title: YY1 IP of XTC.UC1 cells after 48h serum induction-slide 1&2

city: TOULOUSE

first: Savagner

last: Frederique

address: Avenue Jean Poulhes

institute: Inserm

hyb_protocol: WGA amplicons were applied to Agilent Human Promoter ChIP on chip arrays 244K, containing 17,000 60-mer probes per array (Agilent Technologies, Santa Clara, CA, USA) also including miRNA gene promoters.

scan_protocol: The arrays were scanned at 5-μm resolution on a scanner G2505C (Agilent Technologies)

data_processing: Data for slide 1 and 2 were combined in a single matrix template to process for normalization.  Dark corner and spike data were removed on the normalized  matrix. A threshold spline curve was then defined only considering the probes beyond this axis. Reporting this curve beyond the spline threshold allowed selecting positive probes. It also allowed defining p-values by using normalised distances between probes and the x=y axis.

label_protocol: Cy5 (IP factors)and Cy3 labeling (IgG or input) of DNA samples for ChIP-chip analysis was performed using procedures previously described [Lamirault et al, J Mol Cell Cardiol, 2006]

growth_protocol: The growth medium consisted of Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% foetal calf serum (Seromed, Merck, Darmstadt, Germany), 100 U/mL penicillin, 100 mg/mL streptomycin, 0.25 mg/mL fungizone, and 10 mU/mL thyrotropin (TSH) (Sigma-Aldrich, Saint Louis, MO, USA). Except for the TSH and the foetal calf serum, all the products were obtained from Gibco BRL (Life Technologies, Thermo Fisher Scientific, Waltham, Massachusetts, USA).The growth medium consisted of Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% foetal calf serum (Seromed, Merck, Darmstadt, Germany), 100 U/mL penicillin, 100 mg/mL streptomycin, 0.25 mg/mL fungizone, and 10 mU/mL thyrotropin (TSH) (Sigma-Aldrich, Saint Louis, MO, USA). Except for the TSH and the foetal calf serum, all the products were obtained from Gibco BRL (Life Technologies, Thermo Fisher Scientific, Waltham, Massachusetts, USA).

extract_protocol: To obtain enough ChIP-DNA for genomic microarray hybridization, immunoprecipitated and input DNA were dissolved in 50 µl of H2O and purfied usinf QIAquick (Qiagen, Hilden, Germany) and were amplified twice using the Sigma GenomePlex WGA2 kit (Sigma-Aldrich).

treatment_protocol: ChIP assays were performed on 10^6 XTC.UC1 cells/assay after 24h and 48h of 10% serum induction following the protocol provided by the manufacturer (EZ-ChIP, Upstate, Merck) after crosslink by 1% formaldehyde and sonication.

value: oncoytic thyroid cell line

tag: factor used for ip

value: IP YY1 XTC.UC1 cells

tag: chip antibody

value: YY1 (Abcam, monoclonal, reference12132)

tag: time after 20% serum induction

source_name: IgG IP of XTC.UC1 cells after 24h serum induction

value: IP IgG XTC.UC1 cells

value: IgG (MP Biomedicals, polyclonal whole molecule, reference 55335)


title: S16 Gut rep2

status: Public on Nov 07 2017

type: RNA

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

country: USA

institute: LC Sciences

description: Hco ISE (MHco3)

hyb_protocol: Hybridization was performed overnight (16 hours) on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) ((a)Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (Bolstad et al, 2003).  Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

molecule: total RNA

organism: Haemonchus contortus

source_name: Adult female gut tissue dissected out

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: total RNA extracted using trizol (Invitrogen)

tag: strain

value: Hco ISE (MHco3)

tag: tissue

value: gut

tag: developmental stage

value: adult

tag: Sex

value: female


title: BM-MSCs_normal control_endothelial induced_3 days_rep3

city: Shanghai

first: Jie

last: Tao

address: haining road 100

country: China

institute: Shanghai General Hospital

description: Gene expression data from normal bone marrow mesenchymal stem cells which were endothelial induced for 3 days.

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA.

label: biotin

organism: Homo sapiens

source_name: Bone marrow mesenchymal stem cells,endothelial induced,3 days

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: Bone marrow mesenchymal stem cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 5% CO2 and 95% air, according to the standard procedure. The cell lines were routinely passaged using an enzymatic solution consisting of 0.25% (w/v) trypsin for 5 min at 37°C.

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

treatment_protocol: The third generation cells, with 1 × 10^4 cells/well, were transferred onto a 12-well plate. After 24 h, endothelial cell induction was performed with induction medium (low glucose DMEM containing 10% FBS). Endothelial induced for 3 days. Then rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

value: Human bone marrow

tag: cell type

value: endothelial cells induced from bone marrow mesenchymal stem cells

tag: genotype/variation

value: control


title: Heart_YQFM_rep4

city: Hangzhou

first: YU

last: ZHAO

address: Yuhangtang Road 388#

institute: College of Pharmeceutical Sciences

description: miRNA from Yiqifumai Powder Injection group

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total miRNA was dephosphorylated, denaturated and then labeled with Cyanine-3-CTP. After purification the labeled miRNAs were hybridized onto the microarray. After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

scan_protocol: Assemble the slides into an slide holder. Place assembled slide holders into scanner carousel. Verify scan settings for miRNA.Scan area is 61×21.6mm,scan resolution:5 μm,single pass.eXtended Dynamic range:selected. Dye channel:green. Green PMT:XDR Hi 100%,XDR Lo 10%.

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.

organism: Rattus norvegicus

source_name: heart, YQFM, replicate 5

extract_protocol: Total miRNA was extracted from rat using mirVanaTM RNA Isolation Kit according to the manufacturer’s speciﬁcations. Total miRNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the miRNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Freshly heart tissue was add lysis/binding buffer (0.1g tissue added 1mL buffer) and grinded into homogenate.Added 1/10 volume Homogenate additive buffer and incubated on ice for 10 minutes.

value: heart

value: male

tag: group

value: Yiqifumai Powder Injection group


title: S17 Gut rep3

description: Hco ISE (MHco3)


title: S15 Gut rep1

description: Hco ISE (MHco3)


title: Heart_YQFM_rep3

source_name: heart, YQFM, replicate 4

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total miRNA was dephosphorylated, denaturated and then labeled with Cyanine-3-CTP. After purification the labeled miRNAs were hybridized onto the microarray. After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).


title: Heart_YQFM_rep2

source_name: heart, YQFM, replicate 3


title: S14 Adult female rep2

description: Hco ISE (MHco3)

source_name: Adult female whole worm extract

value: Whole organism


title: S11 Adult male rep1

description: Hco ISE (MHco3)

source_name: Adult male worm whole extract


title: S10 L3 Act.24hr rep2

description: Hco ISE (MHco3)

source_name: L3 whole extract after culture in vitro 37oC for 24 hours


title: RNAPolII IP of XTC.UC1 cells after 24h serum induction-slide 1&2

type: genomic

country: France

molecule: genomic DNA

tag: cell line

value: IP RNApol XTC.UC1 cells

value: RNA polymerase II (Santa Cruz Biotechnology , polyclonal N-20, reference sc-899x)


title: BM-MSCs_SCD1 overexpression_endothelial induced_3 days_rep2

description: Gene expression data from bone marrow mesenchymal stem cells which were transfected by SCD1-lentivirus and endothelial induced for 3 days.

source_name: Bone marrow mesenchymal stem cells transfected by SCD1-lentivirus,endothelial induced,3 days

value: SCD1 overexpression


title: BM-MSCs_normal control_endothelial induced_3 days_rep2


title: BM-MSCs_SCD1 overexpression_endothelial induced_3 days_rep1


title: Heart_YQFM_rep1

source_name: heart, YQFM, replicate 2


title: S13 Adult female rep1

description: Hco ISE (MHco3)


title: S12 Adult male rep2

description: Hco ISE (MHco3)


title: BM-MSCs_normal control_endothelial induced_3 days_rep1


title: ERR1 IP of XTC.UC1 cells after 24h serum induction-slide 1&2

value: oncoytic thyroid cell line

value: IP ERR1 XTC.UC1 cells

value: ERR1 (Perseus Proteomics Inc., reference H5844)


title: S08 L3 Non-act rep2

description: Hco ISE (MHco3)

source_name: L3 whole extract

value: Hco ISE (MHco3)


title: S09 L3 Act.24hr rep1

description: Hco ISE (MHco3)


title: Heart_SHAM_rep3

description: miRNA from sham group

source_name: heart, SHAM, replicate 4

value: sham group


title: Heart_SHAM_rep4

description: miRNA from sham group

source_name: heart, YQFM, replicate 1


title: S06 Adult female rep3

description: Hco ISE (MHco3)

value: adult


title: S07 L3 Non-act rep1

description: Hco ISE (MHco3)


title: PRC IP of XTC.UC1 cells after 24h serum induction-slide 1&2

value: IP PRC XTC.UC1 cells

value: Polyclonal PRC antibody was produced (Eurogentec, Seraing, Belgium) against a human PRC peptide (1520-1534)

value: IP IgG XTC.UC1 cells

value: IgG (MP Biomedicals, polyclonal whole molecule, reference 55335)


title: Heart_SHAM_rep2

description: miRNA from sham group

source_name: heart, SHAM, replicate 3

value: heart


title: Heart_SHAM_rep1

description: miRNA from sham group

source_name: heart, SHAM, replicate 2

value: male


title: S05 Adult male rep3

description: Hco ISE (MHco3)

source_name: Adult male whole worm extract


title: S04 L3 Act.24hr rep3

description: Hco ISE (MHco3)


title: RNAPolII IP of XTC.UC1 cells after 48h serum induction-slide 1&2

source_name: IgG IP of XTC.UC1 cells after 24h serum induction


title: Heart_CHF_rep4

description: miRNA from chronic heart failure group

source_name: heart, SHAM, replicate 1

value: chronic heart failure group


title: S03 L3 Non-act. rep3

description: Hco ISE (MHco3)

value: Whole organism


title: CREB IP of XTC.UC1 cells after 48h serum induction-slide 1&2

value: IP CREB XTC.UC1 cells

value: CREB (Abcam, monoclonal, reference 32515)


title: CREB IP of XTC.UC1 cells after 24h serum induction-slide 1&2


title: Heart_CHF_rep2

description: miRNA from chronic heart failure group

source_name: heart, CHF, replicate 2


title: YY1 IP of XTC.UC1 cells after 24h serum induction-slide 1&2

value: IP YY1 XTC.UC1 cells

value: YY1 (Abcam, monoclonal, reference12132)


title: S01 L4 rep1

description: Hco ISE (MHco3)

source_name: L4 whole extract 7 days post infection


title: S02 L4 rep2

description: Hco ISE (MHco3)


title: Heart_CHF_rep3

description: miRNA from chronic heart failure group

source_name: heart, CHF, replicate 3


title: Heart_CHF_rep1

description: miRNA from chronic heart failure group

source_name: heart, CHF, replicate 1


title: PRC IP of XTC.UC1 cells after 48h serum induction-slide 1&2

value: oncoytic thyroid cell line


title: GABP IP of XTC.UC1 cells after 48h serum induction-slide 1&2

value: IP GABP XTC.UC1 cells

value: GABP (Santa Cruz Biotechnology, polyclonal, reference sc-22810)


title: GABP IP of XTC.UC1 cells after 24h serum induction-slide 1&2


title: NRF1 IP of XTC.UC1 cells after 48h serum induction-slide 1&2

value: IP NRF1 XTC.UC1 cells

value: NRF-1 (Abcam, polyclonal, reference 34682)


title: ERR1 IP of XTC.UC1 cells after 48h serum induction-slide 1&2

value: IP ERR1 XTC.UC1 cells

value: ERR1 (Perseus Proteomics Inc., reference H5844)

source_name: IgG IP of XTC.UC1 cells after 48h serum induction


title: NRF1 IP of XTC.UC1 cells after 24h serum induction-slide 1&2

value: IP IgG XTC.UC1 cells


title: 468_1a3kd_dac_ra_rep3

status: Public on Nov 06 2017

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: PO Box 15000

department: Pathology

country: Canada

institute: Dalhousie University

description: CHP files derived from Transcriptome Analysis Console

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuGene-2_0-st
program-name = Expression Console
program-version = 1.3.1.187

label_protocol: standard Affymetrix protocol

growth_protocol: All cells grown in DMEM with 10% FBS, 1x antibiotic-antimycotic, 0.25 ug/mL puromycin.

extract_protocol: RNA extracted with Trizol reagent and PureLink RNA kit (Invitrogen).

value: SMP ALDH1A3 kd

tag: atra tx

tag: decitabine tx

value: 1 uM

tag: replicate


title: 231_1a3oe_dac_ra_rep1

value: MSCV ALDH1A3 overexpression


title: 468_1a3kd_nt_rep3

value: 0 nM

value: 0 uM


title: 231_1a3oe_ra_rep1


title: 231_1a3oe_nt_rep1


title: 468_smp_dac_ra_rep3

value: SMP scramble


title: 231_1a3oe_dac_ra_rep3


title: 231_1a3oe_dac_rep1


title: 468_1a3kd_dac_rep3


title: 468_smp_nt_rep3


title: 231_mscv_dac_ra_rep3

value: MSCV scramble


title: 231_mscv_dac_ra_rep1


title: 231_1a3oe_ra_rep3


title: 468_smp_dac_rep3


title: 468_1a3kd_ra_rep3


title: 231_mscv_nt_rep3


title: 468_smp_ra_rep3


title: 231_1a3oe_nt_rep3


title: 231_1a3oe_dac_rep3


title: 231_mscv_dac_rep3


title: 231_mscv_ra_rep3


title: 468_smp_dac_rep1


title: 468_1a3kd_nt_rep2


title: 468_1a3kd_ra_rep2


title: 231_mscv_dac_rep1


title: 468_smp_ra_rep2


title: 468_1a3kd_dac_ra_rep2


title: 231_1a3oe_ra_rep2


title: 468_smp_dac_rep2


title: 468_smp_nt_rep2


title: 468_smp_dac_ra_rep2


title: 231_mscv_ra_rep1


title: 468_1a3kd_ra_rep1


title: 231_mscv_nt_rep2


title: 468_1a3kd_dac_rep2


title: 231_mscv_ra_rep2


title: 468_smp_ra_rep1


title: 468_1a3kd_dac_rep1


title: 468_1a3kd_dac_ra_rep1


title: 468_1a3kd_nt_rep1


title: 231_mscv_nt_rep1


title: 231_1a3oe_nt_rep2


title: 231_1a3_dac_ra_rep2


title: 468_smp_dac_ra_rep1


title: 231_1a3oe_dac_rep2


title: 468_smp_nt_rep1


title: 231_mscv_dac_rep2


title: 468_1a3kd_nt_rep3 [methylation]

description: 61 NT 3

hyb_protocol: as described in Illumina protocol

scan_protocol: as described in Illumina protocol

data_processing: as described in Illumina protocol

label: cy3, cy5

source_name: MDA-MB-468 1a3 NT

label_protocol: as described in Illumina protocol

growth_protocol: MDA-MB-231 and MDA-MB-468 cells grown in DMEM with 10% FBS, 1x antibiotic-antimycotic, 0.25 ug/mL puromycin.

extract_protocol: DNA extracted with the PureLink DNA kit (Invitrogen)

treatment_protocol: atRA and decitabine as inidcated.

tag: vector

tag: atra

tag: decitabine


title: 231_1a3_nt_rep3 [methylation]

description: 1A3 NT 3

source_name: MDA-MB-231 1a3 NT


title: 231_mscv_dac_rep3 [methylation]

description: MSCV DAC 3

source_name: MDA-MB-231 MSCV DAC


title: 468_smp_nt_rep3 [methylation]

description: SMP NT 3

source_name: MDA-MB-468 SMP NT


title: 468_smp_ra_rep3 [methylation]

description: SMP RA 3

source_name: MDA-MB-468 SMP RA


title: 468_smp_dac_rep3 [methylation]

description: SMP DAC 3

source_name: MDA-MB-468 SMP DAC


title: E2-treated3

status: Public on Nov 04 2017

first: Xiao-Yan

last: Zhu

address: 800 Xiangyin Rd

institute: Second Military Medical University

description: Gene expression data

hyb_protocol: microRNAs were hybridized for 16h at 48C in Hybridization Oven 640 (Affymetrix).

scan_protocol: microRNA Chips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

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

label: Biotin

source_name: Rattus norvegicus cardiomyocytes treated with E2

label_protocol: Biotinylated microRNAs were prepared according to the standard Affymetrix protocol (miRNA expression analysis technical manual, Affymetrix).

growth_protocol: Primary cultured rat neonatal cardiomyocytes were used for microRNA extraction.

extract_protocol: microRNAs were extracted with miRcute miRNA isolation kit (TianGen) according to the manufacture’s protocol. microRNAs were dissolved in DEPC treated water and the concentration was determined by Nanodrop2000c (Thermo).

treatment_protocol: Primary cultured rat neonatal cardiomyocytes were treated with 17beta-estradiol (E2) for 24h.

value: cardiomyocytes

tag: treatment

value: 17beta-estradiol (E2) for 24h


title: 468_1a3kd_nt_rep2 [methylation]

description: 61 NT 2


title: E2-treated1

description: Gene expression data


title: E2-treated2

description: Gene expression data


title: 231_mscv_dac_ra_rep2


title: 468_smp_ra_rep2 [methylation]

description: SMP RA 2


title: 231_mscv_ra_rep3 [methylation]

description: MSCV RA 3

source_name: MDA-MB-231 MSCV atRA


title: 468_smp_dac_rep1 [methylation]

description: SMP DAC 1


title: control3

description: Gene expression data

source_name: Rattus norvegicus cardiomyocytes control

value: control


title: 201B7_P18

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

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

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

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

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

tag: gender

value: Female

value: inducible pluripotent stem cells

tag: cell source

value: Fibroblast-derived iPS cells

tag: disease state

value: normal


title: 231_1a3_nt_rep1 [methylation]

description: 1A3 NT 1


title: 231_mscv_ra_rep1 [methylation]

description: MSCV RA 1


title: 468_smp_nt_rep2 [methylation]

description: SMP NT 2


title: 231_mscv_dac_rep1 [methylation]

description: MSCV DAC 1


title: 468_smp_nt_rep1 [methylation]

description: SMP NT 1


title: 231_mscv_nt_rep1 [methylation]

description: MSCV NT 1

source_name: MDA-MB-231 MSCV NT


title: 231_1a3_nt_rep2 [methylation]

description: 1A3 NT 2


title: IR+UNx 30

city: Aarhus N

first: Casper

middle: Kierulf

last: Lassen

address: Palle Juul-Jensens Boulevard 99

department: Department of Clinical Medicine

country: Denmark

institute: Aarhus University

description: RMA expression value derived from Expression Console software

hyb_protocol: The generated target RNA was loaded onto the Affymetrix Clariom D array cartridge and hybridized for 16 hours at 45°C. After washing and staining in the GeneChip Fluidics Station, the array was scanned in the GeneChip Scanner 7G.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Affymetrix Console Software according to the RMA. Normalized gene expression data was analysed in the open source software Multiexperiment Viewer version 4.9.0, which is part of the TM4 microarray software suite.The statistical analysis was done by employing the Significance Analysis of Microarrays (SAM)-method. The number of permutations was set to 200, S0 was selected according to the method by Tusher et al, and the K-nearest neighbors method for imputation of missing data, with k = 10, was used. Unpaired two-class analysis was performed. A false discovery rate (FDR) of 10% was selected.

source_name: IR+UNx group

label_protocol: A target preparation of 150 ng RNA was used for cDNA synthesis, in vitro transcription and terminal labeling utilizing the WT PLUS reagent kit (Affymetrix).

growth_protocol: The kidney was harvested, placed on ice and a piece consisting of both outer medulla and cortex was excised. The kidney tissue was homogenised in lysis buffer (Macherey Nagel, Düren, Germany) on a TissueLyser LT (Qiagen, Venlo, Netherlands) for 30 seconds at 1,250 rpm and centrifuged at 1000 × g for 10 minutes at 4°C.

extract_protocol: otal RNA was obtained using an RNA Isolation Kit (Macherey Nagel) in accordance with the manufacturer’s instructions

value: Male

tag: tissue

value: kidney

tag: strain

value: Wistar


title: IR+UNx 35


title: 231_mscv_nt_rep3 [methylation]

description: MSCV NT 3


title: control1

description: Gene expression data


title: 468_smp_ra_rep1 [methylation]

description: SMP RA 1


title: 231_mscv_dac_rep2 [methylation]

description: MSCV DAC 2


title: 468_smp_dac_rep2 [methylation]

description: SMP DAC 2


title: UNx 34

source_name: UNx group


title: IR 9

source_name: IR group


title: IR 24


title: MRC-iPS-25_P30

value: MRC5-derived iPS cells


title: 231_mscv_ra_rep2 [methylation]

description: MSCV RA 2


title: HUES-8_P24

value: Embryonic stem cells

value: Blastocyst-derived ES cells


title: MRC5

value: Fetal lung fibroblast cells

value: Fetal lung-derived cells


title: UNx 25


title: PAE551_P13

value: Placental artery endothelial cells

value: Placental artery endothelial-derived cells


title: PAE-iPS-01_P31

value: PAE551-derived iPS cells


title: 468_1a3kd_nt_rep1 [methylation]

description: 61 NT 1

value: SMP ALDH1A3 kd

value: 0 nM

value: 0 uM


title: Calbicans_control

city: Washington

first: Dongmei

last: Li

state: DC

address: 3900 Reservoir Rd Med dent SE318

department: Microbiology

description: gene expression at exponential stage

hyb_protocol: The arry was provided by Agilent Technologies eArray ID 017942. It was designed as 6101 open reading frames in two oligonucleotides probes including 12 mitochondrial genes. The probes were used to generate custom microarrays in a 8x15 K format with a randomized layout. The hybridization was carried out using Agilent SureHyb hybridization chamber.

scan_protocol: The scan was processed with an Agilent SCAN 02349 Microarray Scanner System.

data_processing: The image files were first analyzed by Agilent Feature Extraction Software and Cy3 intensities were then logarithmically transformed and statistically normalized. Statistical analysis of microarray data was conducted by the multi-variate t test to give a False Discovery Rate (FDR).  The processed_data.txt contains the ratio of treated vs control.

organism: Candida albicans

source_name: total RNA from C. albicans from control cells labeled with Cy3

label_protocol: One-color microarray-based gene expression was performed. 100 ng of total RNA was used for cDNA labeling with Cy3 of each strain according to the manufacturer's instructions.

growth_protocol: Overnight cultures of a C. albicans wild type were diluted to a A600 of 0.2 in 20 ml of YPD medium containing 2% glucose and incubated at 200 rpm at 30°C for 5 hours.

extract_protocol: Total RNA was isolated by the pheno/chloroform method and RNA inegrity was assessed using an Agilent 2100 bioanalyzer.

treatment_protocol: Exponentially growing cells were treated for 60 min with 4 μg/ml of NSC319726

tag: growth phase

value: exponential


title: UNx 11


title: 231_mscv_nt_rep2 [methylation]

description: MSCV NT 2

value: MSCV scramble


title: Sham 36

source_name: Sham group


title: Sham 31


title: altitude exposure at post21, biological rep 007 [batch1]

status: Public on Nov 03 2017

city: Aurora

first: Robert

middle: C

last: Roach

state: CO

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

department: Department of Pulmonology

institute: University of Colorado

hyb_protocol: Hybridization to the Affymetrix GeneChip miRNA 3.0 Array was performed per manufacturer guidelines.

scan_protocol: GeneChip Scanner 3000 7G.

data_processing:
Raw expression data was normalized with the RMA algorithm using the R/Bioconductor oligo package. Hybridization and scanning took place in two batches (batch 1 on August 19, 2013 and batch 2 on May 6, 2015). Batches were combined using the ComBat function in the R/Bioconductor sva package. Probe annotation was retrieved from Affymetrix and miRBase.
Probe group file: miRNA-3_0-st-v3.pgf

source_name: post21, PBMC

label_protocol: cDNA synthesis and amplification were performed using the Sigma-Aldrich TransPlex Complete Whole Transcriptome Amplification (WTA) Kit.

growth_protocol: Not applicable

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

treatment_protocol: Exposure to altitude.

value: altitude re-exposure

tag: time point

value: day 21 post-decent

tag: subject

tag: cell type

value: peripheral blood mononuclear cells (PMBCs)

tag: age

tag: Sex

value: M

tag: height (inches)

tag: weight (kg)

tag: batch


title: Differentiated Day 12_stimulate 30 minutes_3

city: Singapore

first: Daniel

middle: Boon Loong

last: Teh

address: 28 Medical Drive, #05-COR

country: Singapore

institute: National University of Singapore

description: Gene expression data from optogenetic mediated differentiation

hyb_protocol: hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 Arrays for 16 hours at 45oC with rotation at 60 rpm.  Arrays were then washed and stained using the FS450_0001 fluidics protocol.

scan_protocol: scanned using an Affymetrix 3000 7G scanner (S/N 54719870)

data_processing: CEL files generated from AGCC (GeneChip Command Console Software) were also imported into Expression Console (EC) 1.4 software for Data QC. RMA and MAS5 normalization was performed on the samples to generate the quality control (QC) metrics

source_name: Neural stem cell optogenetic stimulated continously for 12 days differentiation

label_protocol: The RNA samples were processed according to the Affymetrix 3’ IVT PLUS protocol

growth_protocol: Neural stem cell differentiation medium.

extract_protocol: Qiagen RNAeasy, as per manufacturer's protool.

treatment_protocol: Not applicable. Total RNA was extracted directly from culture condition without prior treatment.

value: derived from adult rat hippocampus

value: neural stem cells


title: Differentiated Day 12_non-stimulate_1

source_name: Neural stem cell optogenetic non-stimulated continously for 12 days differentiation


title: Differentiated Day 12_stimulate 30 minutes_1


title: Calbicans_NSC319726

description: gene expression at exponential stage

source_name: total RNA from C. albicans from treated cells labeled with Cy3


title: Differentiated Day 12_non-stimulate_3


title: altitude exposure at post21, biological rep 001 [batch1]


title: IR+UNx 10

value: Male

value: kidney

value: Wistar


title: SK-N-MC_Rvagabundus+H2O2_rep2

city: Oeiras

first: Claudia

middle: Nunes

last: Santos

address: Av Republica, EAN

country: Portugal

institute: ITQB/IBET

hyb_protocol: Five µg of end-labeled, fragmented cDNA was used in a 100-µL hybridization cocktail containing added hybridization controls. Eighty µL of mixture was hybridized on arrays for 17 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0007; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed first with Affymetrix Expression Console software for quality control. For subsequent analyses Chipster 2.0 (http://chipster.csc.fi/) was used with custom cdf file HuGene10stv1_Hs_ENTREZG.cdf as available from Brainarray database version 14.1.0. Array raw data were normalized using Robust Multi-array average (RMA) and statistical differences evaluated by a two groups test (empirical Bayes), for p<0.05.

source_name: SK-N-MC cells with 0.5ug GAE of Rubus vagabundus digested extract + 300uM H2O2

label_protocol: Biological triplicates were processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip HuGene 1.0 ST Arrays in the Gene Expression Unit of Instituto Gulbenkian de Ciência (Oeiras, Portugal), and, according to the manufacturer’s Whole Transcript Sense Target Labeling Assay. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (GeneChip® WT cDNA Synthesis Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription reaction to generate cRNA (GeneChip® WT cDNA Amplification Kit; Affymetrix). Fifteen µg of this cRNA was used for a second cycle of first-strand cDNA synthesis (GeneChip® WT cDNA Synthesis Kit; Affymetrix). From the single stranded cDNA 5.5 µg was fragmented and end-labeled (GeneChip® WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: SK-N-MC cells (ECACC) were grown in EMEM supplemented with 10% FBS, 1% sodium-pyruvate, 1x Non-essential amino acids, 200mM glutamine, 1% pen-strep

extract_protocol: Total RNA extraction of sorted cells was performed using AxyPrep Multisource Total RNA Miniprep (Axygen). Total RNA was treated with Turbo™ DNase I (Ambion), accordingly to the manufacturer’s instructions. RNA quantity was assessed using a Nano-Drop® ND-1000 spectrophotometer (NanoDrop Technologies) and RNA quality using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Assay (Agilent Technologies).

treatment_protocol: SK-N-MC cells were seeded at 5x104 cells/cm2 and grown for 24 h. BB or RV was supplied to cells (0.5 µg GAE/mL) dissolved in medium containing 0.5% (v/v) FBS for 24 h. 300uM of hydrogen peroxde was provided or not to corresponding samples for 3h. After incubation, cells were washed with PBS, tripsinized, collected to a tube and 0.05 volumes of FBS added, to inactivate trypsin. Dihexyloxacarbocyanine iodide (DiOC6(3)) and PI were added to cells to a final concentration of  20 nM  and 1 µg/mL, respectively, and incubated for 30 min at 37 ºC.  DiOC6(3) was used to evaluate the mitochondrial transmembrane potential (ΔΨm) and PI to determine cell viability, based on plasma membrane integrity. Cells were then sorted in a FACSAria High Speed Cell Sorter (Becton Dickinson), using a 100 µm nozzle with 206.8 kPa (30 psi) sheath pressure. A 488 nm laser was used for DiOC6(3) and PI excitation and detection was performed using a 530/30 nm and a 695/40 nm HQ band pass filter, respectively. Only cells that presented cellular membrane integrity and high mitochondrial transmembrane potential were collected in tubes containing PBS for further analysis.

value: Female

tag: ethnicity

value: Caucasian

value: brain

tag: cell line

value: SK-N-MC cells

tag: stress

tag: agent

value: Rubus vagabundus digested extract


title: SK-N-MC_Blackberry+H2O2_rep4

source_name: SK-N-MC cells with 0.5ug GAE of blackberry digested extract + 300uM H2O2

tag: gender

value: blackberry digested extract


title: SK-N-MC_Rvagabundus+H2O2_rep3


title: SK-N-MC_Blackberry+H2O2_rep2


title: altitude exposure at post7, biological rep 025 [batch1]

source_name: post7, PBMC

tag: treatment

value: day 7 post-decent

value: F


title: altitude exposure at post7, biological rep 023 [batch1]

value: altitude re-exposure


title: Sham 8

tag: tissue


title: control2

description: Gene expression data

value: cardiomyocytes

value: control


title: altitude exposure at post21, biological rep 006 [batch1]

value: day 21 post-decent

value: peripheral blood mononuclear cells (PMBCs)

value: M


title: Differentiated Day 12_non-stimulate_2

value: derived from adult rat hippocampus

value: neural stem cells


title: SK-N-MC_H2O2_rep3

source_name: SK-N-MC cells with 300uM of H2O2


title: HUES-3_P29

value: Male

value: Embryonic stem cells

tag: cell source

value: Blastocyst-derived ES cells

tag: disease state

value: normal


title: altitude exposure at post7, biological rep 020 [batch1]

tag: time point


title: altitude exposure at post21, biological rep 005 [batch1]

tag: subject


title: altitude exposure at post21, biological rep 004 [batch1]

tag: cell type


title: Differentiated Day 12_stimulate 30 minutes_2


title: SK-N-MC_Rvagabundus+H2O2_rep4

value: Female

value: Caucasian

value: brain

value: SK-N-MC cells


title: altitude exposure at post7, biological rep 019 [batch1]

value: day 7 post-decent

tag: age

value: F


title: altitude exposure at post7, biological rep 022 [batch1]

value: altitude re-exposure

tag: Sex


title: SK-N-MC_Blackberry+H2O2_rep3

value: blackberry digested extract


title: altitude exposure at post7, biological rep 018 [batch1]

tag: height (inches)


title: altitude exposure at post7, biological rep 017 [batch1]

tag: weight (kg)


title: altitude exposure at post7, biological rep 015 [batch1]

tag: batch


title: SK-N-MC_H2O2_rep4

tag: ethnicity

value: control


title: SK-N-MC_Rvagabundus_rep2

source_name: SK-N-MC cells with 0.5ug GAE of Rubus vagabundus digested extract

tag: cell line

value: Rubus vagabundus digested extract


title: altitude exposure at post7, biological rep 021 [batch1]

value: peripheral blood mononuclear cells (PMBCs)

value: M


title: SK-N-MC_Rvagabundus_rep3

tag: stress


title: altitude exposure at post7, biological rep 014 [batch1]


title: SK-N-MC_H2O2_rep2

tag: agent


title: altitude exposure at post7, biological rep 012 [batch1]


title: altitude exposure at post21, biological rep 002 [batch1]

value: day 21 post-decent


title: SK-N-MC_Rvagabundus_rep4

tag: gender


title: altitude exposure at post7, biological rep 013 [batch1]

tag: treatment


title: SK-N-MC_Ctr_rep3

source_name: SK-N-MC cells only (control)

tag: tissue


title: SK-N-MC_Blackberry_rep3

source_name: SK-N-MC cells with 0.5ug GAE of blackberry digested extract


title: SK-N-MC_Blackberry_rep2


title: altitude exposure at post7, biological rep 011 [batch1]


title: altitude exposure at post7, biological rep 010 [batch1]


title: altitude exposure at alt16, biological rep 025 [batch1]

source_name: alt16, PBMC

value: initial altitude exposure

value: day 16


title: altitude exposure at alt16, biological rep 023 [batch1]


title: altitude exposure at alt16, biological rep 021 [batch1]


title: altitude exposure at alt16, biological rep 022 [batch1]


title: SK-N-MC_Blackberry_rep4


title: SK-N-MC_Ctr_rep4


title: SK-N-MC_Ctr_rep2


title: altitude exposure at alt16, biological rep 019 [batch1]


title: altitude exposure at alt16, biological rep 020 [batch1]


title: altitude exposure at alt16, biological rep 018 [batch1]


title: altitude exposure at alt16, biological rep 015 [batch1]


title: altitude exposure at alt16, biological rep 017 [batch1]


title: altitude exposure at alt16, biological rep 014 [batch1]


title: altitude exposure at alt16, biological rep 011 [batch1]


title: altitude exposure at alt16, biological rep 005 [batch1]


title: altitude exposure at alt16, biological rep 003 [batch1]


title: altitude exposure at alt16, biological rep 010 [batch1]


title: altitude exposure at alt16, biological rep 002 [batch1]


title: altitude exposure at alt16, biological rep 006 [batch1]


title: altitude exposure at alt16, biological rep 007 [batch1]


title: altitude exposure at alt16, biological rep 004 [batch1]


title: altitude exposure at alt16, biological rep 013 [batch1]


title: altitude exposure at alt16, biological rep 012 [batch1]


title: altitude exposure at alt7, biological rep 023 [batch2]

source_name: alt7, PBMC

value: day 7


title: altitude exposure at alt7, biological rep 019 [batch2]


title: altitude exposure at alt7, biological rep 022 [batch2]


title: IR 23

value: Male

value: kidney

tag: strain

value: Wistar


title: altitude exposure at alt7, biological rep 013 [batch2]


title: altitude exposure at alt16, biological rep 001 [batch1]


title: altitude exposure at alt7, biological rep 014 [batch2]


title: altitude exposure at alt7, biological rep 017 [batch2]


title: altitude exposure at alt7, biological rep 006 [batch2]


title: altitude exposure at alt7, biological rep 007 [batch2]


title: altitude exposure at alt7, biological rep 018 [batch2]


title: altitude exposure at alt1noon, biological rep 022 [batch1]

source_name: alt1noon, PBMC

value: day 1, noon


title: altitude exposure at alt7, biological rep 002 [batch2]


title: altitude exposure at alt7, biological rep 011 [batch2]


title: altitude exposure at alt1noon, biological rep 025 [batch1]


title: altitude exposure at alt1noon, biological rep 020 [batch1]


title: altitude exposure at alt1noon, biological rep 015 [batch1]


title: altitude exposure at alt7, biological rep 001 [batch2]


title: altitude exposure at alt7, biological rep 005 [batch2]


title: altitude exposure at alt1noon, biological rep 021 [batch1]


title: altitude exposure at alt1noon, biological rep 017 [batch1]


title: altitude exposure at alt1noon, biological rep 014 [batch1]


title: altitude exposure at alt1noon, biological rep 013 [batch1]


title: altitude exposure at alt1noon, biological rep 018 [batch1]


title: altitude exposure at alt7, biological rep 010 [batch2]


title: altitude exposure at alt1noon, biological rep 007 [batch1]


title: altitude exposure at alt1noon, biological rep 019 [batch1]


title: altitude exposure at alt1noon, biological rep 005 [batch1]


title: altitude exposure at alt1noon, biological rep 011 [batch1]


title: altitude exposure at alt1noon, biological rep 012 [batch1]


title: altitude exposure at alt1noon, biological rep 010 [batch1]


title: altitude exposure at alt1noon, biological rep 002 [batch1]


title: baseline condition at sea level, biological rep 021 [batch1]

source_name: sea level, PBMC

value: sea level

value: baseline


title: baseline condition at sea level, biological rep 022 [batch1]


title: AHEP_2

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

description:
8x60Kv2
AHEP_4

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 ( G4845A,  G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for micro array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
(Matrix_1) representate the integrated analysis result of GPL17077 and GPL13497. When comparing with data from GPL13497 arrays, we conducted quantile normalization for robustly removing the difference among chips and the batch effects.
(Matrix_2) representate 75th percent shift normalized signal intensity from GPL17077 alone. After averaging the signal intensity within replicate spots, the batch effect, observed within different GPL17077 array chips, was removed by Combat (Leek et al., 2012) with covariates of the same differentiation stages.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Adult hepatocyte


title: baseline condition at sea level, biological rep 019 [batch1]

value: F


title: baseline condition at sea level, biological rep 020 [batch1]


title: AHEP_LB_1

description:
8x60Kv2
AH_ECSTMBud_14

value: Adult hepatocyte-LB


title: altitude exposure at alt1noon, biological rep 023 [batch1]


title: AHEP_1

description:
8x60Kv2
AHEP_2


title: All_iPS_LB_2

description:
8x60Kv2
All-iPSC_LB_5

value: All-iPSC-LB


title: altitude exposure at alt1noon, biological rep 006 [batch1]


title: baseline condition at sea level, biological rep 018 [batch1]


title: baseline condition at sea level, biological rep 023 [batch1]


title: baseline condition at sea level, biological rep 014 [batch1]


title: altitude exposure at alt1noon, biological rep 001 [batch1]


title: baseline condition at sea level, biological rep 025 [batch1]


title: baseline condition at sea level, biological rep 017 [batch1]


title: All_iPS_LB_1

description:
8x60Kv2
All-iPSC_LB_4


title: iPS_STM_NCB_5

description:
8x60Kv2
NCB-STM_d20

value: iPS-STM


title: baseline condition at sea level, biological rep 011 [batch1]

value: peripheral blood mononuclear cells (PMBCs)


title: baseline condition at sea level, biological rep 015 [batch1]


title: baseline condition at sea level, biological rep 010 [batch2]


title: baseline condition at sea level, biological rep 010 [batch1]


title: baseline condition at sea level, biological rep 012 [batch2]

value: M


title: iPS_STM_NCB_3

description:
8x60Kv2
NCB-STM_bFGF_BMP4_d8_a


title: baseline condition at sea level, biological rep 007 [batch1]


title: All_iPS_LB_3

description:
8x60Kv2
All-iPSC_LB_7


title: iPS_STM_NCB_2

description:
8x60Kv2
NCB-STM_d8_b


title: iPS_LPM_NCB_1

description:
8x60Kv2
NCB-LPM_d5

value: iPS-LPM


title: baseline condition at sea level, biological rep 012 [batch1]


title: baseline condition at sea level, biological rep 003 [batch1]


title: iPS_STM_NCB_4

description:
8x60Kv2
NCB-STM_bFGF_BMP4_d8_b


title: iPS_DE_d6_5

description:
8x60Kv2
DE-1_e

value: iPSC-DE


title: baseline condition at sea level, biological rep 004 [batch1]


title: iPS_MC_NCB_3

description:
8x60Kv2
ki_GFP_MC

value: iPSC-MC


title: baseline condition at sea level, biological rep 013 [batch1]


title: iPS_MC_NCB_2

description:
8x60Kv2
ki_GF01_MC


title: iPS_MC_NCB_1

description:
8x60Kv2
ki_FF_MC


title: baseline condition at sea level, biological rep 006 [batch1]


title: iPS_DE_d6_4

description:
8x60Kv2
DE-1_d


title: baseline condition at sea level, biological rep 005 [batch1]


title: iPS_STM_NCB_1

description:
8x60Kv2
NCB-STM_d8_a


title: baseline condition at sea level, biological rep 002 [batch1]


title: HUVEC_2

description:
8x60Kv2
ki_HU

value: HUVEC


title: iPS_EC_1

description:
8x60Kv2
a_FF_EC

value: iPSC-EC


title: iPS_EC_3

description:
8x60Kv2
ka_FF_EC2


title: MSC_1

description:
8x60Kv2
MSC_2

value: MSC


title: iPS_EC_2

description:
8x60Kv2
ka_FF_EC1


title: iPSC_3

description:
4x44Kv2
iPSC4

value: iPSC


title: baseline condition at sea level, biological rep 001 [batch1]


title: iPSC_2

description:
4x44Kv2
iPSC3


title: Tcells_icilin_24hrs_rep3

city: Calgary

first: Robin

middle: M.

last: Yates

state: AB

address: 3330 Hospital Drive NW

institute: University of Calgary

hyb_protocol: Samples were hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix) at 45°C for 16 h at the SACRI Microarray and Genomics Facility (University of Calgary) (n=6). Arrays were stained and washed by using GeneChip Fluidics 450 per manufacturer protocols

scan_protocol: Samples were scanned with a GeneChip Scanner 3000 7G System (Affymetrix)

data_processing: Probe cell intensity data files were generated and summarized with GeneChip Command Console Software, and Robust Multi-Array Average was used to log 2 transform and normalize data

organism: Mus musculus

source_name: murine CD4+ T cells_icilin_24hrs

label_protocol: Biotinylated RNA was prepared using the GeneChip Whole Transcript Express Labeling Assay/GeneChip WT PLUS Reagent Labeling Kit (902280)

growth_protocol: Purified splenic CD4+ T cells were grown in complete T cell medium [10% fetal bovine serum (FBS), 100 U/ml penicillin-streptomycin, 2 mM L-glutamine, 1X nonessential amino acids, 1 mM sodium pyruvate, 500 µM 2-ME in RPMI 1640]

extract_protocol: Total RNA was extracted by using an RNeasy Mini Kit (Qiagen), and RNA quality and RNA integrity number was measured with Agilent RNA Nano Chips on a 2100 Bioanalyzer. A total of 0.25 µg of RNA with an RNA integrity number of ≥8 was used for each sample

treatment_protocol: Cells were treated with 100 µM icilin (in the vehicle DMSO) or corresponding concentrations of vehicle for 24 hours prior to extraction. T cells were stimulated with 10 µg/mL anti-mouse CD3 and 10 µg/mL anti-mouse CD28 monoclonal antibodies for 24 h before addition of icilin or vehicle

value: Wild-type C57BL/6

value: ~8 wks old

value: female

value: splenic CD4+ T cells

tag: treated with

value: 100 µM icilin


title: Tcells_icilin_24hrs_rep2


title: ALT_2

description:
8x60Kv2
LIV_30yrs_b

value: Adult liver tissue


title: Tcells_icilin_24hrs_rep1


title: Ctrl_LB_7

description:
4x44Kv2
LB2_Kuraray

value: iPSC-LB


title: baseline condition at sea level, biological rep 019 [batch2]

value: sea level

tag: time point

value: baseline

value: F


title: Tcells_vehicle_24hrs_rep3

source_name: murine CD4+ T cells_vehicle 24hrs

value: DMSO vehicle


title: HUVEC_1

description:
8x60Kv2
ki_GFP_HU


title: Ctrl_LB_4

description:
8x60Kv2
DEbud_c


title: Ctrl_LB_6

description:
4x44Kv2
LB1_10725


title: Ctrl_LB_5

description:
8x60Kv2
DE+1bud_b


title: MSC_2

description:
8x60Kv2
MSC_3


title: Ctrl_LB_2

description:
8x60Kv2
DE+1bud_a


title: ILT_1

description:
4x44Kv2
LIV3

value: Infant liver tissue


title: Ctrl_LB_3

description:
8x60Kv2
DEbud_b


title: FLT_2

description:
4x44Kv2
LIV2a

value: Fetal liver tissue


title: ILT_2

description:
4x44Kv2
LIV4


title: FLT_1

description:
4x44Kv2
LIV1


title: FLT_3

description:
4x44Kv2
LIV2b


title: iPS_IH_d14_1

description:
8x60Kv2
IH

value: iPSC-IH


title: ALT_1

description:
8x60Kv2
LIV_30yrs_a


title: iPS_MH_d22_1

description:
8x60Kv2
MHD8

value: iPSC-MH


title: Ctrl_LB_1

description:
8x60Kv2
DEbud_a


title: iPS_HE_d10_2

description:
8x60Kv2
HE_b

value: iPSC-HE


title: iPS_tHE_d9_1

description:
8x60Kv2
DE+2_a

value: iPSC-tHE


title: iPS_tHE_d8_3

description:
8x60Kv2
DE+1_c


title: iPS_HE_d10_1

description:
8x60Kv2
HE_a


title: Tcells_vehicle_24hrs_rep1

value: Wild-type C57BL/6


title: iPSC_1

description:
4x44Kv2
iPSC2

value: iPSC


title: iPS_MH_d22_3

description:
4x44Kv2
MH2


title: HCC-LM3_exosome_rep1

first: Wen

last: Yang

address: 225 Changhai Road

department: Eastern Hepatobiliary Surgery Institute

description: miRNA expression in exosomes from HCC cell lines

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6 (Agilent technologies, Santa Clara, CA, US).

source_name: Exosomes of HCC-LM3 cells

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

growth_protocol: All cell lines were cultured in a humidified incubator containing 5% CO2 at 37℃.

extract_protocol: Total RNA was isolated from exosomes of HCC cells by using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.Quality and quantity of total RNA was analysed by using the RNA 6000 Pico kit from Agilent.

treatment_protocol: For exosomes isolation, we firstly transplanted equal number of different cells into 10cm plates and changed the culture medium with fresh DMEM supplemented serum which was depleted of exosomes by centrifugated at 12000 x g overnight. After 48 hours, conditioned medium(CM) was collected for exosomes isolation.

value: Liver

tag: tumor

value: Hepatocellular carcinoma


title: iPS_IH_d14_2

description:
4x44Kv2
IH1


title: iPS_DE_d7_2

description:
8x60Kv2
DE_b

value: iPSC-DE


title: iPS_MH_d22_2

description:
4x44Kv2
MH1


title: iPS_tHE_d8_1

description:
8x60Kv2
DE+1_a


title: iPS_tHE_d9_2

description:
8x60Kv2
DE+2_b


title: iPS_tHE_d8_2

description:
8x60Kv2
DE+1_b


title: iPS_DE_d7_3

description:
8x60Kv2
DE_c


title: iPS_DE_d7_1

description:
8x60Kv2
DE_a


title: iPS_HE_d10_3

description:
8x60Kv2
HE_c


title: KO_6days_rep2

city: Philadelphia

first: Roberto

last: Caricchio

state: PA

address: 3322 N. Broad Street

department: Medicine/Rheumatology

institute: Lewis Katz School of Medicine

hyb_protocol: Samples were hybridized with GeneChip Mouse Transcriptome Array 1.0 (MTA 1.0) (Affymetrix) and scanned on an Affymetrix Gene Chip Scanner 3000 using Command Console software.

scan_protocol: Scanning was performed according to manufacturer's instructions (Affymetrix).

data_processing: Quality control of the experiment was performed by Expression Console software (Affymetrix) for normalization and background correction. Data analysis and statistical evaluations were performed using Transcriptome Analysis Console (Affymetrix). Significance in gene expression determined by ANOVA p<0.05.

source_name: B6.ER⍺KO_ treated-6days

label_protocol: Fragmented biotin-labeled cDNA (from 10ng RNA) was synthesized using the Affymetrix WT Pico kit.

extract_protocol: RNA was extracted from 600µL glomerular extracts with the Direct-zol RNA Mini-prep kit (Zymo Research) according to the manufacturer's instructions.

treatment_protocol: Mice were injected i.p. with 8ul/g nephrotoxic serum from sheep to induce anti-GBM nephritis before kidney harvest.

value: glomerular extracts

tag: genotype/variation

tag: timepoint

value: 6 days


title: KO_2weeks_rep2

source_name: B6.ER⍺KO_ treated-2weeks

value: 2 weeks


title: CSQT-2_exosome_rep1

source_name: Exosomes of CSQT-2 cells


title: KO_18hours_rep2

source_name: B6.ER⍺KO_ treated-18hourrs

value: 18 hours


title: KO_2weeks_rep1


title: MHCC-97L_exosome_rep1

source_name: Exosomes of MHCC-97L cells


title: iPS_DE_d6_3

description:
8x60Kv2
DE-1_c


title: HepG2_exosome_rep1

source_name: Exosomes of HepG2 cells


title: iPS_DE_d6_2

description:
8x60Kv2
DE-1_b


title: KO_6days_rep1


title: iPS_DE_d6_1

description:
8x60Kv2
DE-1_a


title: iPS_MC_NCB_4

description:
8x60Kv2
NCB-MC_d22

value: iPSC-MC


title: KO_untreated_rep2

value: untreated


title: KO_18hours_rep1

source_name: B6.ER⍺KO_ treated-18hours


title: Tcells_vehicle_24hrs_rep2

tag: age

value: ~8 wks old

tag: Sex

value: female

tag: cell type

value: splenic CD4+ T cells

value: DMSO vehicle


title: WT_6days_rep1

source_name: B6_ treated-6days

value: wildtype


title: WT_6days_rep2


title: Control lung at P3

status: Public on Nov 02 2017

city: San Diego

first: David

middle: James

last: McCulley

state: CA

address: 9500 Gilman Drive, MC 0735, Leichtag Building, Room 132

department: Pediatrics

institute: University of California, San Diego

description:
Gene expression analysis from pooled P3 control lungs
P3_control

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the UW-Madison Gene Expression Core Facility.

data_processing: Data were extracted, processed using Affymetrix Command Console (build 1.2.0.20).

source_name: P3 control lungs

label_protocol: Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit

growth_protocol: Mouse lungs collected at E14.5, P0, and P3 from control and Pbx1/2 CKO mice.

extract_protocol: Total lung RNA was isolated using RNeasy Mini Kit (Qiagen).

treatment_protocol: Not applicable

value: whole lung

tag: genotype

value: control


title: WT_untreated_rep1


title: Pbx1/2 CKO lung at P3

description:
Gene expression analysis from pooled P3 Pbx1/2 CKO lungs
P3_Pbx CKO

source_name: P3 Pbx1/2 CKO lungs

value: Pbx1/2 CKO


title: OPC 48h Fibrinogen 2

city: San Francisco

first: Mark

last: Petersen

address: 1650 Owens Street

institute: Gladstone Institutes

description: Gene expression data from fibrinogen-stimulated OPCs

hyb_protocol: GeneChip Expression Analysis Technical Manual 702232 Rev. 3

data_processing: Microarrays were normalized for array-specific effects using Affymetrix's Robust Multi-Array (RMA) normalization. Normalized arrays values were reported on a log2 scale. For statistical analyses, we removed all array probesets where no experimental groups had an average log2 intensity greater than 3.0. Linear models were fitted for each gene using the Bioconductor limma package in R. Moderated t-statistics, fold-change and the associated P-values were calculated for each gene. To account for the fact that thousands of genes were tested, we reported false discovery rate (FDR)-adjusted values, calculated using the Benjamini-Hochberg method.

source_name: RNA prepared from OPCs treated with fibrinogen for 48h

label_protocol: NuGEN Ovation Pico WTA System V2 and NuGEN Encore Biotin protocol

growth_protocol: OPCs were prepared from neonatal rat pups at postnatal day 1-2 and allowed to recover in proliferation media (DMEM, +N2, +B27, +pen/strep, +NT3, +PDGF) for two days before treatments.

extract_protocol: RNA extraction from OPCs was performed using RNeasy kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Genomic DNA was removed during the RNeasy cleanup using Rnase-Free Dnase set (Qiagen, Valencia, CA).

treatment_protocol: Rat OPCs were stimulated with fibrinogen for 48 hrs in differentiation media

value: oligodendrocyte progenitor cells (OPCs)


title: OPC 48h Fibrinogen 1


title: WT_untreated_rep2


title: WT_18hours_rep2

source_name: B6_ treated-18hourrs


title: Control lung at P0

description:
Gene expression analysis from pooled P0 control lungs
P0_control

source_name: P0 control lungs


title: Pbx1/2 CKO lung at P0

description:
Gene expression analysis from pooled P0 Pbx1/2 CKO lungs
P0_Pbx CKO

source_name: P0 Pbx1/2 CKO lungs


title: KO_untreated_rep1


title: OPC 48h Fibrinogen 3


title: SMARCB1+ day7 3

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (V.16.0.0, ENTREZG)

source_name: I2A SMARCB1-reexpressed cell line

label_protocol: According to the standard Affymetrix protocol

extract_protocol: Total RNAs were collected from samples using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

value: I2A SMARCB1-reexpressed

value: rhabdoid tumor cell line


title: WT_2weeks_rep2

source_name: B6_ treated-2weeks

value: glomerular extracts


title: OPC 48h Control 2

description: Gene expression data from unstimulated OPCs

source_name: RNA prepared from unstimulated OPCs


title: SMARCB1+ day14 3


title: OPC 48h Control 3


title: SMARCB1+ day14 1


title: SMARCB1+ day14 2


title: WT_18hours_rep1

source_name: B6_ treated-18hours


title: Control lung at E14.5

description:
Gene expression analysis from pooled E14.5 control lungs
E14_control

source_name: E14.5 control lungs


title: WT_2weeks_rep1


title: OPC 48h Control 1


title: SMARCB1+ day7 1


title: OPC 12h Fibrinogen 3

source_name: RNA prepared from OPCs treated with fibrinogen for 12 hr

treatment_protocol: Rat OPCs were stimulated with fibrinogen for 12 hrs


title: SMARCB1+ day7 2


title: Pbx1/2 CKO lung at E14.5

description:
Gene expression analysis from pooled E14.5 Pbx1/2 CKO lungs
E14_Pbx CKO

source_name: E14.5 Pbx1/2 CKO lungs


title: OPC 12h Control 1


title: OPC 12h Control 2


title: SMARCB1+ day4 2


title: OPC 12h Fibrinogen 2


title: OPC 12h Fibrinogen 1


title: SMARCB1+ day2 3


title: SMARCB1-def 3

source_name: I2A SMARCB1-deficient cell line

value: I2A SMARCB1-deficient


title: SMARCB1+ day4 3


title: SMARCB1-def 2


title: SMARCB1+ day2 2


title: SMARCB1+ day2 1


title: 60D_CTRL2

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: Digestive gland RNA of Mytilus galloprovincialis

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 2 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized by quantile normalization  of "gPRocessed signal" using R2.6.1 statistical software

label: Cyanine 3

organism: Mytilus galloprovincialis

source_name: Digestive gland of Mytilus galloprovincialis of control group after 60 days

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰. Mussels were distributed into 17L- glass-beakers for 60 days.

extract_protocol: Total RNA was isolated using Extract-all (Eurobio) procedure.

tag: time

value: 60 days

value: Digestive gland


title: 60D_KET4

source_name: Digestive gland of Mytilus galloprovincialis exposed to Ketoprofen (KET) after 60 days

growth_protocol: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰. Mussels were distributed into 17L- glass-beakers for days. and exposed to ketoprofen for 60 days

value: Ketoprofen (KET)


title: 30D_KET4

source_name: Digestive gland of Mytilus galloprovincialis exposed to Ketoprofen (KET) after 30 days

growth_protocol: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰. Mussels were distributed into 17L- glass-beakers for days. and exposed to ketoprofen for 30 days

value: 30 days


title: 60D_KET1


title: 30D_KET3


title: 60D_CTRL3


title: 60D_KET2


title: 60D_CTRL1


title: 60D_CTRL4


title: 30D_CTRL4

source_name: Digestive gland of Mytilus galloprovincialis of control group after 30 days

growth_protocol: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰. Mussels were distributed into 17L- glass-beakers for 30 days.


title: 60D_KET3


title: 30D_CTRL3


title: DM_minus24hr_Foxo3

status: Public on Nov 01 2017

type: SRA

city: Guangzhou

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads by ChIP-seq were mapped to mm9 genome using SOAP2 with parameters: -v 2 -r 0 -m 0 -p 20
Peaks were called using MACS2 (v2.1.0), a p-value of 10^-4 was used as the cutoff
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation. Overlapping analysis was performed using in-house programs and the maximum distance limitation was set to 1000bp.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS, scores represent -10*log(p)

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep.

extract_protocol:
Chromatins from myoblasts and myotubes were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies
ChIP-seq libraries were constructed closely according to the standard illumina pair-end ChIP-seq procedure. After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.

treatment_protocol: C2C12 myoblasts were induced to differentiate by culturing in differentiation medium (DMEM, 2% horse serum and 1% pen/strep)

tag: cell line

tag: developmental stage

value: DM -24 hours

tag: antibody

value: anti-Foxo3 (Hu P. et al, 2008)


title: DM_72hr_Foxo3

value: DM 72 hour


title: InVitro_6hr_NB1RGB cells_TGFB_2

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression in TGFB  (10 ng/mL)-treated NB1RGB cells

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

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

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

source_name: NB1RGB, 6hr, TGFB treatment (10 ng/mL) replicate-2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human foreskin fibroblasts NB1RGB were provided by the RIKEN BRC through the National Bio-Resource Project of the MEXT Japan, and were grown in DMEM containing 10% fetal bovine serum (FBS) at 37 °C in a 5% CO2 incubator.

extract_protocol: RNA was prepared using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Cells were plated at 80% confluence and cultured for 16 hours, CNP at each concentration (0.025, 0.1 μg/mL) was added and the cells were incubated for 1 hour. TGF was then added, and cells were cultured for 6 hours.

tag: cell

value: human foreskin fibroblast

tag: gender

value: male

value: 3 days


title: 30D_KET2

tag: agent

tag: tissue


title: InVitro_6hr_NB1RGB cells_TGFB_1

source_name: NB1RGB, 6hr, TGFB treatment (10 ng/mL) replicate-1


title: 30D_CTRL2

value: control


title: InVitro_6hr_NB1RGB cells_None_1

description: Gene expression in untreated NB1RGB cells

source_name: NB1RGB, 6hr, no treatment replicate-1


title: InVitro_6hr_NB1RGB cells_TGFB+CNP_0.025

description: Gene expression in CNP (0.025 μM)-treated NB1RGB cells in the presence of TGFB

source_name: NB1RGB, 6hr, CNP treatment (0.025 μM)  in the presence of TGFB (10 ng/mL)


title: SMARCB1+ day4 1

source_name: I2A SMARCB1-reexpressed cell line


title: 30D_CTRL1


title: OPC 12h Control 3


title: 30D_KET1


title: InVitro_6hr_NB1RGB cells_CNP_0.025

description: Gene expression in CNP (0.025 μM)-treated NB1RGB cells

source_name: NB1RGB, 6hr, CNP treatment (0.025 μM)


title: InVitro_6hr_NB1RGB cells_TGFB+CNP_0.1

description: Gene expression in CNP (0.1 μM)-treated NB1RGB cells in the presence of TGFB

source_name: NB1RGB, 6hr, CNP treatment (0.1 μM)  in the presence of TGFB (10 ng/mL)


title: SMARCB1-def 1


title: InVitro_6hr_NB1RGB cells_None_2

source_name: NB1RGB, 6hr, no treatment replicate-2


title: InVitro_6hr_NB1RGB cells_CNP_0.1

description: Gene expression in CNP (0.1 μM)-treated NB1RGB cells

source_name: NB1RGB, 6hr, CNP treatment (0.1 μM)


title: 14D_CTRL4

source_name: Digestive gland of Mytilus galloprovincialis of control group after 14 days

growth_protocol: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰. Mussels were distributed into 17L- glass-beakers for 14 days.

value: 14 days


title: 14D_KET3

source_name: Digestive gland of Mytilus galloprovincialis exposed to Ketoprofen (KET) after 14 days

growth_protocol: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰. Mussels were distributed into 17L- glass-beakers for days. and exposed to ketoprofen for 14 days


title: 14D_CTRL2


title: 14D_CTRL3


title: 14D_KET1


title: 14D_KET2


title: 14D_CTRL1


title: 14D_KET4


title: oxPAPC-treated HUVECs replicate 2

city: Kuopio

first: Suvi

last: Kuosmanen

address: Neulaniementie 2

country: Finland

institute: University of Eastern Finland

description:
oxPAPC2
Biological replicate 2 of 3  treated with  oxPAPC for 4h prior collection

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark )according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing:
The image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
All capture probes with both Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide, or for which calling failed, are excluded.

source_name: Human Umbilical Vein Endothelial Cells (HUVECs)

label_protocol: 200 ng total RNA from sample and reference was labelled with Hy3 and Hy5 fluorescent label, respectively, using miRCURY LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

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

tag: treatment

value: oxPAPC

source_name: Total RNA common reference pool

tag: sample type

value: reference


title: oxPAPC-treated HUVECs replicate 3

description:
oxPAPC3
Biological replicate 3 of 3  treated with oxPAPC for 4h prior collection


title: oxPAPC control-treated HUVECs replicate 1

description:
oxPAPC_ctrl1
Biological replicate 1 of 3 treated with oxPAPC control medium for 4h prior collection

value: oxPAPC control medium


title: oxPAPC control-treated HUVECs replicate 2

description:
oxPAPC_ctrl2
Biological replicate 2 of 3  treated with  oxPAPC control medium for 4h prior collection


title: oxPAPC control-treated HUVECs replicate 3

description:
oxPAPC_ctrl3
Biological replicate 3 of 3  treated with oxPAPC control medium for 4h prior collection


title: oxPAPC-treated HUVECs replicate 1

description:
oxPAPC1
Biological replicate 1 of 3 treated with oxPAPC for 4h prior collection


title: VEGF-treated HUVECs replicate 3

description:
vegf3
Biological replicate 3 of 3  treated with vegf

value: vegf


title: VEGF-treated HUVECs replicate 1

description:
vegf1
Biological replicate 1 of 3 treated with vegf


title: VEGF control-treated HUVECs, replicate 1

description:
vegf_ctrl1
Biological replicate 1 of 3 treated with vegf control

value: vegf control


title: VEGF control-treated HUVECs, replicate 2

description:
vegf_ctrl2
Biological replicate 2 of 3  treated with vegf control


title: VEGF-treated HUVECs replicate 2

description:
vegf2
Biological replicate 2 of 3  treated with vegf


title: VEGF control-treated HUVECs, replicate 3

description:
vegf_ctrl3
Biological replicate 3 of 3  treated with vegf control


title: CD8 EMRA T cells + BIRB, donor 4

city: London

first: Sian

middle: M

last: Henson

address: Charterhouse Square

country: United Kingdom

institute: QMUL

description: Gene expression data from EMRA CD8+ T cells + BIRB796 p38 inhibitor

hyb_protocol: Fragmented, labelled cDNA was hybridized to Affymetrix U133 plus 2 arrays according to the manufacturer’s protocol at the Central Biotechnology Service, Cardiff University, UK.

scan_protocol: Agilent GeneChip 3000 scanner

data_processing: Raw intensity data from each microarray were normalized to expression values using RMAExpress. Gene Cluster 3.0 software was used to center the genes and cluster them using Kendall’s tau coefficient. Heat maps of the clustered data were created using Java TreeView software. Principle component analysis was generated using the Partek software package.

source_name: CD27-CD45RA+ CD8+ T cell

label_protocol: The Nugen Biotin labeling kit was used

growth_protocol: PBMC were isolated using Ficoll plaque. CD8+ T cells were purified by positive selection. Positively selected CD8+ T cells were labeled with CD27 FITC (M-T271) and CD45RA APC (HI100) and sorted into 4 subsets using a FACSAria.

extract_protocol: RNA isolation was achived using the ARCTURUS PicoPure Isolation Kit (ThermoFisher). The concentration of small quantities of RNA was determined using the Nanodrop. Linear amplification of 10 ng of total RNA was performed using the Ovation Biotin RNA amplification

treatment_protocol: Each T cell subsets was stimulated for 2 hours with 0.5µg/ml plate coated anti-CD3 (OKT3) and 5ng/ml rhIL-2 before RNA isolation. A final condition took stimulated CD8+ EMRA T cells, CD27-CD45RA+ and incubated them with a p38 MAPK inhibitor BIRB796 at a final concentration of 500nM. 0.5x106 cells were stimulated in each case.


title: CD8 EMRA T cells, donor 6

description: Gene expression data from EMRA CD8+ T cells

value: female


title: CD8 Central Memory T cells, donor 5

description: Gene expression data from CM CD8+ T cells

source_name: CD27+CD45RA- CD8+ T cell


title: CD8 EMRA T cells + BIRB, donor 1


title: CD8 Effector Memory T cells, donor 4

description: Gene expression data from EM CD8+ T cells

source_name: CD27-CD45RA- CD8+ T cell


title: CD8 Effector Memory T cells, donor 3


title: CD8 Effector Memory T cells, donor 2


title: CD8 EMRA T cells, donor 1


title: CD8 EMRA T cells + BIRB, donor 3


title: CD8 EMRA T cells + BIRB, donor 5


title: CD8 Central Memory T cells, donor 1


title: CD8 EMRA T cells + BIRB, donor 2


title: CD8 Naïve T cells, donor 3

description: Gene expression data from Naïve CD8+ T cells

source_name: CD27+CD45RA+ CD8+ T cell


title: CD8 EMRA T cells, donor 2


title: CD8 Central Memory T cells, donor 2


title: CD8 EMRA T cells, donor 5


title: CD8 EMRA T cells, donor 4


title: CD8 Central Memory T cells, donor 6


title: CD8 Naïve T cells, donor 6


title: CD8 Central Memory T cells, donor 3


title: CD8 EMRA T cells + BIRB, donor 6


title: CD8 Naïve T cells, donor 2


title: CD8 Effector Memory T cells, donor 1


title: CD8 Central Memory T cells, donor 4


title: CD8 Effector Memory T cells, donor 6


title: CD8 Effector Memory T cells, donor 5


title: CD8 Naïve T cells, donor 4


title: CD8 Naïve T cells, donor 5


title: CD8 EMRA T cells, donor 3


title: Sorafenib-1

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

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 (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and RMA as normalization method on core dataset.

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

extract_protocol: Total RNA was isolated from frozen liver tissue samples using a High Pure RNA Tissue Kit (Roche Applied Science, Indianapolis, IN) according to the manufacturer’s protocol.

treatment_protocol: Hep3B cells were inoculated into the both flanks (1 x 10^7 cells/ flank). After 5 weeks, tumor bearing mice were randomized into 4 groups (PBS control, sorafenib treatment, mIFN-β treatment, and sorafenib plus mIFN-β treatment). Mice were treated daily peri-tumor injection of IFN-β (1 x 10^4 IU/site) and/or oral sorafenib administration (30mg/kg) for two weeks.

tag: host strain

value: NOD.CB-17Prkdc scid/J

tag: cell type source

value: Hep3B cells

tag: mouse status

value: tumor-bearing xenograft model

tag: treated with

value: Sorafenib


title: Sorafenib-3


title: mIFN-β-1+Sorafenib-2


title: DHL Patient#2 Control 6h

city: Barcelona

first: Juan

middle: Garcia

last: Valero

state: Barcelona

address: Rosselló, 153

department: Oncology and haematology

country: Spain

institute: IDIBAPS

description: Double Hit Lymphoma patient sample

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm implemented in the Expression Console Software v1.1 (Affymetrix).

source_name: DHL Patient#2 Control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: DHL cells at exponential phase were set at 1x10^6 cells/ml for the experiment

extract_protocol: Total RNA was extracted using the Trizol reagent

treatment_protocol: DHL cells were treated with 100 nM CPI203 for 6h

tag: individual

value: DHL cells

value: Control


title: mIFN-β-1+Sorafenib-1


title: DHL Patient#2 100 nM CPI203 6h

description: Double Hit Lymphoma patient sample

source_name: DHL Patient#2 100 nM CPI203

tag: cell type


title: Sorafenib-2


title: DHL Patient#1 Control 6h

description: Double Hit Lymphoma patient sample

source_name: DHL Patient#1 Control


title: PBS control-2

description: PBS control-2

source_name: PBS control-2

value: PBS control


title: mIFN-β-2

value: mIFN-β


title: mIFN-β-1+Sorafenib-3


title: DHL Patient#1 100 nM CPI203 6h

description: Double Hit Lymphoma patient sample

source_name: DHL Patient#1 100 nM CPI203


title: OCI-LY8 100nM CPI203 6h

description: Double Hit Lymphoma cell line

source_name: OCI-LY8 100nM CPI203

value: DHL cell line OCI-LY8


title: mIFN-β-1


title: CTCs, biological rep2

city: Xi'an

first: chen

last: shao

state: Shanxi

address: West changle road No.169

department: Department of Urology

institute: The Fourth Military Medical University

description: Gene expression data from CTCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

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: CTCs from PC3

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: PC3 and CTCs were cultured in F-12K Medium supplemented with 10% fetal bovine serum and incubated at 37 ℃ in a 5% CO2 incubator.

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

treatment_protocol: No special treatment.

value: CTCs from PC3


title: SUDHL-6 100nM CPI203 6h

description: Double Hit Lymphoma cell line

source_name: SUDHL-6 100nM CPI203

value: DHL cell line SUDHL-6


title: PC3, biological rep1

description: Gene expression data from PC3 cell line

source_name: human prostate cancer cell PC3

value: human prostate cancer cell PC3


title: OCI-LY8 Control 6h

description: Double Hit Lymphoma cell line

source_name: OCI-LY8 Control


title: SUDHL-6 Control 6h

description: Double Hit Lymphoma cell line

source_name: SUDHL-6 Control


title: mIFN-β-3


title: PBS control-3

description: PBS control-3

source_name: PBS control-3


title: CTCs, biological rep3

description: Gene expression data from CTCs


title: PBS control-1

description: PBS control-1

source_name: PBS control-1


title: SUDHL-4 100nM CPI203 6h

description: Double Hit Lymphoma cell line

source_name: SUDHL-4 100nM CPI203

value: DHL cell line SUDHL-4


title: PC3, biological rep2

description: Gene expression data from PC3 cell line


title: PC3, biological rep3

description: Gene expression data from PC3 cell line


title: SUDHL-4 Control 6h

description: Double Hit Lymphoma cell line

source_name: SUDHL-4 Control


title: CTCs, biological rep1

description: Gene expression data from CTCs


title: HepG2_Ad-NC

city: Beijing

first: Jian

last: Li

address: Dahua Road

institute: Beijing Hospital

description: HepG2 cells were transfected with Ad-NC for 48 h and RNA was collected for detection.

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: transfected with

value: Ad-NC


title: miR-21_WT3_Ipsi_(Mouse430_2)

last: Chambers

state: London

address: Guy's Campus

department: Wolfson CARD

institute: King's College Londonn

description: Gene expression data

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 230 v2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and analyzsed in Affymetrix Transcript Analysis Console

source_name: F4/80+ CD11b+ macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard WT Pico KIt Affymetrix protocol from  <1ng total RNA

extract_protocol: Agilent total RNA microprep kit

treatment_protocol: FACS F4/80+ CD11b+ macrophages (population P5) isolated from a pool of ipsilateral L4/L5 DRG directly into lysis buffer

tag: genotype/variation

value: wild type WT


title: miR-21_cKO3_Ipsi_(Mouse430_2)

description: Gene expression data

growth_protocol: FACS F4/80+ CD11b+ macrophages (population P5) isolated from a pool of ipsilateral L4/L5 DRG

value: miR-21 cKO


title: HepG2_Ad-uc.372

description: HepG2 cells were transfected with Ad-uc.372 for 48 h and RNA was collected for detection.

tag: cell line


title: miR-21_cKO2_Ipsi_(Mouse430_2)

description: Gene expression data

value: F4/80+ CD11b+ macrophages (population P5) isolated from a pool of ipsilateral L4/L5 DRG


title: miR-21_cKO1_Ipsi_(Mouse430_2)

description: Gene expression data


title: miR-21_WT2_Ipsi_(Mouse430_2)

description: Gene expression data


title: Zgalactanivorans_kappa_rep2

city: Roscoff

first: Francois

last: Thomas

address: Place George Teissier

department: UMR8227, CNRS-UPMC

institute: Station Biologique de Roscoff

description:
Zobellia galactanivorans grown with kappa-carrageenan as sole carbon source
This sample is of Z.galactanivorans grown with kappa-carrageenan as a sole carbon source. It is the second of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by PartnerChip, Evry, France, following the Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by PartnerChip, Evry, France, following the Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: Gene expression was summarized from probe sets and normalized using the Analysis of NimbleGen Arrays Interface (Simon and Biot, 2010 Bioinformatics 26 (19): 2468-2469)

organism: Zobellia galactanivorans

label_protocol: Labeling was performed by PartnerChip, Evry, France, following the Nimblegen standard operating protocol. See www.nimblegen.com.

growth_protocol: Zobellia galactanivorans DsijT was grown to late log-phase in marine mineral medium (Thomas et al. 2011, Journal of Microbiological Methods 84: 61-66) containing a single carbon source, aerobically at 20°C, 180 rpm.

extract_protocol: Samples were directly transferred from -80°C to a 65°C water bath for 15 min to lyse to cells and mixed with 50 µl chloroform for 5 min at room temperature. The aqueous phase was recovered after centrifugation for 15 min at 13000g, 4°C. Total RNA was purified using RNeasy Mini Kit (Qiagen) with on-column DNase I treatment

treatment_protocol: Cells were pelleted by centrifugation (10 min, 4000g), resuspended in Trizol and frozen in liquid nitrogen

tag: genotype/strain

value: wild-type DsijT


title: Zgalactanivorans_kappa_rep3

description:
Zobellia galactanivorans grown with kappa-carrageenan as sole carbon source
This sample is of Z.galactanivorans grown with kappa-carrageenan as a sole carbon source. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_alginate_rep1

description:
Zobellia galactanivorans grown with alginate as sole carbon source
This sample is of Z.galactanivorans grown with alginate as a sole carbon source. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_kappa_rep1

description:
Zobellia galactanivorans grown with kappa-carrageenan as sole carbon source
This sample is of Z.galactanivorans grown with kappa-carrageenan as a sole carbon source. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_alginate_rep2

description:
Zobellia galactanivorans grown with alginate as sole carbon source
This sample is of Z.galactanivorans grown with alginate as a sole carbon source. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_alginate_rep3

description:
Zobellia galactanivorans grown with alginate as sole carbon source
This sample is of Z.galactanivorans grown with alginate as a sole carbon source. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_iota_rep2

description:
Zobellia galactanivorans grown with iota-carrageenan as sole carbon source
This sample is of Z.galactanivorans grown with iota-carrageenan as a sole carbon source. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_iota_rep1

description:
Zobellia galactanivorans grown with iota-carrageenan as sole carbon source
This sample is of Z.galactanivorans grown with iota-carrageenan as a sole carbon source. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_iota_rep3

description:
Zobellia galactanivorans grown with iota-carrageenan as sole carbon source
This sample is of Z.galactanivorans grown with iota-carrageenan as a sole carbon source. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Ovaries of PNA mice

city: Nanjing

first: LEI

last: LEI

state: Jiangsu

address: changle road 68#

department: Department of Obstetrics and Gynecology

institute: Nanjing First Hospital, Nanjing Medical University

description:
P_(Mouse430_2).CEL
Gene expression data from ovaries of PNA mice.

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The scanned images were analyzed using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data.

source_name: Ovaries of PNA mice

growth_protocol: The mice were anesthetized with chloral hydrate on diestrus, ovaries were removed, weighed and then ﬁxed in Bouin’s solution. 2 groups of samples were tested, with each group containing 5 mouse ovaries.

extract_protocol: RNA was extracted using Trizol reagents, and qualified with a NanoDrop 2000 and Agilent Bioanalyzer 2100, and the qualifying samples were entered into the microarray experiment.

treatment_protocol: Adult ICR mice (females, 6 weeks of age; males, 10 weeks of age) were purchased from the Animal Experimental Center of Yangzhou University (Jiangsu Province, China), and housed in the Drum Tower Hospital Animal Experimental Center (Jiangsu Province, China) at 22°C, on a 12 h light/12 h dark cycle with lights on at 07:00, and ad libitum access to chow and water. Females were mated with males and checked for copulatory plugs daily. The date of the plug was considered day 1 of gestation. Pregnant dams were injected daily s.c. with 70 μl of sesame oil containing 350 μg of DHT (521-18-6, Sigma, USA) or sesame oil vehicle on days 16-18 of gestation, and female offspring were studied.

tag: strain/background

value: ICR

value: female

value: ovary

value: prenatally androgenized (PNA)


title: Zgalactanivorans_laminarin_rep2

description:
Zobellia galactanivorans grown with laminarin as sole carbon source
This sample is of Z.galactanivorans grown with laminarin as a sole carbon source. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_glucose_rep3

description:
Zobellia galactanivorans grown with glucose as sole carbon source
This sample is of Z.galactanivorans grown with glucose as a sole carbon source. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Pla2g3-/- colon_azoxymethane

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

institute: The University of Tokyo

description: gene expression in colorectal cancer tissues

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit and hybridized with a Whole Mouse Genome Microarray (4x44K, Agilent Technologies). Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: Pla2g3-/- colon with azoxymethane

label_protocol: 27.7 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: All mice were housed in climate-controlled (23 oC) specific pathogenfree facilities with a 12-h light-dark cycle, with free access to standard diet CE2 (CLEA Japan) and water.

extract_protocol: Total RNA was extracted from mouse colons was purified using the RNeasy Mini Kit (Qiagen), and the quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were injected intraperitoneally with azoxymethane (Wako) at a dose of 10 mg/kg body weight once a week for 6 weeks. Mice were sacrificed 28 weeks after the last injection of azoxymethane. On the last day of the experiments, the colon was removed for microarray analysis.

tag: genotype

value: colon

tag: Sex

value: Male

tag: background strain

tag: age


title: CD8 Naïve T cells, donor 1

source_name: CD27+CD45RA+ CD8+ T cell

tag: gender


title: Zgalactanivorans_glucose_rep1

description:
Zobellia galactanivorans grown with glucose as sole carbon source
This sample is of Z.galactanivorans grown with glucose as a sole carbon source. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Pla2g3+/+ colon_azoxymethane

source_name: Pla2g3+/+ colon with azoxymethane

tag: tissue


title: Zgalactanivorans_glucose_rep2

description:
Zobellia galactanivorans grown with glucose as sole carbon source
This sample is of Z.galactanivorans grown with glucose as a sole carbon source. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Pla2g3+/+ colon_vehicle

description: gene expression in colon by administration of saline as a vehicle

source_name: Pla2g3+/+ colon with administration of saline as a vehicle


title: Ovaries of control mice

description:
C_(Mouse430_2).CEL
Gene expression data from ovaries of control mice.

source_name: Ovaries of control mice

tag: treatment

value: control


title: Zgalactanivorans_laminarin_rep1

description:
Zobellia galactanivorans grown with laminarin as sole carbon source
This sample is of Z.galactanivorans grown with laminarin as a sole carbon source. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Pla2g3-/- colon_vehicle

source_name: Pla2g3-/- colon with administration of saline as a vehicle


title: Zgalactanivorans_laminarin_rep3

description:
Zobellia galactanivorans grown with laminarin as sole carbon source
This sample is of Z.galactanivorans grown with laminarin as a sole carbon source. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_porphyran_rep3

description:
Zobellia galactanivorans grown with porphyran as sole carbon source
This sample is of Z.galactanivorans grown with porphyran as a sole carbon source. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_porphyran_rep1

description:
Zobellia galactanivorans grown with porphyran as sole carbon source
This sample is of Z.galactanivorans grown with porphyran as a sole carbon source. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_agar_rep3

description:
Zobellia galactanivorans grown with agar as sole carbon source
This sample is of Z.galactanivorans grown with agar as a sole carbon source. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_porphyran_rep2

description:
Zobellia galactanivorans grown with porphyran as sole carbon source
This sample is of Z.galactanivorans grown with porphyran as a sole carbon source. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Zgalactanivorans_agar_rep2

description:
Zobellia galactanivorans grown with agar as sole carbon source
This sample is of Z.galactanivorans grown with agar as a sole carbon source. It is the second of three biological replicates used in this experiment, each from separate cultures.