title: Invasive urothelial carcinoma, biological rep 18

city: West Lafayette

first: Deborah

last: Knapp

address: 625 Harrison Street

institute: Purdue University

description:
Gene expression data from canine invasive bladder tumor
PU_Zack_050108

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical  Manual, 2001, Affymetrix).

scan_protocol: Following hybridization, scanning was performed following manufacturer's protocol.

data_processing: Data was processed using GeneSpring 12.6.1

organism: Canis lupus familiaris

source_name: Invasive urothelial carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Normal bladder and bladder tumors were collected and stored in trizol.

extract_protocol: Total RNA was extracted following manufacturer's protocol. Quality Control on RNA was performed using Agilent 2100 Bioanalyzer DE72902029.

treatment_protocol: Normal bladder and bladder tumors were processed for RNA only after confirmed diagnosis via histopathology.

value: Bladder Tumor


title: Invasive urothelial carcinoma, biological rep 17

status: Public on Aug 25 2015

type: RNA

country: USA

description:
Gene expression data from canine invasive bladder tumor
PU_Snickers_050108

label: biotin

molecule: total RNA

tag: tissue


title: PC3M untreated for 8 hr, biological replicate 2

city: Bethesda

first: Donald

middle: P

last: Bottaro

state: MD

address: Bldg 10 CRC Rm 2-3952, 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

description:
PC3M untreated for 8 hr
Untreated 8 hr_2

hyb_protocol: Labeled cDNAs were hybridized to HG U133A Plus 2.0 Affymetrix GeneChip™ arrays, stained with streptavidin phycoerythrin with antibody amplification.

scan_protocol: Scanning was performed following manufacturer’s instructions.

data_processing: Microarray data were analyzed using Partek Genomic Suite software v6.6.  Thirty-six CEL files were loaded into Partek and normalized by the RMA (robust multichip average) algorithm.

organism: Homo sapiens

label_protocol: A total of 4 micrograms of the amplified cDNA was fragmented and biotin labeled using FL-Ovation™ cDNA Biotin Module V2 (NuGEN # 4200) according to the manufacturer’s instructions.

growth_protocol: PC3M cells were grown to 70% confluenc and serum deprived for 16 h (T0) prior to treatment for various intervals and sample processing.

extract_protocol:
At termination, total RNA was extracted using Qiagen’s All Prep DNA/RNA Kit™ (Qiagen) following the manufacturer’s instructions. Resulting RNA was quantitated by Nanodrop spectrophotometry and stored at -80oC until use.
Total RNA (50 ng) was amplified using the WT-Ovation FFPE System™ (NuGEN) according to the manufacturer’s instructions.  Quantity and quality of the resulting amplified cDNA were measured by Nanodrop spectrophotometry.

treatment_protocol: At T0, biological triplicate cell groups were left untreated or treated with hHGF (1 nM), hNK2 (30 nM) or mHGF (1 nM) for and additional 8, 16 or 32 hours (termination).  Dosing is based on known difference in ligand-receptor binding affinity and is designed to achieve equivalent receptor occupancy.

tag: cell line

value: prostate adenocarcinoma cell line PC3M

tag: agent

value: untreated

tag: time

value: 8 hr


title: PC3M untreated for 32 hr, biological replicate 3

description:
PC3M untreated for 32 hr
Untreated 32 hr_3

value: 32 hr


title: Invasive urothelial carcinoma, biological rep 16

description:
Gene expression data from canine invasive bladder tumor
PU_Sable_050108


title: PC3M untreated for 8 hr, biological replicate 1

description:
PC3M untreated for 8 hr
Untreated 8 hr_1


title: Gill-26.4C-0min-recovery-Replicate1

city: Davis

first: Lisa

last: Komoroske

state: CA

address: One Shields Ave

department: Wildlife, fish and conservation biology

institute: University of California, Davis

hyb_protocol: Prior to hybridization, 1.65 µg of dye labeled complementary RNA (specific activity >16.0 pmol Cy3/ug cRNA) for each sample was combined with 2.2 µl of 25x fragmentation buffer, 11 µl of 10X Gene Expression Blocking Agent and nuclease-free water to bring the final volume to 55 µl. The fragmentation mix was incubated at 60°C for 30 min, cooled on ice for 1 min, and the fragmentation was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer. Samples were centrifuged for 1 min, placed on ice and 100 µl of the mix was loaded onto arrays and each microarray slide was placed in a single hybridization chamber. Individuals from each treatment were randomized between slides and array position on the slide. All samples were hybridized to the arrays (custom designed Agilent 4x44K oligonucleotide microarrays) for 17 h at 65°C, followed by a wash with Gene Expression Wash Buffer 1 (Agilent) at room temperature and a wash with Gene Expression Wash Buffer 2 (Agilent) heated to 37ºC. Slides were scanned immediately after washing.

scan_protocol: Fluorescent images were scanned using an Axon GenePix 4000B Scanner and the analysis software GenePix Pro (Molecular Devices, LLC, Sunnyvale, CA). The images were quantified using Feature Extraction 11.5.1.1 (Agilent Technologies).

data_processing: Normalization of the microarray data and statistical analysis was performed in Genespring v12.6 (Agilent Technologies). Data was quantile normalized and Log2 transformed prior to statistical analysis. Probes that had a raw signal less than 100 (~2 times the intensity of the background) were filtered out of the statistical analysis to eliminate sources of background noise, but still retain probes with low intensity.

organism: Hypomesus transpacificus

source_name: Gill, 26.4C exposure, 0min recovery

label_protocol: Two hundred ng of total RNA was amplified and labeled with Cy3 using the Low Input Quick Amp Labeling kit (Agilent Technologies). To minimize technical artefacts, labeling reactions were performed simultaneously.  Dye incorporation and cRNA yield were assessed with a NanoDrop Spectrometer.

growth_protocol: Delta smelt were allowed three weeks to acclimatize to holding conditions at 16°C at the Center for Aquatic Biology and Aquaculture at the University of California, Davis.

extract_protocol: At each time point, fish were sacrificed by a lethal dose of MS-222, gills dissected and immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Gill samples were then homogenized using Qiagen's TissuelyserLT and Trizol reagent following manufacturer’s protocols. Samples purity was improved by using RNEasy columns and reagents prior to final elution in water. Concentration and purity (260/280, 260/230) were assessed using a Nanodrop spectrometer (Thermo Scientific) and RNA integrity was determined through electrophoresis.

treatment_protocol: Fish were placed in treatment vessels and given thirty minutes to acclimate, followed by ramping increases in temperatures (0.3°C/min) to treatments selected relative to acute thermal tolerance (CTmax-2°C, CTmax-4°C, CTmax-6°C). When each treatment temperature was reached, fish were removed and either immediately sacrificed and sampled (0 min recovery), or transferred into 9.5 L (larval fish) or 35.2 L (adult) black round recovery tanks at the original acclimation temperature and allowed to recover for 30 or 60 minutes prior to sampling. Handling control trials were conducted by subjecting fish to the same conditions except they were held at the acclimation temperature for the average time of the treatment trials, followed by subsequent transfer into appropriate recovery tanks

tag: treatment

value: 26.4C exposure

tag: recovery time

value: 0minutes recovery


title: Gill-24.4C-60min-recovery-Replicate6

source_name: Gill, 24.4C exposure, 60min recovery

value: 24.4C exposure

value: 60minutes recovery


title: Gill-26.4C-0min-recovery-Replicate3


title: Gill-26.4C-0min-recovery-Replicate2


title: Invasive urothelial carcinoma, biological rep 15

description:
Gene expression data from canine invasive bladder tumor
PU_Penny_050108


title: PC3M untreated for 16 hr, biological replicate 3

description:
PC3M untreated for 16 hr
Untreated 16 hr_3

value: 16 hr


title: PC3M untreated for 32 hr, biological replicate 2

description:
PC3M untreated for 32 hr
Untreated 32 hr_2


title: Gill-26.4C-60min-recovery-Replicate1

source_name: Gill, 26.4C exposure, 60min recovery


title: Invasive urothelial carcinoma, biological rep 14

description:
Gene expression data from canine invasive bladder tumor
PU_Misty_050108


title: Invasive urothelial carcinoma, biological rep 13

description:
Gene expression data from canine invasive bladder tumor
PU_Mimi_050108


title: Gill-24.4C-60min-recovery-Replicate1


title: Invasive urothelial carcinoma, biological rep 10

description:
Gene expression data from canine invasive bladder tumor
PU_Frenkie_050108


title: Invasive urothelial carcinoma, biological rep 12

description:
Gene expression data from canine invasive bladder tumor
PU_Jesse_050108


title: PC3M untreated for 16 hr, biological replicate 1

description:
PC3M untreated for 16 hr
Untreated 16 hr_1


title: Gill-24.4C-60min-recovery-Replicate3


title: PC3M treated with 30 nM NK2 for 8 hr, biological replicate 3

description:
PC3M treated with 30 nM NK2 for 8 hr
30 nM NK2 8 hr_3


title: Gill-24.4C-60min-recovery-Replicate2


title: PC3M untreated for 32 hr, biological replicate 1

description:
PC3M untreated for 32 hr
Untreated 32 hr_1


title: Invasive urothelial carcinoma, biological rep 11

description:
Gene expression data from canine invasive bladder tumor
PU_Jascha_050108


title: Gill-24.4C-30min-recovery-Replicate3

source_name: Gill, 24.4C exposure, 30min recovery

value: 30minutes recovery


title: PC3M untreated for 16 hr, biological replicate 2

description:
PC3M untreated for 16 hr
Untreated 16 hr_2


title: PC3M treated with 30 nM NK2 for 8 hr, biological replicate 2

description:
PC3M treated with 30 nM NK2 for 8 hr
30 nM NK2 8 hr_2


title: Gill-24.4C-0min-recovery-Replicate2

source_name: Gill, 24.4C exposure, 0min recovery


title: Gill-24.4C-30min-recovery-Replicate1


title: Invasive urothelial carcinoma, biological rep 8

description:
Gene expression data from canine invasive bladder tumor
PU_Casey_050108


title: Gill-24.4C-30min-recovery-Replicate2


title: Invasive urothelial carcinoma, biological rep 7

description:
Gene expression data from canine invasive bladder tumor
PU_9_050108


title: Invasive urothelial carcinoma, biological rep 9

description:
Gene expression data from canine invasive bladder tumor
PU_Charlie_050108


title: Gill-24.4C-0min-recovery-Replicate4


title: PC3M treated with 30 nM NK2 for 32 hr, biological replicate 2

description:
PC3M treated with 30 nM NK2 for 32 hr
30 nM NK2 32 hr_2


title: Gill-24.4C-0min-recovery-Replicate5


title: PC3M treated with 30 nM NK2 for 8 hr, biological replicate 1

description:
PC3M treated with 30 nM NK2 for 8 hr
30 nM NK2 8 hr_1


title: Invasive urothelial carcinoma, biological rep 5

description:
Gene expression data from canine invasive bladder tumor
PU_7_050108


title: Invasive urothelial carcinoma, biological rep 4

description:
Gene expression data from canine invasive bladder tumor
PU_6_050108


title: PC3M treated with 30 nM NK2 for 32 hr, biological replicate 1

description:
PC3M treated with 30 nM NK2 for 32 hr
30 nM NK2 32 hr_1


title: PC3M treated with 30 nM NK2 for 32 hr, biological replicate 3

description:
PC3M treated with 30 nM NK2 for 32 hr
30 nM NK2 32 hr_3


title: Gill-22.4C-60min-recovery-Replicate2

source_name: Gill, 22.4C exposure, 60min recovery

value: 22.4C exposure


title: Gill-22.4C-60min-recovery-Replicate4


title: Invasive urothelial carcinoma, biological rep 6

description:
Gene expression data from canine invasive bladder tumor
PU_8_050108


title: Gill-22.4C-30min-recovery-Replicate4

source_name: Gill, 22.4C exposure, 30min recovery


title: Invasive urothelial carcinoma, biological rep 3

description:
Gene expression data from canine invasive bladder tumor
PU_5_050108


title: Invasive urothelial carcinoma, biological rep 2

description:
Gene expression data from canine invasive bladder tumor
PU_4_050108


title: PC3M treated with 30 nM NK2 for 16 hr, biological replicate 3

description:
PC3M treated with 30 nM NK2 for 16 hr
30 nM NK2 16 hr_3


title: PC3M treated with 30 nM NK2 for 16 hr, biological replicate 2

description:
PC3M treated with 30 nM NK2 for 16 hr
30 nM NK2 16 hr_2


title: Gill-22.4C-30min-recovery-Replicate2


title: Invasive urothelial carcinoma, biological rep 1

description:
Gene expression data from canine invasive bladder tumor
PU_2_050108


title: PC3M treated with 30 nM NK2 for 16 hr, biological replicate 1

description:
PC3M treated with 30 nM NK2 for 16 hr
30 nM NK2 16 hr_1


title: Gill-22.4C-30min-recovery-Replicate3


title: Normal bladder, biological rep 4

description:
Gene expression data from canine normal bladder
PU_FT #7_(Canine_2)

source_name: Normal bladder

value: Normal bladder


title: PC3M treated with 1nM Mouse HGF for 8 hr, biological replicate 1

description:
PC3M treated with 1nM Mouse HGF for 8 hr
1nM Mouse HGF 8 hr_1

value: mHGF


title: PC3M treated with 1nM Mouse HGF for 8 hr, biological replicate 3

description:
PC3M treated with 1nM Mouse HGF for 8 hr
1nM Mouse HGF 8 hr_3


title: Gill-22.4C-30min-recovery-Replicate1


title: Gill-22.4C-0min-recovery-Replicate4

source_name: Gill, 22.4C exposure, 0min recovery


title: PC3M treated with 1nM Mouse HGF for 8 hr, biological replicate 2

description:
PC3M treated with 1nM Mouse HGF for 8 hr
1nM Mouse HGF 8 hr_2


title: PC3M treated with 1nM Mouse HGF for 32 hr, biological replicate 1

description:
PC3M treated with 1nM Mouse HGF for 32 hr
1nM Mouse HGF 32 hr_1


title: Gill-22.4C-0min-recovery-Replicate2


title: Gill-22.4C-0min-recovery-Replicate1


title: Normal bladder, biological rep 3

description:
Gene expression data from canine normal bladder
PU_FT #6_(Canine_2)


title: Normal bladder, biological rep 1

description:
Gene expression data from canine normal bladder
PU_Maggie_050108


title: PEG treated, biological rep3

city: Wageningen

first: Maria

middle: Cecilia

last: Costa

state: The Netherlands

address: Droevendaalsesteeg, 1

department: Plant Physiology

country: Netherlands

institute: Wageningen University

description: Gene expression data from germinated Arabidopsis seeds at the stage of radicle protrusion incubated in PEG for 72h

hyb_protocol: Following fragmentation, 2.5 ug of ss-cDNA were hybridized on the Affymetrix ARAGene 1.1ST Array plates. Plates were washed and stained by the GeneTitan machine using the Affymetrix HWS Kit for the GeneTitan.

scan_protocol: Plates were scanned using the Affymetrix GeneTitan scanner operated by the software program Affymetrix GeneChip Command Console.

data_processing: The Robust Multichip Analysis (RMA-Sketch for gene level analysis) algorithm was used for the summarization. Signal intensities were extracted and analysed using the Bioconductor packages of R. The data was normalized using the RMA algorithm with the TAIRG v17 cdf file.

organism: Arabidopsis thaliana

source_name: Germinated seeds at the stage of radicle protrusion incubated in PEG for 72h

label_protocol: Biotin-labeled cDNA was prepared using the Affymetrix NuGEN Ovation PicoSL WTA and Biotin Module from 50ng total RNA according to the manufacturer's specifications.

growth_protocol: Seeds were cold stratified for 72 h at 4˚C in 9 cm Petri dishes on two layers of blue filter paper and 10 ml of distilled water. After stratification, seeds were transferred to germination cabinets with constant white light at 22 ˚C.

extract_protocol: Total RNA was extracted following the hot borate protocol modified from Wan and Wilkins (1994) (Maia et al, Plos ONE 2011)

treatment_protocol: Germinated seeds at the stage of radicle protrusion were either imediately frozen to be used for RNA isolation or incubated in 6-cm Petri dishes containing 1.3 ml of an PEG solution (-2.5MPa) on two sheets of white filter paper, in the dark, at 20˚C, and then frozen to be used for RNA isolation.

value: PEG

tag: ecotype

value: seeds


title: Gill-HandlingControl-60min-recovery-Replicate7

source_name: Gill, HandlingControl, 60min recovery

value: HandlingControl


title: PC3M treated with 1nM Mouse HGF for 32 hr, biological replicate 3

description:
PC3M treated with 1nM Mouse HGF for 32 hr
1nM Mouse HGF 32 hr_3


title: Normal bladder, biological rep 2

description:
Gene expression data from canine normal bladder
PU_FT #14_(Canine_2)


title: Gill-22.4C-0min-recovery-Replicate3


title: PEG treated, biological rep1


title: Gill-HandlingControl-60min-recovery-Replicate6


title: PC3M treated with 1nM Mouse HGF for 16 hr, biological replicate 2

description:
PC3M treated with 1nM Mouse HGF for 16 hr
1nM Mouse HGF 16 hr_2


title: PC3M treated with 1nM Mouse HGF for 16 hr, biological replicate 1

description:
PC3M treated with 1nM Mouse HGF for 16 hr
1nM Mouse HGF 16 hr_1


title: PEG treated, biological rep2


title: PC3M treated with 1nM Mouse HGF for 16 hr, biological replicate 3

description:
PC3M treated with 1nM Mouse HGF for 16 hr
1nM Mouse HGF 16 hr_3


title: non-treated, biological rep3

description: Gene expression data from fresh germinated Arabidopsis seeds at the stage of radicle protrusion

source_name: Fresh germinated seeds at the stage of radicle protrusion


title: Gill-HandlingControl-60min-recovery-Replicate5


title: Gill-HandlingControl-60min-recovery-Replicate1


title: non-treated, biological rep1


title: Gill-HandlingControl-60min-recovery-Replicate4


title: non-treated, biological rep2


title: PC3M treated with 1 nM Human HGF for 8 hr, biological replicate 3

description:
PC3M treated with 1 nM Human HGF for 8 hr
1 nM Human HGF 8 hr_3

value: hHGF


title: PC3M treated with 1 nM Human HGF for 8 hr, biological replicate 1

description:
PC3M treated with 1 nM Human HGF for 8 hr
1 nM Human HGF 8 hr_1

value: prostate adenocarcinoma cell line PC3M


title: PC3M treated with 1 nM Human HGF for 8 hr, biological replicate 2

description:
PC3M treated with 1 nM Human HGF for 8 hr
1 nM Human HGF 8 hr_2


title: PC3M treated with 1 nM Human HGF for 32 hr, biological replicate 1

description:
PC3M treated with 1 nM Human HGF for 32 hr
1 nM Human HGF 32 hr_1


title: Gill-HandlingControl-60min-recovery-Replicate3


title: Gill-HandlingControl-30min-recovery-Replicate5

source_name: Gill, HandlingControl, 30min recovery


title: Gill-HandlingControl-30min-recovery-Replicate3


title: PC3M treated with 1 nM Human HGF for 32 hr, biological replicate 3

description:
PC3M treated with 1 nM Human HGF for 32 hr
1 nM Human HGF 32 hr_3


title: PC3M treated with 1 nM Human HGF for 32 hr, biological replicate 2

description:
PC3M treated with 1 nM Human HGF for 32 hr
1 nM Human HGF 32 hr_2


title: Gill-HandlingControl-30min-recovery-Replicate4


title: Gill-HandlingControl-30min-recovery-Replicate6


title: PC3M treated with 1 nM Human HGF for 16 hr, biological replicate 3

description:
PC3M treated with 1 nM Human HGF for 16 hr
1 nM Human HGF 16 hr_3


title: Gill-HandlingControl-30min-recovery-Replicate2


title: ZOSM_IP vs Input

type: genomic

city: Toronto

first: Jinchang

last: Lu

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre, University of Toronto

description: MeDIP chip on ZOSM

hyb_protocol: Hybridization was processing overnight at 42°C in Roche-NimbleGen hybridization system12.

scan_protocol: Array scanning were done using MS200 scanner (NimbleGen)

data_processing: Arrays were processed using NimbleScan 2.6,which transformed image signal to digital signal, following using Nimblegen's standard protocol.

molecule: genomic DNA

source_name: MeDIP DNA from ZOSM

label_protocol: 1 µg amplified IP &Input DNA was directly labeled using NimbleGen Dual-Color DNA Labeling Kit (05223547001).

growth_protocol: ZOSM cells are cultured in Dulbecco's modified Eagle's medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) at 37°C and 5% CO2.

extract_protocol: The genomic DNA was extracted and purified using Genomic DNA Purification Kit (Promega), and fragmented using MseI restriction enzyme digestion to yield DNA fragments between 200 to 1,000 bp. Methylated DNA was enriched using methyl-DNA immunoprecipitation (MeDIP) according to manufacturer’s protocol. MeDIP-enriched DNA as well as input DNA was amplified with GenomePlex Complete Whole Genome Amplification kit (Sigma-Aldrich).

treatment_protocol: Cells are harvested at 80-90% confluency for RNA extraction.

tag: origin

value: skip metastasis

tag: malignancy

value: high metastatic

tag: chip antibody

source_name: Input DNA from ZOSM

value: none,Input DNA


title: PC3M treated with 1 nM Human HGF for 16 hr, biological replicate 2

description:
PC3M treated with 1 nM Human HGF for 16 hr
1 nM Human HGF 16 hr_2


title: Gill-HandlingControl-0min-recovery-Replicate6

source_name: Gill, HandlingControl, 0min recovery


title: Gill-HandlingControl-0min-recovery-Replicate2


title: PC3M treated with 1 nM Human HGF for 16 hr, biological replicate 1

description:
PC3M treated with 1 nM Human HGF for 16 hr
1 nM Human HGF 16 hr_1


title: Gill-HandlingControl-0min-recovery-Replicate1


title: ZOS_IP vs Input

description: MeDIP chip on ZOS

source_name: MeDIP DNA from ZOS

growth_protocol: ZOS cells are cultured in Dulbecco's modified Eagle's medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) at 37°C and 5% CO2.

value: primary tumor

value: low metastatic

source_name: Input DNA from ZOS


title: ExVivoBlood_sRANKL_repl6

status: Public on Aug 24 2015

city: Sendai

first: Masayuki

last: Asano

state: Miyagi

address: Seiryo-machi 1-1, Aoba-ku

department: Department of Dermatology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression with sRANKL treatment

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20100115) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peripheral Blood, sRANKL, replicate 6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: CD14+ cells were isolated from the peripheral blood mononuclear cells of healthy donors using magnetic-activated cell sorting beads (CD14 microbeads, Miltenyi Biotec, CA) according to the manufacturer’s protocol. CD14+ monocytes (2 x 105 /ml) were cultured in complete medium containing 100 ng/ml of recombinant human M-CSF for 5 days. On the fifth day, the monocyte-derived M2 macrophages (M2MF) were treated  with IL-4 (20 ng/ml, Peprotech London, UK) together with or without sRANKL (100 ng/ml, Peprotech London) for 6 hours.

value: whole blood

tag: cell type

value: monocyte-derived macrophages

value: sRANKL and IL-4

tag: gender

value: male

tag: age


title: ExVivoBlood_sRANKL_repl5

description: Gene expression with sRANKL treatment

source_name: Peripheral Blood, sRANKL, replicate 5


title: ExVivoBlood_sRANKL_repl4

description: Gene expression with sRANKL treatment

source_name: Peripheral Blood, sRANKL, replicate 4


title: ZOSM osteosaracoma cell line

description: Gene expression data from primary osteosarcoma cell line ZOSM which isolated from primary tumor of a 18-year-old boy

hyb_protocol: The bio-tagged cRNA were fragmented and then hybridized to Affymetrix Human Genome U133 Plus 2.0 Array. The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip arrays were scanned by a GeneChip Scanner 3000.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4.

data_processing: The data were normalized using Robust Multi-array Average(RMA) .

source_name: primary human osteosarcoma cell lines

label_protocol: An aliquot of 2 µg of total RNA was used to synthesize double-stranded cDNA, then produce biotin-tagged cRNA using the MessageAmpTM Premier RNA Amplification Kit (Ambion)

growth_protocol: ZOS and ZOSM are cultured in Dulbecco's modified Eagle's medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufactures’ instructions.

tag: location

value: right femoral head


title: ExVivoBlood_control_repl5

description: Gene expression without sRANKL treatment

source_name: Peripheral Blood, control, replicate 5

value: IL-4 (control)


title: ExVivoBlood_control_repl4

source_name: Peripheral Blood, control, replicate 4


title: ExVivoBlood_sRANKL_repl2

description: Gene expression with sRANKL treatment

source_name: Peripheral Blood, sRANKL, replicate 2

value: female


title: ExVivoBlood_control_repl6

source_name: Peripheral Blood, control, replicate 6


title: PC3M treated with 1nM Mouse HGF for 32 hr, biological replicate 2

description:
PC3M treated with 1nM Mouse HGF for 32 hr
1nM Mouse HGF 32 hr_2

value: mHGF

value: 32 hr


title: ExVivoBlood_control_repl3

source_name: Peripheral Blood, control, replicate 3


title: ExVivoBlood_sRANKL_repl3

description: Gene expression with sRANKL treatment

source_name: Peripheral Blood, sRANKL, replicate 3


title: ExVivoBlood_control_repl2

source_name: Peripheral Blood, control, replicate 2


title: EXP6 DSS CD103+CD11b+ [L6P6]

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description: EXP6 DSS CD103+CD11b+

hyb_protocol: Fragmented samples were hybridized according to Affymetrix guidelines for 18hr in 45°C on GeneChip Mouse Gene 1.0 ST Array; The arrays were then washed and stained using the standard fluidics protocol (FS450_0007) for gene arrays on the GeneChip Fluidics Station 450.

scan_protocol: The mouse gene chips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.

data_processing: CEL files were processed in Bioconductor using the xps package. Expression data was summarized at the transcript level and normalized using RMA. Log2 transformation was applied to the expression data.

organism: Mus musculus

source_name: colon lamina propria

label_protocol: Single-stranded DNA were prepared according to the Ovation Pico RNA Amplification Kit (NuGEN) from 5ng of total RNA. 5.5ug of ssDNA were fragmented and labeled using the NuGEN Encore Biotin Module.

growth_protocol: 8 weeks old BALB/c mice

extract_protocol: isolation from colon via collagenase disgestion

treatment_protocol: with or with 2% DSS treatment

tag: strain

value: BALB/c


title: EXP6 DSS CD103+CD11b- [L6P5]

description: EXP6 DSS CD103+CD11b-


title: EXP4 DSS CD103+CD11b+ [L4P6]

description: EXP4 DSS CD103+CD11b+


title: ExVivoBlood_control_repl1

source_name: Peripheral Blood, control, replicate 1


title: EXP5 DSS CD103+CD11b- [L5P5]

description: EXP5 DSS CD103+CD11b-


title: EXP5 DSS CD103+CD11b+ [L5P6]

description: EXP5 DSS CD103+CD11b+


title: EXP4 DSS CD103-CD11b+ [L4P7]

description: EXP4 DSS CD103-CD11b+


title: EXP6 DSS CD103-CD11b+ [L6P7]

description: EXP6 DSS CD103-CD11b+


title: EXP5 DSS CD103-CD11b+ [L5P7]

description: EXP5 DSS CD103-CD11b+


title: EXP3 CD103+CD11b+ [L3P6]

description: EXP3 CD103+CD11b+


title: EXP3 CD103+CD11b- [L3P5]

description: EXP3 CD103+CD11b-


title: EXP3 CD103-CD11b+ [L3P7]

description: EXP3 CD103-CD11b+


title: ExVivoBlood_sRANKL_repl1

description: Gene expression with sRANKL treatment

source_name: Peripheral Blood, sRANKL, replicate 1


title: EXP2 CD103-CD11b+ [L2P7]

description: EXP2 CD103-CD11b+


title: ZOS osteosaracoma cell line

description: Gene expression data from primary osteosarcoma cell line ZOS which isolated from primary tumor of a 18-year-old boy

value: right distal femur


title: EXP4 DSS CD103+CD11b- [L4P5]

description: EXP4 DSS CD103+CD11b-


title: EXP2 CD103+CD11b+ [L2P6]

description: EXP2 CD103+CD11b+


title: EXP2 CD103+CD11b- [L2P5]

description: EXP2 CD103+CD11b-


title: EXP1 CD103-CD11b+ [L1P7]

description: EXP1 CD103-CD11b+


title: EXP1 CD103+CD11b+ [L1P6]

description: EXP1 CD103+CD11b+


title: wt control embryo, biological rep2

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Raw data was normalized using RMA (R/Bioconductor v.2.10.0).

organism: Drosophila melanogaster

source_name: embryos derived from wild-type control germline clones

label_protocol: Standard Affymetrix

growth_protocol: Embryos from flies with brakeless or wt control germline clones were collected for 2 hours on apple-agarose plates with partial addition of yeast at 25C, and aged for an additional 2 hours.

extract_protocol: Trizol (Invitrogen) extraction of total RNA followed by purification using Rneasy kit (Qiagen) was performed according to the manufacturer's instructions.

treatment_protocol: Embryos were dechorionated in bleach and frozen at -80 degrees C.

tag: genotype/variation

value: FRT2R G13/FRT2R G13 ovoD1 females crossed to FRT2R G13 males

value: dechorionated embryo

value: 2-4 hour embryos


title: EXP1 CD103+CD11b- [L1P5]

description: EXP 1 CD103+CD11b-


title: wt control embryo, biological rep3


title: wt control embryo, biological rep1


title: brakeless mutant embryo, biological rep2

source_name: embryos derived from brakeless germline clones

value: FRT2R G13 bks278/FRT2R G13 ovoD1 females crossed to FRT2R G13 bks278/CyO males


title: brakeless mutant embryo, biological rep3


title: NEC2, BIOLOGICAL REPLICATE 2

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
NEC2
Enriched miRNA
miRNA expression data from neonatal bowel tissue

hyb_protocol: Labeled RNA were hybridized at 48°C and 60 rpm for 16 hr on Affymetrix GeneChip® miRNA 3.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station (FS450_0002).

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

data_processing: The digital data retrieved from the CEL files were processed by Partek Genomic Suite version 6.5 using modified RMA-algorithm.

label: BIOTIN

source_name: NEC

label_protocol: Biotin labeled RNA were prepared according to the standard Affymetrix protocol from 130ng enriched LMW RNA (FlashTag Biotin HSR RNA Labeling Kit).

extract_protocol: RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA) and miRNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The RNA quality and integrity were analyzed with Nanodrop ND 1000 spectrophotometer (Rockland, DE) and Bioanalyzer (Agilent, Cheshire, UK).

tag: developmental stage

value: neonate

tag: condition

value: necrotizing enterocolitis (NEC)

value: Bowel


title: SIP3, BIOLOGICAL REPLICATE 3

description:
SIP3
Enriched miRNA
miRNA expression data from neonatal bowel tissue

source_name: SIP

value: spontaneous intestinal perforation (SIP)

tag: tissue


title: NEC4, BIOLOGICAL REPLICATE 4

description:
NEC4
Enriched miRNA
miRNA expression data from neonatal bowel tissue


title: brakeless mutant embryo, biological rep1


title: NEC3, BIOLOGICAL REPLICATE 3

description:
NEC3
Enriched miRNA
miRNA expression data from neonatal bowel tissue


title: SIP2, BIOLOGICAL REPLICATE 2

description:
SIP2
Enriched miRNA
miRNA expression data from neonatal bowel tissue


title: Surg-CTL4, BIOLOGICAL REPLICATE 4

description:
CTL4
Enriched miRNA
miRNA expression data from neonatal bowel tissue

source_name: Surg-CTL

value: control


title: SIP4, BIOLOGICAL REPLICATE 4

description:
SIP4
Enriched miRNA
miRNA expression data from neonatal bowel tissue


title: NEC1, BIOLOGICAL REPLICATE 1

description:
NEC1
Enriched miRNA
miRNA expression data from neonatal bowel tissue


title: Surg-CTL2, BIOLOGICAL REPLICATE 2

description:
CTL2
Enriched miRNA
miRNA expression data from neonatal bowel tissue


title: Surg-CTL1, BIOLOGICAL REPLICATE 1

description:
CTL1
Enriched miRNA
miRNA expression data from neonatal bowel tissue


title: MET4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
MET34-US83300186_252665223520_S01_GE2_1105_Oct12_1_2.txt
Gene expression in the chest wall of 74y old male with metastatic renal cell carcinoma, clear cell type, Fuhrman grade 3

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Regardless the platform, in all our microarray experiments we have used the multiple yellow strategy in which differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. For instance: (CTR1+CTR3) was compared with (PTA1+PTA3), (CTR2+CTR4) was compared  with (PTA2+PTA4) and the results of the two comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions. Therefore, we deposit the data as for one-color experiment

source_name: chest wall metastasis_Replicate 4

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: 74 years old male with metastatic renal cell carcinoma, clear cell type, Fuhrman grade 3

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Total right kidney nephrectomy and resection of a chest wall mass

tag: Sex

value: male

value: 74 years old

tag: disease state

value: metastatic carcinoma, consistent with renal cell carcinoma, clear cell type, Fuhrman grade 3

value: chest wall

value: chest wall metastasis


title: MET3

source_name: chest wall metastasis_Replicate 3


title: ΔcspC x WT_log phase_rep1

city: São Paulo

first: Juliana

middle: da Silva

last: Santos

state: SP

address: Avenida Professor Lineu Prestes, 1374

department: Microbiology

country: Brazil

institute: Institute of Biomedical Sciences from University of São Paulo

hyb_protocol: Agilent protocol

scan_protocol: Agilent protocol

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 9.0. Agilent output files were then opened using Excel and the log10 values extracted with no additional processing or filtering

organism: Caulobacter vibrioides NA1000

source_name: WT_log phase

label_protocol: standard Cy3-dCTP incorporation

growth_protocol: Overnight cultures were diluted in fresh complex medium and grown to log or stationary phase

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

treatment_protocol: Cells were harvested from cultures at log or stationary phase with no additional treatment

value: WT

tag: growth phase

value: log phase

source_name: ΔcspC_log phase

label_protocol: standard Cy5-dCTP incorporation

value: cspC mutant


title: MET2

description:
MET12-US83300186_252665223520_S01_GE2_1105_Oct12_1_1.txt
Gene expression in the chest wall of 74y old male with metastatic renal cell carcinoma, clear cell type, Fuhrman grade 3

source_name: chest wall metastasis_Replicate 2


title: SIP1, BIOLOGICAL REPLICATE 1

description:
SIP1
Enriched miRNA
miRNA expression data from neonatal bowel tissue


title: WT_stationary x log_rep1

source_name: WT_stationary phase

value: stationary phase


title: PTA3

description:
PTA34-US83300186_252665223520_S01_GE2_1105_Oct12_1_4.txt
Gene expression in the right kidney of 74y old male with metastatic renal cell carcinoma, clear cell type, Fuhrman grade 3

source_name: primary tumor side  A_ Replicate 3

value: right kidney

value: primary tumor side  A


title: Low grade tumor sample [Ast_15Agosto2014_5_(HTA-2_0)] exon-level

city: México.

first: Ruth

last: Ruiz-Esparza

address: Centro Médico Nacional Siglo XXI, IMSS, México,

department: Pediatría

country: Mexico

institute: Instituto Mexicano del Seguro Social

description: Gene expression data from pediatric brain tumor grade I

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HTA 2.0 Array. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneArray Scanner G2500A.

data_processing:
For data analysis two softwares were used: Expression Console and Transcript Analysis Console. The first software allows us to perform a gene and exon-level normalization, and signaling summarization by evaluating QC values for the array. The second software allows evaluating gene and exon expiration between samples. Parameters used for the analysis were: One-Way Between-Subject ANOVA (Unpaired); Fold Change (linear) < -2 or Fold Change (linear) > 2; and ANOVA p-value (Condition pair) < 0.05.
Fold Change (linear) < -2 or Fold Change (linear) > 2; and ANOVA p-value (Condition pair) < 0.05.

source_name: Tumor sample

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

extract_protocol: RNA was extracted from tissue samples using TRIzol (Ambion life technologies, Thermo Scientific Inc.) following the methodology described by Hongbao et al. 2008 and with certain modifications described by Vujovic et al. 2013. Briefly, tumor samples were homogenized in 1 ml of TRIZOL® Reagent (1ml per 50 mg of tissue), and incubated at room temperature (25°C) for 5 min. After that, we added 200 µl of chloroform (per ml TRIzol) and shake vigorously the samples for 15 sec. Then, samples were incubating at 4°C for 15 min and they were centrifuged at 12,000xg for 15 min (4°C). The aqueous phase, which corresponds to RNA was transferred to a new 1.5 ml tube and RNA was precipitated adding 500 µl isopropanol (per ml TRIzol) and incubating for 30 min at room temperature. After that, samples were centrifuged at 12,000xg (10 min) at 4°C, the supernatant was removed and pellet was washed once with 75% ethanol (1 ml/ml TRIzol), vortexed and centrifuged at 7,500xg for 5 min at 4°C. The final pellet was dissolved in 300-600 µl of RNase-free water and it was stored at -80 °C until use.

treatment_protocol: A total of eight astrocytic tumors and two control tissues were collected during the period of 2012–2014: four low-grade Ast (three pilocytic Ast (PAst) and one diffuse Ast (DAst)) and four high-grade Ast (four glioblastoma multiforme (GBM)). Brain tumor samples were collected at surgery, snap frozen in liquid nitrogen and stored at −80 °C until use.  All tumors were collected from children – one through 15 years of age – refer from the Children´s hospital, National Medical Center Century XXI, Mexican Institute of Social Security. All patients were from families with no history of cancer (de novo tumors)Control samples were obtained from pediatric patients (one boy and one girl) who had submitted to temporal lobe resection for epilepsy. Tumors were histopathologically classified by two pathologists according to a criteria established by the WHO.

value: glia tissue

tag: tumor grade

value: Pilocitic astrocitoma


title: WT_stationary x log_rep2


title: MET1

source_name: chest wall metastasis_Replicate 1


title: ΔcspC x WT_stationary phase_rep1

source_name: ΔcspC_stationary phase


title: ΔcspC x WT_stationary phase_rep3


title: PTB1

description:
PTB12-US83300186_252665224026_S01_GE2_1105_Oct12_1_1.txt
Gene expression in the right kidney of 74y old male with metastatic renal cell carcinoma, clear cell type, Fuhrman grade 3

source_name: primary tumor side  B_ Replicate 1

value: primary tumor side B


title: ΔcspC x WT_log phase_rep3


title: PTB4

description:
PTB34-US83300186_252665224026_S01_GE2_1105_Oct12_1_2.txt
Gene expression in the right kidney of 74y old male with metastatic renal cell carcinoma, clear cell type, Fuhrman grade 3

source_name: primary tumor side  B_ Replicate 4


title: ΔcspC x WT_stationary phase_rep2


title: PTB2

source_name: primary tumor side  B_ Replicate 2


title: PTB3

source_name: primary tumor side  B_ Replicate 3


title: PTA2

description:
PTA12-US83300186_252665223520_S01_GE2_1105_Oct12_1_3.txt
Gene expression in the right kidney of 74y old male with metastatic renal cell carcinoma, clear cell type, Fuhrman grade 3

source_name: primary tumor side  A_ Replicate 2


title: PTA4

source_name: primary tumor side  A_ Replicate 4


title: High grade tumor sample [CVA_Ast_23072014_(HTA-2_0)] exon-level

description: Gene expression data from pediatric brain tumor grade V

value: GBM


title: CTR4

description:
CTR34-US83300186_252665224026_S01_GE2_1105_Oct12_1_4.txt
Gene expression in the right kidney of 74y old male with metastatic renal cell carcinoma, clear cell type, Fuhrman grade 3

source_name: non-cancerous kidney resection margins_Replicate 4

value: control - non-cancerous kidney resection margins


title: ΔcspC x WT_log phase_rep2


title: Control sample from pediatric patient with epilepsy [Ast_15Agosto2014_2_(HTA-2_0)] exon-level

description: Gene expression data frompediatric control tissue (epilepsy sample)

source_name: Control sample

value: Control Tissue


title: Low grade tumor sample [CAR_Ast_23072014_(HTA-2_0)] exon-level


title: High grade tumor sample [Ast_15Agosto2014_3_(HTA-2_0)] exon-level


title: High grade tumor sample [Ast_15agosto2014_6_(HTA-2_0)] exon-level


title: CTR3

source_name: non-cancerous kidney resection margins_Replicate 3

value: male


title: High grade tumor sample [ARI_Ast_23072014_(HTA-2_0)] exon-level


title: CTR2

description:
CTR12-US83300186_252665224026_S01_GE2_1105_Oct12_1_3.txt
Gene expression in the right kidney of 74y old male with metastatic renal cell carcinoma, clear cell type, Fuhrman grade 3

source_name: non-cancerous kidney resection margins_Replicate 2

value: 74 years old


title: mdDA neurons isolated from the ventral midbrain at E14.5, technical replicate 3

status: Public on Aug 22 2015

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation

source_name: Primary embryonic mdDA neurons isolated from the ventral midbrain at E14.5 by FACS-sorting for GFP

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy Mini or Micro Kit (Qiagen) including DNase treatment

value: C57BL/6 x 129/Ola (mixed)

value: primary mdDA neurons

tag: genotype


title: PTA1

source_name: primary tumor side  A_ Replicate 1

value: metastatic carcinoma, consistent with renal cell carcinoma, clear cell type, Fuhrman grade 3


title: CTR1

source_name: non-cancerous kidney resection margins_Replicate 1


title: Surg-CTL3, BIOLOGICAL REPLICATE 3

description:
CTL3
Enriched miRNA
miRNA expression data from neonatal bowel tissue

source_name: Surg-CTL

value: neonate

value: control

value: Bowel


title: MEFs, biological rep1

status: Public on Aug 23 2015

city: Shanghai

first: Yanbin

last: Fu

address: No.1239, SiPing Road

country: China

institute: Tongji University

description: mouse embryonic fibroblasts were isolated from embryonic day 13.5 (E13.5) C57BL/6 mouse embryos

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: mouse embryonic fibroblasts

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: mouse embryonic fibroblasts are directly isolated from mouse embryos; cardiomyocytes are directly isolated from mouse heart; CiCMs are induced from MEFs with chemical cocktails

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: chemical cocktails

value: mouse embryos


title: CiCMs, biological rep1

description: chemical-induced cardiomyocyte-like cells from MEFs

value: in vitro


title: iPSC-derived mdDA neurons, control, biological replicate 5

description: iPSC-derived mdDA neurons, controls

scan_protocol: According to the Affymetrix expression protocol

source_name: iPSC-derived mdDA neurons, controls

value: not applicable

value: iPSC-derived mdDA neurons


title: mdDA neurons isolated from the ventral midbrain at E13.5, technical replicate 2

source_name: Primary embryonic mdDA neurons isolated from the ventral midbrain at E13.5 by FACS-sorting for GFP


title: CiCMs, biological rep2

source_name: chemical-induced cardiomyocyte-like cells from MEFs


title: cardiomyocytes (CMs), biological rep1

description: cardiomyocytes from mouse heart

source_name: cardiomyocytes

value: mouse heart

value: cardiomyocytes from mouse heart


title: mdDA neurons isolated from the ventral midbrain at E13.5, technical replicate 3


title: mdDA neurons isolated from the ventral midbrain at E14.5, technical replicate 2


title: MEFs, biological rep3

value: mouse embryonic fibroblasts were isolated from embryonic day 13.5 (E13.5) C57BL/6 mouse embryos


title: cardiomyocytes (CMs), biological rep3

description: cardiomyocytes from mouse heart


title: MEFs, biological rep2


title: mdDA neurons isolated from the ventral midbrain at E13.5, technical replicate 1


title: Control sample from pediatric patient with epilepsy [Ast_15Agosto2014_1_(HTA-2_0)] exon-level

description: Gene expression data from pediatric control tissue (epilepsy sample)

value: glia tissue


title: cardiomyocytes (CMs), biological rep2

description: cardiomyocytes from mouse heart


title: CiCMs, biological rep3

value: chemical-induced cardiomyocyte-like cells from MEFs


title: Low grade tumor sample [Ast_15Agosto2014_4_(HTA-2_0)] exon-level

source_name: Tumor sample

value: Pilocitic astrocitoma


title: mdDA neurons isolated from the ventral midbrain at E14.5, technical replicate 1


title: iPSC-derived mdDA neurons, control, biological replicate 4

description: iPSC-derived mdDA neurons, controls


title: iPSC-derived mdDA neurons, control, biological replicate 1

description: iPSC-derived mdDA neurons, controls


title: iPSC-derived mdDA neurons, control, biological replicate 3

description: iPSC-derived mdDA neurons, controls


title: iPSC-derived mdDA neurons, control, biological replicate 2

description: iPSC-derived mdDA neurons, controls


title: iPSC-derived mdDA neurons, WNT1- and DKK3-treatment, biological replicate 1

description: iPSC-derived mdDA neurons differentiated in the presence of human recombinant WNT1 and DKK3


title: iPSC-derived mdDA neurons, WNT1- and DKK3-treatment, biological replicate 2

source_name: iPSC-derived mdDA neurons differentiated in the presence of human recombinant WNT1 and DKK3


title: iPSC-derived mdDA neurons, WNT1- and DKK3-treatment, biological replicate 3


title: iPSC-derived mdDA neurons, WNT1- and DKK3-treatment, biological replicate 5


title: iPSC-derived mdDA neurons, WNT1- and DKK3-treatment, biological replicate 4


title: Colon_Rint_rep5

city: Jouy en Josas

first: Thomas

middle: Walter

last: Hoffmann

address: Domaine de Vilvert

department: UMR 1319 MICALIS

country: France

institute: INRA Jouy en Josas

description:
Sample name: Ri5
Gene expression in colon from a R. intestinalis mono-associated mouse

hyb_protocol: For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 11.0 pmol Cy3/µg of cRNA) were fragmented at 60°C for 30 minutes and hybridized to the microarrays for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies). After hybridization, microarrays were washed and then dried immediately.

scan_protocol: After washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies), with a resolution of 3 µm and a dynamic range of 20 bit.

data_processing: The resulting .tiff images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using the GE1_107_Sep09 protocol.

source_name: Colon, R. intestinalis, replicate 5

label_protocol: Transcriptional profiling was performed on colon samples using the SurePrint G3 Mouse GE 8x60K Microarray (Design ID: 028005, Agilent Technologies). A total number of 40 samples (5 per group) were processed. Cyanine-3 (Cy3) labeled cRNAs were prepared with 100 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies) and following the recommended protocol. Specific activities and cRNA yields were determined using a NanoDrop ND-1000 (Thermo Fisher Scientific).

growth_protocol: Germ-free female C3H/HeN mice were bred in germ-free isolators.

extract_protocol: Total RNA was isolated from colon samples and cell lines using RNeasy® Mini Kit (Qiagen), according to the manufacturer's instructions. RNA integrity was checked onto a Bioanalyzer 2100 using RNA 6000 Nano chips (Agilent Technologies) and all of the samples showed a RIN score higher than 8.

treatment_protocol: Bacterial suspensions, yeast suspensions, feces from conventional mice, or control medium was administered to 6-week-old mice by intragastric gavage (8 mice per group). After 6 weeks of implantation, mice were euthanized and several samples were taken: pieces and content from jejunum, ileum, cecum and colon; and mesenteric lymph nodes (MLNs).

tag: association

value: Rint

value: colon

value: female

value: 12 weeks


title: Patient100_HNTC

city: Sheffield

first: Munitta

last: Muthana

address: Beech Hill Rd

country: United Kingdom

institute: University of Sheffield

description: Non targeting control

hyb_protocol: Standard as recommended by illumina

scan_protocol: Standard as recommended by illumina

data_processing: The data were normalised using quantile normalisation with lumiN from the lumi package in R

source_name: Rheumatoid arthritis synovial fibroblast: NTC, 25 nm siRNA knockdown, 48 h

label_protocol: Standard as recommended by illumina

growth_protocol: All RASF cells were cultured in DMEM, 10% FCS and only passages 3-8 were used in experiments all cells were cultured in tissue culture treated flasks and incubated at 37°C, 5% CO2 and 20% O2

extract_protocol: Cells were harvested and pelleted by centrifugation for 7 minutes at 12,000 rpm. mRNA was extracted from the cells using an RNeasy mini kit, following manufacturer’s instructions. The concentration of mRNA was determined using the NanoDrop Spectrophotometer ND 1000. The concentration of the mRNAs were standardised by dilution in RNase/DNase-free water and stored at -80°C.  Frozen concentrated mRNA was shipped on dry ice to Cambridge Genomic Services. Samples were amplified using Nugen amplification technology due to low DNA concentrations. The samples were run on an Illumina HumanHT-12 v4 BeadChip which contain more than 47,000 probes. For each probe represented on the array, beads are assembled with an average 15-fold redundancy.

treatment_protocol: Transfections were carried out in 6-well plate. RASFs were plated at 1.2x105 cells per well and cultured in DMEM for 24 hours. Non targeting control (NTC), Histone deacetylase 1 (HDAC1), C5orf30,  ON TARGET plus SMART pool siRNAs both at 20μM, were diluted in serum-free medium and mixed 1:1 with Dharmafect transfection 4 reagent and incubated for 20 minutes. This was added to the RASFs in a final volume of 2ml per well with serum-containing medium. The plate was incubated at 37°C for 24-48 hours. Cells were harvested and resuspended in PBS ready for RNA extraction.

tag: sirna

value: NTCKD


title: Patient97_H

description: HDAC1 knockdown

source_name: Rheumatoid arthritis synovial fibroblast: HDAC1, 25 nm siRNA knockdown, 48 h


title: Patient97_C5NTC

description: Non targeting control

source_name: Rheumatoid arthritis synovial fibroblast: NTC, 50nm siRNA, knockdown 24h


title: Patient100_C5NTC

description: Non targeting control


title: Patient98_C5NTC

description: Non targeting control


title: Colon_Calb_rep6

description:
Sample name: Ca6
Gene expression in colon from a C. albicans mono-associated mouse

source_name: Colon, C. albicans, replicate 6

value: Calb


title: Patient100_C5

description: C5orf30 knockdown

source_name: Rheumatoid arthritis synovial fibroblast: C5orf30, 50nm siRNA, knockdown 24h


title: Patient97_C5

description: C5orf30 knockdown


title: Colon_Rint_rep4

description:
Sample name: Ri4
Gene expression in colon from a R. intestinalis mono-associated mouse

source_name: Colon, R. intestinalis, replicate 4


title: Patient100_H

description: HDAC1 knockdown


title: Colon_Rint_rep1

description:
Sample name: Ri1
Gene expression in colon from a R. intestinalis mono-associated mouse

source_name: Colon, R. intestinalis, replicate 1


title: Colon_Calb_rep7

description:
Sample name: Ca7
Gene expression in colon from a C. albicans mono-associated mouse

source_name: Colon, C. albicans, replicate 7


title: Colon_Rint_rep2

description:
Sample name: Ri2
Gene expression in colon from a R. intestinalis mono-associated mouse

source_name: Colon, R. intestinalis, replicate 2


title: Patient98_HNTC

description: Non targeting control


title: Patient97_HNTC

description: Non targeting control


title: Colon_Calb_rep5

description:
Sample name: Ca5
Gene expression in colon from a C. albicans mono-associated mouse

source_name: Colon, C. albicans, replicate 5


title: Patient98_H

description: HDAC1 knockdown


title: Colon_Calb_rep4

description:
Sample name: Ca4
Gene expression in colon from a C. albicans mono-associated mouse

source_name: Colon, C. albicans, replicate 4


title: Colon_Sbou_rep6

description:
Sample name: Sb6
Gene expression in colon from a S. boulardii mono-associated mouse

source_name: Colon, S. boulardii, replicate 6

value: Sbou


title: Colon_Sbou_rep5

description:
Sample name: Sb5
Gene expression in colon from a S. boulardii mono-associated mouse

source_name: Colon, S. boulardii, replicate 5


title: Colon_Calb_rep2

description:
Sample name: Ca2
Gene expression in colon from a C. albicans mono-associated mouse

source_name: Colon, C. albicans, replicate 2


title: Colon_Calb_rep1

description:
Sample name: Ca1
Gene expression in colon from a C. albicans mono-associated mouse

source_name: Colon, C. albicans, replicate 1


title: Colon_Sbou_rep4

description:
Sample name: Sb4
Gene expression in colon from a S. boulardii mono-associated mouse

source_name: Colon, S. boulardii, replicate 4


title: Colon_Rint_rep3

description:
Sample name: Ri3
Gene expression in colon from a R. intestinalis mono-associated mouse

source_name: Colon, R. intestinalis, replicate 3


title: Colon_Calb_rep3

description:
Sample name: Ca3
Gene expression in colon from a C. albicans mono-associated mouse

source_name: Colon, C. albicans, replicate 3


title: Colon_Sbou_rep3

description:
Sample name: Sb3
Gene expression in colon from a S. boulardii mono-associated mouse

source_name: Colon, S. boulardii, replicate 3


title: Colon_Sbou_rep2

description:
Sample name: Sb2
Gene expression in colon from a S. boulardii mono-associated mouse

source_name: Colon, S. boulardii, replicate 2


title: Patient98_C5

description: C5orf30 knockdown


title: Colon_Rgna_rep6

description:
Sample name: Rg6
Gene expression in colon from a R. gnavus mono-associated mouse

source_name: Colon, R. gnavus, replicate 6

value: Rgna


title: Colon_Sbou_rep1

description:
Sample name: Sb1
Gene expression in colon from a S. boulardii mono-associated mouse

source_name: Colon, S. boulardii, replicate 1


title: Colon_Rgna_rep3

description:
Sample name: Rg3
Gene expression in colon from a R. gnavus mono-associated mouse

source_name: Colon, R. gnavus, replicate 3


title: Colon_Rgna_rep5

description:
Sample name: Rg5
Gene expression in colon from a R. gnavus mono-associated mouse

source_name: Colon, R. gnavus, replicate 5


title: Colon_Ecoli_rep6

description:
Sample name: Ec6
Gene expression in colon from a E. coli LF82 mono-associated mouse

source_name: Colon, E. coli, replicate 6

value: Ecoli


title: Colon_Conv_rep5

description:
Sample name: C5
Gene expression in colon from a conventionalized mouse

source_name: Colon, Conventionalized, replicate 5

value: Conv


title: C. elegans exposed to silver nitrate replicate 3

city: Lexington

first: Daniel

middle: L

last: Starnes

state: KY

address: 1100 Nicholasville Road

department: Plant and Soil Science

institute: University of Kentucky

hyb_protocol: 5 ug of labeled cRNA was hybridized to the C. elegans array for 16 hours at 45 degrees C.  Arrays were washed and stained using the Affymetrix 450 Fluidics station

scan_protocol: Affymetrix 7G Scanner.

data_processing: Data was collected using Affymetrix Comand Console software. Algorithm: ExpressionStat 5.0

organism: Caenorhabditis elegans

source_name: Nematodes exposed to AgNO3 treatment for 48 hours

label_protocol: Affymetrix IVT Express kit was used to label 100ng of total RNA

growth_protocol: Age syncroized eggs were allowed to hatch for 12 hours post bleaching

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

treatment_protocol: 12 hour old L1 nematodes were transferred to expsoure solutions (EC30 for reporduction) for each of the three treatments + control

value: N2 (Bristol)

value: wildtype


title: Colon_Btheta_rep6

description:
Sample name: Bt6
Gene expression in colon from a B. thetaiotaomicron mono-associated mouse

source_name: Colon, B. thetaiotaomicron, replicate 6

value: Btheta


title: Colon_Conv_rep3

description:
Sample name: C3
Gene expression in colon from a conventionalized mouse

source_name: Colon, Conventionalized, replicate 3


title: C. elegans exposed to pristine particles replicate 1

source_name: Nematodes exposed to pristine silver nanomaterials for 48 hours


title: C. elegans exposed to pristine particles replicate 3


title: C. elegans exposed to silver nitrate replicate 2


title: Colon_Ecoli_rep4

description:
Sample name: Ec4
Gene expression in colon from a E. coli LF82 mono-associated mouse

source_name: Colon, E. coli, replicate 4


title: Colon_Conv_rep2

description:
Sample name: C2
Gene expression in colon from a conventionalized mouse

source_name: Colon, Conventionalized, replicate 2


title: Colon_Ecoli_rep3

description:
Sample name: Ec3
Gene expression in colon from a E. coli LF82 mono-associated mouse

source_name: Colon, E. coli, replicate 3


title: Colon_Ecoli_rep5

description:
Sample name: Ec5
Gene expression in colon from a E. coli LF82 mono-associated mouse

source_name: Colon, E. coli, replicate 5


title: Colon_Ecoli_rep2

description:
Sample name: Ec2
Gene expression in colon from a E. coli LF82 mono-associated mouse

source_name: Colon, E. coli, replicate 2


title: C. elegans exposed to pristine particles replicate 2


title: C. elegans exposed to silver nitrate replicate 1


title: Colon_Rgna_rep2

description:
Sample name: Rg2
Gene expression in colon from a R. gnavus mono-associated mouse

source_name: Colon, R. gnavus, replicate 2


title: Colon_Rgna_rep4

description:
Sample name: Rg4
Gene expression in colon from a R. gnavus mono-associated mouse

source_name: Colon, R. gnavus, replicate 4


title: Colon_Rgna_rep1

description:
Sample name: Rg1
Gene expression in colon from a R. gnavus mono-associated mouse

source_name: Colon, R. gnavus, replicate 1


title: Colon_Conv_rep1

description:
Sample name: C1
Gene expression in colon from a conventionalized mouse

source_name: Colon, Conventionalized, replicate 1


title: Colon_Conv_rep4

description:
Sample name: C4
Gene expression in colon from a conventionalized mouse

source_name: Colon, Conventionalized, replicate 4


title: Colon_Ecoli_rep1

description:
Sample name: Ec1
Gene expression in colon from a E. coli LF82 mono-associated mouse

source_name: Colon, E. coli, replicate 1


title: Colon_Btheta_rep4

description:
Sample name: Bt4
Gene expression in colon from a B. thetaiotaomicron mono-associated mouse

source_name: Colon, B. thetaiotaomicron, replicate 4


title: C. elegans exposed to aged particles replicate 3

source_name: Nematodes exposed to artifically aged silver nanomaterials for 48 hours


title: C. elegans exposed to aged particles replicate 2


title: Colon_Btheta_rep3

description:
Sample name: Bt3
Gene expression in colon from a B. thetaiotaomicron mono-associated mouse

source_name: Colon, B. thetaiotaomicron, replicate 3


title: Colon_Germfree_rep5

description:
Sample name: GF5
Gene expression in colon from a germ-free mouse

source_name: Colon, Germ-free, replicate 5

value: Germfree


title: Colon_Btheta_rep2

description:
Sample name: Bt2
Gene expression in colon from a B. thetaiotaomicron mono-associated mouse

source_name: Colon, B. thetaiotaomicron, replicate 2


title: Colon_Germfree_rep2

description:
Sample name: GF2
Gene expression in colon from a germ-free mouse

source_name: Colon, Germ-free, replicate 2


title: Colon_Btheta_rep1

description:
Sample name: Bt1
Gene expression in colon from a B. thetaiotaomicron mono-associated mouse

source_name: Colon, B. thetaiotaomicron, replicate 1


title: C. elegans Control replicate 1

source_name: Nematodes exposed to control treatment for 48 hours


title: C. elegans exposed to aged particles replicate 1


title: Colon_Germfree_rep3

description:
Sample name: GF3
Gene expression in colon from a germ-free mouse

source_name: Colon, Germ-free, replicate 3


title: WB_stress_6

status: Public on Aug 21 2015

city: Maebashi

first: Shigeo

last: Miyata

address: 3-39-22 Showa-machi

institute: Gunma University Graduate School of Medicine

description: a pair of mPFC_stress_6

hyb_protocol: For each hybridization, 600 ng of Cy3-labeled cRNA was fragmented and hybridized at 65°C for 17 h to an Agilent SurePrint G3 Mouse GE 8×60K Microarray (Design ID: 028005).

scan_protocol: After washing, the microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: The intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. The normalization was performed using Agilent GeneSpring GX version 11.0.2 (per chip: normalization to the 75th percentile shift; per gene: none). The probes that were declared as “present” in all the assayed samples and that displayed a raw intensity value above 50 in at least 2 samples were used for the following statistical analyses.

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using a one-color Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Briefly, 100 ng of total RNA was reverse-transcribed to obtain double-stranded cDNA using a poly dT-T7 promoter primer. The primer, template RNA, and quality-control transcripts of known concentrations and quality were first denatured at 65°C for 10 min and then incubated for 2 h at 40°C with 5× first-strand buffer, 0.1 M dithiotreitol, 10 mM dNTP mix, and AffinityScript RNase Block Mix. The AffinityScript enzyme was then inactivated at 70°C for 15 min. The cDNA products were used as templates for in vitro transcription to generate fluorescent cRNA. The cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and Cy3-labeled CTP and then incubated at 40°C for 2 h. The labeled cRNAs were purified using Qiagen’s RNeasy mini spin columns and eluted using 30 µl of nuclease-free water. After cRNA was amplified and labeled, the cRNA quantity and cyanine incorporation were determined using a NanoDrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.

extract_protocol: The total RNA in the blood lysates was extracted using a GeneJet Whole Blood RNA Purification Mini Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA) according to the manufacturer’s instructions. Total RNA from the mPFC tissues was extracted using an RNeasy Micro Kit (Qiagen K.K.) according to the manufacturer’s instructions. The RNA quantity and quality were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc.) and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) as recommended.

treatment_protocol: Mouse blood (300 µl) was collected under pentobarbital anesthesia (50 mg/kg, i.p.) via the vena cava. The blood was heparinized immediately and centrifuged at 1,000 × g for 2 min. The pellet was dissolved in ice-cold lysis buffer containing 2-mercaptoethanol. Immediately after the blood was drawn, the mouse was decapitated, and the brain was removed. The decapitation was completed within 5 min of the anesthesia taking effect to minimize the effect of pentobarbital on gene expression. Coronal slices (1 mm thickness) were sectioned using a brain slicer, and the mPFC was dissected under a stereoscopic microscope. The dissected tissues were immersed in the RNA stabilization solution RNAlater (Qiagen K.K., Tokyo, Japan) and stored until RNA extraction.

value: Female

tag: surgery

value: sham operation

tag: stress

value: stress

value: whole blood

tag: individual

value: same as mPFC_stress_6


title: WB_stress_5

description: a pair of mPFC_stress_5

tag: gender

tag: age

value: same as mPFC_stress_5


title: WB_OVX_1

description: a pair of mPFC_OVX_1

tag: strain

value: ovariectomy

value: non-stress

value: same as mPFC_OVX_1


title: Colon_Germfree_rep4

description:
Sample name: GF4
Gene expression in colon from a germ-free mouse

source_name: Colon, Germ-free, replicate 4

value: colon

value: female

value: 12 weeks


title: WB_OVX_2

description: a pair of mPFC_OVX_2

value: same as mPFC_OVX_2


title: WB_OVX_4

description: a pair of mPFC_OVX_4

value: same as mPFC_OVX_4


title: WB_stress_4

description: a pair of mPFC_stress_4

value: same as mPFC_stress_4


title: WB_OVX+stress_6

description: a pair of mPFC_OVX+stress_6

value: same as mPFC_OVX+stress_6


title: WB_OVX_3

description: a pair of mPFC_OVX_3

value: same as mPFC_OVX_3


title: WB_OVX+stress_5

description: a pair of mPFC_OVX+stress_5

value: Female

value: same as mPFC_OVX+stress_5


title: C. elegans Control replicate 3

value: N2 (Bristol)

tag: genotype/variation

value: wildtype


title: WB_stress_2

description: a pair of mPFC_stress_2

value: sham operation

value: stress

value: whole blood

value: same as mPFC_stress_2


title: WB_OVX+stress_2

description: a pair of mPFC_OVX+stress_2

value: ovariectomy

value: same as mPFC_OVX+stress_2


title: WB_OVX+stress_4

description: a pair of mPFC_OVX+stress_4

value: same as mPFC_OVX+stress_4


title: WB_OVX_6

description: a pair of mPFC_OVX_6

value: non-stress

value: same as mPFC_OVX_6


title: WB_control_5

description: a pair of mPFC_control_5

value: same as mPFC_control_5


title: C. elegans Control replicate 2


title: WB_stress_1

description: a pair of mPFC_stress_1

value: same as mPFC_stress_1


title: Colon_Germfree_rep1

description:
Sample name: GF1
Gene expression in colon from a germ-free mouse

source_name: Colon, Germ-free, replicate 1

value: Germfree

value: colon

value: female

value: 12 weeks


title: WB_stress_3

description: a pair of mPFC_stress_3

value: Female

value: same as mPFC_stress_3


title: WB_control_6

description: a pair of mPFC_control_6

value: sham operation

value: same as mPFC_control_6


title: WB_OVX_5

description: a pair of mPFC_OVX_5

value: whole blood

value: same as mPFC_OVX_5


title: WB_OVX+stress_1

description: a pair of mPFC_OVX+stress_1

value: ovariectomy

value: stress

value: same as mPFC_OVX+stress_1


title: WB_OVX+stress_3

description: a pair of mPFC_OVX+stress_3

value: same as mPFC_OVX+stress_3


title: mPFC_OVX+stress_5

description: a pair of WB_OVX+stress_5

value: medial prefrontal cortex

value: same as WB_OVX+stress_5


title: WB_control_3

description: a pair of mPFC_control_3

value: non-stress

value: same as mPFC_control_3


title: WB_control_1

description: a pair of mPFC_control_1

value: same as mPFC_control_1


title: WB_control_4

description: a pair of mPFC_control_4

value: same as mPFC_control_4


title: WB_control_2

description: a pair of mPFC_control_2

value: same as mPFC_control_2


title: mPFC_OVX+stress_1

description: a pair of WB_OVX+stress_1

value: Female

value: same as WB_OVX+stress_1


title: mPFC_OVX_6

description: a pair of WB_OVX_6

value: same as WB_OVX_6


title: mPFC_OVX_2

description: a pair of WB_OVX_2

value: same as WB_OVX_2


title: mPFC_stress_5

description: a pair of WB_stress_5

value: sham operation

value: same as WB_stress_5


title: mPFC_stress_3

description: a pair of WB_stress_3

value: same as WB_stress_3


title: mPFC_OVX+stress_4

description: a pair of WB_OVX+stress_4

value: ovariectomy

value: stress

value: same as WB_OVX+stress_4


title: mPFC_OVX_3

description: a pair of WB_OVX_3

value: medial prefrontal cortex

value: same as WB_OVX_3


title: mPFC_OVX+stress_2

description: a pair of WB_OVX+stress_2

value: same as WB_OVX+stress_2


title: mPFC_OVX+stress_6

description: a pair of WB_OVX+stress_6

value: same as WB_OVX+stress_6


title: mPFC_OVX+stress_3

description: a pair of WB_OVX+stress_3

value: same as WB_OVX+stress_3


title: mPFC_OVX_1

description: a pair of WB_OVX_1

value: non-stress

value: same as WB_OVX_1


title: mPFC_OVX_5

description: a pair of WB_OVX_5

value: Female

value: same as WB_OVX_5


title: mPFC_control_4

description: a pair of WB_control_4

value: same as WB_control_4


title: mPFC_control_6

description: a pair of WB_control_6

value: same as WB_control_6


title: mPFC_stress_1

description: a pair of WB_stress_1

value: sham operation

value: same as WB_stress_1


title: mPFC_stress_2

description: a pair of WB_stress_2

value: same as WB_stress_2


title: mPFC_control_3

description: a pair of WB_control_3

value: same as WB_control_3


title: mPFC_control_5

description: a pair of WB_control_5

value: same as WB_control_5


title: mPFC_OVX_4

description: a pair of WB_OVX_4

value: ovariectomy

value: same as WB_OVX_4


title: mPFC_stress_4

description: a pair of WB_stress_4

value: stress

value: medial prefrontal cortex

value: same as WB_stress_4


title: Colon_Btheta_rep5

description:
Sample name: Bt5
Gene expression in colon from a B. thetaiotaomicron mono-associated mouse

source_name: Colon, B. thetaiotaomicron, replicate 5

value: Btheta

value: colon

value: female

value: 12 weeks


title: mPFC_control_2

description: a pair of WB_control_2

value: Female

value: non-stress

value: same as WB_control_2


title: mPFC_stress_6

description: a pair of WB_stress_6

value: sham operation

value: same as WB_stress_6


title: Preconditioned mouse lung, biological replicate 3

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

description: Gene expression data from ventilation-preconditioned lung

hyb_protocol: Labeled RNA were hybridized to a Mouse Gene 2.0 ST Array. Washing and staining was done ina a GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Scanning was performed using GeneChip Scanner 7G (Affymetrix)

data_processing: Data were analyzed (Background correction and normalization using the RMA algorithm) using the oligo and limma packages from Bioconductor, in the R platform.

source_name: Lung from preconditioned mouse

label_protocol: 100 ng of total RNA were amplified and labeled using the WT Plus Reagent kit (Affymetrix), following manufacturer's instructions

growth_protocol: Lung tissue from 10 week old mice

extract_protocol: RNA was extracted using Trizol and purified using the RNAeasy minikit (Quiagen)

treatment_protocol: Preconditioned mice were ventilated using low pressures for 90 minutes 1 week prior to tissue sampling

value: ventilation-preconditioned lung

value: 10 weeks


title: mPFC_control_1

description: a pair of WB_control_1

value: same as WB_control_1


title: ApoE/Caspase-1 double knockout aorta, biological replicate 3

city: Philadelphia

first: Xiao-Feng

last: Yang

state: PA

address: 3500 N. Broad St

department: Cardiovascular Research Center

institute: Temple University School of Medicine

description: Gene expression data from the aorta of ApoE/Caspase-1 double knockout mice fed with 3 weeks of high fat diet starting from 8-week of age

hyb_protocol: Samples were hybridized to the Affymetrix Genechip Mouse Gene 2.0.ST Arrays (Santa Clara, CA) following the manufacturer’s instructions at the Expression Microarray Core Facility in the Fox Chase Cancer Center, Temple University.

scan_protocol: Scanned microarray images were analyzed using the Affymetrix Gene Expression Console with Robust Multi-array Average normalization algorithm.

data_processing: Our affymetrix data analysis was done in the R statistical environment using “oligo” and “limma” packages. Venn diagram analysis was performed in the R statistical environment using the package “VennDiagram”. Heat map and scatter plot were performed using the statistical tools provided by the R and Bioconductor projects.

source_name: ApoE/Caspase-1 double knockout

label_protocol: Samples were labeled and hybridized to the Affymetrix Genechip Mouse Gene 2.0.ST Arrays (Santa Clara, CA) following the manufacturer’s instructions at the Expression Microarray Core Facility in the Fox Chase Cancer Center, Temple University.

growth_protocol: All animal experiments were performed in accordance with the Institutional Animal Care and Use Committee (IACUC) Guidelines and Authorization for the use of Laboratory Animals and were approved by the IACUC of Temple University School of Medicine.  All animals were housed in the Temple University Central Animal Facility under controlled temperature (23±1°C) with a 12-hour light-dark cycle. Animals had Ad libitum access to standard chow diet and water. Wild-type (WT) and ApoE-/- mice were purchased from the Jackson Laboratories (Bar Harbor, Maine). Caspase 1-/- mice were generously provided by Dr. Flavell’s laboratory (Department of Immunobiology, Yale University School of Medicine). ApoE/caspase-1 double gene deficient (ApoE-/-/caspase-1-/-) mice were generated by crossing caspase-1-/- mice into ApoE-/- mice. All mice used were on a C57BL/6 background.

extract_protocol: Total RNA was extracted from the aortas of mice using the RNeasy Kit (Qiagen, Valencia, CA). RNA quantity was determined by the NanoDrop ND-2000 (Thermo Scientific, Wilmington, DE). The RNA integrity was determined by the RNA 28S/18S ratio using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male mice Wild-type mice, Apolipoprotein E (ApoE) gene knockout mice, and ApoE/caspase-1 double gene deficient mice were fed high fat diet (catalog #88137, Harlan Teklad) for 3 weeks starting from 8-week of age to induce early hyperlipidemia.  At 11 week-old, mice were sacrificed and aortas were collected for microarray analysis.

value: aorta

value: male

value: ApoE/Caspase-1 double knockout

value: 11 weeks


title: PP_OP_M_V_D4_R3

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Organ pipe cactus. 17 days DEVT flies were collected.

hyb_protocol: Hybridizations with custom NimbleGen 12-plex microarrays were performed with a NimbleGen Hybridization System 4.

scan_protocol: Array scanning was performed with a GenePix 4000B scanner (Molecular Devices) and associated software at 532 nm, with photomultiplier gain settings that resulted in less than one in 105 normalized counts at saturation.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Drosophila mojavensis

source_name: Drosophila mojavensis PP08

label_protocol: cDNA samples were labeled with Cy3 using a NimbleGen (Roche Diagnostics) One Color DNA Labeling kit.

growth_protocol: Bottle cultures were established at moderate larval densities to minimize nutritionally caused maternal/environmental effects from the vial cultures and maintained in an incubator programmed on a 14:10 LD photoperiod that cycled from 27° to 17° C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). Invitrogen Superscript Double-Stranded cDNA Synthesis kits were used to synthesize double-stranded cDNA.  Each cDNA sample was quantified using a NanoDrop spectrophotometer (NanoDrop Technologies).

value: Wild-type

tag: phenotype

value: normal

tag: population

value: Punta Prieta, Baja California

tag: host diet

value: Organ Pipe

tag: group

value: virgin

tag: length of egg to adult development time

value: 17 day DEVT

value: whole organism


title: WT aorta, biological replicate 2

description: Gene expression data from the aorta of wild-type mice fed with 3 weeks of high fat diet starting from 8-week of age

source_name: Wild-type

tag: tissue


title: PP_OP_M_V_D5_R2

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Organ pipe cactus. 18 days DEVT flies were collected.

value: 18 day DEVT


title: Preconditioned mouse lung, biological replicate 1


title: ApoE/Caspase-1 double knockout aorta, biological replicate 4


title: ApoE/Caspase-1 double knockout aorta, biological replicate 5


title: WT aorta, biological replicate 3


title: Intact mouse lung, biological replicate 1

description: Gene expression data from intact lung

source_name: Lung from intact mouse

value: intact lung


title: PP_OP_M_V_D5_R1


title: ApoE/Caspase-1 double knockout aorta, biological replicate 1


title: Intact mouse lung, biological replicate 3

description: Gene expression data from intact lung


title: WT aorta, biological replicate 1


title: Preconditioned mouse lung, biological replicate 2


title: ApoE/Caspase-1 double knockout aorta, biological replicate 2


title: PP_OP_M_V_D3_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Organ pipe cactus. 16 days DEVT flies were collected.

value: 16 day DEVT


title: PP_OP_M_V_D4_R1


title: PP_OP_M_V_D4_R2


title: WT aorta, biological replicate 5


title: WT aorta, biological replicate 4


title: PP_OP_M_V_D3_R4


title: PP_OP_M_V_D3_R2


title: Intact mouse lung, biological replicate 2

description: Gene expression data from intact lung


title: PP_OP_M_V_D3_R1


title: PP_OP_M_V_D2_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Organ pipe cactus. 15 days DEVT flies were collected.

value: 15 day DEVT


title: PP_OP_M_V_D2_R3


title: PP_OP_M_V_D2_R2


title: PP_OP_M_V_D2_R1


title: PP_OP_F_V_D3_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised on fermented Organ pipe cactus. 16 days DEVT flies were collected.

value: female


title: PP_OP_M_M_D2_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated males were raised on fermented Organ pipe cactus. 15 days DEVT flies were collected.

value: mated


title: PP_OP_M_V_D1_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Organ pipe cactus. 14 days DEVT flies were collected.

value: 14 day DEVT


title: PP_OP_M_M_D1_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated males were raised fermented Organ pipe cactus. 14 days DEVT flies were collected.

value: male


title: PP_OP_M_M_D2_R1


title: PP_OP_M_M_D4_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated males were raised on fermented Organ pipe cactus. 17 days DEVT flies were collected.


title: PP_OP_M_M_D3_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated males were raised on fermented Organ pipe cactus. 16 days DEVT flies were collected.


title: PP_OP_F_V_D3_R2


title: PP_OP_F_V_D2_R2

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised on fermented Organ pipe cactus. 15 days DEVT flies were collected.


title: PP_OP_M_V_D1_R2


title: PP_OP_M_M_D3_R2


title: PP_OP_F_V_D4_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised on fermented Organ pipe cactus. 17 days DEVT flies were collected.


title: PP_OP_F_V_D4_R2


title: PP_OP_F_M_D4_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated females were raised on fermented Organ pipe cactus. 17 days DEVt flies were collected.


title: PP_OP_F_V_D4_R3


title: PP_OP_M_M_D3_R3


title: PP_OP_M_M_D2_R2


title: PP_OP_F_V_D2_R3


title: PP_OP_F_V_D2_R4


title: PP_OP_F_M_D4_R2

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated females were raised on fermented Organ pipe cactus. 17 days DEVT flies were collected.


title: PP_OP_F_V_D1_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised on fermented Organ pipe cactus. 14 days DEVt flies were collected.


title: PP_OP_F_M_D3_R2

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated females were raised on fermented Organ pipe cactus. 16 days DEVT flies were collected.


title: PP_OP_M_M_D4_R2


title: PP_OP_F_V_D1_R2

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised on fermented Organ pipe cactus. 14 days DEVT flies were collected.


title: PP_OP_F_M_D3_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated females were raised on fermented from Organ pipe cactus. 16 days DEVT flies were collected.


title: PP_OP_F_V_D5_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised fermented Organ pipe cactus. 18 days DEVT flies were collected.


title: PP_OP_F_V_D2_R1


title: PP_OP_M_M_D2_R4


title: PP_OP_F_M_D3_R1


title: LB_OP_M_V_D4_R3

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Organ pipe cactus. 17 days DEVT flies were collected.

source_name: Drosophila mojavensis LB09

value: Las Bocas, Sonora


title: LB_OP_M_V_D5_R2

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Organ pipe cactus. 18 days DEVT flies were collected.


title: LB_OP_M_V_D4_R2


title: PP_OP_F_M_D2_R2

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated females were raised on fermented Organ pipe cactus. 15 days DEVT flies were collected.


title: LB_OP_M_V_D3_R4

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Organ pipe cactus. 16 days DEVT flies were collected.


title: PP_OP_F_M_D2_R1


title: LB_OP_M_V_D5_R1


title: LB_OP_M_V_D3_R2


title: LB_OP_M_V_D4_R1


title: LB_OP_M_V_D3_R1


title: LB_OP_M_V_D3_R3


title: LB_OP_F_V_D4_R1

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin females were raised on fermented Organ pipe cactus. 17 days DEVT flies were collected.


title: LB_OP_F_V_D4_R2

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin females were raised on fermented Organ pipe cactus. 17 days DEVt flies were collected.


title: LB_OP_F_V_D3_R2

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin females were raised on fermented Organ pipe cactus. 16 days DEVT flies were collected.


title: LB_OP_M_V_D2_R4

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Organ pipe cactus. 15 days DEVT flies were collected.


title: LB_OP_M_V_D2_R1


title: LB_OP_F_M_D3_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Organ pipe cactus. 16 days DEVT flies were collected.


title: LB_OP_F_V_D3_R3


title: LB_OP_F_M_D3_R2


title: LB_OP_M_V_D2_R2

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Organ pipe cactus. 15 days DEVt flies were collected.


title: LB_OP_M_V_D2_R3


title: LB_OP_F_V_D5_R1

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin females were raised on fermented Organ pipe cactus. 18 days DEVT flies were collected.


title: LB_OP_F_V_D2_R1

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin females were raised on fermented Organ pipe cactus. 15 days DEVT flies were collected.


title: LB_OP_F_V_D3_R1


title: PP_AG_M_V_D3_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Agria cactus. 16 days DEVT flies were collected.

value: Agria


title: PP_OP_M_M_D4_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated males were raised on fermented Organ pipe cactus. 17 days DEVT flies were collected.

value: Wild-type


title: PP_AG_M_V_D3_R3

value: normal


title: LB_OP_M_M_D3_R1

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These mated males were raised on fermented Organ pipe cactus. 16 days DEVT flies were collected.


title: LB_OP_F_V_D2_R2


title: PP_AG_M_V_D2_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Agria cactus. 15 days DEVT flies were collected.

value: Punta Prieta, Baja California


title: PP_AG_M_V_D2_R2


title: PP_AG_M_V_D2_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Agria cactus. 15 days DEVt flies were collected.


title: PP_AG_M_V_D3_R1


title: PP_AG_M_V_D2_R1


title: PP_AG_M_V_D1_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Agria cactus. 14 days DEVT flies were collected.


title: PP_AG_M_V_D1_R4


title: PP_AG_F_V_D3_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised on fermented Agria cactus. 16 days DEVT flies were collected.


title: PP_AG_M_V_D1_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised onfermented Agria cactus. 14 days DEVT flies were collected.


title: PP_AG_M_M_D3_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated males were raised on fermented Agria cactus. 16 days DEVT flies were collected.


title: PP_AG_M_M_D2_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated males were raised on fermented Agria cactus. 15 days DEVT flies were collected.


title: PP_AG_F_V_D3_R2


title: PP_AG_F_V_D2_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised on fermented Agria cactus. 15 days DEVT flies were collected.


title: PP_AG_M_M_D2_R2


title: PP_AG_M_M_D1_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated males were raised on fermented Agria cactus. 14 days DEVT flies were collected.


title: PP_AG_F_V_D3_R4


title: PP_AG_F_V_D3_R3


title: PP_AG_M_M_D2_R1


title: PP_AG_M_V_D3_R2

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Agria cactus. 16 days DEVt flies were collected.


title: PP_AG_M_V_D1_R2


title: PP_AG_F_V_D2_R1


title: PDACPRE2

city: London

first: Jenny

last: Cook

address: John Vane Science Centre, Charterhouse Square

institute: Barts Cancer Institute

description: Gene expression data from CD14++ CD16- classical monocytes from peripheral blood of patient with pancreatic ductal adenocarcinoma

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human 2.0 plus U133 Gene Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneScan 3000 7G.

data_processing: The data were analyzed with R-lab using Affymetrix default analysis settings and global scaling as normalization method.

source_name: NAIVEPANC9_514_CD14++CD16- monocytes

label_protocol: cDNA product was biotinylated using the NuGen Encore biotin module and then prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA extraction was performed using Qiagen micro extraction kit according to the manufacturer's instructions. RNA was amplified using the NuGen Ovation pico WTA 3300 kit.

treatment_protocol: Peripheral blood was collected in EDTA vacutainers, blood was subject to red blood cell lysis and the classical CD14++ CD16- monocytes isolated using fluorescence assisted cell sorting (FACS).

tag: disease state

value: Locally advanced, unresectable Pancreatic Ductal Adenocarcinoma (PDAC) prior to any chemotherapy treatment

tag: treatment

tag: Sex

value: m

value: monocytes


title: PDACPRE1

source_name: NAIVEPANC7_508_CD14++CD16- monocytes

value: f


title: PDACPOST2

description: Gene expression data from CD14++ CD16- classical monocytes from peripheral blood of patient with pancreatic ductal adenocarcinoma treated with folfirinox

source_name: TREATED2_514_CD14++CD16- monocytes

value: Folfirinox


title: PP_AG_F_V_D2_R3

tag: genotype

value: virgin

value: whole organism


title: PDAC4

source_name: NAIVEPANC4_335_CD14++CD16- monocytes


title: PP_AG_F_V_D2_R2

value: 15 day DEVT


title: PDACPOST1

source_name: TREATED1_508_CD14++CD16- monocytes


title: PP_AG_F_V_D1_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised on fermented Agria cactus. 14 days DEVT flies were collected.

value: female


title: PP_AG_F_V_D1_R2


title: PDAC5

source_name: NAIVEPANC5_336_CD14++CD16- monocytes

value: Locally advanced, unresectable Pancreatic Ductal Adenocarcinoma (PDAC) sample taken 30 minutes after FOLFIRNOX treatment ended


title: PDAC3

source_name: NAIVEPANC3_332_CD14++CD16- monocytes


title: PP_AG_F_M_D3_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated females were raised on fermented Agria cactus. 16 days DEVT flies were collected.

value: mated

value: 16 day DEVT


title: PP_AG_F_M_D2_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated females were raised on fermented Agria cactus. 15 days DEVT flies were collected.


title: PDAC1

source_name: NAIVEPANC1_304_CD14++CD16- monocytes


title: HEALTHY3

description: Gene expression data from CD14++ CD16- classical monocytes from peripheral blood healthy volunteer

source_name: HEALTHY3_50_CD14++CD16- monocytes

value: Healthy


title: LB_AG_M_V_D4_R2

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Agria cactus. 17 days DEVT flies were collected.

value: Las Bocas, Sonora

value: Agria

value: male

value: 17 day DEVT


title: PP_AG_F_M_D1_R1

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These mated females were raised on fermented Agria cactus. 14 days DEVT flies were collected.

value: Wild-type

value: normal

value: Punta Prieta, Baja California

value: 14 day DEVT


title: PP_AG_F_M_D2_R2


title: PP_AG_F_M_D2_R3


title: HEALTHY1

source_name: HEALTHY1_55_CD14++CD16- monocytes

value: f

value: monocytes