title: dha 3 h rep 4 of 5

status: Public on Oct 14 2015

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

description: 3 h treatment period

hyb_protocol: Purified Cy3- and Cy5-labelled cDNA were mixed in a Short Oligo Hybridization Solution (Corning Inc.), and hybridized to P. falciparum spotted 70-mer oligo microarrays for 16-18 hr at 45°C. Arrays were washed at room temperature in a solution of 2x SSC (Sodium Saline Citrate) containing 0.2% SDS, and then in 0.1x SSC.

scan_protocol: Scanned on an GenePix 4000B scanner and images analyzed using GenePix Pro 6.1.0.4

data_processing: Microarray feature signals of irregular shape were flagged (i.e. marked as not available for analysis) manually in the GenePix Pro software. The .gpr files were analysed using the limma package in R 3.0.2. Microarray features flagged by the Genepix Pro software, designated as empty (no oligo probe), not in genome, negative control, positive control, plastid genome, unmapped, or mapping to non-mRNA were given zero weight for normalization using the modifyWeights function in limma. Microarray feature median foreground signals of Cy5/Cy3 ratios were background corrected with normexp.offset=50, and normalized within microarrays by global loess.

organism: Plasmodium falciparum

source_name: untreated reference rep 4 of 5 3 h time-point

label_protocol: 10 µg of total RNA were heated at 70◦C for 5 min together with 5 µg of oligo (dT)21. After annealing at 25◦C for 5 min, cDNA was synthesized in a 50 µl reaction containing 2.5 µl ImpromII reverse transcriptase (Promega), 0.5 mM each of dATP,dCTP,dGTP, 0.2 mM dTTP, 0.3 mM aminoallyl-dUTP (Sigma), 3 mM MgCl2. The reaction was performed for 2 h at 37◦C. RNA was hydrolysed by adding EDTA to 100 mM and NaOH to 200 mM and heated to 65◦C for 15 min. The cDNA mix was neutralized with 25 µl of 1 M HEPES pH7.4. cDNA was desalted in Microcon 30 spin column (Millipore) by washing twice with deionised water. Desalted cDNA was coupled with 1 pmol of monoreactive Cy dye (GE Healthcare) in  in 0.1M sodium bicarbonate pH9.0 for 1h at 25◦C. Unincorporated dyes were removed by purification with QIAquick PCR purification column (Qiagen).

growth_protocol: Parasites were cultured in vitro using the standard method (Trager and Jensen (1976)  Science 193:673-5). The parasite culture was composed of human erythrocytes type O Rh+ in RPMI 1640 supplemented with 25 mM HEPES pH 7.4, 0.2% NaHCO3 0.2% glucose, 0.025 mg/ml hypoxanthine, 40 µg/ml gentamicin and 8% (v/v) pooled human serum. The culture was maintained in a 3% CO2 incubator at 37°C.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Genomic DNA was removed from total RNA using a Turbo DNA freeTM kit (Ambion, Applied Biosystems).

treatment_protocol: Parasites cultures were synchronized to ring stages by two consecutive sorbitol treatment cycles (Lambros & Vanderberg (1979) J Parasitol. 65:418-20). 48 h after the second synchronization, the parasite culture was divided equally into new culture plates for drug treatment. The synchronized parasites were then cultured for 18 h to obtain a majority of trophozoite-stage parasites for drug treatment.  Parasites were treated with 500 nM DHA or vehicle control (1% DMSO). Parallel culture plates were left untreated as reference controls. Samples were taken after 1, 2, and 3 h of treatment. Parasites were harvested from culture and liberated from host cells by treatment with 0.15% (w/v) saponin for 5 min on ice. The liberated parasites were washed three times with 1xPBS (137 mM NaCl, 8 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, pH 7.4) to remove host cell debris and drug.

source_name: dha-treated rep 4 of 5 3 h time-point


title: dha 3 h rep 2 of 5

type: RNA

description: 3 h treatment period

molecule: total RNA

source_name: untreated reference rep 2 of 5 3 h time-point

tag: strain

source_name: dha-treated rep 2 of 5 3 h time-point


title: dha 3 h rep 3 of 5

description: 3 h treatment period

source_name: untreated reference rep 3 of 5 3 h time-point

source_name: dha-treated rep 3 of 5 3 h time-point


title: BMP3l, biological rep2

status: Public on Oct 15 2015

city: London

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

country: Canada

institute: Robarts Research Institute

description: Gene expression from BMP3 treated rep2

hyb_protocol: 12.5 ug of amplified RNA was hybridized for 16 hr at 45C onto Affymetrix Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek, and differentially expressed genes were identified by a combination of statistical analysis (p<0.05) and comparison analysis (displayed >1.5-fold increase or decrease from the control to BMP treatment).

label: biotin

organism: Mus musculus

source_name: Cells treated with BMP3

label_protocol: Biotin end labeled single strand cRNA was prepared according to the Affymetrix GeneChip 3' IVT Express Kit User Manual (P/N 702646 Rev. 1)

growth_protocol: Cells were grown under standard culture conditions

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to the manufacturer's instructions

treatment_protocol: Cells were treated with and without 100 ng/ml recombinant human BMP3 for 6 hours

tag: cell line

value: C3H10T1/2 cells

tag: cell type

value: mesenchymal stem cells


title: dha 3 h rep 1 of 5

description: 3 h treatment period

source_name: untreated reference rep 1 of 5 3 h time-point

source_name: dha-treated rep 1 of 5 3 h time-point


title: dha 3 h rep 5 of 5

description: 3 h treatment period

source_name: untreated reference rep 5 of 5 3 h time-point

source_name: dha-treated rep 5 of 5 3 h time-point


title: mRNA_wild type IhhN induced cells_rep2

city: Shanghai

first: Lu

last: Shen

address: RM 218 Little White House 1954 Huashan RD

department: Bio-X Institutes

country: China

institute: Shanghai Jiao Tong University

description: Gene expression after 48hr in C3H10T1/2 cells in the presence of 750nM wild type IhhN

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 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 (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) 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.

source_name: wild type IhhN induced cells, 750nM for 2 days, replicate 2

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

extract_protocol: RNA was prepared from cells using Trizol reagent (Invitrogen) according to manufacturer's instruction.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C3H10T1/2 cells, diluted 1:1 with MEM/EBSS medium supplemented with 10% heat-inactivated fetal bovine serum in the presence of 750nM IhhN protein, were incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: induction

value: wild type IhhN


title: vehicle control 3 h rep 1 of 4

description: 3 h treatment period

source_name: vehicle-treated rep 1 of 4 3 h time-point


title: vehicle control 3 h rep 2 of 4

description: 3 h treatment period

source_name: vehicle-treated rep 2 of 4 3 h time-point


title: dha 2 h rep 3 of 5

description: 2 h treatment period

source_name: untreated reference rep 3 of 5 2 h time-point

source_name: dha-treated rep 3 of 5 2 h time-point


title: dha 2 h rep 5 of 5

description: 2 h treatment period

source_name: untreated reference rep 5 of 5 2 h time-point

source_name: dha-treated rep 5 of 5 2 h time-point


title: vehicle control 3 h rep 4 of 4

description: 3 h treatment period

source_name: vehicle-treated rep 4 of 4 3 h time-point


title: dha 2 h rep 2 of 5

description: 2 h treatment period

source_name: untreated reference rep 2 of 5 2 h time-point

source_name: dha-treated rep 2 of 5 2 h time-point


title: vehicle control 2 h rep 3 of 5

description: 2 h treatment period

source_name: vehicle-treated rep 3 of 5 2 h time-point


title: vehicle control 2 h rep 5 of 5

description: 2 h treatment period

source_name: vehicle-treated rep 5 of 5 2 h time-point


title: vehicle control 2 h rep 4 of 5

description: 2 h treatment period

source_name: untreated reference rep 4 of 5 2 h time-point

source_name: vehicle-treated rep 4 of 5 2 h time-point


title: dha 1 h rep 5 of 5

description: 1 h treatment period

source_name: untreated reference rep 5 of 5 I h time-point

source_name: dha-treated rep 5 of 5 1 h time-point


title: vehicle control 2 h rep 1 of 5

description: 2 h treatment period

source_name: untreated reference rep 1 of 5 2 h time-point

source_name: vehicle-treated rep 1 of 5 2 h time-point


title: dha 1 h rep 3 of 5

description: 1 h treatment period

source_name: untreated reference rep 3 of 5 I h time-point

source_name: dha-treated rep 3 of 5 1 h time-point


title: dha 2 h rep 4 of 5

description: 2 h treatment period

source_name: dha-treated rep 4 of 5 2 h time-point


title: dha 1 h rep 2 of 5

description: 1 h treatment period

source_name: untreated reference rep 2 of 5 I h time-point

source_name: dha-treated rep 2 of 5 1 h time-point


title: dha 1 h rep 4 of 5

description: 1 h treatment period

source_name: untreated reference rep 4 of 5 I h time-point

source_name: dha-treated rep 4 of 5 1 h time-point


title: vehicle control 2 h rep 2 of 5

description: 2 h treatment period

source_name: untreated reference rep 2 of 5 2 h time-point

source_name: vehicle-treated rep 2 of 5 2 h time-point


title: vehicle control 1 h rep 5 of 5

description: 1 h treatment period

source_name: vehicle-treated rep 5 of 5 1 h time-point


title: dha 1 h rep 1 of 5

description: 1 h treatment period

source_name: untreated reference rep 1 of 5 I h time-point

source_name: dha-treated rep 1 of 5 1 h time-point


title: vehicle control 1 h rep 4 of 5

description: 1 h treatment period

source_name: vehicle-treated rep 4 of 5 1 h time-point


title: ChIP_non-protein induced cells

type: genomic

description: Chip-chip normal C3H10T1/2 cells Gli1

hyb_protocol: Hybridization on MM9 ChIP 3x720K RefSeq Promoter microarray (Roche Nimblegen) according to the manufacturer’s recommendation.

scan_protocol: Arrarys were scanned using a Nimblegen MS 200 Microarrary Scanner at 2 μm resolution.

data_processing: Array signals were extracted using NimbleScan Software version 2.6 (Roche Nimblegen) according to the manufacturer’s instruction and then MA2C was used to make peak calling.

molecule: genomic DNA

source_name: Gli1 ChIP DNA from non-protein induced cells

label_protocol: For each ChIP, 2 μg DNA was labled with Cy5-dUTP for amplified ChIP sample and Cy3-dUTP for input sample according to the manufacturer’s recommendation (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells were cultured for 48 hours in the presence of 750nM IhhN protein.

extract_protocol: After isolating sheared crosslinked chromatin, each sample (1x105 cells) was incubated overnight with 5 μg polyclonal Gli1 antibody (AB3444, Millipore) or matched IgG controls. Then 60 μL Protein G Agarose was added to each sample and incubated for 1 h at 4℃ with rotation. After incubation, Protein G Agarose was pelleted by brief centrifugation and washed according to the instruction manual. The pellets were incubated with 100 μL elution buffer (10 μL 20% SDS, 20 μL 1 M NaHCO3 and 170 μL sterile, distilled water) at room temperature for 15 min twice and the supernatant was collected. To each sample collection (totally 200 μL) 8 μL 5 M NaCl was added and incubated at 65℃ overnight to reverse the DNA-protein crosslink. The next day samples were sequentially treated with RNAse A and Proteinase K. DNAs were purified using PCR Purification Kit (Qiagen) and amplified using GenomePlex® Whole Genome Amplification Kit (Sigma-Aldrich).

treatment_protocol: Cells were harvested by scraping.

tag: condition

value: non-protein

tag: chip antibody

source_name: Input DNA from non-protein induced cells

value: none, input DNA


title: E. coli 45L strain, heat shock, long, rep 2

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

country: Japan

institute: University of Tsukuba

hyb_protocol: Following fragmentation, 3 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009).
The normalized data can be found on the series record in the file "GSE61749_Normalized_data.txt". The data values presented in this file are log10 mRNA concentration (pM).

organism: Escherichia coli

source_name: E. coli 45L strain, 30 min heat shock at 45ºC, rep 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were grown in the minimal media, M63. The final cell concentrations were controlled ~ 10^8 cells/mL within the exponential growth phase.

extract_protocol: Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions.

treatment_protocol: The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 7,000 × g for 3 min at 4°C, and the pelleted cells were stored at –80°C prior to use.

value: heat shock response, 44.8ºC


title: E. coli 45L strain, heat shock, long, rep 1

source_name: E. coli 45L strain, 30 min heat shock at 45ºC, rep 1


title: E. coli 43B strain, heat shock, long, rep 2

source_name: E. coli 43B strain, 30 min heat shock at 45ºC, rep 2


title: vehicle control 1 h rep 1 of 5

description: 1 h treatment period

source_name: vehicle-treated rep 1 of 5 1 h time-point


title: E. coli 41B strain, heat shock, long, rep 2

source_name: E. coli 41B strain, 30 min heat shock at 45ºC, rep 2


title: vehicle control 1 h rep 2 of 5

description: 1 h treatment period

source_name: untreated reference rep 2 of 5 I h time-point

source_name: vehicle-treated rep 2 of 5 1 h time-point


title: vehicle control 1 h rep 3 of 5

description: 1 h treatment period

source_name: untreated reference rep 3 of 5 I h time-point

source_name: vehicle-treated rep 3 of 5 1 h time-point


title: K-p6

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: Sample 15

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing:
Allele ratio was computed by dividing allele A signal by sum of allele A and allele B signals for probes targeting SNPs. Measurement for probes targeting copy number variation were discarded.
Sample tables contain Birdseed v2 computed intensities.

organism: Homo sapiens

source_name: blood

label_protocol: Affymetrix standard procedure

extract_protocol: Genomic DNA was extracted from whole blood treated with EDTA using a QIAamp DNA Mini Kit

tag: diagnosis

value: healthy (control)

tag: tissue

value: blood


title: K-p5

description: Sample 14


title: E. coli 41B strain, heat shock, long, rep 1

source_name: E. coli 41B strain, 30 min heat shock at 45ºC, rep 1


title: ChIP_wild type IhhN induced cells

description: Chip-chip wt IhhN induced cells Gli1

source_name: Gli1 ChIP DNA from WT IhhN induced cells

value: Wild type IhhN

source_name: Input DNA from WT IhhN induced cells


title: E. coli Anc strain, heat shock, long, rep 2

source_name: E. coli ancestor strain, 30 min heat shock at 45ºC, rep 2


title: E. coli Anc strain, heat shock, long, rep 1

source_name: E. coli ancestor strain, 30 min heat shock at 45ºC, rep 1


title: vehicle control 3 h rep 3 of 4

description: 3 h treatment period

source_name: untreated reference rep 4 of 5 3 h time-point

source_name: vehicle-treated rep 3 of 4 3 h time-point


title: ChIP_E95K mutant IhhN induced cells

description: Chip-chip E95K mutant IhhN induced cells Gli1

source_name: Gli1 ChIP DNA from E95K mutant IhhN induced cells

value: E95K mutant IhhN

source_name: Input DNA from E95K mutant IhhN induced cells


title: E. coli 37L evolved strain, under 37ºC, rep 2

value: exponential growth, 36.9ºC


title: E. coli 37L evolved strain, under 37ºC, rep 1


title: K-p2

description: Sample 11


title: K-p3

description: Sample 12


title: E. coli 45L strain, heat shock, rep 1

source_name: E. coli 45L strain, 5 min heat shock at 45ºC, rep 1


title: Combi_replicate4

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

description:
M4
Gene expression after 48 h in 70 mGy gamma radiation + 0.25 mg/L depleted uranium exposed fish liver

hyb_protocol: Totally 600 ng of Cy3-labeled, linearly amplified cRNA was fragmented and hybridized to 8x60k microarrays and rotationally (10 rpm) incubated at 65 ºC for 17 h.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (Dye channel: G (green), scan region: Agilent HD (61 × 21.6 mm), Scan resolution: 3 µm, Tiff file dynamic range: 20 bit, Green PMI gain: 100%).

data_processing: The microarray scan images (raw signal intensity) were extracted using Agilent Feature Extraction software v10.7. Raw data were normalized (quantile) and statistical analyses were performed using GeneSpring GX v11.0 (Agilent Technologies). Non-uniform outliers were excluded.

organism: Salmo salar

source_name: 70 mGy gamma radiation + 0.25 mg/L depleted uranium (Combi) exposed

label_protocol: Cyanine 3-CTP (Cy3) labeled cRNA was made from 200 ng total RNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, California, USA). The cRNA dye incorporation and yield were checked using Agilent Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA was extracted from 20-30 mg snap-frozen liver tissue using RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.The RNA quality (purity and yield) was controlled by photometric analyses (260/230 > 2.0, 260/280>1.8, yield >200 ng/μL) using Nanodrop® spectrophotometer (ND-1000, Nanodrop Technologies, Wilminton, Delaware, USA) and RNA integrity (RIN>8.0) inspected by Bioanalyzer gelelectrophoresis with RNA 6000 Nano chips (Agilent technologies, Santa Clara, California, USA) according to the manufacturer’s instructions.

treatment_protocol: Atlantic salmon parr were transferred to lake water (Maridalsvannet, Norway) for 72 h acclimation prior to being exposed to control, 70 mGy external gamma radiation emitted from a cobalt-60 source, and 0.25 mg/L depleted uranium in the dark for 48 h. Fish were exposed in a flow-through system supplied with air pumps. No feeding was performed during the acclimation and exposure period.

tag: stress

value: Liver


title: E. coli 45L strain, heat shock, rep 2

source_name: E. coli 45L strain, 5 min heat shock at 45ºC, rep 2


title: E. coli 45L evolved strain, evolutionary temperature, rep 2

source_name: E. coli 45L evolved strain, under 45ºC, rep 2

value: exponential growth, 44.8ºC


title: E. coli 45L evolved strain, evolutionary temperature, rep 3

source_name: E. coli 45L evolved strain, under 45ºC, rep 3


title: Combi_replicate3

description:
M3
Gene expression after 48 h in 70 mGy gamma radiation + 0.25 mg/L depleted uranium exposed fish liver

value: 70 mGy gamma radiation + 0.25 mg/L depleted uranium (Combi)


title: dha 2 h rep 1 of 5

description: 2 h treatment period

source_name: untreated reference rep 1 of 5 2 h time-point

source_name: dha-treated rep 1 of 5 2 h time-point


title: E. coli 43B strain, heat shock, long, rep 1

source_name: E. coli 43B strain, 30 min heat shock at 45ºC, rep 1


title: Combi_replicate1

description:
M1
Gene expression after 48 h in 70 mGy gamma radiation + 0.25 mg/L depleted uranium exposed fish liver


title: K-p4

description: Sample 13

source_name: blood


title: Combi_replicate2

description:
M2
Gene expression after 48 h in 70 mGy gamma radiation + 0.25 mg/L depleted uranium exposed fish liver


title: E. coli 45L evolved strain, regular temperature, rep 3

source_name: E. coli 45L evolved strain, under 37ºC, rep 3


title: DU_replicate3

description:
U3
Gene expression after 48 h in 0.25 mg/L depleted uranium exposed fish liver

source_name: 0.25 mg/L depleted uranium (DU) exposed

value: 0.25 mg/L depleted uranium (DU)


title: K-p1

description: Sample 10


title: CD-9

description: Sample 9

value: celiac disease


title: E. coli 45L evolved strain, regular temperature, rep 2

source_name: E. coli 45L evolved strain, under 37ºC, rep 2


title: CD-6

description: Sample 6


title: E. coli 43B strain, heat shock, rep 2

source_name: E. coli 43B strain, 5 min heat shock at 45ºC, rep 2


title: CD-1

description: Sample 1


title: DU_replicate4

description:
U4
Gene expression after 48 h in 0.25 mg/L depleted uranium exposed fish liver


title: CD-3

description: Sample 3


title: CD-5

description: Sample 5


title: Liver_8mkd-furan_sample44 [fresh-frozen; 1-color array]

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

institute: Health Canada

description: SAMPLE 8

hyb_protocol: 600ng Cy3-labeled sample cRNA was hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) protocol (v6.6).  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505B) according to manufacturer's recommendations.  Data was extracted from the scanned images using Feature Extraction Version 10.7.3.1.

data_processing: Probes with technical replicates were averaged using the median signal intensity. Non-background subtracted median signal intensities were cyclic lowess normalized in R using the normalize.loess() function in the affy R library.

source_name: Liver

label_protocol: 200 ng sample RNA was used to amplify and label cRNA using the Low Input Quick Amp Labeling Kit (Agilent Cat #: 5190-0444). Samples were labeled with Cyanine 3-CTP. Labeled cRNA was purified using the RNease Mini Kit (Qiagen). Amplification and labeling efficiency of cRNA were quantified using a NanoDrop spectrophotometer.

growth_protocol: 5-6 week old female specific pathogen free B6C3F1 mice were purchased from Charles River Breeding Laboratories (Portage, ME) and were allowed to acclimatize for at least 7 days prior to the start of the study. Feed (NIH-07; Zeigler Brothers, Inc., Gardners, PA) and tap water were available ad libitum. Mice were housed five per cage in polycarbonate cages in a specific pathogen free (SPF) and Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) accredited facility. All procedures were conducted in compliance with the Animal Welfare Act Regulations (9CFR1–4). Mice were handled and treated according to the guidelines provided in the National Institute of Health (NIH) Guide for the Care and Use of Laboratory Animals (ILAR, 1996; http://dels.nas.edu/ilar/).

extract_protocol: Mice were anaesthetized under carbon dioxide inhalation followed by exsanguination. Livers were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from ~100mg frozen tissue using the RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 1.83 and RINs > 8.9.

treatment_protocol: Mice were dosed via oral gavage for 21 days. Four different doses of furan dissolved in corn oil were used: 1, 2, 4 and 8 mg/kg bw.  Control animals were gavaged with cornoil oil only.   Tissues were collected 4 hours following the final dose.

tag: female

value: female

tag: exposed to

value: 8 mg/kg bw furan for 3 wks

value: liver

tag: sample type

value: fresh-frozen tissue


title: DU_replicate1

description:
U1
Gene expression after 48 h in 0.25 mg/L depleted uranium exposed fish liver


title: Gamma_replicate2

description:
G2
Gene expression after the first 5 h during a 48h duration in 70 mGy gamma radiation exposed fish liver

source_name: 70 mGy gamma radiation (Gamma) exposed

value: 70 mGy gamma radiation (Gamma)


title: Adult bone marrow rep1

city: Amsterdam

first: Maja

middle: Maria

last: Paciejewska

state: noord holland

address: Plesmanlaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin Research

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing: RMA + GC correction by Partek software

source_name: Adult bone marrow

label_protocol: GeneChip WT Terminal Labeling Kit

growth_protocol: Cultured in Low Glucose DMEM, 30% FBS, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM ultraglutamine

extract_protocol: Rneasy column purification

value: Adult bone marrow

value: mesenchymal stromal cells


title: Gamma_replicate1

description:
G1
Gene expression after the first 5 h during a 48h duration in 70 mGy gamma radiation exposed fish liver


title: Liver_8mkd-furan_sample43 [fresh-frozen; 1-color array]

description: SAMPLE 7


title: E. coli 43B evolved strain, evolutionary temperature, rep 3

source_name: E. coli 43B evolved strain, under 43ºC, rep 3

value: exponential growth, 43.2ºC


title: Gamma_replicate4

description:
G4
Gene expression after the first 5 h during a 48h duration in 70 mGy gamma radiation exposed fish liver


title: Gamma_replicate3

description:
G3
Gene expression after the first 5 h during a 48h duration in 70 mGy gamma radiation exposed fish liver


title: Fetal bone marrow rep1

source_name: Fetal bone marrow

value: Fetal bone marrow


title: Liver_Control_sample6 [fresh-frozen; 1-color array]

description: SAMPLE 4

value: vehicle control for 3wks


title: Liver_8mkd-furan_sample41 [fresh-frozen; 1-color array]

description: SAMPLE 5


title: E. coli 43B evolved strain, evolutionary temperature, rep 2

source_name: E. coli 43B evolved strain, under 43ºC, rep 2


title: Fetal bone marrow rep3


title: Liver_8mkd-furan_sample42 [fresh-frozen; 1-color array]

description: SAMPLE 6


title: Adult bone marrow rep3


title: E. coli 37L evolved strain, under 37ºC, rep 3


title: CD-7

description: Sample 7

value: blood


title: E. coli 45L evolved strain, evolutionary temperature, rep 1

source_name: E. coli 45L evolved strain, under 45ºC, rep 1


title: Adult bone marrow rep2


title: Fetal bone marrow rep2


title: Control_replicate4

description:
C4
Gene expression after 48 h in control fish liver

source_name: Control

value: Control


title: Liver_Control_sample4 [fresh-frozen; 1-color array]

description: SAMPLE 3


title: Liver_Control_sample3 [fresh-frozen; 1-color array]

description: SAMPLE 2


title: E. coli 43B evolved strain, regular temperature, rep 3

source_name: E. coli 43B evolved strain, under 37ºC, rep 3

value: exponential growth, 36.9ºC


title: E. coli 43B evolved strain, evolutionary temperature, rep 1

source_name: E. coli 43B evolved strain, under 43ºC, rep 1


title: E. coli 43B evolved strain, regular temperature, rep 2

source_name: E. coli 43B evolved strain, under 37ºC, rep 2


title: CD-2

description: Sample 2


title: E. coli 43B evolved strain, regular temperature, rep 1

source_name: E. coli 43B evolved strain, under 37ºC, rep 1


title: E. coli 41B strain, heat shock, rep 1

source_name: E. coli 41B strain, 5 min heat shock at 45ºC, rep 1

value: heat shock response, 44.8ºC


title: E. coli 41B strain, heat shock, rep 2

source_name: E. coli 41B strain, 5 min heat shock at 45ºC, rep 2


title: Control_replicate2

description:
C2
Gene expression after 48 h in control fish liver

value: Liver


title: Control_replicate1

description:
C1
Gene expression after 48 h in control fish liver


title: Liver_Control_sample2 [fresh-frozen; 1-color array]

description: SAMPLE 1


title: Control_replicate3

description:
C3
Gene expression after 48 h in control fish liver


title: Liver_8mkd-furan_3wk-FFPE_sample45 [1-color array]

description: Sample 50

hyb_protocol: Hybridization mixtures were prepared using the Gene Expression Hybridization kit (Agilent Technologies) and CGHBlock (Agilent Technologies). 600 ng of Cy3-labelled cDNA was hybridized to SurePrint G3 Mouse GE 8x60K microarrays (Agilent Technologies).  Samples were arranged according to a randomized block design. Hybridization occurred at 65°C for 17 hours at 20 rpm in the dark in an Agilent SureHyb hybridization chamber.

scan_protocol: Slides were washed with Wash Buffers 1 and 2 (Agilent Technologies) and scanned at 5 μm resolution on an Agilent G2505B scanner. Feature extraction was accomplished using Agilent feature extraction software version 11.

label_protocol: 1650 ng cDNA was labeled with 2.48 ul Cy3 dye using the Genomic DNA ULS Labeling Kit (Agilent Technologies). Excess dye was removed using KREApure columns (Agilent Technologies), labeled product was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific Inc.), and degree of labeling was calculated using: Degree of labeling = [(340 x pmol per μl dye)/(ng per μl cDNA x 1000)] x 100% (with an acceptable range of 1.5-3%).

extract_protocol: Mice were anaesthetized under carbon dioxide inhalation followed by exsanguination. Livers were removed and preserved in formalin for 18 hours or 3 weeks prior to being embedded in paraffin.  Tissues were stored in paraffin blocks at room temperature until RNA extraction was performed.  Total RNA was extracted from 1x10um section (18 hours in formalin) or 2x10um sections (3 weeks in formalin) using the FFPE RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios 1.74-2.12 and RINs 1.3-2.4.

treatment_protocol: Mice were dosed via oral gavage for 21 days. The furan dose was 8 mg/kg bw in cornoil.  Control animals were gavaged with cornoil oil only.   Tissues were collected 4 hours following the final dose.

tag: gender

value: 8mg/kg bodyweight per day furan for 3 wks

value: 18 hours in formalin_FFPE sample


title: CD-8

description: Sample 8

source_name: blood

value: celiac disease


title: Liver_4mkd-furan_3wk-FFPE_sample34 [1-color array]

description: Sample 43

value: female

value: 4mg/kg bodyweight per day furan for 3 wks


title: Liver_4mkd-furan_3wk-FFPE_sample35 [1-color array]

description: Sample 44

value: liver


title: E. coli 41B evolved strain, evolutionary temperature, rep 2

source_name: E. coli 41B evolved strain, under 41ºC, rep 2

value: exponential growth, 41.2ºC


title: Liver_4mkd-furan_3wk-FFPE_sample33 [1-color array]

description: Sample 42


title: Liver_8mkd-furan_3wk-FFPE_sample44 [1-color array]

description: Sample 49


title: Liver_2mkd-furan_3wk-FFPE_sample24 [1-color array]

description: Sample 39

value: 2mg/kg bodyweight per day furan for 3 wks


title: Liver_8mkd-furan_3wk-FFPE_sample43 [1-color array]

description: Sample 48


title: CD-4

description: Sample 4


title: Liver_8mkd-furan_3wk-FFPE_sample41 [1-color array]

description: Sample 46


title: Liver_4mkd-furan_3wk-FFPE_sample36 [1-color array]

description: Sample 45


title: Liver_8mkd-furan_3wk-FFPE_sample42 [1-color array]

description: Sample 47


title: Liver_4mkd-furan_3wk-FFPE_sample31 [1-color array]

description: Sample 41


title: Liver_2mkd-furan_3wk-FFPE_sample25 [1-color array]

description: Sample 40


title: E. coli 41B evolved strain, evolutionary temperature, rep 3

source_name: E. coli 41B evolved strain, under 41ºC, rep 3


title: E. coli 45L evolved strain, regular temperature, rep 1

source_name: E. coli 45L evolved strain, under 37ºC, rep 1


title: DU_replicate2

description:
U2
Gene expression after 48 h in 0.25 mg/L depleted uranium exposed fish liver

source_name: 0.25 mg/L depleted uranium (DU) exposed

value: 0.25 mg/L depleted uranium (DU)


title: E. coli 41B evolved strain, regular temperature, rep 3

source_name: E. coli 41B evolved strain, under 37ºC, rep 3


title: Liver_2mkd-furan_3wk-FFPE_sample23 [1-color array]

description: Sample 38


title: E. coli 41B evolved strain, evolutionary temperature, rep 1

source_name: E. coli 41B evolved strain, under 41ºC, rep 1


title: E. coli 41B evolved strain, regular temperature, rep 2

source_name: E. coli 41B evolved strain, under 37ºC, rep 2


title: E. coli Anc strain, heat shock, rep 1

source_name: E. coli ancestor strain, 5 min heat shock at 45ºC, rep 1


title: E. coli 43B strain, heat shock, rep 1

source_name: E. coli 43B strain, 5 min heat shock at 45ºC, rep 1


title: E. coli 41B evolved strain, regular temperature, rep 1

source_name: E. coli 41B evolved strain, under 37ºC, rep 1


title: Liver_1mkd-furan_3wk-FFPE_sample11 [1-color array]

description: Sample 31

value: 1mg/kg bodyweight per day furan for 3 wks


title: Liver_Control_3wk-FFPE_sample4 [1-color array]

description: Sample 29


title: Liver_2mkd-furan_3wk-FFPE_sample22 [1-color array]

description: Sample 37


title: Liver_2mkd-furan_3wk-FFPE_sample21 [1-color array]

description: Sample 36


title: Liver_Control_3wk-FFPE_sample3 [1-color array]

description: Sample 28


title: Liver_Control_3wk-FFPE_sample1 [1-color array]

description: Sample 26


title: Liver_1mkd-furan_3wk-FFPE_sample13 [1-color array]

description: Sample 33


title: Liver_1mkd-furan_3wk-FFPE_sample14 [1-color array]

description: Sample 34


title: Liver_1mkd-furan_3wk-FFPE_sample15 [1-color array]

description: Sample 35


title: E. coli Anc strain, regular temperature, rep 1

source_name: E. coli ancestor strain, under 37ºC, rep 1


title: Liver_Control_3wk-FFPE_sample2 [1-color array]

description: Sample 27


title: Liver_1mkd-furan_3wk-FFPE_sample12 [1-color array]

description: Sample 32


title: Liver_8mkd-furan_18hr-FFPE_sample41 [1-color array]

description: Sample 21


title: E. coli Anc strain, heat shock, rep 2

source_name: E. coli ancestor strain, 5 min heat shock at 45ºC, rep 2


title: Liver_4mkd-furan_18hr-FFPE_sample34 [1-color array]

description: Sample 18


title: E. coli Anc strain, regular temperature, rep 3

source_name: E. coli ancestor strain, under 37ºC, rep 3


title: E. coli Anc strain, regular temperature, rep 2

source_name: E. coli ancestor strain, under 37ºC, rep 2


title: Liver_8mkd-furan_18hr-FFPE_sample42 [1-color array]

description: Sample 22


title: Liver_8mkd-furan_18hr-FFPE_sample45 [1-color array]

description: Sample 25


title: Liver_4mkd-furan_18hr-FFPE_sample33 [1-color array]

description: Sample 17


title: Liver_4mkd-furan_18hr-FFPE_sample31 [1-color array]

description: Sample 16


title: Liver_Control_3wk-FFPE_sample6 [1-color array]

description: Sample 30


title: Liver_4mkd-furan_18hr-FFPE_sample35 [1-color array]

description: Sample 19


title: Liver_2mkd-furan_18hr-FFPE_sample25 [1-color array]

description: Sample 15


title: Liver_1mkd-furan_18hr-FFPE_sample15 [1-color array]

description: Sample 10


title: DePDMSCs P3,  biological rep 3

city: Hangzhou

first: Chenxia

last: Hu

state: Zhejiang

address: School of Medicine; First Affiliated Hospital; Zhejiang University

institute: Zhejiang University

description: Gene expression data from Adipogenic Placental derived mesenchymal stem cells in general adipogenic medium for 21d

hyb_protocol: Array hybridization and washes were performed using the GeneChip® Hybridization, Wash and Stain Kit ( Affymetrix, Santa Clara, CA, USA) in the Hybridization Oven 645 ( Affymetrix, Santa Clara, CA, USA) and Fluidics Station 450 ( Affymetrix, Santa Clara, CA, USA) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by the GeneChip® Scanner 3000 ( Affymetrix, Santa Clara, CA, USA) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, USA) with default settings.

data_processing: The scanned images were first assessed by visual inspection, and then analyzed to generate raw data files that were saved as CEL files.

label_protocol: Total RNA was amplified, labeled and purified using the GeneChip 3’IVT Express Kit ( Affymetrix, Santa Clara, CA, USA) following the manufacturer’s instructions to obtain biotin-labeled cRNA.

extract_protocol: Using the RNAiso plus kit (TaKaRa, Tokyo, Japan), total RNA was isolated according to the manufacturer’s instructions.

value: Placenta


title: Liver_8mkd-furan_18hr-FFPE_sample43 [1-color array]

description: Sample 23


title: Liver_2mkd-furan_18hr-FFPE_sample24 [1-color array]

description: Sample 14


title: AL cells, biological rep 1

department: First Affiliated Hospital; Zhejiang University

description: Gene expression data from Placental derived mesenchymal stem cells at passage 3 in general adipogenic medium for 14d


title: Liver_4mkd-furan_18hr-FFPE_sample36 [1-color array]

description: Sample 20


title: DePDMSCs P3,  biological rep 2

source_name: Adipogenic Placental derived mesenchymal stem cells in general adipogenic medium for 21d


title: Liver_8mkd-furan_18hr-FFPE_sample44 [1-color array]

description: Sample 24


title: DePDMSCs P3,  biological rep 1


title: Liver_1mkd-furan_18hr-FFPE_sample11 [1-color array]

description: Sample 6


title: Liver_1mkd-furan_18hr-FFPE_sample13 [1-color array]

description: Sample 8


title: Liver_Control_18hr-FFPE_sample1 [1-color array]

description: Sample 1

value: vehicle control for 3wks


title: Liver_Control_18hr-FFPE_sample2 [1-color array]

description: Sample 2


title: Liver_2mkd-furan_18hr-FFPE_sample21 [1-color array]

description: Sample 11


title: Liver_2mkd-furan_18hr-FFPE_sample23 [1-color array]

description: Sample 13


title: Liver_2mkd-furan_18hr-FFPE_sample22 [1-color array]

description: Sample 12


title: Liver_Control_18hr-FFPE_sample6 [1-color array]

description: Sample 5


title: AL cells, biological rep 3

source_name: Placental derived mesenchymal stem cells at passage 3 in general adipogenic medium for 14d


title: AL cells, biological rep 2


title: Liver_Control_18hr-FFPE_sample4 [1-color array]

description: Sample 4


title: Liver_8mkd-furan_3wk-FFPE_sample44 [2-color array]

description:
3 weeks in formalin, FFPE samples
Sample 16

hyb_protocol: Hybridization mixtures were prepared using the Gene Expression Hybridization kit (Agilent Technologies) and CGHBlock (Agilent Technologies). 300 ng each of sample and reference cDNA was hybridized to SurePrint G3 Mouse GE 8x60K microarrays (Agilent Technologies). Hybridization occurred in a randomized block design, at 65°C for 17 hours at 20 rpm in the dark in an Agilent SureHyb hybridization chamber.

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

label_protocol: 825 ng sample cDNA was labeled with 1.44 ml Cy5 dye and 825 ng of reference cDNA (made from a pool of all sample cDNA) was labeled with 1.24 μl Cy3 using the Genomic DNA ULS Labeling Kit (Agilent Technologies). Excess dye was removed using KREApure columns (Agilent Technologies), labeled product was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific Inc.), and degree of labeling was calculated using: Degree of labeling = [(340 x pmol per μl dye)/(ng per μl cDNA x 1000)] x 100% (with an acceptable range of 1.5-3%).

treatment_protocol: Mice were dosed via oral gavage for 21 days. The furan dose was 8 mg/kg bw in cornoil.  Control animals were gavaged with corn oil only.   Tissues were collected 4 hours following the final dose.

value: 8mg/kg bw furan for 3 wks

value: FFPE (3wks in formalin)

source_name: Pooled reference (all samples pooled together)

value: pooled reference


title: Liver_1mkd-furan_18hr-FFPE_sample12 [1-color array]

description: Sample 7


title: Liver_1mkd-furan_18hr-FFPE_sample14 [1-color array]

description: Sample 9


title: PDMSCs P3,  biological rep 2

description: Gene expression data from Placental derived mesenchymal stem cells at passage 3 in general PDMSCs medium


title: Liver_8mkd-furan_3wk-FFPE_sample42 [2-color array]

description:
3 weeks in formalin, FFPE samples
Sample 14


title: PDMSCs P3,  biological rep 1

source_name: Placental derived mesenchymal stem cells at passage 3 in general PDMSCs medium


title: Liver_Control_18hr-FFPE_sample3 [1-color array]

description: Sample 3


title: Control, wild type, biological rep 2

city: Poznań

first: Radosław

last: Januchowski

address: 6 Święcickiego St.

department: Histology and Embryology

institute: University of Medical Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HumanGenome-U219 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were processed by RMA algorithm using Affymetrix expression console and R language with Bioconductor package.

source_name: Control, non treated, wild type cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All of the cell lines were maintained as monolayers in complete medium [MEM medium (A2780) or RPMI-1640 (W1) supplemented with 10% (v/v) foetal bovine serum, 2 pM L-glutamine, penicillin (100 units/ml), streptomycin (100 units/ml) and amphotericin B (25 μg/ml)] at 37°C in a 5% CO2 atmosphere

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

treatment_protocol: The final concentrations used for selection were 1000 ng/ml Cis, 1100 ng/ml Pac, 100 ng/ml Dox, and 24 ng/ml Top. These concentrations were chosen based on the results of Dietel et al., 1997 [29] and were two-fold higher than the plasma concentrations of the respective drugs 2 hours after intravenous administration

tag: cell subline

value: primary ovarian cancer W1


title: Liver_Control_3wk-FFPE_sample6 [2-color array]

description:
3 weeks in formalin, FFPE samples
Sample 12

value: corn-oil for 3 wks (vehicle control)


title: Liver_8mkd-furan_3wk-FFPE_sample43 [2-color array]

description:
3 weeks in formalin, FFPE samples
Sample 15


title: Liver_8mkd-furan_3wk-FFPE_sample41 [2-color array]

description:
3 weeks in formalin, FFPE samples
Sample 13


title: Liver_8mkd-furan_18hr-FFPE_sample44 [2-color array]

description:
18 hours in formalin, FFPE samples
Sample 8

value: FFPE (18hrs in formalin)


title: PDMSCs P3,  biological rep 3


title: Liver_Control_3wk-FFPE_sample2.2 [2-color array]

description:
3 weeks in formalin, FFPE samples
Sample 10


title: Liver_Control_3wk-FFPE_sample4 [2-color array]

description:
3 weeks in formalin, FFPE samples
Sample 11


title: Control, wild type, biological rep 3

value: Control, non treated, wild type cell line


title: Liver_8mkd-furan_18hr-FFPE_sample43 [2-color array]

description:
18 hours in formalin, FFPE samples
Sample 7


title: Liver_Control_3wk-FFPE_sample2.1 [2-color array]

description:
3 weeks in formalin, FFPE samples
Sample 9


title: Control, wild type, biological rep 1


title: Liver_8mkd-furan_18hr-FFPE_sample42 [2-color array]

description:
18 hours in formalin, FFPE samples
Sample 6


title: Vincristine resistant, biological rep 3

source_name: Vincristine resistant cell line

value: Vincristine resistant cell line


title: Paclitaxel resistant, biological rep 3

source_name: Paclitaxel resistant cell line

value: Paclitaxel resistant cell line


title: Liver_8mkd-furan_18hr-FFPE_sample41 [2-color array]

description:
18 hours in formalin, FFPE samples
Sample 5

value: female


title: Liver_Control_18hr-FFPE_sample3 [2-color array]

description:
18 hours in formalin, FFPE samples
Sample 2

value: liver


title: Cisplatin resistant, biological rep 3

source_name: Csplatin resistant cell line

value: Csplatin resistant cell line


title: Topotecan resistant, biological rep 3

source_name: Topotecan resistant cell line

value: Topotecan resistant cell line


title: Methotrexate resistant, biological rep 3

source_name: Methotrexate resistant cell line

value: Methotrexate resistant cell line


title: Liver_Control_18hr-FFPE_sample4 [2-color array]

description:
18 hours in formalin, FFPE samples
Sample 3


title: Control line, biological rep 3

source_name: Control, non treated cell line

value: Control, non treated cell line


title: Control line, biological rep 1


title: Liver_Control_18hr-FFPE_sample6 [2-color array]

description:
18 hours in formalin, FFPE samples
Sample 4


title: Doxorubicin resistant, biological rep 1

source_name: Doxorubicin resistant cell line

value: Doxorubicin resistant cell line


title: Vincristine resistant, biological rep 2


title: Cisplatin resistant, biological rep 2


title: Vincristine resistant, biological rep 1


title: Paclitaxel resistant, biological rep 1


title: Liver_Control_18hr-FFPE_sample2 [2-color array]

description:
18 hours in formalin, FFPE samples
Sample 1


title: Methotrexate resistant, biological rep 1


title: Paclitaxel resistant, biological rep 2


title: Methotrexate resistant, biological rep 2


title: Doxorubicin resistant, biological rep 2


title: Topotecan resistant, biological rep 1


title: Doxorubicin resistant, biological rep 3


title: Topotecan resistant, subpopulation 2, biological rep 2


title: Topotecan resistant, subpopulation 2, biological rep 3


title: Control line, biological rep 2


title: Topotecan resistant, subpopulation 2, biological rep 1


title: Topotecan resistant, subpopulation 1, biological rep 2


title: Topotecan resistant, subpopulation 1, biological rep 3


title: Paclitaxel resistant, subpopulation 2, biological rep 3


title: Topotecan resistant, subpopulation 1, biological rep 1


title: Paclitaxel resistant, subpopulation 1, biological rep 2


title: Paclitaxel resistant, subpopulation 2, biological rep 2


title: Paclitaxel resistant, subpopulation 1, biological rep 3


title: MDA-MB-231 Fatostain 10µM and Proadifen 8.5 x 10E-5% (w/v)_2

city: Shrewsbury

first: Andrew

last: Canter

address: Unti 46, Atcham Business Park

country: United Kingdom

institute: Pathway Intermediates

description:
replicate 2
CLS Germany
sample name: J

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: MDA-MB-231Fatostain 10µM and Proadifen 8.5 x 10E-5% (w/v)

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

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

tag: race

value: Caucasian

tag: age

value: Breast adenocarcinoma


title: Doxorubicin resistant, subpopulation 1, biological rep 2


title: Doxorubicin resistant, subpopulation 2, biological rep 2


title: Doxorubicin resistant, subpopulation 2, biological rep 1


title: MDA-MB-231 Fatostain 10µM_2

description:
replicate 2
CLS Germany
sample name: H

source_name: MDA-MB-231 Fatostain 10µM


title: MDA-MB-231 Fatostain 10µM and Proadifen 8.5 x 10E-5% (w/v)_1

description:
replicate 1
CLS Germany
sample name: I


title: Cisplatin resistant, subpopulation 2, biological rep 2


title: Paclitaxel resistant, subpopulation 1, biological rep 1


title: Calu-1 Zoledronic acid 100µM_2

description:
replicate 2
CLS Germany
sample name: D

source_name: Calu-1 Zoledronic acid 100µM

value: Lung adenocarcinoma


title: Cisplatin resistant, subpopulation 2, biological rep 3


title: Doxorubicin resistant, subpopulation 1, biological rep 3


title: Cisplatin resistant, subpopulation 2, biological rep 1


title: Calu-1 Fatostatin 10µM and Proadifen 8.5 x 10E-5% (w/v)_1

description:
replicate 1
CLS Germany
sample name: K


title: Calu-1 Fatostatin 10µM_1

description:
replicate 1
CLS Germany
sample name: E

source_name: Calu-1 Fatostatin 10µM


title: Doxorubicin resistant, subpopulation 1, biological rep 1


title: Calu-1 Fatostatin 10µM_2

description:
replicate 2
CLS Germany
sample name: F


title: MDA-MB-231 Fatostain 10µM_1

description:
replicate 1
CLS Germany
sample name: G


title: MSU_97

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 2104H McGavran-Greenberg 135 Dauer Drive Campus Box 7435 27599-7435

department: Center for Environmental Health Sciences Integrated Sciences Facility Corencer Center

country: USA

institute: University of North Carolina at Chapel Hill

description: HFD Early

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

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).  Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: HFD Early

label_protocol: Labelled by following Agilent's Low Input Quick Amp Standard Protocol.

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

tag: treatment

value: DMBA

tag: location

value: Mammary

value: Tumor

source_name: Universal Mouse Reference RNA

tag: content

value: 11 mouse cell lines

tag: manufacturer

value: Stratagene


title: Calu-1 Zoledronic acid 100µM_1

description:
replicate 1
CLS Germany
sample name: C

tag: cell line


title: Calu-1 Fatostatin 10µM and Proadifen 8.5 x 10E-5% (w/v)_2

description:
replicate 2
CLS Germany
sample name: L


title: Paclitaxel resistant, subpopulation 2, biological rep 1


title: Cisplatin resistant, subpopulation 1, biological rep 3


title: MSU_96

description: HFD Late

source_name: HFD Late


title: Doxorubicin resistant, subpopulation 2, biological rep 3


title: MDA-MB-231 untreated [C4]

description: replicate 4

source_name: CLS Germany


title: Cisplatin resistant, subpopulation 1, biological rep 2


title: S6-2-3

city: Glasgow

first: Nuria

last: Terron Canedo

address: Bearsden Road

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow, College of Medical, Veterinary and Life Sciences

description: Pooled sample of both cell lines

hyb_protocol: Samples were run on a miRCURY LNAª microRNA Array 7th Gen (Exiqon, Vedbaek Denmark). This array comprises 2,164 probes that contain human and viral sequences together with predicted equine microRNA sequences derived from miRBase 19.0.43

scan_protocol: The slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Stockport, United Kingdom) and the image analysis was carried out using the ImaGene¨ 9 miRCURY LNAª microRNA Array Analysis Software (Exiqon, Vedbaek Denmark).

data_processing:
Pre-processing of the data included background subtraction (Normexp with offset value 10) and normalisation using the global lowess regression algorithm. Moderated t-statistics were applied to determine differential expression of microRNAs between EqPalFs and S6-2 cells. Following this, the Benjamini and Hochberg multiple testing adjustment method was applied to the P values. P values of 0.05 or lower were considered to be statistically significant. Calculations were performed with R/Bioconductor using the limma package
The complete_data.txt contains the following data columns;
logFC: Log2(FoldChange) value when comparing two sample groups of interest. This corresponds to deltaLogMedianRatios or deltaLogMedianSignals
AvExpr: The average expression level (M or G) calculated based on all samples included in the comparison
AvgHy3 : Log2 (average Hy3 signal intensity)
P.Value: p-value calculated from t-statistics comparing the two sample groups
adj.P.Val: Adjusted p-value from t-statistics comparing the two sample groups
followed byt the signal intensity for each sample

organism: Equus caballus

source_name: S6-2_in vitro transformed with BPV-1 genomes

label_protocol: A sample of 750 ng of total RNA from the cell lines was fluorescently labelled, using the miRCURY LNA™ microRNA Hi-Power Labelling Kit, Hy3™/Hy5™ (Exiqon, Vedbaek Denmark) following the manufacturer’s instructions. The query samples (EqPalFs and S6-2 cells) were labelled using Hy3™ whereas the reference sample (a pooled sample of RNA from both cell lines) was dyed using Hy5™.

growth_protocol: Cell lines and culture previously described in Yuan et al., 2008

extract_protocol: Total RNA was isolated from EqPalFs and S6-2 cells at low passage (<10) using Trizol Reagent (Life Technologies Ltd, Paisley, United Kingdom) as per the manufacture's advice, vortexed and kept at -80 C until further use. Quality of RNA was assessed using a 2100 Bioanalyzer (Agilent Technologies, Stockport, United Kingdom). All samples had an RNA integrity number (RIN value) of 10.0.

treatment_protocol: In vitro BPV-1 transformation of the cells previously described in Yuan et al., 2008

tag: cell type

value: Equine primary fibroblasts

tag: genotype/variation

value: in vitro transformed with BPV-1 genomes

tag: bpv-1 neg/pos

value: positive

source_name: Reference (EqPalF+S-62)

value: Pooled sample of both cell lines


title: MSU_86

description: HFD Late

tag: tissue


title: S6-2-2

description: Pooled sample of both cell lines


title: MDA-MB-231 untreated [C3]

description: replicate 3


title: EqPalF-3

description: Pooled sample of both cell lines

source_name: EqPalF_no treatment

value: EqPalF

value: control (no treatment)

value: negative


title: S6-2-1

description: Pooled sample of both cell lines


title: MSU_768

description: HFD Early


title: Cisplatin resistant, subpopulation 1, biological rep 1

value: Csplatin resistant cell line


title: MSU_84

description: HFD Late


title: MSU_93

description: HFD Late


title: MSU_67

description: HFD Late


title: MDA-MB-231 untreated [C1]

description: replicate 1


title: EqPalf-1

description: Pooled sample of both cell lines


title: MDA-MB-231 treated with 8.0µM Pravastatin [B4]

description: replicate 4


title: MSU_62a

description: HFD Late


title: EqPalF-2

description: Pooled sample of both cell lines


title: MDA-MB-231 untreated [C2]

description: replicate 2


title: Topotecan resistant, biological rep 2

value: Topotecan resistant cell line

value: primary ovarian cancer W1


title: MDA-MB-231 treated with 8.0µM Pravastatin [B2]

description: replicate 2

value: Caucasian

value: Breast adenocarcinoma


title: MSU_59a

description: LFD-HFD Late

source_name: LFD-HFD Late

value: DMBA


title: MDA-MB-231 treated with 0.0008% (w/v) Proadifen [A4]

description: replicate 4


title: MSU_54

description: HFD-LFD Early

source_name: HFD-LFD Early

value: Mammary


title: MSU_59b

description: HFD-LFD Late

source_name: HFD-LFD Late

value: Tumor


title: MSU_62b

description: HFD-LFD Early

value: 11 mouse cell lines


title: MSU_58

description: HFD-LFD Late

value: Stratagene


title: MSU_45

description: LFD-HFD Late


title: MDA-MB-231 treated with 8.0µM Pravastatin [B1]

description: replicate 1


title: MDA-MB-231 treated with 8.0µM Pravastatin [B3]

description: replicate 3


title: MDA-MB-231 treated with 0.0008% (w/v) Proadifen [A2]

description: replicate 2


title: MDA-MB-231 treated with 0.0008% (w/v) Proadifen [A3]

description: replicate 3


title: MSU_42

description: LFD-HFD Late


title: MSU_28

description: LFD Late

source_name: LFD Late


title: Calu-1 0.00085%(w/v) Proadifen [19]

description: replicate 1

value: Lung adenocarcinoma


title: MSU_34

description: LFD Late


title: MSU_137

description: LFD Late


title: MDA-MB-231 treated with 0.0008% (w/v) Proadifen [A1]

description: replicate 1


title: Calu-1 0.00085%(w/v) Proadifen [21]

description: replicate 3


title: MSU_24

description: LFD-HFD Late


title: Cisplatin resistant, biological rep 1

source_name: Csplatin resistant cell line


title: MSU_122a

description: LFD Late


title: MSU_26

description: HFD-LFD Late


title: Calu-1 8.0µM Pravastatin [18]

description: replicate 3


title: MEF_Junb knock-out_clone 2

status: Public on Oct 13 2015

city: Heidelberg

first: Marina

last: Schorpp-Kistner

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Junb KO 2

hyb_protocol: Quality-checked total RNA was suspended in 25 µl miRNA hybridization buffer (Febit) per array and incubated for 16 h at 42°C using the Geniom RT-Analyzer (Febit).

scan_protocol: The arrays were scanned on the Geniom RT-Analyzer (Febit) using a Cy3 filter.

data_processing: Measured raw data were corrected for spatial effects on the chip by global background subtraction and normalized applying variance stabilizing normalization (VSN).

label: phycoerythrin (Cy3)

source_name: Junb knock-out MEFs

label_protocol: Hybridized RNA was labeled applying the microfluidic-based primer extension assay (Febit): In detail, biotinylated nucleotides were added to bound miRNAs by Klenow fragment at 37°C for 15 min. Subsequently, hybridized miRNAs were detected by binding of streptavidin-phycoerythrin (SAPE) followed by an antibody-mediated linear signal amplification based on the binding of a biotinylated anti-streptavidin antibody (Consecutive Signal Enhancement, Febit).

growth_protocol: Cells were cultured at 37°C and 8% CO2  in humidified atmosphere in DMEM (4.5 g/l glucose) supplemented with 10 % fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA integrity was verified by microcapillary gel electrophoresis using the RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Murine embryonic fibroblasts were isolated from Junb-deficient and wildtype E9.5 embryos and immortalized following the 3T3 protocol. Cells were published previously in Andrecht et al. (2002) J Biol Chem. 277(39):35961-8 and Licht et al. (2010) J Clin Invest. 120(7):2307-18.

tag: strain background

value: Junb knock-out

value: mouse embryos

tag: developmental stage

value: murine embryonic fibroblasts (MEFs)


title: MEF_Junb knock-out_clone 1

description: Junb KO 1


title: Calu-1 untreated  [13]

description: replicate 1


title: 152492

city: Nice

first: annie

last: peyron

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was hybridized with the hybridization kit according the Agilent protocol

scan_protocol: We used a Surescan provided by Agilent and controled by SureScan Software

data_processing: the data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method - CGH v2 proposed by Agilent

source_name: RCC

label_protocol: DNA was labeled with the sureTag labeling kit accirding the agilent protocol

extract_protocol: DNA was extracted from fresh, frozen or formol fixed-paraffin embedded fragments using Qiamp DNA mini kit.

value: RCC ,TFE

value: RCC

source_name: Male DNA control provided in SureTag Labeling Kit

value: commercial DNA from cell lines


title: Calu-1 untreated  [14]

description: replicate 2


title: Calu-1 0.00085%(w/v) Proadifen [20]

description: replicate 2


title: ASSAY WT

city: Haidian District

first: Yi

last: Fu

state: Beijing

address: 38 Xueyuan Rd

department: Physiology and Pathophysiology

institute: Peking University Health Science Center

description: This sample is of 2×106 cells extracted from 6 WT mice

hyb_protocol: Hybridization was performed in NimbleGen Hybridization System.

scan_protocol: After washing, slides were scanned with Axon GenePix 4000B scanner. Data was extracted and normalized using NimbleScan v2.5 Software. Results were provided in the NimbleScan Generated Data Folder.

data_processing: Further Data analysis was performed using Agilent GeneSpring GX v11.5.1 software. Results were provided in the Gene Expression Profiling Data.xls file and Data Analysis Folder.

source_name: Peritoneal Macrophages

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.

growth_protocol: Peritoneal macrophages were isolated from WT and COMP-/- mice injected with thioglycollate for 4 days. Isolated cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum for 24 hours.

extract_protocol: mRNA was isolated from 2×106 cells extracted from 6 mice per sample using Trizol. RNA quantity and quality were measured using NanoDrop ND-1000, whereas RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Reverse transcription using Invitrogen SuperScript ds-cDNA synthesis kit.

tag: strain

value: WT


title: Calu-1 8.0µM Pravastatin [17]

description: replicate 2


title: Calu-1 untreated  [15]

description: replicate 3


title: ASSAY KO

description: This sample is of 2×106 cells extracted from 6 COMP KO mice

value: COMP KO


title: Calu-1 8.0µM Pravastatin [16]

description: replicate 1


title: MEF_Junb wildtype_clone 2

description: Junb WT 2

source_name: Junb wildtype MEFs

value: Junb wildtype


title: MSU_163

description: HFD Early

source_name: HFD Early


title: MSU_105

description: LFD Late

source_name: Universal Mouse Reference RNA


title: MEF_Junb wildtype_clone 1

description: Junb WT 1


title: 151892

source_name: RCC (primitive)

tag: sample type

value: RCC (primitive)

source_name: Female DNA control provided in SureTag Labeling Kit


title: 142823


title: 151385

source_name: RCC (metastasis)

value: RCC (metastasis)


title: 549 EVE 48h rep3

city: HOUSTON

first: WEI

last: MO

state: TX

address: 7435 FANNIN ST

department: SYSTEMS BIOLOGY

institute: MD ANDERSON CANCER CENTER

description: replicate 3

label_protocol: Labeling of streptavidin-Cy3 was performed using the manufacturer’s procedure

extract_protocol: Total RNA from the cells was extracted with a mirVana miRNA isolation kit in accordance with the prescribed protocol provided with the kit. Complementary RNA was generated using a TotalPrep RNA amplification kit (Illumina, AMIL1791).

value: everolimus (10uM)

tag: phenotype

value: triple negative breast cancer


title: 549 EVE 48h rep1

description: replicate 1


title: 231 EVE 48h rep3

description: replicate 3


title: 549 EVE 48h rep2

description: replicate 2


title: 549 DMSO 48h rep1

description: replicate 1

value: DMSO


title: MSU_51

description: HFD-LFD Early

value: DMBA

value: Mammary

value: Tumor

value: 11 mouse cell lines


title: A.chinensis_Hemiberlesia lataniae_7days_rep6

city: Lincoln

first: Michael

middle: Garry

last: Hill

address: Gerald St

department: Applied Entomology

country: New Zealand

institute: NZ Institute of Plant & Food Research

description: Analysis compared RNA fromActinidia chinensis 'Hort16A' cane bark challenged with Hemiberlesia lataniae neonates (crawlers) for 2 days and 7 days compared with unchallenged bark.

hyb_protocol: method described by Janssen et al. 2008 BMC Plant Biol. 8: 16.

scan_protocol: Images converted to 16-bit intensities using GenePix 4000B scanner and Genepix Pro 4.0 softward.

data_processing: data normalised using print tip loess method and candidate differentially expressed genes identified using FDR control set at P<.05. Genepix intensity files were preprocessed and analysed using the limma analysis package in Bioconductor.

organism: Actinidia chinensis

source_name: bark samples from 9-week-old canes challenged with Hemiberlesia lataniae neonates for 7 days

growth_protocol: insect were grown in pure culture on squash in constant environment room at 20C and 70%RH. Vines were grown in bags in shade house

extract_protocol: 7cm section of bark removed and snap frozen. RNA extracted using pine tissue method  (Chang et al. 1993 Molecular Biology Reports 11: 113-116)

treatment_protocol: 150 mobile stage (crawlers) H. lataniae applied to an area of bark on 9-week old canes delimited by wool yarn

tag: cultivar

source_name: bark samples from 9-week-old canes

tag: tag


title: 549 DMSO 48h rep3

description: replicate 3


title: A.chinensis_Hemiberlesia lataniae_7days_rep5

label_protocol: method described by Janssen et al. 2008 BMC Plant Biol. 8: 16.


title: 231 DMSO 48h rep2

description: replicate 2


title: 549 DMSO 48h rep2

description: replicate 2


title: 231 EVE 48h rep2

description: replicate 2


title: 231 EVE 48h rep1

description: replicate 1


title: A.chinensis_Hemiberlesia lataniae_7days_rep4


title: 231 DMSO 48h rep3

description: replicate 3


title: 231 DMSO 48h rep1

description: replicate 1


title: 9 Tumor-associated fibroblasts

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL

description: Tumor-associated fibroblasts

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

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

data_processing:
Genome Studio V2011.2
Unmethylated and methylated signal intensities

label: Cy3, Cy5

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: Tumor-associated fibroblasts


title: A.chinensis_Hemiberlesia lataniae_7days_rep3


title: A.chinensis_Hemiberlesia lataniae_7days_rep2


title: A.chinensis_Hemiberlesia lataniae_7days_rep1


title: A.chinensis_control_7days_rep6


title: A.chinensis_control_7days_rep5


title: A.chinensis_control_7days_rep3


title: A.chinensis_control_7days_rep2


title: 14 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: A.chinensis_control_7days_rep4


title: A.chinensis_control_7days_rep1


title: A.chinensis_Hemiberlesia lataniae_2days_rep3

source_name: bark samples from 9-week-old canes challenged with Hemiberlesia lataniae neonates for 2 days


title: A.chinensis_Hemiberlesia lataniae_2days_rep4


title: 25 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: Rind, biological rep3

city: St Lucia

first: Rosanne

middle: Elena

last: Casu

state: QLD

address: Queensland Bioscience Precinct, 306 Carmody Rd

country: Australia

institute: CSIRO Agriculture Flagship

hyb_protocol: Hybridizations, washing and staining were performed as specified in the manufacturer’s protocol (Affymetrix, Inc.).

scan_protocol: Scanning was performed as specified in the manufacturer’s protocol (Affymetrix, Inc.). The scanner operating software, GCOS, converted the signal on each array into a DAT file, which was then used to generate CEL and CHP files for analysis.

data_processing: GeneSpring GX 11.0.2 (Agilent Technologies Inc., Santa Clara, CA, USA) was used for initial data analysis. A file describing the 8,236 sugarcane probe sets on the GeneChip Sugarcane Genome Array (Affymetrix.GeneChip.Sugar_Cane) was downloaded from Agilent Technologies. The generated CEL files were imported into GeneSpring, summarised using Robust Multi-array Average (RMA) and parameterised (tissue and replicate). They were then subjected to quantile normalisation and a baseline transformation using the median of all samples.

organism: Saccharum hybrid cultivar Q117

source_name: Rind from maturing stalk (internode 8)

label_protocol: Labelled target used in hybridisations was generated from 200 ng of amplified RNA using the One-Cycle Eukaryotic Target Labeling Assay.

growth_protocol: Sugarcane plants (variety Q117) were grown as a commercial crop and were harvested in late March 2005, 11 months after planting at Kalamia Mill estate in the Burdekin River region (North Queensland, Australia, Lat.: 19 32’ S; Long.: 147 25’ E).

extract_protocol: Total RNA was isolated from each tissue sample using an RNeasy Plant Mini Kit (including DNase digestion to remove any remaining DNA) according to the manufacturer’s directions (QIAGEN, Doncaster, VIC, Australia). Amplified RNA for use in GeneChip array hybridisations was generated from 250 ng of each total RNA sample derived from the initial set of field-grown plants using a SenseAmp Plus RNA Amplification Kit (Genisphere, Hatfield, PA, USA) according to the manufacturer’s directions. Each sample was checked for a lack of contaminating genomic DNA and the presence of known transcripts by RT-PCR and RT-qPCR respectively, with diagnostic primer sets to determine quality. All RNA samples were stored at -80°C until required.

treatment_protocol: Tissue samples were dissected from internode 8 (I8 – maturing stalk) sections harvested from three biological replicates of field-grown Q117 sugarcane plants, with the internodes being numbered from the apex down according to the method of Bonnett et al (2006). The tissue samples comprised: (i) storage parenchyma (P); (ii) vascular bundles (V) and (iii) rind (R). For both sets of samples, the following protocol was used: the internode was quickly cut away from the rest of the stalk and then sliced longitudinally in wedges. The vascular bundles were gently pulled away from the surrounding tissue with fine forceps and scraped to remove the adhering parenchyma cells which were immediately placed into a cryovial pre-cooled on dry ice. The cleaned vascular bundles were also placed into a pre-cooled cryovial. The rind was cut from the exterior surface of the internode, shredded finely using a scalpel and also placed into a pre-cooled cryovial. Each piece of internode was dissected within 15 min of removal from the plant in order to minimise RNA degradation and changes in the RNA composition. Once all of the dissections from a particular internode were finished, the cryovials were removed from the dry ice, plunged into liquid nitrogen and then stored at -80°C until required.

tag: variety

value: Rind

tag: organ

value: stalk


title: Rind, biological rep2


title: A.chinensis_Hemiberlesia lataniae_2days_rep5


title: 5 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: 6 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: A.chinensis_Hemiberlesia lataniae_2days_rep1


title: A.chinensis_Hemiberlesia lataniae_2days_rep2


title: 13 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: 26 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: 27 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: 28 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: 16 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: Rind, biological rep1


title: 12 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: Vascular bundles, biological rep2

source_name: Vascular bundles from maturing stalk (internode 8)

value: Vascular bundles


title: Vascular bundles, biological rep1


title: A.chinensis_control_2days_rep5


title: 9 Control fibroblasts

description: Control fibroblasts

value: Control fibroblasts


title: A.chinensis_control_2days_rep4


title: Parenchyma, biological rep3

source_name: Storage parenchyma from maturing stalk (internode 8)

value: Storage parenchyma


title: A.chinensis_control_2days_rep3


title: 14 Control fibroblasts

description: Control fibroblasts


title: 27 Control fibroblasts

description: Control fibroblasts


title: Parenchyma, biological rep1


title: A.chinensis_control_2days_rep2


title: 6 Control fibroblasts

description: Control fibroblasts


title: 18 Tumor-associated fibroblasts

description: Tumor-associated fibroblasts


title: poolCTL2(1+2+3+4) vs PIO-1.txt

status: Public on Oct 12 2015

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: manufacturer's instructions

growth_protocol: Caco-2 cells grow at 37°C in a controlled 5% CO2 atmosphere, in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, Cergy-Pontoise, France) supplemented with 20% foetal calf serum (FCS, Dutscher, Brumath, France), 1% penicillin-streptomycin (Invitrogen) and 1% non-essential amino acids (5 ml/l) (Invitrogen).

extract_protocol: Total RNA were extracted with the Nucleospin RNA kit (Macherey-Nagel, Hoerdt, France).

treatment_protocol: 1 million of cells (plated in 6 wells plates) were treated with GED (1 mM and 30mM), 5-ASA (30 mM), or pioglitazone (1 µM) in DMEM without serum. When necessary, the vehicle DMSO (Sigma) was used as control (Ctrl). Serum deprivation was used 16 hours prior to stimulation in order to synchronize the cells.

tag: treatment

value: control

value: pioglitazone (1 µM)


title: poolCTL2(1+2+3+4) vs PIO-3.txt


title: poolCTL1(1+2) vs 5ASA-3.txt


title: Vascular bundles, biological rep3


title: poolCTL1(1+2) vs GED30-4.txt

value: GED (30mM)


title: A.chinensis_control_2days_rep1


title: 26 Control fibroblasts

description: Control fibroblasts


title: 5 Control fibroblasts

description: Control fibroblasts


title: PIO-4 vs poolCTL2(1+2+3+4).txt


title: 18 Control fibroblasts

description: Control fibroblasts


title: poolCTL1(1+2) vs GED30-2.txt


title: poolCTL1(1+2) vs 5ASA-2.txt


title: 28 Control fibroblasts

description: Control fibroblasts


title: poolCTL vs AGO4.txt

source_name: poolCTL

value: GED (1mM)


title: 25 Control fibroblasts

description: Control fibroblasts


title: GED30-3 vs poolCTL1(1+2).txt


title: GED30-1 vs poolCTL1(1+2).txt


title: AGO1 vs poolCTL.txt


title: AGO3 vs poolCTL.txt


title: poolCTL vs AGO2.txt


title: PIO-2 vs poolCTL2(1+2+3+4).txt


title: 12 Control fibroblasts

description: Control fibroblasts


title: 16 Control fibroblasts

description: Control fibroblasts


title: 5ASA-4 vs poolCTL1(1+2).txt


title: 5 Fibroblasts in normal-like stiffness

description: Fibroblasts in normal-like stiffness

value: Fibroblasts in normal-like stiffness


title: DUCaP cells treated for 24 hours with R1881, experiment 3

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

hyb_protocol: Target samples were hybridized to Human Gene 1.0 ST v1 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data was preprocessed using the RMA method and a custom CDF from the Brainarray group (ENSG CDF, version 13).

source_name: DUCaP

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: Cells (LNCaP, VCaP, DuCaP) were grown on polylysine-coated (Sigma) petridishes in RPMI1640 supplemented with 10% charcoal-stripped FCS overnight.

extract_protocol: RNA was extracted using TRI-reagent (Sigma) according to the manufacturer`s protocol. After DNA digestion with DnaseI (Qiagen), RNA was purified using Rneasy kit (Qiagen).

treatment_protocol: Cells were cultured in the absence (EtOH) or presence of 1nM R1881 for 8 and 24 hours, respectively.

tag: time

value: DUCaP

tag: date of experiment


title: DUCaP cells treated for 24 hours with EtOH, experiment 3

value: EtOH

tag: cell line


title: 5 Fibroblasts in tumor-like stiffness

description: Fibroblasts in tumor-like stiffness

tag: cell type

value: Fibroblasts in tumor-like stiffness


title: DUCaP cells treated for 24 hours with R1881, experiment 2


title: BMN_FJ3_MoGene

city: MARSEILLE

first: Marc

last: DALOD

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2.07 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package. Two matrices was generated. Matrix1 corresponds to all probesets. Matrix2 corresponds to probes showing a fold change ≥2 and a p-value <0.05 for at least one cell type between D5 or D11 versus D0 using the LIMMA statistical package of the R program.

label_protocol: 1 to 20 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.

growth_protocol: To extract skin mononuclear phagocytic cells, ears were splitted into dorsal and ventral parts and incubated with a solution of PBS containing 1 mg/mL dispase (Roche) for 2 h at 37° C or overnight at 4° C, as specified. The dorsal and ventral parts were then cut into small pieces and incubated for 90 min at 37° C with RPMI containing 1 mg/mL DNase and 1 mg/mL Collagenase IV (Worthington Biochemical). The resulting single cell suspension was subjected to centrifugation on a Percoll gradient (Amersham-Pharmacia).

extract_protocol: Each cell subset was purified by flow cytometry and total RNA was extracted with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.

treatment_protocol: Mice at 8 to 11 weeks of age received on a daily basis and for 14 consecutive days a dose of 5 % IMQ cream (Aldara, MEDA Pharma, Paris, France) applied topically on the ear skin and corresponding to 7 mg IMQ per ear side

tag: cell population

value: Epidermal Langerhans Cells

value: 5 days of IMQ


title: BMN_FJ4_MoGene


title: BMN_GD2_MoGene

value: 11 days of IMQ


title: BMN_GD1_MoGene


title: DUCaP cells treated for 24 hours with EtOH, experiment 2


title: BMN_FS2_MoGene

value: Untreated


title: BMN_FS3_MoGene


title: 28 Fibroblasts in normal-like stiffness

description: Fibroblasts in normal-like stiffness


title: 13 Control fibroblasts

description: Control fibroblasts


title: DUCaP cells treated for 8 hours with EtOH, experiment 2

value: 8 h


title: BMN_FS1_MoGene


title: BMN_FJ2_MoGene


title: BMN_GA2_MoGene

value: CD11b+CD64-Ly-6C-MHCII+ CD24-

value: Dermal CD11b+ conventional DCs


title: DUCaP cells treated for 24 hours with EtOH, experiment 1


title: DUCaP cells treated for 8 hours with R1881, experiment 1


title: DUCaP cells treated for 24 hours with R1881, experiment 1


title: DUCaP cells treated for 8 hours with R1881, experiment 2


title: BMN_GA3_MoGene


title: Parenchyma, biological rep2

value: stalk


title: BMN_GA1_MoGene


title: BMN_FG4_MoGene


title: LNCaP cells treated for 8 hours with EtOH, experiment 2

source_name: LNCaP

value: LNCaP


title: BMN_FG2_MoGene


title: BMN_FG3_MoGene


title: LNCaP cells treated for 24 hours with EtOH, experiment 3


title: BMN_BH4_MoGene


title: 28 Fibroblasts in tumor-like stiffness

description: Fibroblasts in tumor-like stiffness


title: BMN_GC3_MoGene

value: Dermal MHCIIhi Macrophages


title: BMN_BH2_MoGene


title: BMN_GC2_MoGene


title: LNCaP cells treated for 8 hours with EtOH, experiment 1


title: LNCaP cells treated for 8 hours with R1881, experiment 1


title: LNCaP cells treated for 24 hours with EtOH, experiment 1


title: DUCaP cells treated for 8 hours with EtOH, experiment 1


title: LNCaP cells treated for 24 hours with R1881, experiment 3


title: LNCaP cells treated for 24 hours with EtOH, experiment 2


title: BMN_BF1_MoGene


title: BMN_GC1_MoGene


title: BMN_BH1_MoGene


title: BMN_GB1_MoGene

value: Dermal MHCIIlow Macrophages


title: BMN_BF4_MoGene


title: LNCaP cells treated for 24 hours with R1881, experiment 1


title: LNCaP cells treated for 24 hours with R1881, experiment 2


title: BMN_FQ4_MoGene


title: BMN_GB3_MoGene


title: BMN_BG4_MoGene


title: BMN_BG1_MoGene


title: BMN_FQ2_MoGene


title: BMN_GF3_MoGene

value: Dermal Ly-6Chigh moDCs


title: BMN_BG2_MoGene


title: BMN_FQ3_MoGene


title: BMN_GB2_MoGene


title: BMN_FI4_MoGene


title: BMN_FI2_MoGene


title: BMN_GF2_MoGene


title: BMN_FI3_MoGene


title: BMN_GF1_MoGene


title: BMN_BD4_MoGene


title: BMN_FH4_MoGene

value: Dermal Monocytes


title: BMN_BC4_MoGene


title: BMN_BC2_MoGene


title: BMN_FH2_MoGene


title: BMN_BF2_MoGene


title: BMN_GD3_MoGene


title: BMN_FH3_MoGene


title: BMN_BC1_MoGene


title: BMN_BD1_MoGene


title: BMN_BD2_MoGene


title: 5ASA-1 vs poolCTL1(1+2).txt


title: Old Spleen Replicate 10 (control)

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

institute: NASA Ames Research Center

description: Old Spleen Replicate 10

data_processing: The data were corrected with COMBAT correction and then quantile normalization with GenePattern Illumina Normalizer Module

source_name: Spleen from non-tumor bearing control mice

tag: Sex

value: male

tag: disease state

value: non-tumor bearing control mice

tag: age

value: 736 days old

value: Spleen


title: Old Spleen Replicate 8 (control)

description: Old Spleen Replicate 8

tag: tissue


title: Old Spleen Replicate 7 (control)

description: Old Spleen Replicate 7

tag: strain


title: Old Spleen Replicate 1 (control)

description: Old Spleen Replicate 1


title: Old Spleen Replicate 4 (control)

description: Old Spleen Replicate 4


title: Old Spleen Replicate 9 (control)

description: Old Spleen Replicate 9


title: Old Spleen Replicate 5 (control)

description: Old Spleen Replicate 5


title: Old Spleen Replicate 3 (control)

description: Old Spleen Replicate 3


title: Middle-Aged Spleen Replicate 2 (control)

description: Middle-Aged Spleen Replicate 2

value: 551 days old


title: Old Spleen Replicate 6 (control)

description: Old Spleen Replicate 6


title: Middle-Aged Spleen Replicate 8 (control)

description: Middle-Aged Spleen Replicate 8


title: Middle-Aged Spleen Replicate 6 (control)

description: Middle-Aged Spleen Replicate 6


title: Middle-Aged Spleen Replicate 4 (control)

description: Middle-Aged Spleen Replicate 4


title: Middle-Aged Spleen Replicate 9 (control)

description: Middle-Aged Spleen Replicate 9


title: Middle-Aged Spleen Replicate 10 (control)

description: Middle-Aged Spleen Replicate 10


title: Middle-Aged Spleen Replicate 7 (control)

description: Middle-Aged Spleen Replicate 7


title: Young Adult Spleen Replicate 10 (control)

description: Young Adult Spleen Replicate 10

value: 143 days old


title: Old Spleen Replicate 2 (control)

description: Old Spleen Replicate 2


title: Middle-Aged Spleen Replicate 3 (control)

description: Middle-Aged Spleen Replicate 3


title: Young Adult Spleen Replicate 5 (control)

description: Young Adult Spleen Replicate 5


title: Middle-Aged Spleen Replicate 1 (control)

description: Middle-Aged Spleen Replicate 1


title: Young Adult Spleen Replicate 7 (control)

description: Young Adult Spleen Replicate 7


title: Young Adult Spleen Replicate 8 (control)

description: Young Adult Spleen Replicate 8


title: Young Adult Spleen Replicate 6 (control)

description: Young Adult Spleen Replicate 6


title: Middle-Aged Spleen Replicate 5 (control)

description: Middle-Aged Spleen Replicate 5


title: Young Adult Spleen Replicate 2 (control)

description: Young Adult Spleen Replicate 2


title: Young Adult Spleen Replicate 9 (control)

description: Young Adult Spleen Replicate 9


title: Young Adult Spleen Replicate 1 (control)

description: Young Adult Spleen Replicate 1


title: Young Adult Spleen Replicate 4 (control)

description: Young Adult Spleen Replicate 4


title: Adolescent Spleen Replicate 10 (control)

description: Adolescent Spleen Replicate 10

value: 68 days old


title: Young Adult Spleen Replicate 3 (control)

description: Young Adult Spleen Replicate 3


title: Adolescent Spleen Replicate 9 (control)

description: Adolescent Spleen Replicate 9


title: Adolescent Spleen Replicate 8 (control)

description: Adolescent Spleen Replicate 8


title: LNCaP cells treated for 8 hours with R1881, experiment 2


title: Adolescent Spleen Replicate 7 (control)

description: Adolescent Spleen Replicate 7


title: Adolescent Spleen Replicate 5 (control)

description: Adolescent Spleen Replicate 5


title: Old Spleen Replicate 8 (tumor-bearing)

description: Old Spleen Replicate 8

source_name: Spleen from LLC tumor bearing mice

value: LLC tumor bearing mice


title: Adolescent Spleen Replicate 3 (control)

description: Adolescent Spleen Replicate 3


title: Old Spleen Replicate 5 (tumor-bearing)

description: Old Spleen Replicate 5


title: Adolescent Spleen Replicate 2 (control)

description: Adolescent Spleen Replicate 2


title: Adolescent Spleen Replicate 1 (control)

description: Adolescent Spleen Replicate 1


title: Adolescent Spleen Replicate 4 (control)

description: Adolescent Spleen Replicate 4


title: Middle-Aged Spleen Replicate 5 (tumor-bearing)

description: Middle-Aged Spleen Replicate 5


title: Old Spleen Replicate 3 (tumor-bearing)

description: Old Spleen Replicate 3


title: Old Spleen Replicate 9 (tumor-bearing)

description: Old Spleen Replicate 9


title: Old Spleen Replicate 10 (tumor-bearing)

description: Old Spleen Replicate 10


title: Old Spleen Replicate 6 (tumor-bearing)

description: Old Spleen Replicate 6


title: Old Spleen Replicate 1 (tumor-bearing)

description: Old Spleen Replicate 1


title: Middle-Aged Spleen Replicate 1 (tumor-bearing)

description: Middle-Aged Spleen Replicate 1


title: Middle-Aged Spleen Replicate 3 (tumor-bearing)

description: Middle-Aged Spleen Replicate 3


title: Young Adult Spleen Replicate 6 (tumor-bearing)

description: Young Adult Spleen Replicate 6


title: Middle-Aged Spleen Replicate 6 (tumor-bearing)

description: Middle-Aged Spleen Replicate 6


title: Young Adult Spleen Replicate 7 (tumor-bearing)

description: Young Adult Spleen Replicate 7


title: Middle-Aged Spleen Replicate 2 (tumor-bearing)

description: Middle-Aged Spleen Replicate 2


title: Old Spleen Replicate 7 (tumor-bearing)

description: Old Spleen Replicate 7


title: Old Spleen Replicate 4 (tumor-bearing)

description: Old Spleen Replicate 4


title: Middle-Aged Spleen Replicate 4 (tumor-bearing)

description: Middle-Aged Spleen Replicate 4


title: Young Adult Spleen Replicate 5 (tumor-bearing)

description: Young Adult Spleen Replicate 5


title: Young Adult Spleen Replicate 3 (tumor-bearing)

description: Young Adult Spleen Replicate 3


title: Adolescent Spleen Replicate 9 (tumor-bearing)

description: Adolescent Spleen Replicate 9


title: Old Spleen Replicate 2 (tumor-bearing)

description: Old Spleen Replicate 2


title: Young Adult Spleen Replicate 4 (tumor-bearing)

description: Young Adult Spleen Replicate 4


title: Young Adult Spleen Replicate 1 (tumor-bearing)

description: Young Adult Spleen Replicate 1


title: Young Adult Spleen Replicate 2 (tumor-bearing)

description: Young Adult Spleen Replicate 2


title: Adolescent Spleen Replicate 6 (control)

description: Adolescent Spleen Replicate 6


title: Adolescent Spleen Replicate 6 (tumor-bearing)

description: Adolescent Spleen Replicate 6


title: Adolescent Spleen Replicate 5 (tumor-bearing)

description: Adolescent Spleen Replicate 5


title: Adolescent Spleen Replicate 8 (tumor-bearing)

description: Adolescent Spleen Replicate 8


title: Adolescent Spleen Replicate 2 (tumor-bearing)

description: Adolescent Spleen Replicate 2


title: Adolescent Spleen Replicate 3 (tumor-bearing)

description: Adolescent Spleen Replicate 3


title: Adolescent Spleen Replicate 1 (tumor-bearing)

description: Adolescent Spleen Replicate 1


title: C.mes.rep2

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: replicate 2

data_processing: The data were normalized using quantile normalization

source_name: Cochlear NECs

label_protocol: Total RNA was pre-amplified with the Ovation RNA Amplification System V2 (NuGEN). The A total of 1.5 µg of cDNA was then processed and labeled following the manufacturer's protocol.

growth_protocol: mouse inner ear tissue

extract_protocol: RNeasy Plus Micro Kit (Qiagen)

treatment_protocol: cells obtained by cell sorting

value: Atoh1/nGFP (C57BL/6)

value: Cochlea

value: NECs


title: Adolescent Spleen Replicate 4 (tumor-bearing)

description: Adolescent Spleen Replicate 4


title: V.sc.rep2

description: replicate 2

source_name: Vestibular ENSCs

value: Vestibular system

value: ENSCs


title: Poor-differentiated Prostate Cancer Tissue, Biological Replicate 1

city: Los Angeles

first: Yu-Ting

last: Tseng

state: California

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

description: Biological replicate 1 of 2. Poor-differentiated Prostate Cancer Tissue

hyb_protocol: Experimental and reference probes were combined and hybridized to custom Agilent 4x44K  whole mouse genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer's suggested protocol

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2565BA (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used was used for background subtraction and LOWESS normalization.  Spots of poor quality (p-value < 0.05) were removed from further analysis

source_name: MGS

label_protocol: A total of 825 ng of amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following Agilent suggested protocols.

extract_protocol: All samples were laser-capture microdissected (~5000 cells per sample).  Total RNA was isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA).  Total RNA was then amplified two rounds using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), incorporating amino-allyl UTP into second round aRNA according to the manufacturer's specification.

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

tag: gender

value: Swiss-Webster

value: primary prostate tumor

value: mixed background

tag: genotype


title: Poor-differentiated Prostate Cancer Tissue, Biological Replicate 2

description: Biological replicate 2 of 2. Poor-differentiated Prostate Cancer Tissue

value: male


title: V.sc.rep3

description: replicate 3


title: V.hc.rep1

description: replicate 1

source_name: Vestibular HCs

value: HCs


title: V.mes.rep2

description: replicate 2

source_name: Vestibular NECs


title: C.hc.rep1

description: replicate 1

source_name: Cochlear HCs


title: C.sc.rep1

description: replicate 1

source_name: Cochlear ENSCs


title: V.sc.rep1

description: replicate 1


title: C.sc.rep2

description: replicate 2


title: V.hc.rep3

description: replicate 3


title: C.hc.rep2

description: replicate 2


title: V.mes.rep1

description: replicate 1


title: C.mes.rep3

description: replicate 3


title: C.mes.rep1

description: replicate 1


title: C.sc.rep3

description: replicate 3


title: V.hc.rep2

description: replicate 2


title: V.mes.rep3

description: replicate 3


title: Metastatic Prostate Cancer Tissue, Biological Replicate 3

description: Biological replicate 3 of 3. Lung Metastases

source_name: Metastatic Prostate Cancer Tissue

value: lung metastases


title: C.hc.rep3

description: replicate 3


title: Well-differentiated Prostate Cancer Tissue, Biological Replicate 3

description: Biological replicate 3 of 3. Well-differentiated Prostate Cancer Tissue


title: Metastatic Prostate Cancer Tissue, Biological Replicate 2

description: Biological replicate 2 of 3. Lung Metastases


title: WT Prostate Epithelial Tissue, Biological Replicate 2

description: Biological replicate 2 of 3. Control WT Prostate Epithelial Tissue

source_name: WT Prostate Epithelial Tissue

value: WT prostate

value: Pb-Cre-;PtenL/L


title: Metastatic Prostate Cancer Tissue, Biological Replicate 1

description: Biological replicate 1 of 3. Lung Metastases


title: Well-differentiated Prostate Cancer Tissue, Biological Replicate 1

description: Biological replicate 1 of 3. Well-differentiated Prostate Cancer Tissue


title: WT Prostate Epithelial Tissue, Biological Replicate 3

description: Biological replicate 3 of 3. Control WT Prostate Epithelial Tissue


title: Well-differentiated Prostate Cancer Tissue, Biological Replicate 2

description: Biological replicate 2 of 3. Well-differentiated Prostate Cancer Tissue


status: Public on Oct 11 2015

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

description: 1125_SMK_12_Live H. Flu SMK_12_lflu3_1125_R SMK_12_lflu3_1125_R

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix Mouse Genome 430 2.0  chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.

scan_protocol: GeneChips were scanned using the GC 30007G scanner.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. Normalized data (VALUE) represents probesets that probesets passed the QC and curation processes.

label: Biotin

source_name: Lung sample from smoke exposed animal 1125 (treatment: Live H. Flu) at 12h time point

label_protocol: Total RNA (100ng) was amplified and labeled using NuGen Ovation Chemistry (San Carlos, California) according to manufacturer’s instruction.

extract_protocol: Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.

tag: animal id

tag: prior exposure

value: smoke

value: Live H. Flu

value: lung


title: 1106_SMK_24_Mock SMK_24_mock3_1106_R

description: 1106_SMK_24_Mock SMK_24_mock3_1106_R SMK_24_mock3_1106_R

source_name: Lung sample from smoke exposed animal 1106 (treatment: Mock) at 24h time point

value: Mock


description: 1117_SMK_24_Live S. Pneumo SMK_24_lpne3_1117_R SMK_24_lpne3_1117_R

source_name: Lung sample from smoke exposed animal 1117 (treatment: Live S. Pneumo) at 24h time point

value: Live S. pneumoniae


description: 1107_SMK_12_Heat-killed H. Flu SMK_12_hkflu3_1107_R SMK_12_hkflu3_1107_R

source_name: Lung sample from smoke exposed animal 1107 (treatment: Heat-killed H. Flu) at 12h time point

value: Heat-killed H. Flu


title: WT Prostate Epithelial Tissue, Biological Replicate 1

description: Biological replicate 1 of 3. Control WT Prostate Epithelial Tissue