high salinity condition (LS4D+300 mM NaCl), biological replicate 2 of 3.


title: stress_D_vulgaris_ancestor_rep3

description: ancestor grown in high salinity condition (LS4D+300 mM NaCl), biological replicate 3 of 3.


title: non-stress_D_vulgaris_evolved_ES9-11_rep1

description: ES9-11 grown in non-stress condition, biological replicate 1 of 3.


title: non-stress_D_vulgaris_ancestor_rep3

description: ancestor grown in non-stress condition, biological replicate 3 of 3.


title: stress_D_vulgaris_ancestor_rep1

description: ancestor grown in high salinity condition (LS4D+300 mM NaCl), biological replicate 1 of 3.


title: non-stress_D_vulgaris_evolved_ES9-11_rep2

description: ES9-11 grown in non-stress condition, biological replicate 2 of 3.


title: non-stress_D_vulgaris_ancestor_rep1

description: ancestor grown in non-stress condition, biological replicate 1 of 3.


title: non-stress_D_vulgaris_ancestor_rep2

description: ancestor grown in non-stress condition, biological replicate 2 of 3.


title: Control (patient with no osteoarthritis) CONTROL7

status: Public on Oct 17 2017

city: Athens

first: George

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

source_name: Serum

extract_protocol: Total RNA was extracted from serum samples using the RiboEXTMLS kit (GeneAll, Seoul, Korea). RNA quantity and quality were evaluated using a spectrophotometer (NanoDrop® ND-1000 UV-Vis, Nanogen Inc). RNA quantity and quality were evaluated using a spectrophotometer (NanoDrop® ND-1000 UV-Vis, Nanogen Inc.). Total RNA samples were spiked using the microRNA Spike-In Kit (Agilent Technologies Santa Clara, CA, USA) to assess the labeling and hybridization efficiencies. Labeling and hybridization were performed using the miRNA complete Labeling and Hybridization Kit (Agilent Technologies Santa Clara, CA, USA) according to manufacturer’s instructions. Samples were hybridized to the SurePrint G3 Human miRNA, 8X60K platform (miRBase release 21.0, Agilent Technologies Inc., Santa Clara, CA) containing probes for the detection of 2,549 human miRNAs. Images were scanned using Agilent Microarray Scanner (G2565CA) controlled by Agilent Scan Control 7.0 software. The signal after background subtraction was exported directly into Agilent Feature Extraction Software version 4.0.1.21 (Agilent Technologies, Santa Clara, CA). Normalization was performed using quantile algorithm. MicroRNAs were considered as differentially expressed (DE) if they obtained a p-value<0.05 and a False Discovery Rate (FDR)≤0.05.

value: F

tag: bmi


title: Control (patient with no osteoarthritis) CONTROL5

hyb_protocol: Samples were hybridized to the SurePrint G3 Human miRNA, 8X60K platform (miRBase release 21.0, Agilent Technologies Inc., Santa Clara, CA) containing probes for the detection of 2,549 human miRNAs.

scan_protocol: Images were scanned using Agilent Microarray Scanner (G2565CA) controlled by Agilent Scan Control 7.0 software.

data_processing: The signal after background subtraction was exported directly into Agilent Feature Extraction Software version 4.0.1.21 (Agilent Technologies, Santa Clara, CA). Normalization was performed using quantile algorithm. MicroRNAs were considered as differentially expressed (DE) if they obtained a p-value<0.05 and a False Discovery Rate (FDR)≤0.05.

label_protocol: Total RNA samples were spiked using the microRNA Spike-In Kit (Agilent Technologies Santa Clara, CA, USA) to assess the labeling and hybridization efficiencies. Labeling and hybridization were performed using the miRNA complete Labeling and Hybridization Kit (Agilent Technologies Santa Clara, CA, USA) according to manufacturer’s instructions.


title: Control (patient with no osteoarthritis) CONTROL10


title: Control (patient with no osteoarthritis) CONTROL3


title: Control (patient with no osteoarthritis) CONTROL11


title: Control (patient with no osteoarthritis) CONTROL12


title: Control (patient with no osteoarthritis) CONTROL9


title: Control (patient with no osteoarthritis) CONTROL4


title: Osteoarthritis OA12


title: Control (patient with no osteoarthritis) CONTROL8


title: Control (patient with no osteoarthritis) CONTROL2

value: Μ


title: Osteoarthritis OA7


title: Control (patient with no osteoarthritis) CONTROL1


title: Control (patient with no osteoarthritis) CONTROL6


title: Osteoarthritis OA11


title: Osteoarthritis OA8


title: hsp-90 RNAi rep1

city: Garching bei München

first: Klaus

last: Richter

address: Lichtenbergstr. 4

department: Chemie

country: Germany

institute: Technische Universität münchen

hyb_protocol: 3,8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix C. elegans Gene 1.0 ST arrays for 16 h at 45 ° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

scan_protocol: The fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G, controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software.

organism: Caenorhabditis elegans

source_name: wild-type, hsp-90 RNAi

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 15 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin. (Affymetrix GeneChip WT PLUS Reagent Kit User Manual)

growth_protocol: growth on NGM RNAi standard plates at 20 degrees

extract_protocol: Nematodes were washed off the plates with M9 buffer and snap frozen in liquid Nitrogen. Pelleted C. elegans worms were homogenized in 700 µl Trizol reagent using Precellys VK05 glass beads (2 cycles of 10 seconds at 6500 rpm; 10 seconds break). After 5 minutes incubation at room temperature 140 ml of chloroform was added and the samples were again incubated at room temperature for 2 minutes. Phase separation was achieved by 15 minutes centrifugation at 12,000 x g at 4 °C. An equal amount of 70 % ethanol was added to the aqueous supernatant and the mixture was applied to RNeasy Mini spin columns (RNeasy Mini Kit, QIAGEN, Hilden, Germany), followed by an on-column DNase digestion and several wash steps. Finally total RNA was eluted in 30 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip reagent set (Agilent, Palo Alto, CA, USA).

treatment_protocol: feeding dsRNA expression bacteria with either empty plasmid or hsp-90 knock-down construct

value: L4-young adult

value: RNAi-mediated Hsp90 knock-down

value: entire nematode


title: Osteoarthritis OA4


title: hsp-90 RNAi rep2


title: Osteoarthritis OA2

value: M


title: hsp-90 RNAi rep3


title: Osteoarthritis OA9


title: Osteoarthritis OA3


title: Osteoarthritis OA5


title: Osteoarthritis OA10


title: Osteoarthritis OA1


title: Osteoarthritis OA6


title: WASH3

city: Philadelphia

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

description: Gene expression data from T6E cells treated with GSI for 24h and then treatment was washed out and cells were cultured with DMSO for 6h.

hyb_protocol: not provided

scan_protocol: not provided

data_processing: data is processed with biocondocutor oligo package and background correcting and rma normalized

source_name: T6E cells, GSI  washoutt

label_protocol: not provided

growth_protocol: T6E cells were cultured  in RPMI (Life Technologies) medium supplemented with 10% heat-inactivated FBS (Hyclone), 100 U/ml penicillin, 100 mg/ml streptomycin, 2 mM L-glutamine, 50 mM 2-mercaptoethanol,

extract_protocol: RNA was extracted using the QIAGEN RNeasy mini Kit.

treatment_protocol: T6E cells were treated with either DMSO or GSI (1 μM) containing medium for 24 hours. Subsequently, cells were cultured in media containing cycloheximide (20 μg/mL) and cells previously cultured DMSO were replated in DMSO (lebeled DMSO) and cells cultured in GSI were either replated in 1 μM GSI (labeled GSI) or in DMSO (labeled WASH) for 6 hours.

value: spleen

tag: cell line


title: GSI3

description: Gene expression data from T6E cells treated with GSI for 30h.

source_name: T6E cells, GSI  treat


title: RNAi empty vector rep2

source_name: wild-type, control

value: control


title: WASH2


title: DMSO3

description: Gene expression data from T6E cells treated with DMSO for 30h.

source_name: T6E cells, DMSO treat


title: patient 403, sample collected in EDTA tube

city: Boston

first: Brian

last: Crompton

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: patient 403, germline DNA collected in EDTA tube

hyb_protocol: hybridized to a custom 4x180K CGH plus SNP microarray (GGXChip+SNP v1.0, Agilent)

scan_protocol: SureScan Microarray Scanner (Agilent)

data_processing: data was analyzed through CytoGenomics v4.0.3.1.2 (Agilent) and Genoglyphix v3.1 (Perkin Elmer)

source_name: Germline DNA collected in EDTA tube

label_protocol: test samples were labeled with Cyanine 5-dUTP and control samples were labeled with Cyanine 3-dUTP

extract_protocol: After plasma was removed, DNA was extracted from the remaining sample with the Gentra Puregene Blood Kit (Qiagen)

treatment_protocol: Peripheral blood samples were collected in either EDTA or Streck tubes

tag: patient

tag: collection tube

value: EDTA

source_name: Sex-matched control


title: patient 403, sample collected in Streck tube

description: patient 403, germline DNA collected in Streck tube

source_name: Germline DNA collected in Streck tube

value: Streck


title: RNAi empty vector rep1


title: DMSO2


title: patient 394, sample collected in EDTA tube

description: patient 394, germline DNA collected in EDTA tube


title: RNAi empty vector rep3


title: patient 179, sample collected in Streck tube

description: patient 179, germline DNA collected in Streck tube


title: RNA38 non-pCR

status: Public on Oct 14 2017

city: Yufu

first: Hajime

last: Fujishima

state: Oita

address: 1-1 Idaigaoka Hasama-machi

department: Gastroenterological and Pediatric Surgery

institute: Oita University Faculty of Medicine

description: Gene expression before chemotherapy

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed with GeneSpring GX software(Aglrent).

source_name: non-pCR

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit (Agilent Technologies).

extract_protocol: Frozen specimens were homogenized, and total RNA was extracted using QIAGEN RNeasyTM mini kit (QIAGEN), according to the manufacture’s protocol.

tag: organ

value: esophagus

value: cancer tissue


title: patient 179, sample collected in EDTA tube

description: patient 179, germline DNA collected in EDTA tube


title: DMSO1


title: RNA34 non-pCR

description: Gene expression before chemotherapy


title: RNA35N pCR not tumor tissue

description: Gene expression before chemotherapy

source_name: pCR

value: normal tissue


title: RNA41 non-pCR

description: Gene expression before chemotherapy


title: RNA33 non-pCR

description: Gene expression before chemotherapy


title: patient 394, sample collected in Streck tube

description: patient 394, germline DNA collected in Streck tube


title: RNA39 non-pCR

description: Gene expression before chemotherapy


title: GSI2


title: RNA37 non-pCR

description: Gene expression before chemotherapy


title: RNA43 non-pCR

description: Gene expression before chemotherapy


title: RNA36 non-pCR

description: Gene expression before chemotherapy


title: RNA29 pCR

description: Gene expression before chemotherapy


title: RNA35 pCR

description: Gene expression before chemotherapy


title: RNA42 non-pCR

description: Gene expression before chemotherapy


title: RNA30 non-pCR

description: Gene expression before chemotherapy


title: GSI1


title: RNA31 non-pCR

description: Gene expression before chemotherapy


title: RNA45 pCR

description: Gene expression before chemotherapy


title: RNA29N pCR not tumor tissue

description: Gene expression before chemotherapy


title: RNA32 non-pCR

description: Gene expression before chemotherapy


title: RNA33N non-pCR not tumor tissue

description: Gene expression before chemotherapy


title: WASH1


title: RNA28N non-pCR not tumor tissue

description: Gene expression before chemotherapy


title: RNA25N non-pCR not tumor tissue

description: Gene expression before chemotherapy


title: RNA26 non-pCR

description: Gene expression before chemotherapy


title: RNA27 non-pCR

description: Gene expression before chemotherapy


title: RNA24 pCR

description: Gene expression before chemotherapy


title: RNA21 non-pCR

description: Gene expression before chemotherapy


title: RNA22 non-pCR

description: Gene expression before chemotherapy


title: RNA19 non-pCR

description: Gene expression before chemotherapy


title: RNA25 non-pCR

description: Gene expression before chemotherapy


title: RNA28 non-pCR

description: Gene expression before chemotherapy


title: RNA15 non-pCR

description: Gene expression before chemotherapy


title: RNA16 non-pCR

description: Gene expression before chemotherapy


title: RNA17 pCR

description: Gene expression before chemotherapy


title: RNA09 non-pCR

description: Gene expression before chemotherapy


title: RNA18 non-pCR

description: Gene expression before chemotherapy


title: RNA07 pCR

description: Gene expression before chemotherapy


title: RNA08 non-pCR

description: Gene expression before chemotherapy


title: RNA11 non-pCR

description: Gene expression before chemotherapy


title: RNA13 non-pCR

description: Gene expression before chemotherapy


title: RNA06 non-pCR

description: Gene expression before chemotherapy


title: RNA10 pCR

description: Gene expression before chemotherapy


title: RNA14 non-pCR

description: Gene expression before chemotherapy


title: RNA03 non-pCR

description: Gene expression before chemotherapy


title: RNA04 pCR

description: Gene expression before chemotherapy


title: RNA01 pCR

description: Gene expression before chemotherapy


title: RNA12 pCR

description: Gene expression before chemotherapy


title: QL_furfural_21

status: Public on Oct 13 2017

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used.

organism: Saccharomyces cerevisiae

source_name: cell culture of strain QLF21

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: JSC25 cells were suspended in 100ul YPD medium containing 20g/L furfural and incubated at 30 degree with vigorous shaking for 2h following streaking on YPD plates immediately and incubating at 30degree  for 2 days to form colonies for next round furfural-treatment.

tag: ploidy

value: diploid strain

tag: background

value: JSC25-derived isolate 21

source_name: control strain JSC24


title: RNA05 non-pCR

description: Gene expression before chemotherapy

tag: tissue


title: QL_furfural_20

source_name: cell culture of strain QLF20

value: JSC25-derived isolate 20


title: RNA20 non-pCR

description: Gene expression before chemotherapy


title: QL_furfural_18

source_name: cell culture of strain QLF18

value: JSC25-derived isolate 18


title: QL_furfural_16

source_name: cell culture of strain QLF16

value: JSC25-derived isolate 16


title: QL_furfural_19

source_name: cell culture of strain QLF19

value: JSC25-derived isolate 19


title: QL_furfural_17

source_name: cell culture of strain QLF17

value: JSC25-derived isolate 17


title: QL_furfural_13

source_name: cell culture of strain QLF13

value: JSC25-derived isolate 13


title: QL_furfural_12

source_name: cell culture of strain QLF12

value: JSC25-derived isolate 12


title: QL_furfural_14

source_name: cell culture of strain QLF14

value: JSC25-derived isolate 14


title: QL_furfural_15

source_name: cell culture of strain QLF15

value: JSC25-derived isolate 15


title: QL_furfural_18R

description: Red part of JSC25-derived sectored colony 18

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37° C. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.  Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. Sectored colonies were mapped using Agilent platform with Agilent-047217, which contains many probes on chromosome IV, but few probes near the telomere and centromere of all chromosomes.

source_name: Cell culture of red part of JCS25-derived sectored colonies 18

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

treatment_protocol: JSC25 cells were suspended in 100ul YPD medium containing 17g/L furfural and incubated at 30 degree with vigorous shaking for 1h following streaking on YPD plates immediately and incubating at 30 degree for 2 days to form colonies for select sectored colonies


title: QL_furfural_18W

description: White part of JSC25-derived sectored colony 18

source_name: Cell culture of white part of JCS25-derived sectored colonies 18


title: QL_furfural_10

source_name: cell culture of strain QLF10

value: JSC25-derived isolate 10


title: QL_furfural_17W

description: White part of JSC25-derived sectored colony 17

source_name: Cell culture of white part of JCS25-derived sectored colonies 17


title: QL_furfural_6

source_name: cell culture of strain QLF6

value: JSC25-derived isolate 6


title: QL_furfural_11

source_name: cell culture of strain QLF11

value: JSC25-derived isolate 11


title: QL_furfural_19R

description: Red part of JSC25-derived sectored colony 19

source_name: Cell culture of red part of JCS25-derived sectored colonies 19


title: QL_furfural_9

source_name: cell culture of strain QLF9

value: JSC25-derived isolate 9

source_name: control strain JSC24


title: QL_furfural_7

source_name: cell culture of strain QLF7

value: JSC25-derived isolate 7


title: QL_furfural_2

source_name: cell culture of strain QLF2

value: JSC25-derived isolate 2


title: QL_furfural_8

source_name: cell culture of strain QLF8

value: diploid strain

value: JSC25-derived isolate 8


title: QL_furfural_19W

description: White part of JSC25-derived sectored colony 19

source_name: Cell culture of white part of JCS25-derived sectored colonies 19


title: QL_furfural_3

source_name: cell culture of strain QLF3

value: JSC25-derived isolate 3


title: QL_furfural_1

source_name: cell culture of strain QLF1

value: JSC25-derived isolate 1


title: QL_furfural_4

source_name: cell culture of strain QLF4

value: JSC25-derived isolate 4


title: QL_furfural_15R

description: Red part of JSC25-derived sectored colony 15

source_name: Cell culture of red part of JCS25-derived sectored colonies 15


title: QL_furfural_5

source_name: cell culture of strain QLF5

value: JSC25-derived isolate 5


title: QL_furfural_14R

description: Red part of JSC25-derived sectored colony 14

source_name: Cell culture of red part of JCS25-derived sectored colonies 14


title: QL_furfural_13R

description: Red part of JSC25-derived sectored colony 13

source_name: Cell culture of red part of JCS25-derived sectored colonies 13


title: QL_furfural_15W

description: White part of JSC25-derived sectored colony 15

source_name: Cell culture of white part of JCS25-derived sectored colonies 15


title: QL_furfural_16R

description: Red part of JSC25-derived sectored colony 16

source_name: Cell culture of red part of JCS25-derived sectored colonies 16


title: QL_furfural_17R

description: Red part of JSC25-derived sectored colony 17

source_name: Cell culture of red part of JCS25-derived sectored colonies 17


title: QL_furfural_14W

description: White part of JSC25-derived sectored colony 14

source_name: Cell culture of white part of JCS25-derived sectored colonies 14


title: QL_furfural_12W

description: White part of JSC25-derived sectored colony 12

source_name: Cell culture of white part of JCS25-derived sectored colonies 12


title: QL_furfural_12R

description: Red part of JSC25-derived sectored colony 12

source_name: Cell culture of red part of JCS25-derived sectored colonies 12

source_name: control strain JSC24


title: QL_furfural_11R

description: Red part of JSC25-derived sectored colony 11

source_name: Cell culture of red part of JCS25-derived sectored colonies 11


title: QL_furfural_11W

description: White part of JSC25-derived sectored colony 11

source_name: Cell culture of white part of JCS25-derived sectored colonies 11


title: QL_furfural_10W

description: White part of JSC25-derived sectored colony 10

source_name: Cell culture of white part of JCS25-derived sectored colonies 10


title: QL_furfural_10R

description: Red part of JSC25-derived sectored colony 10

source_name: Cell culture of red part of JCS25-derived sectored colonies 10


title: QL_furfural_7W

description: White part of JSC25-derived sectored colony 7

source_name: Cell culture of white part of JCS25-derived sectored colonies 7


title: QL_furfural_8R

description: Red part of JSC25-derived sectored colony 8

source_name: Cell culture of red part of JCS25-derived sectored colonies 8


title: QL_furfural_16W

description: White part of JSC25-derived sectored colony 16

source_name: Cell culture of white part of JCS25-derived sectored colonies 16


title: QL_furfural_7R

description: Red part of JSC25-derived sectored colony 7

source_name: Cell culture of red part of JCS25-derived sectored colonies 7


title: QL_furfural_6W

description: White part of JSC25-derived sectored colony 6

source_name: Cell culture of white part of JCS25-derived sectored colonies 6


title: QL_furfural_6R

description: Red part of JSC25-derived sectored colony 6

source_name: Cell culture of red part of JCS25-derived sectored colonies 6


title: QL_furfural_3W

description: White part of JSC25-derived sectored colony 3

source_name: Cell culture of white part of JCS25-derived sectored colonies 3


title: QL_furfural_5R

description: Red part of JSC25-derived sectored colony 5

source_name: Cell culture of red part of JCS25-derived sectored colonies 5


title: QL_furfural_4W

description: White part of JSC25-derived sectored colony 4

source_name: Cell culture of white part of JCS25-derived sectored colonies 4


title: QL_furfural_4R

description: Red part of JSC25-derived sectored colony 4

source_name: Cell culture of red part of JCS25-derived sectored colonies 4


title: QL_furfural_3R

description: Red part of JSC25-derived sectored colony 3

source_name: Cell culture of red part of JCS25-derived sectored colonies 3


title: QL_furfural_2R

description: Red part of JSC25-derived sectored colony 2

source_name: Cell culture of red part of JCS25-derived sectored colonies 2


title: QL_furfural_9W

description: White part of JSC25-derived sectored colony 9

source_name: Cell culture of white part of JCS25-derived sectored colonies 9

source_name: control strain JSC24


title: QL_furfural_1R

description: Red part of JSC25-derived sectored colony 1

source_name: Cell culture of red part of JCS25-derived sectored colonies 1

value: JCS25-derived sectored colony


title: QL_furfural_1W

description: White part of JSC25-derived sectored colony 1

source_name: Cell culture of white part of JCS25-derived sectored colonies 1


title: QL_furfural_9R

description: Red part of JSC25-derived sectored colony 9

source_name: Cell culture of red part of JCS25-derived sectored colonies 9


title: QL_furfural_5W

description: White part of JSC25-derived sectored colony 5

source_name: Cell culture of white part of JCS25-derived sectored colonies 5


title: L-Asp_01

city: LOWELL

first: GUOQING

last: LI

address: 220 Pawtucket St

institute: University of Massachusetts Lowell

description: Gene expression data from PAO1 at 20mM L-Asp

scan_protocol: Affymetrix Protocol:Scan-M10

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 in MMP supplemented with 20mM Pyruvate and 20mM L-Asp_01

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 10 ug total RNA

growth_protocol: Overnight grown cultures of P. aeruginosa PAO1 were used to inoculate 10 ml minimal medium P and grown at 37ºC with shaking at 300rpm.Cells were harvested when the optical density at 600 nm reached 0.4~0.6 by centrifugation for 5 minutes at 4C.

extract_protocol: Total RNA samples were isolated by RNeasy Plus Micro Kit following instructions of the manufacturer (Qiagen). Reverse transcription for cDNA synthesis and fragmentation by DNase I treatment were performed according to the instructions of GeneChip manufacturer (Affymetrix).

treatment_protocol: P. aeruginosa PAO1 was grown in minimal medium P in the presence of Pyruvate at 20 mM and L-Ala, L-Asn or L-Asp at 20 mM.


title: L-Asn_02

description: Gene expression data from PAO1 at 20mM L-Asn

source_name: PAO1 in MMP supplemented with 20mM Pyruvate and 20mM L-Asn_02


title: L-Asp_02

source_name: PAO1 in MMP supplemented with 20mM Pyruvate and 20mM L-Asp_02


title: L-Ala_01

description: Gene expression data from PAO1 at 20mM L-Ala

source_name: PAO1 in MMP supplemented with 20mM Pyruvate and 20mM L-Ala_01


title: QL_furfural_2W

description: White part of JSC25-derived sectored colony 2

source_name: Cell culture of white part of JCS25-derived sectored colonies 2


title: L-Ala_02

source_name: PAO1 in MMP supplemented with 20mM Pyruvate and 20mM L-Ala_02


title: Sorted SSEA5-positive undifferentiated hESC, biological replicate 1

status: Public on Oct 12 2017

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

institute: Helmholtz Center Munich

description: Gene expression data from SSEA5-positive cell population of undifferentiated hESC line H9

hyb_protocol: cDNA was hybridized using GeneChip Hybridization, Wash and Stain kit (Affymetrix), according to manufacturer's instructions. GeneChips were washed using GeneChip Fluidics station 450

scan_protocol: Chips were scanned using GeneChip Scanner 3000 7G

data_processing: Data was analysed using Bioconductoroligo package in R.

source_name: undifferentiated hESC line H9

label_protocol: 50 ng of starting RNA was processed and biotin-labelled using Ovation Pico WTA System v2 and Encore Biotin Module according to manufacturer's instructions

growth_protocol: hESC cells were maintained in KSR-bFGF growth medium on irradiated MEF feeders. Differentiation was done in Matrigel-coated dishes using KSR medium without bFGF and 50 ng/ml BMP4 for 2.5 days

extract_protocol: Total RNA was extracted using Qiagen Rneasy Mini kit according to manufacturer's instructions

treatment_protocol: Differentiation was done in Matrigel-coated dishes using KSR medium without bFGF and 50 ng/ml BMP4 for 2.5 days. Cells were collected using Versene solution and subjected to FACS sorting using anti-APA and anti-SSEA5 antibodies

tag: cell population


title: Sorted SSEA5-positive undifferentiated hESC, biological replicate 2


title: Sorted SSEA5-positive undifferentiated hESC, biological replicate 3


title: Sorted APA-negative cell population, biological replicate 3

description: Gene expression data from APA-negative cell population of hESC line H9 treated with BMP4 for 2.5 days

value: APA-


title: Sorted APA-positive cell population, biological replicate 2

description: Gene expression data from APA-positive cell population of hESC line H9 treated with BMP4 for 2.5 days

value: APA+


title: Sorted APA-positive cell population, biological replicate 1

source_name: hESC line H9 treated with BMP4 for 2.5 days


title: Sorted APA-negative cell population, biological replicate 2


title: Maltose-148 h-replicate 2

city: León

first: Antonio

last: Rodríguez-García

address: Avenida Real 1

country: Spain

institute: INBIOTEC

description:
MgLoc_Mal.148.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

hyb_protocol: Mixes of Cy3-cDNA (300 ng) and Cy5-gDNA (4 pmol) in a volume of 18.8 μl were denaturalized (94 °C, 3 min), pulse centrifuged and added to 31.2 μl of 1.6 × hybridization solution (PMID 19146703). Forty microlitres of this solution were applied on each microarray surface. The slides were placed in an Agilent hybridization chamber and rotated at 4 rpm and 55 °C for 64–67 h. Washing, stabilization and drying of the slides were carried out as indicated previously (PMID 23555999).

scan_protocol: A G2565BA scanner (Agilent), in extended dynamic mode, and the FeatureExtraction v9.5.1 software (CGH protocol) were used to quantify the hybridization signals.

data_processing: The limma package v3.20 was used for normalization of the signal intensities and for statistical analyses. Net fluorescence signals were calculated as the subtraction of the median of background pixels from the mean of foreground pixels. When this mean value was negative or lower than the background standard deviation, the background standard deviation was used as the surrogate signal. Mg values were calculated as the log2 of Cy3-cDNA/Cy5-gDNA net signals and then normalized using cyclic loess and global median. For both normalization processes, probes were weighted to exclude tiling probes (fkb cluster) in the calculus of the normalization factors.

organism: Streptomyces tsukubensis NRRL18488

source_name: Culture no. 14, 148 h of culture, maltose added

label_protocol: Total RNA samples were labelled using random hexamers (Invitrogen), SuperScript III reverse transcriptase (Invitrogen) and Cy3-dCTP (GE Healthcare Life Sciences) as indicated previously (PMID 17623301). Then, remnant RNAwas hydrolyzed with NaOH at 70 °C and the synthesized Cy3-cDNA was purified using the MinElute PCR Purification Kit (Qiagen). gDNA from S. tsukubaensis NRRL 18488 was labelled with Cy5-dCTP (GE Healthcare Life Sciences) using the BioPrime Array CGH Genomic Labeling Module (Invitrogen) and the Cy5-gDNA was purified with the MinElute kit (Qiagen). The incorporation of Cy3/Cy5- dCTP was quantified with NanoDrop spectrophotometer and kept at −20 °C. Only samples with a specific activity greater than 40 pmol μg−1 were used in the microarray hybridization.

growth_protocol: Streptomyces tsukubensis  NRRL 18488 was grown at 28 ºC on ISP4 (Difco™) medium for spore preparation. 10e9 spores were inoculated into 0.5-l flasks containing 100 ml of MGm-2.5 media (PMID 22990582) and incubated at 28 ºC and 220 rpm.

extract_protocol: Frozen samples were thawed on ice, suspended in 170 μl of lysozyme solution (15 mg ml−1 in TE buffer) and incubated at room temperature for 10 min. Cell suspensions were transferred to lysing matrix B columns (MP Biochemicals), cooled on ice and lysed on a FastPrep FP120 homogenizer (Thermo Electron). Two pulses of 30 s at speed 6.5 m s−1 were applied, cooling down the tubes on ice for 1 min between pulses. After centrifugation, the aqueous solution was prepurified by fenolization. RNA was extracted using RNeasy Mini Spin columns and treated on-column with DNase I (both from Qiagen). After elution, RNA concentration, purity and integrity were determined using a ND-1000 spectrophotometer, the RNA 6000 Nano LabChip kit and a 2100 Bioanalyzer (Agilent)

treatment_protocol: Culture samples ranging from 0.4 to 1 ml were taken and immediately mixed with two volumes of RNAprotect Bacteria Reagent (Qiagen), vortexed for 30 s and kept for 5 min at room temperature for stabilization of RNA. After centrifugation, the supernatant was discarded and the pellets were kept at −80 °C until further processed

tag: addition

value: Maltose

tag: time

source_name: Total DNA extracted from a stationary-phase culture


title: Sorted APA-negative cell population, biological replicate 1


title: QL_furfural_13W

description: White part of JSC25-derived sectored colony 13

source_name: Cell culture of white part of JCS25-derived sectored colonies 13


title: Maltose-100 h-replicate 1

description:
MgLoc_Mal.100.m11
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 11, 100 h of culture, maltose added


title: Maltose-92 h-replicate 2

description:
MgLoc_Mal.092.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 14, 92 h of culture, maltose added


title: L-Asn_01

source_name: PAO1 in MMP supplemented with 20mM Pyruvate and 20mM L-Asn_01


title: Sorted APA-positive cell population, biological replicate 3


title: QL_furfural_8W

description: White part of JSC25-derived sectored colony 8

source_name: Cell culture of white part of JCS25-derived sectored colonies 8

source_name: control strain JSC24


title: Maltose-100 h-replicate 2

description:
MgLoc_Mal.100.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 14, 100 h of culture, maltose added


title: Maltose-124 h-replicate 2

description:
MgLoc_Mal.124.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 14, 124 h of culture, maltose added


title: Embryonic dental Sox2+ cells, biological rep 3

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

country: France

institute: Inserm

description: Embryonic Sox2+ cells from incisor epithelium. Incisors manually dissected. Sox2+ cells sorted based on alive (AAD-) and Sox2+ (GFP+) cells, using fluorescence-activated cell sorting (FACs).

hyb_protocol: GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 3, Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing:
The data-analysis consisted of data pre-processing, quality analysis and detection of statistically differentially expressed genes between the sample groups. The .CEL files of each of the six arrays were loaded into the Affymetrix Expression Console software. They were processed with two different analysis methods:
* Gene level SST-RMA (Signal Space Transformation - Robust Multichip Analysis), includes background reduction and SST intensity normalization to produce the gene expression difference results
* Exon level SST-Alt Splicing - includes additionally the extraction of all exon, exon-exon splice junction and transcript isoform expression changes. These results can be found from the .CHP files included in the project folder. The file names indicate which method has been used.
These files in turn are used with the Affymetrix Transcriptome Analysis Console (TAC) Software to produce the differential expression tables and charts.
[1] MTA 1.0 - http://www.affymetrix.com/catalog/prod870009/AFFY/Mouse+Transcriptome+Assay+1.0
[2] CEL file format - http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html
[3] Affymetrix Expression Console Software - http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?productId=131414
[4] Affymetrix Expression Console Software Manual - http://media.affymetrix.com/support/downloads/manuals/expression_console_userguide.pdf
[5] CHP file format - http://dept.stat.lsa.umich.edu/~kshedden/Courses/Stat545/Notes/AffxFileFormats/chp.html
[6] Affymetrix Transcriptome Analysis Console (TAC) Software - http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?categoryIdClicked=&productId=prod760001&navAction=jump
[7] Affymetrix Transcriptome Analysis Console (TAC) Software Manual - http://media.affymetrix.com/support/downloads/manuals/tac_user_manual.pdf

source_name: E14.5 embryos

label_protocol: Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays P/N 703262 Rev. 1

growth_protocol: Mice were kept in an animal facility (following Finnish National Board of Animal Experimentation guidelines) until sample collection.

extract_protocol: RNA was extracted using the RNeasy Micro kit (Qiagen, 74004).


title: Maltose-80 h-replicate 1

description:
MgLoc_Mal.080.m11
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 11, 80 h of culture, maltose added


title: Maltose-76 h-replicate 2

description:
MgLoc_Mal.076.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 14, 76 h of culture, maltose added


title: Maltose-92 h-replicate 1

description:
MgLoc_Mal.092.m11
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 11, 92 h of culture, maltose added


title: Maltose-89 h-replicate 1

description:
MgLoc_Mal.089.m11
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 11, 89 h of culture, maltose added


title: Embryonic dental Sox2+ cells, biological rep 1

value: Embryonic Sox2+ cells from incisor epithelium


title: Maltose-80 h-replicate 2

description:
MgLoc_Mal.080.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 14, 80 h of culture, maltose added


title: Maltose-89 h-replicate 2

description:
MgLoc_Mal.089.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 14, 89 h of culture, maltose added


title: Adult dental Sox2+ cells, biological rep 1

description: Adult Sox2+ cells from labial cervical loop (laCL). laCLs manually dissected. Sox2+ cells sorted based on alive (AAD-) and Sox2+ (GFP+) cells, using fluorescence-activated cell sorting (FACs).

source_name: P30 mice


title: Maltose-76 h-replicate 1

description:
MgLoc_Mal.076.m11
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 11, 76 h of culture, maltose added

source_name: Total DNA extracted from a stationary-phase culture


title: mESC, biological rep 3

description: Comercially available mESCs

source_name: mESCs

value: mouse embryonic stem cells (mESCs)


title: Embryonic dental Sox2+ cells, biological rep 2


title: Maltose-72 h-replicate 2

description:
MgLoc_Mal.072.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 14, 72 h of culture, maltose added


title: Adult dental Sox2+ cells, biological rep 2

value: Adult Sox2+ cells from labial cervical loop


title: Adult dental Sox2+ cells, biological rep 3


title: genomic DNA from whole blood 47

city: Shanghai

first: Lei

last: Shi

address: No. 1665 Kongjiang Road

institute: Xinhua Hospital, Shanghai Jiao Tong University School of Medicine

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 BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v3.2

source_name: genomic DNA from whole blood

growth_protocol: Not handled cell

extract_protocol: genomic DNA was extracted and purified from whole blood samples using Qiagen Dneasy Kit according to standard instructions

treatment_protocol: Not handled cell

tag: gender

value: Male

tag: age (y)


title: genomic DNA from whole blood 45

value: Female


title: mESC, biological rep 2

description: Comercially available mESCs


title: Maltose-70.7 h-replicate 2

description:
MgLoc_Mal.071.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 14, 70.7 h of culture, maltose added


title: genomic DNA from whole blood 46


title: genomic DNA from whole blood 39


title: genomic DNA from whole blood 42


title: Glycerol-100 h-replicate 2

description:
MgLoc_Gol.100.m7
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 7, 100 h of culture, glycerol added

value: Glycerol


title: Glycerol-124 h-replicate 1

description:
MgLoc_Gol.124.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 124 h of culture, glycerol added


title: genomic DNA from whole blood 43


title: Maltose-70 h-replicate 2

description:
MgLoc_Mal.070.m14
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 14, 70 h of culture, no carbon source yet added


title: Glycerol-100 h-replicate 1

description:
MgLoc_Gol.100.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 100 h of culture, glycerol added


title: genomic DNA from whole blood 41


title: Maltose-70 h-replicate 1

description:
MgLoc_Mal.070.m11
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 11, 70 h of culture, no carbon source yet added


title: Maltose-72 h-replicate 1

description:
MgLoc_Mal.072.m11
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 11, 72 h of culture, maltose added


title: genomic DNA from whole blood 37


title: Glycerol-148 h-replicate 1

description:
MgLoc_Gol.148.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 148 h of culture, glycerol added


title: Maltose-70.7 h-replicate 1

description:
MgLoc_Mal.071.m11
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 11, 70.7 h of culture, maltose added


title: genomic DNA from whole blood 44


title: genomic DNA from whole blood 38


title: genomic DNA from whole blood 48


title: mESC, biological rep 1

description: Comercially available mESCs


title: Glycerol-80 h-replicate 1

description:
MgLoc_Gol.080.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 80 h of culture, glycerol added


title: Glycerol-92 h-replicate 1

description:
MgLoc_Gol.092.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 92 h of culture, glycerol added


title: Glycerol-92 h-replicate 2

description:
MgLoc_Gol.092.m7
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 7, 92 h of culture, glycerol added


title: Glycerol-72 h-replicate 2

description:
MgLoc_Gol.072.m7
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 7, 72 h of culture, glycerol added


title: Glycerol-80 h-replicate 2

description:
MgLoc_Gol.080.m7
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 7, 80 h of culture, glycerol added

source_name: Total DNA extracted from a stationary-phase culture


title: Glycerol-89 h-replicate 1

description:
MgLoc_Gol.089.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 89 h of culture, glycerol added


title: Glycerol-76 h-replicate 2

description:
MgLoc_Gol.076.m7
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 7, 76 h of culture, glycerol added


title: Glycerol-76 h-replicate 1

description:
MgLoc_Gol.076.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 76 h of culture, glycerol added


title: genomic DNA from whole blood 35

source_name: genomic DNA from whole blood


title: Glycerol-89 h-replicate 2

description:
MgLoc_Gol.089.m7
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 7, 89 h of culture, glycerol added


title: Glycerol-72 h-replicate 1

description:
MgLoc_Gol.072.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 72 h of culture, glycerol added


title: genomic DNA from whole blood 32


title: Glycerol-70.7 h-replicate 2

description:
MgLoc_Gol.071.m7
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 7, 70.7 h of culture, glycerol added


title: genomic DNA from whole blood 30


title: genomic DNA from whole blood 29


title: genomic DNA from whole blood 33


title: Glycerol-70.7 h-replicate 1

description:
MgLoc_Gol.071.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 70.7 h of culture, glycerol added


title: Glycerol-70 h-replicate 2

description:
MgLoc_Gol.070.m7
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 7, 70 h of culture, no carbon source yet added


title: genomic DNA from whole blood 40


title: genomic DNA from whole blood 27


title: Glycerol-70 h-replicate 1

description:
MgLoc_Gol.070.m6
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 6, 70 h of culture, no carbon source yet added


title: genomic DNA from whole blood 25


title: genomic DNA from whole blood 34


title: genomic DNA from whole blood 26


title: genomic DNA from whole blood 31


title: genomic DNA from whole blood 28


title: genomic DNA from whole blood 20


title: genomic DNA from whole blood 23


title: Glucose-124 h-replicate 1

description:
MgLoc_Glc.124.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 124 h of culture, glucose added

value: Glucose


title: genomic DNA from whole blood 24


title: Glucose-100 h-replicate 1

description:
MgLoc_Glc.100.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 100 h of culture, glucose added


title: genomic DNA from whole blood 21


title: InVitro_24hr_MEG-A2_Ato-C

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression after 24hr in Ato-C-treated MEG-A2  cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MEG-A2, 24hr, ATO/CDDP, 1.0/5.0 μmol/L

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling 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.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The CML cell lines were incubated in a RPMI 1640 medium supplemented with 20% heat-inactivated fetal bovine serum. The cells were then treated with the indicated concentration of ATO and/or CDDP for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: CML cell line

value: male


title: Glucose-100 h-replicate 2

description:
MgLoc_Glc.100.m5
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 5, 100 h of culture, glucose added


title: genomic DNA from whole blood 22

label_protocol: Standard Illumina Protocol


title: genomic DNA from whole blood 36


title: Glucose-92 h-replicate 1

description:
MgLoc_Glc.092.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 92 h of culture, glucose added


title: genomic DNA from whole blood 19


title: Glucose-89 h-replicate 2

description:
MgLoc_Glc.089.m5
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 5, 89 h of culture, glucose added


title: InVitro_24hr_MEG-A2_CDDP

description: Gene expression after 24hr in CDDP-treated MEG-A2 cells

source_name: MEG-A2, 24hr, CDDP, 5.0 μmol/L


title: genomic DNA from whole blood 16


title: genomic DNA from whole blood 18


title: InVitro_24hr_MEG-A2_None

description: Gene expression after 24hr in untreated MEG-A2 cells

source_name: MEG-A2, 24hr, no treatment


title: InVitro_24hr_MEG-A2_ATO

description: Gene expression after 24hr in ATO-treated MEG-A2  cells

source_name: MEG-A2, 24hr, ATO, 1.0 μmol/L


title: genomic DNA from whole blood 12


title: genomic DNA from whole blood 13


title: Glucose-92 h-replicate 2

description:
MgLoc_Glc.092.m5
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 5, 92 h of culture, glucose added

source_name: Total DNA extracted from a stationary-phase culture


title: genomic DNA from whole blood 15

source_name: genomic DNA from whole blood


title: InVitro_24hr_KU-812_Ato-C

description: Gene expression after 24hr in Ato-C-treated KU-812 cells


title: Glucose-148 h-replicate 1

description:
MgLoc_Glc.148.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 148 h of culture, glucose added


title: Glucose-76 h-replicate 1

description:
MgLoc_Glc.076.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 76 h of culture, glucose added


title: Glucose-80 h-replicate 1

description:
MgLoc_Glc.080.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 80 h of culture, glucose added


title: Glucose-76 h-replicate 2

description:
MgLoc_Glc.076.m5
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 5, 76 h of culture, glucose added


title: Glucose-89 h-replicate 1

description:
MgLoc_Glc.089.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 89 h of culture, glucose added


title: genomic DNA from whole blood 10


title: InVitro_24hr_KU-812_None

description: Gene expression after 24hr in untreated KU-812 cells

source_name: KU-812, 24hr, no treatment


title: genomic DNA from whole blood 11


title: Glucose-80 h-replicate 2

description:
MgLoc_Glc.080.m5
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 5, 80 h of culture, glucose added


title: InVitro_24hr_KU-812_ATO

description: Gene expression after 24hr in ATO-treated KU-812 cells


title: InVitro_24hr_KU-812_CDDP

description: Gene expression after 24hr in CDDP-treated KU-812 cells

source_name: KU-812, 24hr, CDDP, 1.5 μmol/L


title: genomic DNA from whole blood 14


title: genomic DNA from whole blood 7


title: genomic DNA from whole blood 8


title: Glucose-72 h-replicate 2

description:
MgLoc_Glc.072.m5
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 5, 72 h of culture, glucose added


title: Glucose-72 h-replicate 1

description:
MgLoc_Glc.072.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 72 h of culture, glucose added


title: InVitro_24hr_K562_CDDP

description: Gene expression after 24hr in CDDP-treated K562 cells

source_name: K562, 24hr, CDDP, 10 μmol/L

value: female


title: genomic DNA from whole blood 4


title: InVitro_24hr_K562_ATO

description: Gene expression after 24hr in ATO-treated K562 cells


title: Glucose-70 h-replicate 2

description:
MgLoc_Glc.070.m5
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 5, 70 h of culture, no carbon source yet added


title: Culture broth_parent_6hr_rep1

city: bhubaneswar

first: Durg

middle: Vijai

last: Singh

state: odisha

address: nalco square

department: infectious biology division

country: India

institute: institute of life sciences

description: Gene expression of the parent CTX- positive Vibrio cholerae

hyb_protocol: 600 ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Agilent designed V. cholerae Gene expression Microarray 8x15K (AMADID No: 022386) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

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

organism: Vibrio cholerae

source_name: Culture broth, parent strain, 6hr, replicate 1

label_protocol: Samples for Gene expression were labeled using the Agilent Quick-Amp labeling Kit (p/n5190-0442). 500 ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: The test strains were grown in 2ml Luri Bertani broth for 6hrs at 370 C.

extract_protocol: RNA was prepared using RNeasy Protect Bacteria Mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop  and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The parent strain was given an induction of salt stress by growing it in LB broth with 2% NaCl.

tag: genotype/variation

value: CTX positive


title: InVitro_24hr_K562_None

description: Gene expression after 24hr in untreated K562 cells

source_name: K562, 24hr, no treatment


title: Culture broth_salt induced_6hr_rep2

description: Gene expression of the salt stress induced parent CTX- positive Vibrio cholerae

source_name: Culture broth, parent salt induced, 6hr, replicate 1


title: genomic DNA from whole blood 5


title: Culture broth_salt induced_6hr_rep1


title: Culture broth_mutant_6hr_rep2

description: Gene expression of the mutant, CTX- negative Vibrio cholerae

source_name: Culture broth, mutant strain,6hr,replicate 2

value: CTX negative


title: Glucose-70.7 h-replicate 1

description:
MgLoc_Glc.071.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 70.7 h of culture, glucose added

tag: strain

source_name: Total DNA extracted from a stationary-phase culture


title: Culture broth_parent_6hr_rep2

source_name: Culture broth, parent strain, 6hr, replicate 2


title: genomic DNA from whole blood 6

source_name: genomic DNA from whole blood


title: Glucose-70.7 h-replicate 2

description:
MgLoc_Glc.071.m5
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 5, 70.7 h of culture, glucose added


title: Culture broth_mutant_6hr_rep1

source_name: Culture broth, mutant strain,6hr,replicate 1


title: post bone marrow transplant 1

status: Public on Oct 11 2017

city: London

first: Prashant

last: Hiwarkar

address: 30 Guildford street

country: United Kingdom

institute: Institute of Child health, UCL

description: transplant recipient

hyb_protocol: Arrays were hybridized using Affymetrix GeneChip Fluidics Station 450 according to manufacturer's protocol

scan_protocol: Affymetrix Genechip 3000S scanner

data_processing:
Data were analyzed using the Bioconductor package affyPLM. Preprocessing followed the following procedures: (1) background correction; (2) normalization using the quantile method; (3) summarization of probe set values using the RMA method (Robust Multi-Array Average)
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: bone marrow transplant recipient

label_protocol: RNA was converted to cDNA and amplified (NuGEN WT-Ovation kit) and then fragmented (WT-Ovation kit) and labeled with biotin (FL-Ovation cDNA biotin module, NuGEN)

extract_protocol: Immediately after sorting cell pellets were lysed in RNA lysis buffer (Qiagen) and RNA was obtained using the RNAeasy mini-kit (Qiagen) in accordance with manufacturer’s protocol

treatment_protocol: Peripheral blood and cord blood mononuclear cells were isolated from normal donors and two months after bone marrow and cord blood transplant using Ficoll-Paque method.

tag: age

value: 9 years

value: peripheral blood

tag: genotype

value: wild-type


title: post cord blood transplant 2

description: transplant recipient

source_name: cord blood transplant recipient

value: 4 months


title: genomic DNA from whole blood 3


title: post bone marrow transplant 3

description: transplant recipient

value: 5 years


title: genomic DNA from whole blood 9


title: paired normal donor peripheral blood 7

description: normal donor

source_name: peripheral blood donor

value: 7 years


title: paired normal donor cord blood 9

description: normal donor

source_name: cord blood donor

value: At birth

value: cord blood


title: post bone marrow transplant 2

description: transplant recipient

value: 1 year


title: post cord blood transplant 3

description: transplant recipient

value: 9 months


title: genomic DNA from whole blood 17

value: Male


title: paired normal donor peripheral blood 8

description: normal donor


title: paired normal donor cord blood 8

description: normal donor


title: Glucose-70 h-replicate 1

description:
MgLoc_Glc.070.m4
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment

source_name: Culture no. 4, 70 h of culture, no carbon source yet added


title: paired normal donor cord blood 7

description: normal donor


title: post cord blood transplant 1

description: transplant recipient


title: normal donor peripheral blood 4

description: normal donor

value: 40 years


title: paired normal donor peripheral blood 9

description: normal donor

value: 8 years


title: normal donor peripheral blood 1

description: normal donor


title: normal donor cord blood 6

description: normal donor


title: normal donor peripheral blood 6

description: normal donor


title: normal donor peripheral blood 3

description: normal donor


title: normal donor peripheral blood 2

description: normal donor


title: normal donor cord blood 4

description: normal donor


title: normal donor peripheral blood 5

description: normal donor


title: normal donor cord blood 5

description: normal donor


title: genomic DNA from whole blood 2


title: normal donor cord blood 3

description: normal donor


title: normal donor cord blood 2

description: normal donor