title: Parent cell line

city: Incheon

first: Seung Hyun

last: Oh

address: 191 Hambakmoero, Yeonsu-gu

department: College of Pharmacy

institute: Gachon University

description: Gene expression data from human lung cnacer cell line H1299

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

scan_protocol: GeneChips were scanned using the Affymetwix GneChip Scanner 3000 7G

data_processing: The data were extracted by Affymetrix GCOS software and global scaling as normalization.

source_name: Human lung cancer cell (H1299)

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

growth_protocol: 10% FBS contained RPMI-1640 5% Co2 and 37C

treatment_protocol: Resiststant cells were continuously treated 17-AAG


title: 17-AAG resistant cell line

status: Public on Jan 11 2017

type: RNA

country: South Korea

description: Gene expression data from human lung cnacer cell line 17-AAG resistant H1299

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: 17-AAG resistant human lung cancer cell line

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

tag: cell line


title: sham surgery sample 3

city: Frankfurt am Main

first: Stefan

last: Momma

address: Heinrich-Hoffmann-Str. 7

department: Neurological Institute (Edinger Institute)

country: Germany

institute: University Hospital Frankfurt am Main

hyb_protocol: not provided

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..

label: biotin

organism: Mus musculus

source_name: sham surgery

label_protocol: not provided

growth_protocol: cells isolated from fresh brains

extract_protocol: Total RNA was extracted using the Ambion® Total RNA Isolation Kit

treatment_protocol: Mice were subjected to MCAO or sham surgery. 48h after surgery/sham, mice were killed and the SVZ immediatly extracted (<6min) and stored in RNAlater.

tag: strain

tag: gender

value: male

tag: tissue

value: brain

tag: brain region

value: subventricular zone


title: pretreatment epithelium (tumor) 1436 2013

city: L'HOSPITALET DE LLOBREGAT

first: DAVID

middle: G

last: MOLLEVI

state: Barcelona

address: Gran Via 197-203

department: PROCURE

country: Spain

institute: ICO

description: Laser Capture Microdissection

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: none provided by submitter

source_name: pretreatment epithelium (tumor)

label_protocol: standard Affymetrix protocol

extract_protocol: Arcturus Histogene LCM Frozen Section kit

tag: mandard's class

tag: rna extraction mehod

tag: amplification protocol


title: pretreatment epithelium (tumor) 1434 2013

description: Laser Capture Microdissection

value: Arcturus Histogene LCM Frozen Section kit


title: sham surgery sample 2


title: sham surgery sample 1


title: FLU-specific CD8+ T cells in HBV chronic phase, rep5

city: PARMA

first: Barbara

last: Montanini

state: PR

address: Parco Area delle Scienze 23/A

department: Life Sciences

country: Italy

institute: University of Parma

hyb_protocol: Labeled cDNA was hybridized to 60-mer oligonucleotide Whole Human Genome Microarrays (Human GE 4x44K v2, Agilent Technologies), following the manufacturer’s protocol.

scan_protocol: Microarray slides were scanned with an Agilent dual-laser DNA microarray scanner.

data_processing: The Agilent Feature Extraction software with default settings (user manual version 7.5) was used to obtain normalized expression values from the raw scans. The software package GeneSpring GX v11.5 (Agilent Technologies) was used for quality control checks, data normalization by the quantile method and microarray data analysis.

source_name: FLU-specific CD8+ T cells from HBV chronic patient 53

label_protocol: Total RNA was amplified with the Transplex Whole Transcriptome Amplification (WTA2) kit (Sigma-Aldrich, St.Louis, Mo) and purified with GenElute™ PCR Clean-Up silica spin-colums (Sigma). cDNA was labeled with the ULS Fluorescent Labeling kit (Agilent Technologies).

extract_protocol: RNA was purified from dextramer-sorted human CD8+ T cells with the Nucleospin RNA XS kit (Macherey Nagel, Duren, Germany) according to the manufacturer's instructions. Total RNA concentration was determined with a Nanodrop spectrophotometer and/or with the Ribogreen RNA quantification kit (Molecular Probes, Life Technologies, Carlsbad, CA). RNA integrity was evaluated with a Bioanalyzer 2100 traces system (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PBMCs were isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation and cryopreserved in liquid nitrogen until the day of analysis. After thawing of PBMCs, CD8+ T cells were isolated with the CD8+ T Cell Isolation Kit (Miltenyi Biotec) and labeled with 7-AAD, anti-CD45, anti-CD3, anti-CD8, and HLA-Class I dextramers in order to identify antigen-specific T cell sub-populations. CD8+ dextramer+ cells were sorted with a FACSAria III Cell Sorter (BD Biosciences).

tag: cell type

value: FLU-specific CD8+ T cells


title: pretreatment epithelium (tumor) 1437 2013

description: Laser Capture Microdissection


title: FLU-specific CD8+ T cells in HBV chronic phase, rep4

source_name: FLU-specific CD8+ T cells from HBV chronic patient 46


title: MCAO sample 3

source_name: middle cerebral artery occlusion (MCAO)


title: FLU-specific CD8+ T cells in HBV chronic phase, rep2

source_name: FLU-specific CD8+ T cells from HBV chronic patient 49


title: FLUh-3

description: FLU-specific CD8+ T cells, rep3

source_name: FLU-specific CD8+ T cells from healthy donor 22

tag: diagnosis

value: healthy


title: postreatment stroma 1431 2013

description: Laser Capture Microdissection

source_name: postreatment stroma


title: FLU-specific CD8+ T cells in HBV chronic phase, rep3

source_name: FLU-specific CD8+ T cells from HBV chronic patient 50


title: FLUh-4

description: FLU-specific CD8+ T cells, rep4

source_name: FLU-specific CD8+ T cells from healthy donor 23


title: MCAO sample 2


title: postreatment stroma 1433 2013

description: Laser Capture Microdissection


title: postreatment stroma 1429 2013

description: Laser Capture Microdissection


title: MCAO sample 1


title: postreatment stroma 1430 2013

description: Laser Capture Microdissection


title: FLU-specific CD8+ T cells in HBV chronic phase, rep1

source_name: FLU-specific CD8+ T cells from HBV chronic patient 48


title: postreatment stroma 1428 2013

description: Laser Capture Microdissection


title: FLUh-2

description: FLU-specific CD8+ T cells, rep2

source_name: FLU-specific CD8+ T cells from healthy donor 20


title: MEFs-AMN107-IFNg, biological rep2

city: Beijing

first: yan

last: cui

state: beijing

address: 27 Taiping Road

department: Department of Molecular Biology

country: China

institute: Beijing Institute of Biotechnology

description: stimulated for 6 h with IFNg

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were analyzed with （Affymetrix® GeneChip® Command Console® Software and MAS5 as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse embryonic fibroblasts

growth_protocol: Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum

extract_protocol: RNA extraction was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: MEFs were treated with or without AMN107 RNA, then were stimulated for 6 h with IFNa or IFNg

value: MEFs


title: Bone-HST Femur, rep2 [miRNA]

city: Philadelphia

first: Annamarie

middle: D

last: Horan

state: PA

address: 3737 Market Street, 6th Floor

department: Orthopaedic Surgery

country: USA

institute: University of Pennsylvania

description:
3808_24889_8
Acute fracture remnant bone

hyb_protocol: Labeled RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 1.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: GeneChip 3000 7G scanner with software version AGCC.

data_processing: Partek Genomics Suite, version 6.6 or lower was used to import data using Quartile Normalization, Median Polish summarization. ANOVA with multiple test correction (with a stepped up p value of 0.05 to 0.1 and fold change ± 1.5) was used for discovery rather than statistical purposes, with repeated measures of Acutely Injured Subjects (AIS) included in the analysis to identify potential miRNAs that were differentially expressed between AIS and healthy volunteers. We then validated performance on RT-qPCR.

source_name: Remnant bone, femur, HST

label_protocol: Affymetrix FlashTag™ Biotin RNA Labeling Kit.

growth_protocol: Not applicable.

extract_protocol: PaxGene microRNA Isolation kit.

treatment_protocol: Bone fragments were captured at room temperature in the OR and transported on ice to the lab where they were cut into two pieces of approximately equal size. One piece was immediately dropped into liquid nitrogen. The other was placed onto a Mantainor(R) tissue card (Denator, Uppsala Science Park, Sweden) and heat stabilized using the Denator Stabilizer (TM). Prior to RNA extraction, each bone fragment was crushed with the Covaris CryoPrep dry tissue Pulverizer Impactor system.

value: Remnant bone (HST Femur)

tag: Sex

value: Male

tag: age

value: 97 yr

tag: race

value: Black

tag: disease state

value: fracture


title: pretreatment stroma 1426 2013

description: Laser Capture Microdissection

source_name: pretreatment stroma


title: pretreatment stroma 1424 2013

description: Laser Capture Microdissection


title: pretreatment stroma 1422 2013

description: Laser Capture Microdissection


title: CHR-4

description: HBV-specific CD8+ T cells chronic phase, rep4

source_name: HBV-specific CD8+ T cells from chronic patient 53

value: chronic hepatitis B

value: HBV-specific CD8+ T cells


title: postreatment stroma 1427 2013

description: Laser Capture Microdissection


title: RES-4

description: HBV-specific CD8+ T cells resolution phase, rep4

source_name: HBV-specific CD8+ T cells from resolved patient 51

value: resolved hepatitis B


title: CHR-1

description: HBV-specific CD8+ T cells chronic phase, rep1

source_name: HBV-specific CD8+ T cells from chronic patient 44


title: MEFs-AMN107-IFNa, biological rep1

description: stimulated for 6 h with IFNa


title: pretreatment stroma 1421 2013

description: Laser Capture Microdissection


title: MEFs-AMN107-IFNg, biological rep1

description: stimulated for 6 h with IFNg


title: MEFs-AMN107-IFNa, biological rep2

description: stimulated for 6 h with IFNa


title: pretreatment stroma 1420 2013

description: Laser Capture Microdissection


title: MEFs-AMN107, biological rep1


title: CHR-3

description: HBV-specific CD8+ T cells chronic phase, rep3

source_name: HBV-specific CD8+ T cells from chronic patient 47


title: pretreatment stroma 1418 2013

description: Laser Capture Microdissection


title: CHR-2

description: HBV-specific CD8+ T cells chronic phase, rep2

source_name: HBV-specific CD8+ T cells from chronic patient 45


title: pretreatment stroma 1419 2013

description: Laser Capture Microdissection


title: MEFs-IFNa, biological rep2

description: stimulated for 6 h with IFNa


title: pretreatment stroma 1423 2013

description: Laser Capture Microdissection


title: RES-3

description: HBV-specific CD8+ T cells resolution phase, rep3

source_name: HBV-specific CD8+ T cells from resolved patient 43


title: FLUh-5

description: FLU-specific CD8+ T cells, rep5

source_name: FLU-specific CD8+ T cells from healthy donor 39


title: RES-1

description: HBV-specific CD8+ T cells resolution phase, rep1

source_name: HBV-specific CD8+ T cells from resolved patient 24


title: RES-2

description: HBV-specific CD8+ T cells resolution phase, rep2

source_name: HBV-specific CD8+ T cells from resolved patient 42


title: MEFs-AMN107, biological rep2


title: FLUh-1

description: FLU-specific CD8+ T cells, rep1

source_name: FLU-specific CD8+ T cells from healthy donor 16


title: AC-5

description: HBV-specific CD8+ T cells acute phase, rep5

source_name: HBV-specific CD8+ T cells from acute patient 33

value: acute hepatitis B


title: MEFs-IFNg, biological rep1

description: stimulated for 6 h with IFNg


title: MEFs-IFNg, biological rep2

description: stimulated for 6 h with IFNg


title: pretreatment stroma 1417 2013

description: Laser Capture Microdissection


title: pretreatment stroma 1416 2013

description: Laser Capture Microdissection


title: pretreatment stroma 1415 2013

description: Laser Capture Microdissection


title: MEFs-IFNa, biological rep1

description: stimulated for 6 h with IFNa


title: MEFs-DMSO, biological rep2


title: AC-3

description: HBV-specific CD8+ T cells acute phase, rep3

source_name: HBV-specific CD8+ T cells from acute patient 27


title: AC-4

description: HBV-specific CD8+ T cells acute phase, rep4

source_name: HBV-specific CD8+ T cells from acute patient 32


title: AC-2

description: HBV-specific CD8+ T cells acute phase, rep2

source_name: HBV-specific CD8+ T cells from acute patient 25


title: pretreatment stroma 1413 2013

description: Laser Capture Microdissection


title: CBP_KO-4

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

hyb_protocol: Fragmented and labeled cDNA was hybridized to Affymetrix MG430.2 arrays using the Affymetrix HWS kit, Standard Array (49 Format) for 16 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G, connected to Command Console software.

data_processing: Raw expression values were normalized using the Robust Multiarray Averaging (RMA) algorithm. For GSEA analysis, multiple probes corresponding to the same gene are collapsed with maximum t-statistic.

label_protocol: 3.75ug of amplified cDNA was biotin-labeled with the Encore® Biotin Module (NuGEN) according to the manufacturer's instructions

growth_protocol: Mice (8-12 week old) were immunized with SRBC (day 0: 1X10^8 cells; d5:1X10^9 cells) and sacrificed at d12 for analysis.

extract_protocol: Total RNA was isolated using the Total RNA isolation NucleoSpin RNA XS kit (NACHEREY-NAGEL) according to the user's manual. Twenty-five nanograms of RNA from each sample were then reverse transcribed and amplified using the Ovation RNA Amplification System (NuGEN)

treatment_protocol: Single cell suspensions prepared from the spleen of immunized mice were processed with the mouse B-cell isolation kit (Miltenyi Biotec), and germinal center B cells (B220+CD95+PNA+) were sorted from individual mouse samples by fluorescence-activated cell sorting

tag: strain background

value: 2-3 months

value: Female

tag: genotype

value: Crebbpfl/fl Cg1-Cre

value: spleen


title: pretreatment stroma 1414 2013

description: Laser Capture Microdissection

value: Arcturus Histogene LCM Frozen Section kit


title: pretreatment stroma 1412 2013

description: Laser Capture Microdissection


title: AC-1

description: HBV-specific CD8+ T cells acute phase, rep1

source_name: HBV-specific CD8+ T cells from acute patient 24


title: OE-19_TCR_replicate1

city: Lyon

first: Juliette

last: Sauveur

state: Rhone-Alpes

address: 8 Avenue Rockefeller, Faculté Rockefeller

department: Immunité, Virus, Inflammation

country: France

institute: Cancer Research Center of Lyon

description:
replicate 1
OE-19_TCR_n1

hyb_protocol: Hybridization of 750 ng of cRNA on Beadchip Illumina HT-12, V4.0 according to the standard Illumina protocol

scan_protocol: Scaned using I-Scan according to the standard Illumina protocol

data_processing: The data were normalised by quantile normalisation with Genome Studio Illumina V2011.1, Gene Expression 1.9.0

source_name: esophageal cancer

label_protocol: Biotinylated cRNA were obtained using the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: OE-19 parental and resistant cell lines were grown in RPMI medium containing 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin. OE-19 TR and TCR were cultured under constant exposure to T-DM1 to maintain selective pressure.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN Qiamp RNeasy mini kit according to the prescribed protocol. Quality control was performed with 2100 Bioanalyzer.

treatment_protocol: Cells were not exposed to T-DM1 for this experiment. Both T-DM1 resistant cell lines were kept in the absence of drugs during 72h before the transcriptomic analysis.

value: HER2 positive

tag: drug exposure


title: CBP_KO-5

value: germinal center B cells (B220+CD95+PNA+)


title: OE-19_TCR_replicate2

description:
replicate 2
OE-19_TCR_n2


title: MEFs-DMSO, biological rep1

source_name: mouse embryonic fibroblasts

tag: cell line

value: MEFs


title: CBP_KO-1


title: OE-19_S_replicate2

description:
replicate 2
OE-19_S_n2


title: OE-19_TR_replicate2

description:
replicate 2
OE-19_TR_n2


title: OE-19_TR_replicate1

description:
replicate 1
OE-19_TR_n1


title: CBP_KO-2


title: CBP_KO-3


title: CBP_HET-5

value: Crebbpfl/+ Cg1-Cre


title: CBP_HET-3


title: OE-19_S_replicate3

description:
replicate 3
OE-19_S_n3


title: CBP_HET-2


title: OE-19_TCR_replicate3

description:
replicate 3
OE-19_TCR_n3


title: OE-19_TR_replicate3

description:
replicate 3
OE-19_TR_n3


title: CBP_HET-4

value: Male


title: OE-19_S_replicate1

description:
replicate 1
OE-19_S_n1


title: CBP_WT-1

value: Crebbp+/+ Cg1-Cre


title: CBP_HET-1


title: CBP_WT-3


title: Apc-/-_sample1

status: Public on Jan 10 2017

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: Following fragmentation, cDNA was hybridized for 20 hr at 48C to Affymetrix Mouse Genome 2.1 ST arrays.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the affy package implemented in the R-statistical environment version 3.1.1. RMA was used to estimate log2 transformed expression values for each probe-set.

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Apc fl/fl mouse 39

label_protocol: 100 ng total RNA was reverse-transcribed, amplified and labeled, with Ambion WT Expression Kits.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), and purified using Rneasy columns (Qiagen). Quality was checked with an Agilent 2100 Bioanalyzer.

tag: strain

value: mixed C57BL/6 and 129 background

tag: treatment

value: 160 mg/kg tamoxifen, once

value: female


title: CBP_WT-4

tag: gender

tag: tissue


title: Cdx2-/-+Braf_V600E_sample3

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Cdx2 fl/fl; Braf fl/fl mouse 47

value: 120 mg/kg tamoxifen, on 2 consecutive days


title: Braf_V600E_sample2

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Braf fl/fl mouse 49

value: male


title: Apc-/-_sample3

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Apc fl/fl mouse 41


title: 7706-2 Pf1 KO MEFs

first: Gregory

last: David

address: 550 1st Avenue, MSB417

department: Biochemistry and Molecular Pharmacology

institute: New York University School of Medicine

hyb_protocol: standard hyb protocol

scan_protocol: GeneChips were scanned using the GeneChip  Expression Wash, Stain and Scan User Manual and the Affymetrix 3000 7G scanner.

data_processing: Data were analyzed using the Affymetrix Expression Console and Genepattern software for the calculation of average expression leveles of each chromosome, with each array normalized with the robust multichip array (RMA) algorithm. Data were analyzed using the Affymetrix Expression Console and Genepattern software for the calculation of average expression leveles of each chromosome, with each array normalized with the robust multichip array (RMA) algorithm.

source_name: MEFs

label_protocol: Biotinylated cRNA were prepared according to the GeneChip  3  IVT Express Kit.

growth_protocol: MEFs were generated from 13.5 and 14.5 days post-coitus embryos. The head and the red organs were removed, and used for genotyping. The torso was then minced and dispersed in 0.1% trypsin (45 min at 37 C). Cells were subsequently grown in DMEM medium supplemented with 10% fetal calf serum (Atlanta Biologicals), 50 μM β-mercaptoethanol (Sigma Aldrich, St. Louis, MO), and penicillin-streptomycin and sub-cultured 1:4 upon confluency. The cultures were maintained in 6% O2, 5% CO2 at 37°C.

extract_protocol: Total RNA from Pf+/+ and Pf1 -/- MEFs at passage 2-3 (Pf+/+ lines 7706-5 and 7706-6 and Pf1 -/- lines 7706-2 and 7706-4) was isolated using Trizol reagent (Thermo Fisher Scientific, Waltham, MA) according to the manufacturers protocol.

tag: genotype/variation


title: 7706-4 Pf1 KO MEFs


title: Cdx2-/-+Braf_V600E_sample1

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Cdx2 fl/fl; Braf fl/fl mouse 45


title: 7706-6 Pf1 WT MEFs


title: 7706-5 Pf1 WT MEFs


title: CBP_WT-2


title: Cdx2-/-_sample3

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Cdx2 fl/fl mouse 32


title: Cdx2-/-_sample1

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Cdx2 fl/fl mouse 30


title: Braf_V600E_sample3

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Braf fl/fl mouse 50


title: Cdx2-/-_sample2

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Cdx2 fl/fl mouse 31


title: control_sample3

source_name: Normal colon sample from Cdx2 fl/fl (no CDX2P_CreERT2) mouse 35


title: Apc-/-_sample2

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Apc fl/fl mouse 40


title: Cdx2-/-+Braf_V600E_sample2

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Cdx2 fl/fl; Braf fl/fl mouse 46


title: control_sample2

source_name: Normal colon sample from Cdx2 fl/fl (no CDX2P_CreERT2) mouse 34


title: control_sample1

source_name: Normal colon sample from Cdx2 fl/fl (no CDX2P_CreERT2) mouse 33


title: Patient 6 150690A_TKI-21-3

first: qu

last: lili

address: No 8 East Road, Fengtai District

institute: Affiliated Hospital of the Academy of Military Medical Science

description: Gene expression in human plasma

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary lung cancer

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

growth_protocol: Not applicable

extract_protocol: Total RNA containing miRNAs was isolated from 200μl plasma with the QIAzol Lysis Reagent (QIAGEN) and purified with the miRNeasy Serum/Plasma Kit (QIAGEN) according to the manufacturer′s instructions.

treatment_protocol: All the participants enrolled had 7ml peripheral venous blood samples collected in the fasting state at morning. Plasma was separated within 30 minutes since the sample collection with the centrifugation at 4,500×g for 10 minutes at 4 ℃ and then stored immediately at -80℃ for further measurements.

tag: plasma

value: primary lung cancer

value: 64 years

tag: smoking history

value: No

tag: histology

value: Adenocarcinoma

tag: clinical stage

value: IV

tag: egfr mutational status


title: Patient 13 150690A_M-4

description: Gene expression in human plasma

value: healthy donor

tag: age

value: 35 years

value: Female

value: Not applicable


title: Braf_V600E_sample1

source_name: Colon tumor from tamoxifen treated CDX2P_CreERT2; Braf fl/fl mouse 48

tag: Sex


title: Patient 12 150690A_M-3

description: Gene expression in human plasma

value: Yes


title: Patient 5 150690A_TKI-21-2

description: Gene expression in human plasma

value: 56 years

value: Male


title: Patient 9 150690A_ALK-3

description: Gene expression in human plasma

value: 43 years

value: WT


title: Patient 11 150690A_M-2

description: Gene expression in human plasma

value: 62 years


title: Patient 10 150690A_M-1

description: Gene expression in human plasma

value: 63 years


title: Patient 8 150690A_ALK-2

description: Gene expression in human plasma

value: 37 years


title: Patient 4 150690A_TKI-21-1

description: Gene expression in human plasma

value: primary lung cancer

value: 77 years


title: Patient 7 150690A_ALK-1

description: Gene expression in human plasma

value: 59 years


title: Patient 3 150690A_TKI-19-3

description: Gene expression in human plasma

value: 52 years

value: Adenocarcinoma

value: IIIB


title: Patient 2 150690A_TKI-19-2

description: Gene expression in human plasma

value: No

value: IV


title: Distal blastema 14dpa LE135-treated 4

city: Boston

first: James

middle: R

last: Monaghan

state: MA

address: 360 Huntington Ave

department: Biology

institute: Northeastern University

description: Distal blastema 14 days after amputation treated with LE135

hyb_protocol: Affymetrix Gene Chip 3'IVT Reagent Kit was used according to manufacturer's instructions.

scan_protocol: Affymetrix Command Console was used according to manufacturer's instructions

data_processing:
Expression values were generated using the Robust Microarray Average (RMA) algorithm.
GPL15153_AMBY_002a520748F

organism: Ambystoma mexicanum

source_name: forelimb

label_protocol: Biotinylation was carried out according to the instructions in Affymetrix's 3'IVT Reagent Kit user's manual

growth_protocol: Animals were maintained at 18-20 degrees C individually in salamander housing solution.

extract_protocol: Total RNA was extracted via Qiagen RNeasy kit per manufacturer’s instructions.  RNA quality was assessed using an Epoch microplate spectrophotometer, gel electrophoresis, and a 2100 Agilent Bioanalyzer.

treatment_protocol: Animals were anesthetized via treatment of 0.01% benzocaine and forelimbs were amputated at the distal zeugopod. Between days 7-14 dpa, individually housed animals were dosed with RA, LE135, or DMSO (n = 16/treatment). Drugs were changed every other day. Blastemas containing as little stump tissue as possible were collected from all 48 animals at 14 dpa and single forelimbs from four separate individuals were pooled together to yield four independent biological replicate samples for each treatment group.

tag: size

value: 8.8cm total length


title: Distal blastema 14dpa LE135-treated 3


title: Distal blastema 14dpa LE135-treated 2


title: Distal blastema 14dpa RA-treated 2

description: Distal blastema 14 days after amputation treated with RA


title: Distal blastema 14dpa LE135-treated 1


title: Patient 1 150690A_TKI-19-1

description: Gene expression in human plasma

value: 41 years


title: Distal blastema 14dpa RA-treated 3


title: Distal blastema 14dpa DMSO-treated 2

description: Distal blastema 14 days after amputation treated with DMSO


title: Distal blastema 14dpa DMSO-treated 1


title: Distal blastema 14dpa RA-treated 1


title: SNJ9

type: genomic

first: yang

last: sihang

address: Haidian district Shuangqing road #30

institute: Tsinghua University

description:
subtropical zone, replicate9
Soil microbes

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

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

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

molecule: genomic DNA

organism: soil metagenome

source_name: Soil microbes in three broadleaved forests

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy3 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Soil DNA was extracted by freeze-grinding mechanical lysis as previously described (Zhou et al 1996). Freshly extracted DNA was purified twice using 0.5% low melting point agarose gel followed by phenol-chloroform-butanol extraction. DNA quality and quantity were assessed by the ratios of 260 nm/280 nm and 260 nm/230 nm, and final DNA contents were quantified with a PicoGreen method using a FLUO star Optima .

treatment_protocol: In August 2011, a total of 30 samples were cellected in the Wulu Mountain, Funiu Mountain and Shennongjia Mountain. At each site, thirty plots (20 m ×20 m) comprising typical vegetation and soil attributes were selected for sampling. At each plot, ten to fifteen soil cores at a depth of 0-10 cm were taken, mixed thoroughly and sieved with 2 mm mesh to remove roots and stones. Soil samples were kept on ice when transporting to laboratory, divided into two subsamples and stored at either 4°C for soil biogeochemical measurements or −80°C for DNA extraction.

tag: climate zone

value: subtropical zone


title: FNM10

description:
north border of subtropical zone, replicate 10
Soil microbes

value: north border of subtropical zone


title: Distal blastema 14dpa RA-treated 4


title: FNM9

description:
north border of subtropical zone, replicate 9
Soil microbes


title: SNJ5

description:
subtropical zone, replicate5
Soil microbes


title: SNJ4

description:
subtropical zone, replicate4
Soil microbes


title: FNM8

description:
north border of subtropical zone, replicate 8
Soil microbes


title: SNJ7

description:
subtropical zone, replicate7
Soil microbes


title: SNJ6

description:
subtropical zone, replicate6
Soil microbes


title: SNJ3

description:
subtropical zone, replicate3
Soil microbes


title: FNM4

description:
north border of subtropical zone, replicate 4
Soil microbes


title: SNJ1

description:
subtropical zone, replicate1
Soil microbes


title: Distal blastema 14dpa DMSO-treated 4


title: FNM7

description:
north border of subtropical zone, replicate 7
Soil microbes


title: SNJ2

description:
subtropical zone, replicate2
Soil microbes


title: FNM5

description:
north border of subtropical zone, replicate 5
Soil microbes


title: SNJ8

description:
subtropical zone, replicate8
Soil microbes


title: FNM6

description:
north border of subtropical zone, replicate 6
Soil microbes


title: FNM3

description:
north border of subtropical zone, replicate 3
Soil microbes


title: SNJ10

description:
subtropical zone, replicate10
Soil microbes


title: FNM2

description:
north border of subtropical zone, replicate 2
Soil microbes


title: WLM9

description:
temperate zone, replicate 9
Soil microbes

value: temperate zone


title: WLM8

description:
temperate zone, replicate 8
Soil microbes


title: FNM1

description:
north border of subtropical zone, replicate 1
Soil microbes


title: RARA-ChIP

city: Kumamoto

first: Ko

last: Ishihara

address: 2-2-1 Honjyo

department: Priority Organization for Innovation and Excellence

country: Japan

institute: Kumamoto University

hyb_protocol: Samples were prepared and hybridized to GeneChip ENCODE 2.0R  Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 250 bp bandwidth and perfect match only.
The resulting BAR files are generated by the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 250 bp bandwidth and perfect match only.

source_name: NT2, 10μM retinoic acid for 6 days, anti-RARa

label_protocol: DNA was amplified by IVT (In vitro transcription) method. For the labeling, DNA was fragmented by DNaseI. DNA was end-labeled by Terminal Transferase with biotin‐N11‐ddATP

growth_protocol: NT2/D1 cells were cultured in Dulbecco’s modified Eagle’s minimum essential medium (DMEM; Wako) supplemented with 10% (v/v) fetal bovine serum (FBS). For retinoic acid treatment, NT2/D1 cells were treated with 10 μM all trans retinoic acid (RA; Wako)

extract_protocol: For immunoprecipitation, chromatin samples were incubated with anti-CTCF or anti-RARa antibodies overnight at 4°C with agitation. The antibody complex were precipitated by incubation with Staph A cells at room temperature for 15 min. The supernatant was removed and the pellets were washed twice with Wash buffer A (50mM Tris-HCl pH8.0, 2mM EDTD, 0.2% Sarkosyl) and five times with Wash buffer B (100mM Tris-HCl pH 9.0, 500mM LiCl, 1% NP40, 1% deoxycholic acid). For elution, the pellets were resuspended in elution buffer (50mM NaHCO3, 1% SDS) and incubate for 15min with agitation. The supernatants were transfered to clean tubes and repeated elution.The elution samples were combined and NaCl (0.3M) and proteinase K (10μg/ml) were added and incubateed at 65°C for 5hr.  The reverse crosslinked samples were purified with MinElute Reaction Cleanup Kit (QIAGEN).

treatment_protocol: For ChIP with anti-CTCF antibodies, NT2/D1 cells were crosslinked with 1% formaldehyde at 37°C for 10 min and washed with PBS. For ChIP with anti-RARa antibodies, NT2/D1 cells were treated with dimethyl 3,3’-dithiobispropionimidate-2HCl (5 mM) (Thermo Scientific) in PBS, rinsed with an ice-cold buffer (100 mM Tris-HCl pH 8.0, 150 mM NaCl), and crosslinked with 1% formaldehyde at 37°C for 20 min. The cell pellet was resuspended in cell lysis buffer (5mM Pipes pH 8.0, 85mM KCl, 0.5%NP40 and protease inhibitors) and placed on ice for 10 min. Crude nucli fraction was pelleted by centrifugation. The pellet was resuspended in Ncli lysis buffer (50mM Tris-HCl pH8.0, 10mM EDTA 1%SDS and protease inhibitors) and incubate on ice for 10min. Lysed nucli were sonicated to generate DNA fragment of 200-1000 bp.

value: 10μM retinoic acid for 6 days

tag: antibody

value: anti-RARa


title: RARA-INPUT

source_name: NT2, 10μM retinoic acid for 6 days, none


title: CTCF-ChIP

source_name: NT2, untreated, anti-CTCF

value: anti-CTCF


title: WLM7

description:
temperate zone, replicate 7
Soil microbes


title: WLM5

description:
temperate zone, replicate 5
Soil microbes


title: CTCF-INPUT

source_name: NT2, untreated, none


title: WLM4

description:
temperate zone, replicate 4
Soil microbes


title: WLM3

description:
temperate zone, replicate 3
Soil microbes


title: WLM2

description:
temperate zone, replicate 2
Soil microbes


title: WLM10

description:
temperate zone, replicate 10
Soil microbes


title: Male_Young4

city: Hershey

first: Penn State

last: COM

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description: Replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: We used GenomeStudio V2011.1 Gene Expression Module v1.9.0 for the average normalization.

source_name: Hippocampus

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

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

treatment_protocol: Mice were aged without any genetic or pharmacological intervention

value: Male

value: Young


title: Male_Adult2

description: Replicate 2

value: Adult


title: Male_Young1

description: Replicate 1


title: Male_Young2

description: Replicate 2


title: Male_Aged1

description: Replicate 1

value: Aged


title: Male_Aged3

description: Replicate 3


title: Male_Young3

description: Replicate 3


title: Male_Aged4

description: Replicate 4


title: Male_Aged2

description: Replicate 2


title: Male_Adult4

description: Replicate 4


title: Female_Aged3

description: Replicate 3

value: Female


title: Female_Aged4

description: Replicate 4


title: WLM1

description:
temperate zone, replicate 1
Soil microbes


title: Male_Adult1

description: Replicate 1


title: WLM6

description:
temperate zone, replicate 6
Soil microbes


title: Male_Adult3

description: Replicate 3


title: Female_Aged2

description: Replicate 2


title: Female_Aged1

description: Replicate 1


title: Female_Adult3

description: Replicate 3


title: Female_Adult2

description: Replicate 2


title: Female_Young3

description: Replicate 3


title: Female_Young4

description: Replicate 4


title: Female_Young2

description: Replicate 2


title: Female_Young1

description: Replicate 1


title: Female_Adult4

description: Replicate 4


title: Female_Adult1

description: Replicate 1


title: CPCG0411.2

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting

data_processing: Raw data were processed through Dasen

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Illumina Infinium HumanMethylation 450k BeadChip kits were used to assess global methylation, using 500 ng of input genomic DNA at the McGill University and Genome Quebec Innovation Centre (Montreal, QC)

tag: ^sample

tag: disease state

value: Sporadic

value: prostate tumor


title: CPCG0267.2


title: CPCG0258.2


title: CPCG0411


title: CPCG0414


title: CPCG0267


title: DC from WT mice, 18h post-TB infection, rep2

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

description: Gene expression of BMDC from WT mice, after 18h of TB infection

hyb_protocol: The slides were hybridized following the One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent)

scan_protocol: The slides were scanned on a Tecan MS200 scanner

data_processing:
Agilent raw files extracted by using Feature Extraction software were processed through Bioconductor (version 3.1) in the R statistical environment (version 3.2.0) via the limma package.
Raw expression values were background corrected in a normexp fashion and then quantile normalized. Normalized expression values were then corrected for batch effects due to the cell sorts at different days, using the ComBat algorithm through the sva package declaring 2 batches (2 sorting days) with the genotype and post-infection time as covariates.

label_protocol: The labeling was done using the Low Input Quick Amp Labeling kit, One Color (Agilent)

growth_protocol: Bone marrow derived dendritic cells were prepared from murine hind legs by flushing the uncovered and opened femurs and tibiae with DPBS (Gibco). Red blood cells were lysed by addition of red blood cell lysis buffer (Sigma). Subsequently, cells were separated with a cell strainer and cultivated in complete RPMI-1640 medium (Gibco) supplemented with 10% fetal calf serum (PAN-Biotech), 1% sodium pyruvate (Gibco), 0,1% b-mercaptoethanol (Gibco) and 20 ng/ml recombinant murine GM-CSF (Peprotech). Cells were allowed to differenciate for 7 days. The culture medium was replaced every two or three days.

extract_protocol: RNA from bone marrow-derived dentritic cells were extracted using the RNeasy mini kit (Qiagen). The amount and purity of RNA were quantified using a NanoDrop ND-1000 apparatus (Thermo Scientific) by measuring absorbance at 260/280 nm. Double-stranded cDNA was reverse-transcribed using the M-MLV Reverse Trancriptase kit (Invitrogen), according to the manufacturer’s protocol.  The quality of the extraction was controled with Agilent 2100 Bioanalyzer and quantification with NanoDrop ND-1000 spectrophotometer

treatment_protocol: After seven days of culture, the cells were infected or not with Mycobacterium tuberculosis at a Multiplicity of Infection of 3 bacteria/cell, during 0, 4 or 18 hours. The bacteria were grown in Middlebrook 7H9 culture medium (Difco) supplemented with 10% Albumin-Dextrose-Catalase (ADC, Difco), 0,05% Tween-80 (Sigma).

value: bone marrow derived dendritic cells

tag: sort

value: WT


title: DC from KO mice, 0h post-TB infection, rep3

description: Gene expression of BMDC from KO mice, after 0h of TB infection

value: DCIR Knockout


title: DC from KO mice, 4h post-TB infection, rep2

description: Gene expression of BMDC from KO mice, after 4h of TB infection


title: DC from KO mice, 18h post-TB infection, rep2

description: Gene expression of BMDC from KO mice, after 18h of TB infection


title: CPCG0381.2


title: DC from WT mice, 4h post-TB infection, rep2

description: Gene expression of BMDC from WT mice, after 4h of TB infection


title: DC from KO mice, 0h post-TB infection, rep4


title: DC from WT mice, 4h post-TB infection, rep4


title: DC from KO mice, 4h post-TB infection, rep4


title: DC from KO mice, 4h post-TB infection, rep1


title: DC from KO mice, 18h post-TB infection, rep1


title: DC from WT mice, 18h post-TB infection, rep3


title: DC from KO mice, 18h post-TB infection, rep4


title: CPCG0258


title: CPCG0362.2


title: CPCG0391.2


title: DC from KO mice, 0h post-TB infection, rep2


title: DC from WT mice, 4h post-TB infection, rep3


title: Distal blastema 14dpa DMSO-treated 3

description: Distal blastema 14 days after amputation treated with DMSO

value: 8.8cm total length


title: DC from WT mice, 4h post-TB infection, rep1


title: DC from WT mice, 0h post-TB infection, rep3

description: Gene expression of BMDC from WT mice, after 0h of TB infection


title: DC from WT mice, 0h post-TB infection, rep2


title: DC from WT mice, 0h post-TB infection, rep4


title: DC from KO mice, 0h post-TB infection, rep1


title: DC from KO mice, 4h post-TB infection, rep3


title: CPCG0375.2


title: DC from WT mice, 18h post-TB infection, rep4


title: DC from KO mice, 18h post-TB infection, rep3


title: BEAS-2B cells treated with PM2.5, biological rep3

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: cells treated with PM2.5

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

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: BEAS-2B cells

growth_protocol: BEAS-2B cells were seeded in petri dishes at density of 1×105 cells/mL and allowed to attach for 24 h, then treated with PM2.5 suspended in DMEM culture medium or DMEM culture mediun only for another 24 h.

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

treatment_protocol: Suspension of PM2.5 was dispersed by sonicator, and diluted to 50 μg/ml, then add to BEAS-2B cells immediately.Cells maintained in DMEM culture medium without PM2.5 were used as control group.

tag: cell type

value: bronchial epithelial cells

tag: treatment

value: PM2.5 suspended in DMEM


title: DC from WT mice, 18h post-TB infection, rep1

tag: tissue


title: CPCG0366.3


title: CPCG0365.4


title: CPCG0344.2


title: CPCG0374.2


title: CPCG0365.3


title: DC from WT mice, 0h post-TB infection, rep1

tag: genotype/variation


title: CPCG0189.3


title: CPCG0368.2


title: BEAS-2B cells as control, biological rep3

description: cells as normal control

value: DMEM


title: CPCG0360.2


title: CPCG0345.4


title: CPCG0189.2


title: CPCG0353.2


title: CPCG0392.3


title: CPCG0404.2


title: BEAS-2B cells treated with PM2.5, biological rep1

description: cells treated with PM2.5


title: CPCG0392.2


title: BEAS-2B cells treated with PM2.5, biological rep2

description: cells treated with PM2.5


title: CPCG0346.3


title: BEAS-2B cells as control, biological rep2

description: cells as normal control


title: BEAS-2B cells as control, biological rep1

description: cells as normal control


title: CPCG0345.2


title: CPCG0127


title: CPCG0087


title: CPCG0388.3


title: CPCG0256.2


title: CPCG0334.3


title: CPCG0078.2


title: CPCG0078


title: CPCG0255.2


title: CPCG0265.2


title: CPCG0184.2


title: CPCG0040


title: CPCG0388


title: CPCG0345


title: CPCG0242.3


title: CPCG0404


title: CPCG0256.3


title: CPCG0388.2


title: CPCG0242.2


title: CPCG0243


title: CPCG0073.2


title: CPCG0345.3


title: CPCG0346.2


title: CPCG0364.2


title: CPCG0340.2


title: CPCG0266.2


title: CPCG0040.2


title: CPCG0413


title: CPCG0027


title: CPCG0117


title: CPCG0410


title: CPCG0407


title: CPCG0379.2


title: CPCG0073


title: CPCG0256


title: CPCG0361.2


title: CPCG0341.2


title: CPCG0357.2


title: CPCG0366.2


title: CPCG0401


title: CPCG0365.2


title: CPCG0336.2


title: CPCG0380


title: CPCG0334.2


title: CPCG0392


title: CPCG0324.2


title: CPCG0409


title: CPCG0374


title: CPCG0412


title: CPCG0379


title: CPCG0391


title: CPCG0387


title: CPCG0371


title: CPCG0381


title: CPCG0372


title: CPCG0375


title: CPCG0378


title: CPCG0365


title: CPCG0366


title: CPCG0368


title: CPCG0369


title: CPCG0364


title: CPCG0358


title: CPCG0361


title: CPCG0362


title: CPCG0360


title: CPCG0357


title: CPCG0363


title: CPCG0356


title: CPCG0353


title: CPCG0355


title: CPCG0348


title: CPCG0350


title: CPCG0352


title: CPCG0346


title: CPCG0344


title: CPCG0340


title: CPCG0342


title: CPCG0341


title: CPCG0334


title: CPCG0336


title: CPCG0339


title: CPCG0269


title: CPCG0268


title: CPCG0263


title: CPCG0331


title: CPCG0265


title: CPCG0266


title: CPCG0182


title: CPCG0354


title: CPCG0373


title: CPCG0233.2


title: CPCG0242


title: CPCG0217


title: CPCG0232.2


title: CPCG0238


title: CPCG0246


title: CPCG0249


title: CPCG0250


title: CPCG0324


title: CPCG0236


title: CPCG0241


title: CPCG0255


title: CPCG0191.2


title: CPCG0208.2


title: CPCG0196.2


title: CPCG0185


title: CPCG0158


title: CPCG0154


title: CPCG0114


title: CPCG0248


title: CPCG0094


title: CPCG0251


title: CPCG0083


title: CPCG0260


title: CPCG0262


title: CPCG0057


title: CPCG0047


title: CPCG0190


title: CPCG0210.2


title: CPCG0048


title: CPCG0189


title: CPCG0259


title: CPCG0233


title: CPCG0184


title: CPCG0102


title: CPCG0183


title: CPCG0210


title: CPCG0099


title: CPCG0196


title: CPCG0191


title: CPCG0213


title: BR0001.2


title: INA-6 treated with EZH2 inhibitor UNC1999, biological rep 4

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

country: Sweden

institute: Rudbeck Laboratory, Uppsala University

description:
miRNA
MM cell line

hyb_protocol: Cyanine3-pCp labelled miRNA was hybridized for 20 hours at 55º C to 8x60K Human miRNA Microarray Slide (Release 21.0)

scan_protocol: The hybridized arrays were washed and then scanned with the Agilent DNA microarray scanner G2505C.

data_processing: Signal intensities was quantified from the scanned image by using Feature Extraction Software version 10.7.3.1. The data was processed using GeneSpring v13 software. The data was normalized using quantile normalization

source_name: Mature Plasma cells

label_protocol: 100 ng of total RNA was labelled using Agilent's miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) according to the manufacturer's instructions.

growth_protocol: The Multiple Myeloma INA-6 cell line was cultered in the presence of Intrerleukin-6 (IL-6) in RPMI-1640 AQmediaTM (Sigma) supplemented with 10% FBS (Sigma), 1%GlutaMax™ (Gibco) and antibiotics (penicillin 100U/ml and streptomycin 50 mg/mL; Sigma) at 37°C in a humidified 5% CO2 in-air atmosphere. ). For experimental setup of the 5 days exponentially growing cells were seeded at 100 000 cells/mL overnight before addition of reagents

extract_protocol: Total RNA was extracted using TRIzol® reagent (Invitrogen) and cleaned using the RNeasy MinElute Cleanup Kit (QIAGEN).

treatment_protocol: The Multiple Myeloma INA-6 cell line was treated with 1 µM of the EZH2 inhibitior UNC1999 or with 1 µM of the inactive from UNC2400 for 120 hours. Medium and reagents were refershed at 72 hours post-treatment.

tag: cell line


title: 9853741088_C

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using the Illumina iScan.

data_processing:
Quantile normalized and corrected for intra-experimental variation (Combat) generating robust gene-expression profiles (PMID: 20181233).
The liver and intestine samples were normalized separately.

source_name: intestine (s1=duodenum), chow, mouse 4

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems).

extract_protocol: Total RNA was extracted with TriReagent (Sigma, St. Louis, MO, USA). The quality and concentration of the RNA were determined using the Experion automated electrophoresis system (Bio-Rad Laboratories, Inc.). The RQI values returned ranged between 9.3-9.6.

treatment_protocol: 4 WT mice on chow and 4 WT mice on chow supplemented with FXR agonist PX20606 (PX) compound 10mg/kg/day for 2 weeks. Liver and intestine (s1=proximal, s3=distal) were collected from all 8 mice.

tag: strain/background

value: male

value: intestine (s1=duodenum)

value: chow

tag: mouse id


title: 9853741071_F

source_name: intestine (s3=distal), px, mouse 7

value: intestine (s3=distal)

value: chow + FXR agonist PX20606


title: 9853741071_D

source_name: intestine (s1=proximal), chow, mouse 5

value: intestine (s1=proximal)


title: BR90041


title: 9853741088_F

source_name: intestine (s3=distal), chow, mouse 5


title: BR90032


title: 9853741088_E

source_name: intestine (s3=distal), px, mouse 10


title: BR0450.2


title: 9853741088_D

source_name: intestine (s1=duodenum), px, mouse 9


title: 9853741070_E

source_name: intestine (s3=distal), chow, mouse 2


title: 9853741070_F

source_name: intestine (s3=distal), px, mouse 8


title: 9853741070_D

source_name: intestine (s1=proximal), px, mouse 7


title: INA-6 treated with control DMSO, biological rep 4

description:
miRNA
MM cell line


title: INA-6 treated with EZH2 inhibitor UNC1999, biological rep 3

description:
miRNA
MM cell line


title: 9853741070_C

source_name: intestine (s1=proximal), chow, mouse 1


title: 9853741071_C

source_name: intestine (s1=proximal), px, mouse 10


title: BR90022


title: BR90031


title: 9853741066_F

source_name: intestine (s3=distal), px, mouse 9


title: INA-6 treated with control DMSO, biological rep 2

description:
miRNA
MM cell line


title: INA-6 treated with EZH2 inhibitor UNC1999, biological rep 2

description:
miRNA
MM cell line


title: BR90012


title: 9853741071_E

source_name: intestine (s3=distal), chow, mouse 1


title: INA-6 treated with control DMSO, biological rep 3

description:
miRNA
MM cell line


title: 9853741066_E

source_name: intestine (s3=distal), chow, mouse 4


title: BR0450


title: BR90011


title: INA-6 treated with control DMSO, biological rep 1

description:
miRNA
MM cell line


title: INA-6 treated with EZH2 inhibitor UNC1999, biological rep 1

description:
miRNA
MM cell line


title: BR0001


title: PAO1 Rep3

city: Dayton

first: thusitha

last: Gunasekera

state: OH

address: Firwood Drive

department: University of Dayton Research Institute

institute: University of Dayton

description: Gene expression data from exponentailly grwoing cells in JetA

hyb_protocol: Following fragmentation 5 µg of cDNA were hybridized for 16 hrs on to P. aeruginosa  PAO1 Chips.   Hybridization 50o C for 16 hrs

scan_protocol: Microarray chips were scanned using the Affymetrix® GeneChip Scanner 3000.

data_processing: The Cell files (.cel) were uploaded into the Expression Console (ver 1.2.0.20), and background corrections, and normalizations were performed using MicroArray Suite 5.0 (MAS5.0) algorithms normalized CHP files were imported into the Affymetrix® Transcriptome Analysis Console.

organism: Pseudomonas aeruginosa

source_name: PAO1 in JetA R3

label_protocol: Five 5 µg of cDNA were fragmented and labeled with biotin

growth_protocol: The cells were grown in in 4 replicates in 50 ml polystyrene tubes with 20 ml of media overlaid with 5 ml Jet A fuel with shaking (200 rpm) at 28oC. The initial inoculum level was adjusted to an OD600 of 0.03.

extract_protocol: Total RNA was extracted for microarray uisng RNeasy Mini Kit as described by the manufacturer (Qiagen, Valencia, CA).

treatment_protocol: For RNA extractions, the cells were grown to mid log phase (0.4 -0.6 OD600) and then cooled rapidly on ice. Cells were harvested by centrifugation (4oC) with 10% ethanol/phenol (19:1) solution and the pellet was frozen immediately on dry ice and stored at -80oC.

tag: strain

value: P. aeruginosa PAO1


title: PAO1 Rep4

source_name: PAO1 in JetA R4


title: PAO1 Rep1

source_name: PAO1 in JetA R1


title: rapamycine NH4 vs rapamycine H2O replicate 1

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

institute: INRA

description: Biological replicate 1 of 2 of rapamycine and H2O addition vs. Biological replicate 1 of 2 of rapamycine and NH4 addition. Swap 2

hyb_protocol: Microarray hybridizations were performed using a Pronto Universal Microarray kit (Corning) according to manufacturer’s indications. Two biological replicates were done based on a dye swap design (S288C strain, 2 biological replicates with ammonium chloride addition and 2 biological replicates with water addition (control)).

scan_protocol: Microarrays were scanned using a GenePix pro 3 scanner (Axon Instruments).

data_processing: Data were processed using the R software (R2.9.2) and the Limma package (R Development Core Team 2010; Smyth 2005, Smyth et al. 2005; Smyth and Speed 2003). Within and between array normalizations were performed respectively by the print-tip-loess and quantile methods. Differentially expressed genes were identified through a linear model approach and a Benjamini-Hochberg method was used to adjust the p-values (Benjamini and Hochberg, 1995).

organism: Saccharomyces cerevisiae S288C

source_name: Total RNA of S288C strain

label_protocol: Retrotranscription and labeling were performed using a ChipShot direct labeling and clean-up system kit (Promega) according to manufacturer’s indications.

growth_protocol: An overnight cell pre-culture of S288c yeast strain was firstly obtained on a YEPD medium, before to transfer cells in an YNB medium for 32h. A constant population of cells was then nitrogen starved for 16h in an YNB-N medium in order to reach the stationary phase. Ammonium chloride (20 mM) or water (control) was then added to the medium after supplementation with rapamycin.

extract_protocol: After 30 minNH4 or H2O addition, sampling was performed in less than 1 min as followed: cells were filtrated under vacuum on a 0.45 µm HA membrane, collected and suspended in 1.5 ml DEPC water then stored at -80°C before RNA extraction. RNA were extracted from yeast cell culture as described previously (Chomczynski and Sacchi, 1987). The RNA concentrations were determined by measuring absorbance at 260 nm with a Nanodrop apparatus.

tag: addition at t0

tag: biological rep


title: rapamycine H2O vs rapamycine NH4 replicate 2

description: Biological replicate 2 of 2 of rapamycine and NH4 addition vs. Biological replicate 2 of 2 of rapamycine and H2O addition. Swap 2


title: 9853741071_B

source_name: liver, px, mouse 9

tag: Sex

value: liver


title: 9853741088_A

source_name: liver, chow, mouse 2


title: PAO1 Rep2

source_name: PAO1 in JetA R2


title: 9853741088_B

source_name: liver, px, mouse 8


title: 9853741071_A

source_name: liver, chow, mouse 4


title: BR0556


title: ATCC 33988 Rep4

source_name: ATCC in JetA R4

value: P.aeruginosa ATCC 33988


title: 9853741066_C

source_name: intestine (s1=proximal), chow, mouse 2


title: ATCC 33988 Rep3

source_name: ATCC in JetA R3


title: 9853741070_A

source_name: liver, px, mouse 10


title: 9853741066_B

source_name: liver, px, mouse 7


title: Gomez-Cabello DCGI1791-1793

city: Sevilla

first: Daniel

last: Gomez-Cabello

state: Sevilla

address: Americo Vespucio

institute: CABIMER

hyb_protocol: The hybridization was carried out according to the manufacturer's protocol. Arrays were scanned using an Agilent DNA Microarray scanner G2565CA (Agilent Technologies)

scan_protocol: Microarray data were extracted and visualized using Feature Extraction software v10.7 and Agilent Genomic Workbench (AGW) software v7.0 (Agilent Technologies)

data_processing: Copy number altered regions were detected using the Aberration Detection Method 2 (ADM-2) algorithm set as 6, with a minimum number of three consecutive probes

source_name: Mouse induced pluripotent stem cells

label_protocol: clone samples were differentially labeled by random priming with Cy5-dCTP and Cy3-dCTP

growth_protocol: induced pluripotent stem cells were kept in an undifferentiated, pluripotent state by using gelatin-coated plates with DMEM/F12+Glutamax (Gibco) supplemented with 20% knockout serum replacement (Gibco), 1000 U/mL LIF (Millipore), 1% non-essential amino acids, 0.1 mM β-mercaptoethanol and 100 units/mL penicillin (Sigma-Aldrich).

extract_protocol: Genomic DNA extraction were performed using DNeasy Blood & Tissue Kit (Cat No: 69504-Qiagen) folowing the manufacter´s intrucctions

tag: passage

value: Passage 2

tag: clone

value: shNT clone

value: shCtIp clone


title: Gomez-Cabello DCGI1790-1792

value: shCtip clone


title: rapamycine NH4 vs rapamycine H2O replicate 2

description: Biological replicate 2 of 2 of rapamycine and NH4 addition vs. Biological replicate 2 of 2 of rapamycine and H2O addition. Swap 1


title: 9853741066_D

source_name: intestine (s1=proximal), px, mouse 8

value: WT


title: ATCC 33988 Rep2

source_name: ATCC in JetA R2


title: ATCC 33988 Rep1

source_name: ATCC in JetA R1


title: CPCG0232

value: Sporadic

value: prostate tumor


title: H2O vs NH4 replicate 1

description: Biological replicate 1 of 2 of NH4 addition vs. Biological replicate 1 of 2 of H2O addition. Swap 2

growth_protocol: An overnight cell pre-culture of S288c yeast strain was firstly obtained on a YEPD medium, before to transfer cells in an YNB medium for 32h. A constant population of cells was then nitrogen starved for 16h in an YNB-N medium in order to reach the stationary phase. Ammonium chloride (20 mM) or water (control) was then added to the medium to compare the effect of nutrient replenishment on gene expression after 30 min.

extract_protocol: After 30 min treatment, sampling was performed in less than 1 min as followed: cells were filtrated under vacuum on a 0.45 µm HA membrane, collected and suspended in 1.5 ml DEPC water then stored at -80°C before RNA extraction. RNA were extracted from yeast cell culture as described previously (Chomczynski and Sacchi, 1987). The RNA concentrations were determined by measuring absorbance at 260 nm with a Nanodrop apparatus.


title: Transient overexpression of Pha21 Replicate 3

city: Taipei

first: Hsin-Hung

last: Yeh

address: No. 128, Sec. 2, Academia Road, Nankang,

department: ABRC

country: Taiwan

institute: Academia Sinica

hyb_protocol: All microarray hybridizations were followed Agilent Hybridization procedure at 65℃ for 17 hours.

scan_protocol: All chips were scanned by Agilent Microarray Scanner and scan settings were followed the manufacture suggestion.

data_processing: All Microarray data were normalized with UBQ 10 (PATC230548)  in GeneSpring GX 11 (Agilent, CA, USA)

organism: Phalaenopsis aphrodite

source_name: Leaves of Phalaenopsis aphrodite infiltrated with agrobacterium carrying Pha21-OE for transient overexpression

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye,  Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented at 60°C for 30 minutes before hybridization

extract_protocol: Total RNA from 0.2g leave tissue was extracted by using Trizol following manufacturer's instructions

treatment_protocol: Agroinfiltration was used to transiently overexpress Pha21 in leave tissue of Phalaenopsis aphrodite. The empty vector,  pK2GW7, and the Pha21-OE were transformed into Agrobacterium tumefaciens C58C1 (pTiB6S3ΔT)H by electroporation. Single colony of the A. tumefaciens strains were picked and cultured overnight at 28°C in 2 ml of yeast-extract buffer (YEB) medium containing appropriate antibiotics. The A. tumefaciens culture (2 ml) was then transferred into 20 ml of YEB medium containing appropriate antibiotics and incubated at 28°C until reaching an OD600 to 1.0. The cells were centrifuged at 3,000 × g for 10 min, and then re-suspended in 20 ml AB-MES medium (17.2 mM K2HPO4, 8.3 mM NaH2PO4, 18.7 mM NH4Cl, 2 mM KCl, 1.25 mM MgSO4, 100 μM CaCl2, 10 μM FeSO4, 50 mM MES, 2% glucose (w/v), pH 5.5) with 200 μm acetosyringone, then incubated at 28°C overnight. The cells were centrifuged at 3,000 × g for 10 min, and then the pellet was washed in 0.5× volume of sterile water. The cells was re-suspended in 2 ml of infiltration medium containing 50% MS medium (1/2 MS salt supplemented with 0.5% sucrose (w/v), pH 5.5), 50% AB-MES and 200 μm acetosyringone. Each P. aphrodite plant was infiltrated with A. tumefaciens suspension (100 μl/leaf).

value: leaf


title: NH4 vs H2O replicate 2

description: Biological replicate 2 of 2 of H2O addition vs. Biological replicate 2 of 2 of NH4 addition. Swap 2


title: H2O vs NH4 replicate 2

description: Biological replicate 2 of 2 of H2O addition vs. Biological replicate 2 of 2 of NH4 addition. Swap 1


title: 9853741070_B

source_name: liver, chow, mouse 5

value: male


title: Transient overexpression of Pha21 Replicate 2


title: CPCG0208


title: NH4 vs H2O replicate 1

description: Biological replicate 1 of 2 of NH4 addition vs. Biological replicate 1 of 2 of H2O addition. Swap 1

source_name: Total RNA of S288C strain


title: Control EV Replicate 2

source_name: Leaves of Phalaenopsis aphrodite infiltrated with agrobacterium carrying empty vector


title: progressive idiopathic pulomonary fibrosis 4

city: Birmingham

first: Victor

middle: John

last: Thannickal

state: AL

address: 1530 3rd Avenue South, THT 422

department: Medicine

institute: University of Alabama at Birmingham

description: Excluded (outlier)

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

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

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment. RMA was used to fit log2 transformed expression values

source_name: Bronchoalveolar lavage derived mesenchymal stromal cells

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA

growth_protocol: BAL fluid was collected from patient with stable and progressive IPF following patient informed consent and methods approved by the Institutional Review Board of the University of Alabama at Birmingham.  The cellular fraction of the BAL fluid is pelleted by centrifugation and plated on tissue culture plates at a density of 5 x 10^6 cells/100 mm dish.  The media is changed daily for the first two days and thrice weekly, thereafter.  This results in the removal of terminally differentiated, apoptotic cells and/or non-adherent cells, mainly inflammatory cell populations (macrophages).  By 10-14 days in cell culture, a number of colony forming units of MSCs (CFU-MSCs) are seen on Giemsa staining (Figure 1B, top panels).  Serial dilutions allowed an estimate of the number of clonally expanding cells in the original BAL; for example, in the patient represented, 4 colonies were visualized at 1:1000 dilutions, indicating ~4000 cells in the original 5 x 106 cells (0.08%). MSCs, at passage 1, show uniform staining for prolyl-4-hydroxylase and vimentin, supporting mesenchymal cell phenotype.  These cells lack expression of hematopoietic cell markers (CD14, CD34, and CD45), and express CD73, CD90, and CD105, typically associated MSCs, and demonstrate the capacity to differentiate into adipocytes, chondrocytes, and osteocytes, as we have shown previously (Lama et al., 2007).

extract_protocol: Qiagen Rneasy Mini Kit

treatment_protocol: 24 hrs serum deprivation before total RNA isolation

tag: diagnosis

value: Lungs


title: INA-6 treated with EZH2 inhibitor UNC1999, biological repl 3

description: MM cell line

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm,

scan_protocol: The arrays were scanned using Affymetrix Genechip Scanner.

data_processing:
The data was processed using GeneSpring v13 software. Where after background correction the data was normalized using quantile normalization and the summarization was done using ExonRMA 16 normilazation.
probe group file: HTA-2_0.r1.pgf
meta-probeset file: HTA-2_0.r1.Psrs.mps

source_name: Mature Plasma cells

label_protocol: The labeling of the RNA for microarray was done according the Affymetrix manufacturer protocol (Affymetrix).

extract_protocol: Total RNA was extracted using TRIzol® reagent (Invitrogen) and cleaned using the Rneasy MinElute Cleanup Kit (QIAGEN).


title: Transient overexpression of Pha21 Replicate 1


title: INA-6 treated with control UNC2400, biological repl 3

description: MM cell line


title: Transient overexpression of Pha13 Replicate 3

source_name: Leaves of Phalaenopsis aphrodite infiltrted with agrobacterium carrying Pha13-OE for transient overexpression

treatment_protocol: Agroinfiltration was used to transiently overexpress Pha13 in leave tissue of Phalaenopsis aphrodite. The empty vector,  pK2GW7, and the Pha13-OE were transformed into Agrobacterium tumefaciens C58C1 (pTiB6S3ΔT)H by electroporation. Single colony of the A. tumefaciens strains were picked and cultured overnight at 28°C in 2 ml of yeast-extract buffer (YEB) medium containing appropriate antibiotics. The A. tumefaciens culture (2 ml) was then transferred into 20 ml of YEB medium containing appropriate antibiotics and incubated at 28°C until reaching an OD600 to 1.0. The cells were centrifuged at 3,000 × g for 10 min, and then re-suspended in 20 ml AB-MES medium (17.2 mM K2HPO4, 8.3 mM NaH2PO4, 18.7 mM NH4Cl, 2 mM KCl, 1.25 mM MgSO4, 100 μM CaCl2, 10 μM FeSO4, 50 mM MES, 2% glucose (w/v), pH 5.5) with 200 μm acetosyringone, then incubated at 28°C overnight. The cells were centrifuged at 3,000 × g for 10 min, and then the pellet was washed in 0.5× volume of sterile water. The cells was re-suspended in 2 ml of infiltration medium containing 50% MS medium (1/2 MS salt supplemented with 0.5% sucrose (w/v), pH 5.5), 50% AB-MES and 200 μm acetosyringone. Each P. aphrodite plant was infiltrated with A. tumefaciens suspension (100 μl/leaf).


title: 9853741066_A

source_name: liver, chow, mouse 1

value: chow


title: INA-6 treated with EZH2 inhibitor UNC1999, biological repl 2

description: MM cell line


title: progressive idiopathic pulomonary fibrosis 2

description: mRNA expression


title: Control EV Replicate 1


title: progressive idiopathic pulomonary fibrosis 3

description: mRNA expression


title: INA-6 treated with control UNC2400, biological repl 2

description: MM cell line


title: Control EV Replicate 3


title: Transient overexpression of Pha13 Replicate 1


title: Transient overexpression of Pha13 Replicate 2


title: Control Empty vector Replicate 3

source_name: Leaves of Phalaenopsis aphrodite infiltrted with agrobacterium carrying empty vector


title: INA-6 treated with control UNC2400, biological repl 1

description: MM cell line


title: Blood_H56+GLA-SE_168hr_animal7

status: Public on Jan 09 2017

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

institute: MPIIB

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse whole blood
F28_WB

hyb_protocol: Quantity and labelling efficiency were verified before hybridization to human whole genome microarrays (Agilent Technologies)

scan_protocol: Scanned on an Agilent Scanner G2505B. Image analysis was performed with Feature Extraction software (version 6.1.1, Agilent Technologies).

data_processing: Data were processed, quantile normalized and analyzed using the R package Lima (Ritchie et al (2015). Nucleic Acids Research, 43(7), pp. e47)

source_name: Whole blood

label_protocol: RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: RNA was extracted from lymph nodes and whole blood using the RNeasy Mini QIAcube kit (Qiagen) and PAXgene kit (Qiagen), respectively.

treatment_protocol: Anesthesized mice were injected sub cuntaneous with 100 microliter vaccine/adjuvants combination

tag: group

value: whole blood

tag: timepoint


title: stable idiopathic pulomonary fibrosis 3

description: Excluded (outlier)

value: stable idiopathic pulomonary fibrosis


title: stable idiopathic pulomonary fibrosis 4

description: mRNA expression


title: stable idiopathic pulomonary fibrosis 2

description: mRNA expression


title: Blood_H56+GLA-SE_168hr_animal5

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse whole blood
F25_WB


title: Blood_H56+GLA-SE_168hr_animal6

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse whole blood
F26_WB


title: stable idiopathic pulomonary fibrosis 1

description: mRNA expression


title: INA-6 treated with EZH2 inhibitor UNC1999, biological repl 1

description: MM cell line


title: progressive idiopathic pulomonary fibrosis 1

description: mRNA expression


title: Blood_H56+GLA-SE_168hr_animal4

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse whole blood
F27_WB


title: Blood_H56+GLA-SE_72hr_animal6

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse whole blood
F19_WB


title: Blood_H56+GLA-SE_168hr_animal2

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse whole blood
F24_WB


title: CA-3_2

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: Cabernet Sauvignon berries collected at time point T3 of the post-harvest withering process, replicate 2

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Grape berries were harvested at full maturity during vintage 2010 in a commercial vineyard located in the province of Verona.

extract_protocol: Total RNA was extracted from ~200 mg of berry (pericarp) using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO) with some modifications as reported in Fasoli, et al. (2012). RNA quality and quantity were assessed using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and a Bioanalyzer Chip RNA 7500 series II (Agilent, Santa Clara, CA).

treatment_protocol: Grape berries harvested at full maturity were placed in barns under controlled conditions to undergo post-harvest withering process.

value: Berries (pericarp)

tag: sampling time points (days after harvest = t0)

value: time point T3, 47 days after harvest

tag: % weight compared to harvest

tag: cultivar

value: Vitis Vinifera cv Cabernet Sauvignon


title: Control Empty vector Replicate 2

tag: tissue


title: Blood_H56+GLA-SE_72hr_animal5

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse whole blood
F20_WB

tag: treatment


title: Blood_H56+GLA-SE_168hr_animal3

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse whole blood
F22_WB


title: Blood_H56+GLA-SE_72hr_animal7

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse whole blood
F18_WB


title: CA-3_1

source_name: Cabernet Sauvignon berries collected at time point T3 of the post-harvest withering process, replicate 1


title: Blood_H56+GLA-SE_168hr_animal1

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse whole blood
F23_WB


title: CA-3_3

source_name: Cabernet Sauvignon berries collected at time point T3 of the post-harvest withering process, replicate 3


title: CA-2_3

source_name: Cabernet Sauvignon berries collected at time point T2 of the post-harvest withering process, replicate 3

value: time point T2, 26 days after harvest


title: Control Empty vector Replicate 1


title: Blood_H56+GLA-SE_72hr_animal2

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse whole blood
F16_WB


title: CA-1_1

source_name: Cabernet Sauvignon berries collected at time point T1 of the post-harvest withering process, replicate 1

value: time point T1, 13 days after harvest


title: CA-1_2

source_name: Cabernet Sauvignon berries collected at time point T1 of the post-harvest withering process, replicate 2


title: CA-2_1

source_name: Cabernet Sauvignon berries collected at time point T2 of the post-harvest withering process, replicate 1


title: Blood_H56+GLA-SE_72hr_animal1

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse whole blood
F21_WB


title: Blood_H56+GLA-SE_72hr_animal4

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse whole blood
F15_WB


title: CA-2_2

source_name: Cabernet Sauvignon berries collected at time point T2 of the post-harvest withering process, replicate 2


title: CA-0_3

source_name: Cabernet Sauvignon berries collected at time point T0 of the post-harvest withering process, replicate 3

value: time point T0, 0 days after harvest


title: BR90021

tag: ^sample

tag: disease state


title: CA-1_3

source_name: Cabernet Sauvignon berries collected at time point T1 of the post-harvest withering process, replicate 3


title: Blood_H56+GLA-SE_72hr_animal3

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse whole blood
F17_WB


title: Blood_H56+GLA-SE_24hr_animal6

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse whole blood
F12_WB


title: Blood_H56+GLA-SE_24hr_animal4

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse whole blood
F8_WB


title: Blood_H56+GLA-SE_24hr_animal5

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse whole blood
F11_WB


title: CA-0_2

source_name: Cabernet Sauvignon berries collected at time point T0 of the post-harvest withering process, replicate 2


title: Blood_H56+GLA-SE_24hr_animal7

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse whole blood
F13_WB


title: CA-0_1

source_name: Cabernet Sauvignon berries collected at time point T0 of the post-harvest withering process, replicate 1


title: rapamycine H2O vs rapamycine NH4 replicate 1

description: Biological replicate 1 of 2 of rapamycine and H2O addition vs. Biological replicate 1 of 2 of rapamycine and NH4 addition. Swap 1

source_name: Total RNA of S288C strain


title: Blood_H56+GLA-SE_24hr_animal2

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse whole blood
F14_WB


title: OS-3_2

source_name: Oseleta berries collected at time point T3 of the post-harvest withering process, replicate 2

value: Vitis Vinifera cv Oseleta


title: Blood_H56+GLA-SE_24hr_animal3

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse whole blood
F9_WB


title: Blood_H56+GLA-SE_24hr_animal1

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse whole blood
F10_WB


title: OS-2_2

source_name: Oseleta berries collected at time point T2 of the post-harvest withering process, replicate 2


title: Blood_H56+GLA-SE_6hr_animal7

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse whole blood
F6_WB


title: OS-3_1

source_name: Oseleta berries collected at time point T3 of the post-harvest withering process, replicate 1


title: Blood_H56+GLA-SE_6hr_animal6

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse whole blood
F5_WB

source_name: Whole blood


title: OS-2_3

source_name: Oseleta berries collected at time point T2 of the post-harvest withering process, replicate 3


title: Blood_H56+GLA-SE_6hr_animal5

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse whole blood
F7_WB


title: OS-2_1

source_name: Oseleta berries collected at time point T2 of the post-harvest withering process, replicate 1


title: Blood_H56+GLA-SE_6hr_animal3

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse whole blood
F4_WB


title: Blood_H56+GLA-SE_6hr_animal2

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse whole blood
F3_WB


title: OS-1_2

source_name: Oseleta berries collected at time point T1 of the post-harvest withering process, replicate 2


title: Blood_H56+GLA-SE_6hr_animal4

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse whole blood
F1_WB


title: OS-0_2

source_name: Oseleta berries collected at time point T0 of the post-harvest withering process, replicate 2


title: OS-0_3

source_name: Oseleta berries collected at time point T0 of the post-harvest withering process, replicate 3


title: OS-1_1

source_name: Oseleta berries collected at time point T1 of the post-harvest withering process, replicate 1


title: OS-3_3

source_name: Oseleta berries collected at time point T3 of the post-harvest withering process, replicate 3


title: OS-1_3

source_name: Oseleta berries collected at time point T1 of the post-harvest withering process, replicate 3


title: Blood_H56+GLA-SE_6hr_animal1

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse whole blood
F2_WB


title: Blood_H56+IC31_168hr_animal5

description:
Gene expression after 168hr in H56+IC31-treated mouse whole blood
E26_WB


title: Blood_H56+IC31_168hr_animal4

description:
Gene expression after 168hr in H56+IC31-treated mouse whole blood
E27_WB


title: SY-3_2

source_name: Syrah berries collected at time point T3 of the post-harvest withering process, replicate 2

value: Vitis Vinifera cv Syrah


title: Blood_H56+IC31_168hr_animal6

description:
Gene expression after 168hr in H56+IC31-treated mouse whole blood
E25_WB


title: SY-3_3

source_name: Syrah berries collected at time point T3 of the post-harvest withering process, replicate 3


title: OS-0_1

source_name: Oseleta berries collected at time point T0 of the post-harvest withering process, replicate 1


title: Blood_H56+IC31_168hr_animal3

description:
Gene expression after 168hr in H56+IC31-treated mouse whole blood
E22_WB


title: SY-2_2

source_name: Syrah berries collected at time point T2 of the post-harvest withering process, replicate 2


title: Blood_H56+IC31_168hr_animal2

description:
Gene expression after 168hr in H56+IC31-treated mouse whole blood
E24_WB


title: Blood_H56+IC31_168hr_animal1

description:
Gene expression after 168hr in H56+IC31-treated mouse whole blood
E23_WB


title: Blood_H56+IC31_72hr_animal7

description:
Gene expression after 72hr in H56+IC31-treated mouse whole blood
E18_WB


title: SY-2_3

source_name: Syrah berries collected at time point T2 of the post-harvest withering process, replicate 3


title: Blood_H56+IC31_72hr_animal4

description:
Gene expression after 72hr in H56+IC31-treated mouse whole blood
E15_WB


title: SY-2_1

source_name: Syrah berries collected at time point T2 of the post-harvest withering process, replicate 1


title: SY-1_3

source_name: Syrah berries collected at time point T1 of the post-harvest withering process, replicate 3


title: SY-3_1

source_name: Syrah berries collected at time point T3 of the post-harvest withering process, replicate 1


title: Blood_H56+IC31_72hr_animal5

description:
Gene expression after 72hr in H56+IC31-treated mouse whole blood
E19_WB

source_name: Whole blood


title: SY-1_2

source_name: Syrah berries collected at time point T1 of the post-harvest withering process, replicate 2


title: SY-1_1

source_name: Syrah berries collected at time point T1 of the post-harvest withering process, replicate 1


title: SY-0_2

source_name: Syrah berries collected at time point T0 of the post-harvest withering process, replicate 2


title: Blood_H56+IC31_72hr_animal6

description:
Gene expression after 72hr in H56+IC31-treated mouse whole blood
E20_WB


title: Blood_H56+IC31_24hr_animal7

description:
Gene expression after 24hr in H56+IC31-treated mouse whole blood
E13_WB


title: SY-0_1

source_name: Syrah berries collected at time point T0 of the post-harvest withering process, replicate 1


title: Blood_H56+IC31_72hr_animal1

description:
Gene expression after 72hr in H56+IC31-treated mouse whole blood
E21_WB


title: Blood_H56+IC31_168hr_animal7

description:
Gene expression after 168hr in H56+IC31-treated mouse whole blood
E28_WB


title: SY-0_3

source_name: Syrah berries collected at time point T0 of the post-harvest withering process, replicate 3


title: Blood_H56+IC31_72hr_animal2

description:
Gene expression after 72hr in H56+IC31-treated mouse whole blood
E16_WB


title: M-4_3

source_name: Merlot berries collected at time point T4 of the post-harvest withering process, replicate 3

value: time point T4, 70 days after harvest

value: Vitis Vinifera cv Merlot


title: Blood_H56+IC31_72hr_animal3

description:
Gene expression after 72hr in H56+IC31-treated mouse whole blood
E17_WB


title: Blood_H56+IC31_24hr_animal4

description:
Gene expression after 24hr in H56+IC31-treated mouse whole blood
E14_WB


title: M-3_3

source_name: Merlot berries collected at time point T3 of the post-harvest withering process, replicate 3


title: Blood_H56+IC31_24hr_animal5

description:
Gene expression after 24hr in H56+IC31-treated mouse whole blood
E11_WB


title: M-4_1

source_name: Merlot berries collected at time point T4 of the post-harvest withering process, replicate 1


title: M-3_2

source_name: Merlot berries collected at time point T3 of the post-harvest withering process, replicate 2


title: M-4_2

source_name: Merlot berries collected at time point T4 of the post-harvest withering process, replicate 2


title: Blood_H56+IC31_24hr_animal6

description:
Gene expression after 24hr in H56+IC31-treated mouse whole blood
E12_WB


title: Blood_H56+IC31_24hr_animal3

description:
Gene expression after 24hr in H56+IC31-treated mouse whole blood
E8_WB


title: M-3_1

source_name: Merlot berries collected at time point T3 of the post-harvest withering process, replicate 1


title: M-2_2

source_name: Merlot berries collected at time point T2 of the post-harvest withering process, replicate 2


title: Blood_H56+IC31_24hr_animal1

description:
Gene expression after 24hr in H56+IC31-treated mouse whole blood
E10_WB


title: Blood_H56+IC31_6hr_animal7

description:
Gene expression after 6hr in H56+IC31-treated mouse whole blood
E6_WB


title: M-2_1

source_name: Merlot berries collected at time point T2 of the post-harvest withering process, replicate 1


title: Blood_H56+IC31_6hr_animal5

description:
Gene expression after 6hr in H56+IC31-treated mouse whole blood
E7_WB


title: M-2_3

source_name: Merlot berries collected at time point T2 of the post-harvest withering process, replicate 3


title: Blood_H56+IC31_6hr_animal4

description:
Gene expression after 6hr in H56+IC31-treated mouse whole blood
E1_WB


title: M-1_2

source_name: Merlot berries collected at time point T1 of the post-harvest withering process, replicate 2


title: Blood_H56+IC31_6hr_animal3

description:
Gene expression after 6hr in H56+IC31-treated mouse whole blood
E4_WB


title: M-1_3

source_name: Merlot berries collected at time point T1 of the post-harvest withering process, replicate 3


title: Blood_H56+IC31_24hr_animal2

description:
Gene expression after 24hr in H56+IC31-treated mouse whole blood
E9_WB

source_name: Whole blood


title: M-0_3

source_name: Merlot berries collected at time point T0 of the post-harvest withering process, replicate 3


title: M-0_2

source_name: Merlot berries collected at time point T0 of the post-harvest withering process, replicate 2


title: SG-5_2

source_name: Sangiovese berries collected at time point T5 of the post-harvest withering process, replicate 2

value: time point T5, 100 days after harvest

value: Vitis Vinifera cv Sangiovese


title: M-1_1

source_name: Merlot berries collected at time point T1 of the post-harvest withering process, replicate 1


title: Blood_H56+IC31_6hr_animal1

description:
Gene expression after 6hr in H56+IC31-treated mouse whole blood
E2_WB


title: Blood_H56+IC31_6hr_animal2

description:
Gene expression after 6hr in H56+IC31-treated mouse whole blood
E3_WB


title: Blood_H56+IC31_6hr_animal6

description:
Gene expression after 6hr in H56+IC31-treated mouse whole blood
E5_WB


title: SG-5_1

source_name: Sangiovese berries collected at time point T5 of the post-harvest withering process, replicate 1


title: Blood_H56+CAF01_168hr_animal7

description:
Gene expression after 168hr in H56+CAF01-treated mouse whole blood
D28_WB


title: M-0_1

source_name: Merlot berries collected at time point T0 of the post-harvest withering process, replicate 1


title: Blood_H56+CAF01_168hr_animal6

description:
Gene expression after 168hr in H56+CAF01-treated mouse whole blood
D25_WB


title: SG-4_1

source_name: Sangiovese berries collected at time point T4 of the post-harvest withering process, replicate 1


title: Blood_H56+CAF01_168hr_animal3

description:
Gene expression after 168hr in H56+CAF01-treated mouse whole blood
D22_WB


title: Blood_H56+CAF01_72hr_animal7

description:
Gene expression after 72hr in H56+CAF01-treated mouse whole blood
D18_WB


title: SG-4_2

source_name: Sangiovese berries collected at time point T4 of the post-harvest withering process, replicate 2


title: Blood_H56+CAF01_168hr_animal4

description:
Gene expression after 168hr in H56+CAF01-treated mouse whole blood
D27_WB


title: Blood_H56+CAF01_168hr_animal2

description:
Gene expression after 168hr in H56+CAF01-treated mouse whole blood
D24_WB


title: Blood_H56+CAF01_168hr_animal5

description:
Gene expression after 168hr in H56+CAF01-treated mouse whole blood
D26_WB


title: Blood_H56+CAF01_168hr_animal1

description:
Gene expression after 168hr in H56+CAF01-treated mouse whole blood
D23_WB


title: SG-5_3

source_name: Sangiovese berries collected at time point T5 of the post-harvest withering process, replicate 3


title: SG-4_3

source_name: Sangiovese berries collected at time point T4 of the post-harvest withering process, replicate 3


title: Blood_H56+CAF01_72hr_animal5

description:
Gene expression after 72hr in H56+CAF01-treated mouse whole blood
D19_WB


title: SG-3_2

source_name: Sangiovese berries collected at time point T3 of the post-harvest withering process, replicate 2


title: Blood_H56+CAF01_72hr_animal4

description:
Gene expression after 72hr in H56+CAF01-treated mouse whole blood
D15_WB


title: Blood_H56+CAF01_72hr_animal3

description:
Gene expression after 72hr in H56+CAF01-treated mouse whole blood
D16_WB


title: Blood_H56+CAF01_72hr_animal6

description:
Gene expression after 72hr in H56+CAF01-treated mouse whole blood
D20_WB


title: SG-2_1

source_name: Sangiovese berries collected at time point T2 of the post-harvest withering process, replicate 1


title: Blood_H56+CAF01_24hr_animal6

description:
Gene expression after 24hr in H56+CAF01-treated mouse whole blood
D12_WB


title: Blood_H56+CAF01_72hr_animal2

description:
Gene expression after 72hr in H56+CAF01-treated mouse whole blood
D21_WB


title: SG-2_2

source_name: Sangiovese berries collected at time point T2 of the post-harvest withering process, replicate 2


title: SG-3_3

source_name: Sangiovese berries collected at time point T3 of the post-harvest withering process, replicate 3


title: SG-3_1

source_name: Sangiovese berries collected at time point T3 of the post-harvest withering process, replicate 1


title: SG-1_3

source_name: Sangiovese berries collected at time point T1 of the post-harvest withering process, replicate 3


title: SG-2_3

source_name: Sangiovese berries collected at time point T2 of the post-harvest withering process, replicate 3


title: Blood_H56+CAF01_24hr_animal5

description:
Gene expression after 24hr in H56+CAF01-treated mouse whole blood
D14_WB

source_name: Whole blood


title: SG-1_1

source_name: Sangiovese berries collected at time point T1 of the post-harvest withering process, replicate 1


title: Blood_H56+CAF01_24hr_animal7

description:
Gene expression after 24hr in H56+CAF01-treated mouse whole blood
D13_WB


title: Blood_H56+CAF01_72hr_animal1

description:
Gene expression after 72hr in H56+CAF01-treated mouse whole blood
D17_WB


title: SG-1_2

source_name: Sangiovese berries collected at time point T1 of the post-harvest withering process, replicate 2


title: SG-0_2

source_name: Sangiovese berries collected at time point T0 of the post-harvest withering process, replicate 2


title: SG-0_3

source_name: Sangiovese berries collected at time point T0 of the post-harvest withering process, replicate 3


title: SG-0_1

source_name: Sangiovese berries collected at time point T0 of the post-harvest withering process, replicate 1


title: Blood_H56+CAF01_24hr_animal3

description:
Gene expression after 24hr in H56+CAF01-treated mouse whole blood
D11_WB


title: Blood_H56+CAF01_24hr_animal2

description:
Gene expression after 24hr in H56+CAF01-treated mouse whole blood
D9_WB


title: Blood_H56+CAF01_24hr_animal4

description:
Gene expression after 24hr in H56+CAF01-treated mouse whole blood
D8_WB


title: C-5_1

source_name: Corvina berries collected at time point T5 of the post-harvest withering process, replicate 1

value: Vitis Vinifera cv Corvina


title: Blood_H56+CAF01_6hr_animal6

description:
Gene expression after 6hr in H56+CAF01-treated mouse whole blood
D5_WB


title: C-5_3

source_name: Corvina berries collected at time point T5 of the post-harvest withering process, replicate 3


title: C-4_1

source_name: Corvina berries collected at time point T4 of the post-harvest withering process, replicate 1


title: C-3_1

source_name: Corvina berries collected at time point T3 of the post-harvest withering process, replicate 1


title: Blood_H56+CAF01_6hr_animal2

description:
Gene expression after 6hr in H56+CAF01-treated mouse whole blood
D3_WB


title: Blood_H56+CAF01_24hr_animal1

description:
Gene expression after 24hr in H56+CAF01-treated mouse whole blood
D10_WB


title: C-4_2

source_name: Corvina berries collected at time point T4 of the post-harvest withering process, replicate 2


title: C-5_2

source_name: Corvina berries collected at time point T5 of the post-harvest withering process, replicate 2


title: Blood_H56+CAF01_6hr_animal5

description:
Gene expression after 6hr in H56+CAF01-treated mouse whole blood
D7_WB


title: C-4_3

source_name: Corvina berries collected at time point T4 of the post-harvest withering process, replicate 3


title: Blood_H56+CAF01_6hr_animal4

description:
Gene expression after 6hr in H56+CAF01-treated mouse whole blood
D1_WB


title: C-2_1

source_name: Corvina berries collected at time point T2 of the post-harvest withering process, replicate 1


title: C-3_2

source_name: Corvina berries collected at time point T3 of the post-harvest withering process, replicate 2


title: Blood_H56+Alum_168hr_animal7

description:
Gene expression after 168hr in H56+Alum-treated mouse whole blood
C25_WB


title: C-3_3

source_name: Corvina berries collected at time point T3 of the post-harvest withering process, replicate 3


title: Blood_H56+Alum_168hr_animal3

description:
Gene expression after 168hr in H56+Alum-treated mouse whole blood
C24_WB


title: C-2_2

source_name: Corvina berries collected at time point T2 of the post-harvest withering process, replicate 2


title: Blood_H56+CAF01_6hr_animal1

description:
Gene expression after 6hr in H56+CAF01-treated mouse whole blood
D2_WB

source_name: Whole blood


title: Blood_H56+Alum_168hr_animal4

description:
Gene expression after 168hr in H56+Alum-treated mouse whole blood
C22_WB


title: Blood_H56+CAF01_6hr_animal3

description:
Gene expression after 6hr in H56+CAF01-treated mouse whole blood
D4_WB


title: C-1_3

source_name: Corvina berries collected at time point T1 of the post-harvest withering process, replicate 3


title: Blood_H56+CAF01_6hr_animal7

description:
Gene expression after 6hr in H56+CAF01-treated mouse whole blood
D6_WB


title: C-1_1

source_name: Corvina berries collected at time point T1 of the post-harvest withering process, replicate 1


title: Blood_H56+Alum_168hr_animal6

description:
Gene expression after 168hr in H56+Alum-treated mouse whole blood
C26_WB


title: C-1_2

source_name: Corvina berries collected at time point T1 of the post-harvest withering process, replicate 2


title: C-2_3

source_name: Corvina berries collected at time point T2 of the post-harvest withering process, replicate 3


title: Blood_H56+Alum_168hr_animal5

description:
Gene expression after 168hr in H56+Alum-treated mouse whole blood
C27_WB


title: C-0_3

source_name: Corvina berries collected at time point T0 of the post-harvest withering process, replicate 3


title: C-0_1

source_name: Corvina berries collected at time point T0 of the post-harvest withering process, replicate 1


title: Blood_H56+Alum_72hr_animal7

description:
Gene expression after 72hr in H56+Alum-treated mouse whole blood
C20_WB


title: Blood_H56+Alum_168hr_animal1

description:
Gene expression after 168hr in H56+Alum-treated mouse whole blood
C28_WB


title: Blood_H56+Alum_72hr_animal5

description:
Gene expression after 72hr in H56+Alum-treated mouse whole blood
C19_WB


title: C-0_2

source_name: Corvina berries collected at time point T0 of the post-harvest withering process, replicate 2


title: Blood_H56+Alum_72hr_animal6

description:
Gene expression after 72hr in H56+Alum-treated mouse whole blood
C18_WB


title: Blood_H56+Alum_168hr_animal2

description:
Gene expression after 168hr in H56+Alum-treated mouse whole blood
C23_WB


title: Blood_H56+Alum_24hr_animal7

description:
Gene expression after 24hr in H56+Alum-treated mouse whole blood
C13_WB


title: Blood_H56+Alum_72hr_animal1

description:
Gene expression after 72hr in H56+Alum-treated mouse whole blood
C17_WB


title: Blood_H56+Alum_72hr_animal3

description:
Gene expression after 72hr in H56+Alum-treated mouse whole blood
C16_WB


title: Blood_H56+Alum_72hr_animal4

description:
Gene expression after 72hr in H56+Alum-treated mouse whole blood
C15_WB


title: Blood_H56+Alum_72hr_animal2

description:
Gene expression after 72hr in H56+Alum-treated mouse whole blood
C21_WB