title: hESC_D9_2

description: Gene expression data from hESC at day 9 of differentiation to hepatocyte like cells

hyb_protocol: Labelled cDNA was hybridised to Affymetrix hgu133plus2 gene chip arrays using a protocol supplied by NuGEN.

scan_protocol: The arrays were washed, stained, and scanned using the standard Affymetrix protocol.

data_processing: All array data were normalised using the Microarray Suite version 5.0 (MAS 5.0) algorithm to a global scaling intensity of 100. This raw data was then normalised using the RMA algorithm in the bioconductor affy package (R version 2.15.1). A customs CDF was used to annotate the array (version 13 ENTREZ based cdf from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/entrezg.asp).

source_name: Embryonic stem cell at day 9 of hepatocyte like differentiation protocol

label_protocol: RNA was amplified, fragmented, and biotin-labelled using the Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module (NuGEN Technologies) according to the manufacturer's protocol. 100ng of total RNA was reverse transcribed and amplified. 3.75ug of cDNA was fragmented and biotinylated.

growth_protocol: hESCs were cultured and differentiated according to Hay, David C, Debiao Zhao, Judy Fletcher, Zoë A Hewitt, Doris McLean, Alai Urruticoechea-Uriguen, James R Black, et al. 2008. “Efficient Differentiation of Hepatocytes from Human Embryonic Stem Cells Exhibiting Markers Recapitulating Liver Development in Vivo.” Stem Cells (Dayton, Ohio) 26 (4): 894–902. doi:10.1634/stemcells.2007-0718.

treatment_protocol: LPCs were first enriched by magnetic assisted cell sorting (MACS) (Miltenyi Biotec) and then isolated by fluorescence activated cell sorting (FACS). The mixed cell suspension from freshly prepared foetal liver was passed through a 40 um nylon mesh cell strainer (Becton Dickinson) and washed with cell separation buffer (CS buffer; phosphate buffered saline (PBS) containing 0.5% bovine serum albumin (BSA) and 2 mM EDTA (Sigma-Aldrich)). After centrifugation at 340g for 5 minutes at 4C, the cell pellet was resuspended in CS buffer. As foetal liver is the site of active haematopoiesis during development, haematopoietic cells are abundant and needed to be removed prior to isolation of LPCs. The filtered cell suspension was incubated in the dark at 4C for 15 minutes with CD235a microbeads and CD45 microbeads, washed with CS buffer, and depleted by MidiMACS LD columns and separation units. The effluent depleted of CD235a+ erythroid cells and CD45+ haematopoietic cells was collected and centrifuged at 340g for 5 minutes at 4C and the cell pellet was resuspended in CS buffer. FcR blocking reagent was added to block non-specific binding of antibody to Fc receptor-expressing cells prior to incubating the cell suspension with EpCAM (CD326) microbeads in the dark at 4C for 30 minutes. After washing with CS buffer, isolation of EpCAM+ cells was performed using a MidiMACS magnetic LS column separation system. The eluted EpCAM– fraction was collected, counted, and resuspended in WME+ in preparation for generation of conditioned medium. The retained EpCAM+ fraction was also collected, counted, and resuspended in WME+, and prepared for FACS isolation of LPCs. MACS-enriched EpCAM+ cells were labelled with fluorescent antibodies EpCAM-APC (BioLegend), CD29-PerCP-eFluor® 710 (eBioscience), CD49d-PE (BioLegend) and CD49e-FITC (BioLegend). Samples were sorted using a FACSAria I flow cytometer (Beckton Dickinson Immunocytometry Systems (BD), UK) equipped with 488nm and 633nm lasers running BD FACSDiva v5 Software. An electronic acquisition gate was applied to the Forward/Side scatter plot to exclude debris from intact material. FITC-conjugated anti-CD49e antibody, PE-conjugated anti-CD49d antibody, and PerCP-eFluor® 710-conjugated anti-CD29 antibody binding was detected following 488nm excitation at emission between 530/30nm, 585/42nm, and 695/40nm, respectively. APC-conjugated anti-EpCAM antibody binding was detected following 633nm excitation at emission between 660/20nm. Non-aggregated material was identified based on FSC Area versus Width plot profiles, before applying electronic gates for sorting. Cells that were triple positive for EpCAM, CD29, and CD49d but negative for CD49e were collected for microarray studies.

value: hESC


title: controll mouse IRF4 Knockout (rep2)

status: Public on May 01 2015

type: RNA

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

description:
Gene expression data from CD19+ sIgM-bone marrow cells of IRF4 knockout mouse
S2246_KO2_KM_IRF4

hyb_protocol: The amplified and fragmented biotinylated cRNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays using standard procedures.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: Raw data analysis was performed with R and Bioconductor (Gentleman et al. 2004; R Development Core Team 2007). Arrays were assessed for quality and  GCRMA -normalized. “Quality assessment” consisted of RNA degradation plots, Affymetrix quality control metrics, sample cross-correlation, data distributions, and probe-level visualizations.  The data were analyzed for differential gene expression using an empirical Bayes moderated t-test (Smyth 2004), implemented in the Bioconductor package Linear Models for Microarray Data (LIMMA).  The results were sorted by the false discovery rate and exported in tab-delimited format.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: CD19+ sIgM-  bone marrow cell sort from  IRF4 Knockout control mouse

label_protocol: Total RNA (1.5 μg) and newly transcribed RNA (280 ng) were amplified and labeled using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's recommendations. As newly transcribed RNA mainly consists of mRNA, it was amplified and labeled according to the manufacturer's protocol for mRNA.

extract_protocol: Total RNA extraktion was performed with the RNeasy Mini Kit (Quiagen) according to the manufacturer's instructions.

tag: strain background

tag: genotype/variation

value: IRF4 Knockout

tag: tissue

value: CD19+ sIgM-  bone marrow cells


title: Tumor from mouse8 (rep2)

description:
Gene expression data from murine tumor cells
S2243_T2_Tumor aus M8

source_name: tumor cells from mouse

value: tumor cells


title: hESC_D9_3

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

organism: Homo sapiens

extract_protocol: Total RNA was extracted from foetal cells using TriZol (Invitrogen) according to the manufacturer's protocol. Total RNA from adult hepatocytes was purchased from 3H Biomedical, Uppsala, Sweden. The Nanodrop instrument (Labtech UK) was used to quantify RNA and assess 260/280 and 260/230 ratios. RNA integrity was examined using a 2100 Bioanalyzer (Agilent UK). All samples used had RIN scores > 9, 260/280 ratios > 2, and 260/230 ratios > 1.9.

tag: cell


title: Tumor from mouse12 (rep3)

description:
Gene expression data from murine tumor cells
S2244_T3_Tumor aus M12


title: hESC_D9_1


title: 70_Dorper sheep DNA

type: genomic

city: Beijing

first: Li

last: Zhang

address: Yuanmingyuan Street

country: China

institute: CAAS

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from sheep blood was genotyped using OvineSNP50 Beadchip (Illumina). Genome wide association studies (GWAS) software TASSEL 3.0 (http://www.maizegenetics.net) and Plink software (v1.07,http://pngu.mgh.harvard.edu/~purcell/plink) were used for data analysis and quality control.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Ovis aries

source_name: Dorper sheep

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA was extracted from blood samples using the TIANamp Blood DNA Kit (Tiangen Biotech Co,Ltd., Beijing, China).

tag: gender

value: male

value: blood

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 83_Dorper sheep DNA


title: 7_Dorper sheep DNA


title: 55_Dorper sheep DNA


title: 64_Dorper sheep DNA


title: 44_Dorper sheep DNA


title: follicle_AMHtreated_24hrs_rep4

city: Aarhus N

first: Helen

middle: Nordahl

last: Madsen

address: Brendstrupgaardsvej 100

department: Dept. Clinical Biochemistry

country: Denmark

institute: Aarhus University Hospital

description: Gene expression data from 6 - 9 dissected and cultured follicles.

hyb_protocol: A total of 3.7 µg fragmented cRNA was loaded onto the Affymetrix MG430 2.0 probe array cartridge. The probe array was then incubated for 16 h at 45°C The washing and staining procedure was performed in the Affymetrix Fluidics Station 450.

scan_protocol: The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (Affymetrix Scanner 3000 7G)

data_processing: The readings from the quantitative scanning were MAS5 normalized using the Affymetrix Gene Expression Analysis Software.

source_name: mouse follicle AMH treated 24 hrs

label_protocol: Five ng total RNA was used as starting material for the biotin labeled cDNA preparation. For the labeling procedure the Ovation Pico WTA System (cat#: 3403) followed by the Encore Biotin Module (cat#: 4200) (NuGen Inc, San Carlos CA, USA) was used according to the manufacturer’s instructions.

growth_protocol: For each experiment follicles from eight mice were pooled to obtain one sample pool with sufficient number of follicles. From this sample follicles were allocated to single drop cultures with 0 (control) or 50 ng/mL recombinant Anti-Müllerian hormone (R&D). The culture medium also contained gonadotropins; 80 IU/L FSH (Merch Serono, UK) and 10 IU/L LH (Sigma-Aldrich). The same procedure was done for 12 and 24 hours experiment.

extract_protocol: RNA was purified using RNeasy micro kit. Concentration of total RNA was checked using Nanodrop 2000.

treatment_protocol: After 12 or 24 hours of culture, the follicles were collected in RNAprotect.

tag: strain

value: Ovarian follicle

tag: age

value: 8 weeks


title: 67_Dorper sheep DNA


title: Tumor from mouse7 (rep1)

description:
Gene expression data from murine tumor cells
S2242_TS_Tumor aus M7

tag: strain background


title: 9_Dorper sheep DNA

tag: tissue


title: hESC_D17_1

description: Gene expression data from hESC at day 17 of differentiation to hepatocyte like cells

source_name: Embryonic stem cell at day 17 of hepatocyte like differentiation protocol

tag: cell


title: hESC_D17_3


title: hESC_D17_2


title: BT549_siERβ2_rep3

city: Stockholm

last: Xu

address: Hälsovägen 7-9

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

hyb_protocol: Hybridization was performed according to Affymetyrix standard protocols

scan_protocol: Sanning was performed using an Affymetrix GeneTitan scanner

data_processing: Raw data was processed in Affymetrix Expression Console using the RMA method

source_name: BT549 cells_siERβ2l_48h

label_protocol: Labeling was performed from 150 ng of starting material according to standard Affymetrix protocols

growth_protocol: The human breast cancer cell line BT549 was maintained in RPMI 1640 medium  supplemented with 10% fetal bovine serum (FBS) (Invitrogen) at 37°C, under a humidified atmosphere of 5% carbon dioxide.

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

treatment_protocol: BT549 cells were transfected with a control siRNA or with the of siRNAs targeting ERβ2 and total RNA was extracted 48h after transfection. BT549 cells were transfected with a control pcDNA3 empty vector or with the of flag tagged ERβ2 cDNA and total RNA was extracted 24h after transfection.

tag: cell line

tag: cell type

value: breast cancer cell line

tag: transfected with

value: siRNA targeting ERβ2

tag: time point

value: 48h after transfection


title: LPC_mRNA_9

description: Gene expression data from foetal liver progenitor cells

source_name: Liver progenitor cell (LPC) 14 weeks + 5 days gestation

value: foetal liver progenitor


title: follicle_control_24hrs_rep4

source_name: mouse follicle untreated 24 hrs


title: follicle_control_12hrs_rep4

source_name: mouse follicle untreated 12 hrs


title: follicle_AMHtreated_12hrs_rep4

source_name: mouse follicle AMH treated 12 hrs


title: 13104.Webster.227.SRFS1KO

city: La Jolla

first: Nick

last: Webster

state: CA

address: 9500 Gilman Drive

department: Medicine

country: USA

institute: UCSD

description: Plier-normalized full exons.

hyb_protocol: Hybridized using standard Affymetrix procedure.

scan_protocol: Scanned using standard Affymetrix procedure.

data_processing:
Data normalized by PLIER, full exons used.
MoEx-1_0-st-v1.r2.dt1.mm9.full.mps

source_name: liver, SRSF1HKO

label_protocol: Labeled using standard Affymetrix procedure by the VA/VMRF GeneChip Core.

growth_protocol: Hepatocytes harvested from 3-month-old SRSF1HKO and WT mice by liver perfusion.

extract_protocol: Total RNA from hepatocytes from SRSF1HKO and WT mice was isolated using an RNeasy Kit (QIAGEN). RNA quality was assessed by using the Agilent Model 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: No treatment.

tag: strain/background

tag: genotype/variation

value: 3 months

value: liver

value: primary hepatocyte cultures


title: 54_Dorper sheep DNA

tag: gender

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: 51_Dorper sheep DNA

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: LPC_mRNA_7

source_name: Liver progenitor cell (LPC) 16 weeks + 1 day gestation

tag: cell


title: LPC_mRNA_8


title: follicle_AMHtreated_24hrs_rep3

tag: strain

tag: tissue

tag: age


title: follicle_AMHtreated_12hrs_rep3


title: 13102.Webster.176.SRSF1KO

description: Plier-normalized full exons.

tag: strain/background

tag: genotype/variation

tag: cell type


title: follicle_control_24hrs_rep3


title: LPC_mRNA_6

source_name: Liver progenitor cell (LPC) 20 weeks gestation


title: 13100.Webster.177.WT

description: Plier-normalized full exons.

source_name: liver, WT

value: WT


title: 65_Dorper sheep DNA

tag: gender

tag: birth weight (kg)

tag: weaning weight (kg)


title: LPC_mRNA_5


title: 18_Dorper sheep DNA

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: 13099.Webster.174.WT

description: Plier-normalized full exons.


title: 13101.Webster.180.WT

description: Plier-normalized full exons.


title: LPC_mRNA_4

source_name: Liver progenitor cell (LPC) 19 weeks + 4 days gestation


title: follicle_AMHtreated_24hrs_rep2


title: 58_Dorper sheep DNA

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)


title: 53_Dorper sheep DNA

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 102_Dorper sheep DNA

tag: tissue


title: follicle_control_24hrs_rep2

tag: strain

tag: age


title: 50_Dorper sheep DNA


title: LPC_mRNA_3

source_name: Liver progenitor cell (LPC) 18 weeks + 4 days gestation

tag: cell


title: LPC_mRNA_1

source_name: Liver progenitor cell (LPC) 14 weeks + 3 days gestation


title: 17_Dorper sheep DNA


title: 13109.Webster.483T

description:
13109.Webster.483.Tumor
Plier-normalized full exons.

data_processing:
Data normalized by PLIER, core exons used
MoEx-1_0-st-v1.r2.dt1.mm9.full.mps

source_name: liver tumor, SRSF3HKO

growth_protocol: Livers harvested from 24-month-old SRSF3HKO mice.

extract_protocol: Total RNA from normal liver tissue or liver tumors from SRSF3HKO mice was isolated using an RNeasy Kit (QIAGEN). RNA quality was assessed by using the Agilent Model 2100 Bioanalyzer (Agilent Technologies).

tag: strain/background

tag: genotype/variation

value: 24 months

value: hepatocellular carcinoma


title: follicle_control_12hrs_rep2


title: 13103.Webster.225.SRSF1KO

description: Plier-normalized full exons.

tag: cell type


title: follicle_AMHtreated_12hrs_rep2


title: 13110.Webster.616T

description:
13110.Webster.616.Tumor
Plier-normalized full exons.


title: follicle_control_12hrs_rep3


title: 26_Dorper sheep DNA

tag: gender

tag: birth weight (kg)

tag: weaning weight (kg)


title: mature_hepatocyte_mRNA_3

description: Gene expression data from mature hepatocytes

source_name: Mature hepatocyte mRNA

value: mature hepatocyte


title: 16_Dorper sheep DNA

source_name: Dorper sheep

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: follicle_AMHtreated_24hrs_rep1

source_name: mouse follicle AMH treated 24 hrs


title: LM5 cell line early passage

city: Zurich

first: Michael

last: Baudis

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

description: LM5 cell line early passage

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The files obtained from the scanner were analyzed with softwares from different companies: the Affymetrix® Chromosome Analysis Suite (ChAS) 2.0.0.195 and the BioDiscovery Nexus Copy Number 7.0. Copy number variants (CNV) according to the Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home), DNA copy number alterations smaller than 100 Kb or 50 adjacent probes and loss of heterozygosity (LOH) smaller than 3 Mb were not considered if not known as recurrent aberrations for any neoplasia.

source_name: LM5 cell line early passage

label_protocol: Microarray CGH was performed with the CytoScan HD Array Kit (Affymetrix, Santa Clara, CA) according to the instructions of the manufacturer at the Laboratory for Oncology Diagnostics (Kinderspital Zurich, Switzerland).

growth_protocol: Human SAOS (HTB-85), HOS (CRL-1543) and 143B (CRL-8303) cells were obtained from ATCC (Rockville, MD). Human LM5 cells, derived from parental SAOS cells, were kindly provided by E.S. Kleinerman (M.D. Anderson Cancer Center, Houston, TX). Cells were cultured in DMEM (4.5 g/l glucose)/F12 (1:1) medium supplemented with 10% heat-inactivated fetal calf serum in a humidified atmosphere of 5% CO2. Authentication of the human cell lines was performed at the early and late passages by multiplex PCR (Microsynth, Balgach, Switzerland) using the PowerPlex®16HS system (Promega, Madison, WI) and verified by comparison with the database at the German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, Germany).

extract_protocol: RNA-free DNA from the individual OS cell lines was extracted using the Gentra Puregene kit (Qiagen, Hilden, Germany) according to the protocol recommended by the supplier. DNA concentration and purity was determined with a NanoDrop 1000 spectrophotometer (Thermo Scientific, Wohlen, Switzerland). Since non-degraded DNA was needed, the size of the double-stranded genomic DNA was assessed on a 1% agarose gel. DNA was concentrated and resuspended in nuclease-free water, and the concentration was measured with a NanoDrop 1000 spectrophotometer.

tag: cell line


title: 13108.Webster.405T

description:
13108.Webster.405.Tumor
Plier-normalized full exons.


title: follicle_control_24hrs_rep1


title: 13107.Webster.623

description:
13107.Webster.623.Normal
Plier-normalized full exons.

source_name: normal liver, SRSF3HKO

value: non-tumorous liver


title: mature_hepatocyte_mRNA_2


title: 13106.Webster.483

description:
13106.Webster.483.Normal
Plier-normalized full exons.


title: mature_hepatocyte_mRNA_1


title: follicle_control_12hrs_rep1


title: follicle_AMHtreated_12hrs_rep1


title: WT LPS+LTbR 24 hrs

city: New Delhi

first: Balaji

last: Banoth

state: Delhi

address: Aruna Asaf Ali Marg

department: Immunology

country: India

institute: National Institute of Immunology

hyb_protocol: illumina standard direct hybridization protocol

scan_protocol: By using illumina Bead Array Reader version 3.7.9.27572

data_processing: The raw data was extracted from illumina's Genome studio software and the same used to check the quality of data. The data were normalized using quantile normalisation method.

source_name: Mouse embryonic fibroblasts

label_protocol: Biotinylated cRNA were prepared with TargetAmpTM- Nano labelling Kit for illumina Expression Beadchip

growth_protocol: Mouse embryonic fibroblasts were treated at 70% confluency.

extract_protocol: Total RNA was isolated using  RNeasy Kit (QIAGEN) and on column DNase digestion was performed according to manufacturer protocol. Quality control was performed using Agilent Bioanalyzer.

treatment_protocol: Mouse embryonic fibroblasts were treated at 70% confluency with Lipo-polysaccharide (LPS-1mg/ml), Lymphotoxin b receptor agonist antibody (LTbR - 0.35mg/ml) individually and in a cotreatment regime with both ligands (LPS+LTbR).

tag: genotype

tag: treatment

value: LPS+LTbR 24 hrs

value: MEF


title: WT LTbR 24 hrs

value: LTbR 24 hrs


title: SAOS cell line late passage

description: SAOS cell line late passage

source_name: SAOS cell line late passage

value: SAOS


title: 86_Dorper sheep DNA

value: male

value: blood

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: yto098

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 v2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite (v.6.6) by the RMA algorithmn

label: Biotin

source_name: adult normal CPE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

growth_protocol: not applicable

extract_protocol: Isolation was performed using RNA STAT-60, according to the manufacturer's instructions. Briefly, tissue samples were homogenized in the STAT-60 using  teflon homogenizers. Chloroform was added and the samples centrifuged. The upper layer (aqueous phase) was removed to a fresh tube and the RNA precipitated with isopropanol. Following centrifugation, the RNA pellet was washed once in 75% ethanol, then the air-dried pellet resuspended in DEPC-treated water.

treatment_protocol: all samples are untreated tissues

tag: strain background (for tissue)

value: FVB

tag: genotype/variation (for tissue)

value: loxP TP53/RB/PTEN (no Cre)

tag: tissue class

value: adult normal CPE


title: 31_Dorper sheep DNA

tag: gender

tag: tissue

tag: birth weight (kg)


title: LPC_mRNA_2

source_name: Liver progenitor cell (LPC) 16 weeks + 3 days gestation

tag: cell

value: foetal liver progenitor


title: 45_Dorper sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: WT 0 hr

tag: strain

tag: genotype

tag: cell type


title: 13105.Webster.405

description:
13105.Webster.405.Normal
Plier-normalized full exons.

tag: strain/background

tag: genotype/variation

tag: age


title: yto097

tag: strain background (for tissue)


title: 23_Dorper sheep DNA

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: WT LPS 24 hrs

tag: treatment

value: LPS 24 hrs


title: Taiwanese hyperlipidemia patient 51

city: Changhua City

first: Wei-Chung

last: Shia

address: 8F., No.235, Xuguang Rd.

department: Cancer Research Center

country: Taiwan

institute: Changhua Christian Hospital

description: Genome-Wide Human SNP 6.0 Array

hyb_protocol: DNA was hybridized to each array according to the instructions from Affymetrix. The arrays were then washed using Affymetrix Fluidics Stations.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

data_processing: CEL files, CHP files, and CN5.CNCHP files were generated by Affymetrix Genotyping Console (GTC) 4.1. SNP analysis (CHP) was performed using the Birdseed V2 algorithm with default parameters, and CNV analysis (CNCHP) was performed using the copy number polymorphism (CNP) genotyping algorithm CN5.

source_name: gDNA from whole blood of male Taiwanese hyperlipidemia patient

label_protocol: DNA was restriction enzyme digested, PCR amplified, fragmented, and labeled according to the instructions from Affymetrix.

extract_protocol: Genomic DNA was extracted from whole blood using the Gentra Puregene Blood Kit (Qiagen). DNA quality and quantity were assessed using a Nanodrop Spectrophotometer ND-1000.

tag: gender

tag: population

value: Taiwanese

tag: tissue

value: whole blood

tag: disease state

value: hyperlipidemia


title: Taiwanese hyperlipidemia patient 45

description: Genome-Wide Human SNP 6.0 Array


title: yto089

source_name: embryo control

tag: genotype/variation (for tissue)

tag: tissue class

value: Embryonic day 18 (embryo control)


title: 10-0595_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: 211At_spleen_0kBq_#2

city: Gothenburg

first: Britta

last: Langen

address: Gula stråket 2B

department: Department of Radiation Physics

institute: Sahlgrenska Academy at University of Gothenburg

scan_protocol: Standard Illumina iScan N240 scanning protocol with scan setting file = Direct Hyb

data_processing: The data were normalized using quantile normalization with BASE

source_name: Mouse spleen, 0 kBq

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Excised organs were flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

tag: strain

value: Balb/c

value: female

value: spleen

tag: injected activity

value: 0 kBq

tag: time point

tag: nuclide


title: 211At_spleen_0kBq_#1


title: 11_Dorper sheep DNA

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 42_Dorper sheep DNA

tag: gender

tag: tissue


title: LM5 cell line late passage

description: LM5 cell line late passage

source_name: LM5 cell line late passage

tag: cell line


title: SAOS cell line early passage

description: SAOS cell line early passage

source_name: SAOS cell line early passage


title: Taiwanese hyperlipidemia patient 53

description: Genome-Wide Human SNP 6.0 Array

tag: population

tag: disease state


title: Taiwanese hyperlipidemia patient 41

description: Genome-Wide Human SNP 6.0 Array


title: yto085

source_name: postanatal control_CPE

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class

value: postnatal control (week 2)


title: 211At_spleen_1.7kBq_7d_#3

source_name: Mouse spleen, 1.7 kBq, 7d

tag: strain

tag: injected activity

value: 1.7 kBq


title: Taiwanese hyperlipidemia patient 52

description: Genome-Wide Human SNP 6.0 Array

value: male


title: yto087


title: 211At_spleen_0kBq_#3

tag: time point

tag: nuclide


title: yto084

value: postnatal control (week 3)


title: yto083

value: FVB


title: 211At_spleen_1.7kBq_7d_#1


title: 211At_spleen_7.5kBq_6h_#2

source_name: Mouse spleen, 7.5 kBq, 6h

value: 7.5 kBq


title: 211At_spleen_7.5kBq_6h_#1


title: 52_Dorper sheep DNA

value: blood

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)


title: Taiwanese hyperlipidemia patient 39

description: Genome-Wide Human SNP 6.0 Array

tag: gender

tag: tissue


title: Taiwanese hyperlipidemia patient 50

description: Genome-Wide Human SNP 6.0 Array

tag: population

tag: disease state


title: 62_Dorper sheep DNA

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: yto088

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

value: loxP TP53/RB/PTEN (no Cre)

tag: tissue class


title: 4_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: 41_Dorper sheep DNA

tag: 6-month weight (kg)

tag: fat thickness (cm)


title: 89_Dorper sheep DNA

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: 211At_spleen_1.7kBq_7d_#2

tag: strain

tag: gender

tag: injected activity

tag: time point

tag: nuclide


title: yto069

source_name: CPC mouse model

tag: host strain

value: Female CD1 nude mouse

value: Tp53/RB/Pten null

value: primary tumor


title: 211At_spleen_1.7kBq_6h_#3

source_name: Mouse spleen, 1.7 kBq, 6h

tag: tissue


title: 59_Dorper sheep DNA

source_name: Dorper sheep

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: yto072

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class


title: 22_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: 211At_spleen_1.7kBq_6h_#2

tag: strain

tag: gender

tag: injected activity

tag: time point


title: 211At_spleen_105kBq_1h_#2

source_name: Mouse spleen, 105 kBq, 1h

tag: tissue

value: 105 kBq

tag: nuclide


title: yto096

value: adult normal CPE


title: 211At_spleen_105kBq_1h_#1

value: Balb/c


title: yto067

tag: host strain

value: reimplant


title: 211At_spleen_1.7kBq_1h_#3

source_name: Mouse spleen, 1.7 kBq, 1h

value: female

value: spleen


title: 211At_spleen_1.7kBq_6h_#1


title: 211At_spleen_1.7kBq_1h_#1


title: yto064

value: implanted


title: 28_Dorper sheep DNA

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: yto062

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class


title: yto068


title: yto063


title: yto065


title: 61_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: daily weight gain (kg)


title: 211At_spleen_1.7kBq_1h_#2

tag: strain

tag: gender

tag: injected activity

value: 1.7 kBq

tag: time point


title: yto066

tag: host strain


title: 211At_medulla_0kBq_#3

source_name: Mouse kidney medulla, 0 Gy

tag: tissue

value: kidney medulla

value: 0 kBq

tag: nuclide


title: yto061

value: FVB


title: 99_Dorper sheep DNA

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)


title: 97_Dorper sheep DNA

tag: birth weight (kg)

tag: post-weaning gain (kg)


title: 47_Dorper sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)


title: 46_Dorper sheep DNA

value: male

tag: fat thickness (cm)

tag: daily weight gain (kg)


title: yto059

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class


title: 211At_medulla_0kBq_#2

tag: strain

tag: gender

tag: injected activity

tag: time point


title: 211At_medulla_0kBq_#1

tag: tissue

tag: nuclide


title: 63_Dorper sheep DNA

value: blood

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)


title: 49_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: 33_Dorper sheep DNA

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: daily weight gain (kg)


title: yto056

tag: host strain

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class


title: yto057


title: 211At_medulla_1.7kBq_7d_#1

source_name: Mouse kidney medulla, 1.7 kBq, 7d

tag: strain

tag: gender

tag: tissue

tag: injected activity

tag: time point


title: 211At_medulla_1.7kBq_7d_#2

tag: nuclide


title: 211At_medulla_1.7kBq_7d_#3


title: yto052


title: yto053


title: 60_Dorper sheep DNA

tag: birth weight (kg)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)


title: 69_Dorper sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: 103_Dorper sheep DNA

tag: daily weight gain (kg)


title: 211At_medulla_7.5kBq_6h_#1

source_name: Mouse kidney medulla, 7.5 kBq, 6h

tag: strain

value: 7.5 kBq


title: 211At_medulla_1.7kBq_6h_#3

source_name: Mouse kidney medulla, 1.7 kBq, 6h

tag: gender


title: yto043

tag: host strain

value: Female CD1 nude mouse

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class


title: 211At_medulla_1.7kBq_6h_#2

tag: tissue

tag: injected activity

tag: time point

tag: nuclide


title: yto050

value: Tp53/RB/Pten null


title: 211At_medulla_7.5kBq_6h_#2


title: 1_Dorper sheep DNA

tag: birth weight (kg)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)


title: 211At_medulla_105kBq_1h_#2

source_name: Mouse kidney medulla, 105 kBq, 1h


title: 211At_medulla_1.7kBq_6h_#1


title: 25_Dorper sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: yto049

tag: host strain

tag: strain background (for tissue)


title: 6_Dorper sheep DNA

tag: gender

tag: daily weight gain (kg)


title: yto054

tag: genotype/variation (for tissue)

tag: tissue class


title: yto046


title: 32_Dorper sheep DNA

tag: tissue


title: 36_Dorper sheep DNA

tag: birth weight (kg)


title: 29_Dorper sheep DNA

tag: eye muscle area (cm2)


title: 101_Dorper sheep DNA

tag: height at withers (cm)


title: yto033


title: 211At_medulla_1.7kBq_1h_#2

source_name: Mouse kidney medulla, 1.7 kBq, 1h

tag: strain

tag: injected activity

tag: time point

tag: nuclide


title: yto032


title: 211At_medulla_1.7kBq_1h_#1


title: yto030


title: yto031


title: yto029


title: 211At_lung_0kBq_#3

source_name: Mouse lung, 0 kBq

value: lung


title: yto041


title: 211At_lung_0kBq_#1


title: 57_Dorper sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: chest girth (cm)

tag: shin circumference (cm)


title: 72_Dorper sheep DNA

tag: gender

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: 211At_lung_0kBq_#2


title: 79_Dorper sheep DNA

tag: daily weight gain (kg)


title: 211At_lung_1.7kBq_7d_#2

source_name: Mouse lung, 1.7 kBq, 7d

tag: tissue


title: yto025

tag: host strain

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class


title: 211At_medulla_1.7kBq_1h_#3

tag: strain

tag: injected activity


title: yto024


title: 37_Dorper sheep DNA

tag: birth weight (kg)

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: 10_Dorper sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)


title: yto027

value: primary tumor


title: 87_Dorper sheep DNA

tag: gender

tag: chest girth (cm)

tag: shin circumference (cm)


title: 211At_lung_1.7kBq_7d_#3

tag: time point

tag: nuclide


title: 104_Dorper sheep DNA

tag: tissue

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 13_Dorper sheep DNA


title: yto021

tag: host strain

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class


title: 76_Dorper sheep DNA

tag: birth weight (kg)

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: non-aggressive prolactin pituitary tumor 24

city: Lyon

first: magali

last: roche

address: 8 avenue Rockfeller

country: France

institute: university lyon 1

hyb_protocol: Before hybridization, samples were dried and resuspent in a total volume of 45 µl containing 1X GE Blocking Agent, 1X Hi-RPM Hybridization Buffer, 1 µl of Hybridaton Spike-In (from Agilent's microRNA Spike- In kit p/n 5190- 1934) and incubated 5 min at 100°C. Total mixture was hybridized on  Human miRNA Microarray v3, 8x15k for 20 hours at 55°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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner Type C using AgilentHD_miRNA profile for settings (default).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters. Raw data files (from Feature Extraction) were then normalized using labelling spikes and each sample from one array was normalized by the normal pituitary of same arrray in Genespring Software 7.0 (Agilent Technologies). It is expected that the values are 1 for GSM1128224 and GSM112822. We have normalized each sample in the batch by the normal pituitary (eg. batch 1 is normalized by sample 0_1 and batch 2 is normalized by sample 0_2). Thus sample 0_1 is normalized by itself and so for sample 0_2.

source_name: human pituitary tumor

label_protocol: 100 ng of total RNA added with labelling Spike-In (from Agilent's microRNA Spike- In kit p/n 5190- 1934) was dephosphorylated, denaturated and then labeled with Cyanine 3-pCp following manufacturer's instructions (Agilent Technologies, miRNA Microarray System with miRNA Complete Labeling and Hyb Kit protocol, version 2.2 october 2009). Then labeled samples were purified using Micro Bio-Spin 6 column from Bio-Rad (optional in protocol).

extract_protocol: Total RNA from pituitary tumors and normal pituitary was extracted using miRNeasy Mini kit with DNAse treatment (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol.

tag: tumor stage

value: non-aggressive


title: aggressive prolactin pituitary tumor 6

value: aggressive

tag: gender


title: 211At_lung_1.7kBq_7d_#1

tag: strain

value: Balb/c

tag: injected activity


title: 211At_lung_7.5kBq_6h_#2

source_name: Mouse lung, 7.5 kBq, 6h

value: female

tag: time point


title: yto018

value: reimplant


title: non-aggressive prolactin pituitary tumor 10


title: yto015

value: loxP TP53/RB/PTEN (no Cre)

value: Non CPC Medulloblastoma primary tumor


title: non-aggressive prolactin pituitary tumor 9


title: yto016


title: 211At_lung_1.7kBq_6h_#1

source_name: Mouse lung, 1.7 kBq, 6h

value: 1.7 kBq

tag: nuclide


title: 211At_lung_105kBq_1h_#1

source_name: Mouse lung, 105 kBq, 1h

tag: tissue

value: 105 kBq


title: 211At_lung_1.7kBq_6h_#3


title: 48_Dorper sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)


title: yto014

source_name: CPC mouse model

tag: host strain

tag: strain background (for tissue)

value: FVB

tag: genotype/variation (for tissue)

tag: tissue class


title: 20_Dorper sheep DNA

value: male

tag: birth weight (kg)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: yto013


title: 211At_lung_105kBq_1h_#2

tag: strain

tag: gender

tag: injected activity

tag: time point

tag: nuclide


title: 71_Dorper sheep DNA

tag: tissue

value: blood

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: chest girth (cm)


title: 211At_lung_7.5kBq_6h_#1

value: 7.5 kBq


title: 211At_lung_1.7kBq_6h_#2


title: non-aggressive prolactin pituitary tumor 8

tag: tumor stage


title: yto012

tag: host strain

value: Female CD1 nude mouse

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class


title: yto017

value: Tp53/RB/Pten null


title: 90_Dorper sheep DNA

tag: birth weight (kg)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: 74_Dorper sheep DNA

tag: gender

tag: daily weight gain (kg)


title: 21_Dorper sheep DNA

tag: tissue

tag: weaning weight (kg)


title: 92_Dorper sheep DNA

tag: 6-month weight (kg)

tag: fat thickness (cm)


title: 211At_medulla_105kBq_1h_#1

tag: strain

value: kidney medulla

tag: injected activity

tag: time point

tag: nuclide


title: aggressive prolactin pituitary tumor 1

tag: tumor stage


title: yto011

tag: host strain

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class

value: primary tumor


title: 5_Dorper sheep DNA

tag: birth weight (kg)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)


title: yto042

value: implanted


title: 211At_lung_1.7kBq_1h_#2

source_name: Mouse lung, 1.7 kBq, 1h

tag: gender

tag: tissue

value: lung


title: non-aggressive prolactin pituitary tumor 11

value: non-aggressive


title: yto010


title: aggressive prolactin pituitary tumor 3

value: aggressive


title: 211At_liver_0kBq_#3

source_name: Mouse liver, 0 kBq

tag: strain

value: Balb/c

value: female

value: liver

value: 0 kBq


title: 211At_lung_1.7kBq_1h_#3

tag: injected activity

value: 1.7 kBq


title: normal pituitary 0 [S02]

value: normal


title: yto009

value: FVB


title: yto007


title: normal pituitary 0 [S01]

value: male


title: 211At_liver_0kBq_#2

tag: time point


title: non-aggressive prolactin pituitary tumor 7


title: 211At_lung_1.7kBq_1h_#1

tag: nuclide


title: yto008


title: non-aggressive prolactin pituitary tumor 17

tag: tumor stage


title: 211At_liver_1.7kBq_7d_#3

source_name: Mouse liver, 1.7 kBq, 7d


title: yto006

tag: host strain


title: 211At_liver_0kBq_#1


title: 56_Dorper sheep DNA

source_name: Dorper sheep

value: blood

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 77_Dorper sheep DNA

tag: birth weight (kg)

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: yto004

value: Female CD1 nude mouse

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class


title: 3_Dorper sheep DNA

tag: gender

tag: tissue

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)


title: 93_Dorper sheep DNA


title: 35_Dorper sheep DNA


title: 24_Dorper sheep DNA


title: aggressive prolactin pituitary tumor 2

tag: tumor stage


title: 81_Dorper sheep DNA

tag: weaning weight (kg)


title: yto003

tag: host strain

value: Tp53/RB/Pten null


title: non-aggressive prolactin pituitary tumor 16


title: yto001

source_name: embryo control

value: loxP TP53/RB/PTEN (no Cre)

value: Embryonic day 18 (embryo control)


title: 211At_liver_1.7kBq_7d_#2

tag: strain

tag: injected activity

tag: time point

tag: nuclide


title: 211At_liver_7.5kBq_6h_#1

source_name: Mouse liver, 7.5 kBq, 6h

value: 7.5 kBq


title: 100_Dorper sheep DNA

tag: birth weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 211At_liver_1.7kBq_6h_#3

source_name: Mouse liver, 1.7 kBq, 6h

tag: gender

tag: tissue


title: 38_Dorper sheep DNA

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)


title: ileum_3y8m_rep 3

city: hangzhou

first: chen

last: bo

state: zhejiang

address: 79 Qingchun Road

department: The First Affiliated Hospital, School of Medicine

institute: zhejiang university

description: Gene expresion of SFB negative patient

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours 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), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: SFB negative patient

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

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

treatment_protocol: Terminal ileum obtained from endscopic  examination were immediately frozen by liquid nitrogen

value: femal

tag: age

value: ileum


title: 211At_liver_1.7kBq_6h_#2


title: 211At_liver_1.7kBq_6h_#1


title: 211At_liver_1.7kBq_7d_#1


title: ileum_4y9m_rep 3

description: Gene expresion of SFB positive patient

source_name: SFB positive patient


title: yto002

tag: host strain

tag: strain background (for tissue)

tag: genotype/variation (for tissue)

tag: tissue class

value: primary tumor


title: ileum_4y_rep 3

description: Gene expresion of SFB negative patient


title: Topical-control-w0-2

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 200 Hawkins Dr, 40025 PFP

institute: University of Iowa

hyb_protocol: Following fragmentation, 3.75 ug of cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Bioconductor/R and were RMA normalized.

source_name: skin, vehicle control after disease establishment, week 0

label_protocol: NuGen Encore Biotin Protocol using 3.75 ug cDNA from NuGen Ovation RNA Amplification V2 system.

extract_protocol: miRNeasy Mini Kit (Qiagen) with on-column DNase treatment (Qiagen) of skin biopsy samples taken at the start of treatment or after 12 weeks.

treatment_protocol: Baricitinib was administered to mice in topical form after the establishment of disease.

tag: strain/background

value: C3H/HeJ grafted model of alopecia areata

value: skin

tag: treatment

value: vehiclecontrol

tag: administered form

value: topical

tag: time of treatment

value: after disease establishment

tag: sampling time point

value: week 0

tag: experiment type

value: topical treatment


title: Topical-control-w12-2

source_name: skin, vehicle control after disease establishment, week 12

value: week 12


title: ileum_2y4m_rep 3

description: Gene expresion of SFB negative patient

value: male


title: Topical-control-w12-3


title: Topical-control-w0-3


title: 2_Dorper sheep DNA

value: female

value: blood

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: Topical-control-w12-1

tag: tissue


title: 19_Dorper sheep DNA

tag: gender

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)


title: ileum_2y3m_rep 3

description: Gene expresion of SFB positive patient

tag: age


title: Topical-control-w0-1

tag: strain/background

tag: treatment

tag: administered form

tag: time of treatment


title: 88_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: iPMS_+

city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

description: test

hyb_protocol: hybridized on Agilent human whole genome 44K oligo microarrays that contain more than 41,000 unique human genes and transcripts.  Hybridization and washing was performed according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned with an Agilent DNA microarray scanner.

data_processing:
Feature Extraction (Version 9.1; Agilent) was used to filter, normalize, and calculate the signal intensity and ratios.  Spots flagged as not passing the automated quality control standards were excluded.
The file of normalized values ("Normalized_data.txt") is available on the series level and contains the feature extraction normalized log10 ratio (Cy5/Cy3)

source_name: Control

label_protocol: RNAs were labeled with SuperScript indirect cDNA labeling system (Invitrogen)

growth_protocol: TK6 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum. The cell culture density was maintained at 1-10x10^5 cells/ml, and was tested periodically for mycoplasma contamination

extract_protocol: RNA was extracted using the Trizol protocol (Invitrogen) followed by RNA cleanup with an RNeasy column (Qiagen)

treatment_protocol: Exponentially growing cells were treated at the density of 4-5x10^5 cells/ml. For γ-ray exposure, cells were irradiated at 0.87 Gy/min to a dose of 4 Gy using an γ-ray irradiator. Heat-shock treatment was performed by submerging 35 mL cultures in a T175 flask in a 47 °C circulating water bath with gentle agitation for 20 min, while the control was held in the same volume at 37 °C; we have previously found that this is a maximally tolerated dose for transcriptional analysis at this time (Fornace et al., 1989a). All chemicals were purchased from Sigma-Aldrich, except cadmium chloride and potassium chromate were from J.T. Baker.  Fresh stocks were prepared according to manufacturers’ instruction.  Stock solutions were added to the culture medium and incubated for 4 hr.  Simultaneous controls for each experiments were treated with an equal volume of the vehicle, phosphate buffered saline (PBS) or DMSO.  At the end of the 4 h treatment period, cells were pelleted by centrifugation and subjected to RNA extraction.  Dose-response studies were performed for most agents to determine the dose for the microarray experiments.

tag: cell line

source_name: iPMS


title: 85_Dorper sheep DNA

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: iPMS_-

description: test


title: 75_Dorper sheep DNA

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 15_Dorper sheep DNA

tag: gender

tag: tissue

tag: height at withers (cm)


title: 211At_liver_105kBq_1h_#1

source_name: Mouse liver, 105 kBq, 1h

tag: strain

value: Balb/c

value: liver

tag: injected activity

value: 105 kBq

tag: time point

tag: nuclide


title: 211At_liver_7.5kBq_6h_#2

value: 7.5 kBq


title: 3-NP_+

description: test


title: 3-NP_-

description: test


title: 91_Dorper sheep DNA

tag: chest girth (cm)

tag: shin circumference (cm)


title: 30_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: 211At_liver_105kBq_1h_#2


title: 211At_liver_1.7kBq_1h_#2

source_name: Mouse liver, 1.7 kBq, 1h

value: 1.7 kBq


title: 211At_liver_1.7kBq_1h_#3


title: 211At_cortex_0kBq_#2

source_name: Mouse kidney cortex, 0 kBq

value: kidney cortex

value: 0 kBq


title: Topical-bari-w12-3

source_name: skin, topical baricitinib after disease establishment, week 12

tag: strain/background

value: C3H/HeJ grafted model of alopecia areata

value: skin

tag: treatment

value: baricitinib

tag: administered form

tag: time of treatment

tag: sampling time point

tag: experiment type


title: 8_Dorper sheep DNA

tag: gender

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 211At_liver_1.7kBq_1h_#1

tag: strain

tag: tissue

tag: injected activity

tag: time point

tag: nuclide


title: Systemic-control-w12-3

treatment_protocol: Baricitinib was administered to mice in systemic form after disease establishment.

tag: strain/background

tag: treatment

value: vehicle control

value: systemic

value: after disease establishment

value: systemic treatment


title: 84_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)


title: 211At_cortex_1.7kBq_7d_#3

source_name: Mouse kidney cortex, 1.7 kBq, 7d

tag: gender


title: Topical-bari-w0-2

source_name: skin, topical baricitinib after disease establishment, week 0

tag: administered form

value: topical

tag: time of treatment

tag: sampling time point

value: week 0

tag: experiment type

value: topical treatment


title: 43_Dorper sheep DNA

value: female

value: blood

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: Topical-bari-w12-2

tag: strain/background

tag: tissue

tag: treatment

value: week 12


title: Topical-bari-w0-3


title: Systemic-control-w0-3


title: 80_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: height at withers (cm)


title: 211At_cortex_0kBq_#1

tag: strain

value: Balb/c

tag: gender

tag: injected activity

tag: time point

tag: nuclide


title: Systemic-control-w12-2

tag: administered form

tag: time of treatment

tag: sampling time point

tag: experiment type


title: ileum_2y6m_rep 3

description: Gene expresion of SFB negative patient

value: femal

tag: age

value: ileum


title: 211At_cortex_7.5kBq_6h_#2

source_name: Mouse kidney cortex, 7.5 kBq, 6h

value: kidney cortex

value: 7.5 kBq


title: 34_Dorper sheep DNA

source_name: Dorper sheep

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 12_Dorper sheep DNA

tag: gender

tag: tissue

tag: birth weight (kg)

tag: weaning weight (kg)

tag: height at withers (cm)


title: 14_Dorper sheep DNA


title: Systemic-control-w0-2

tag: strain/background

value: C3H/HeJ grafted model of alopecia areata

value: skin

tag: treatment

tag: administered form

tag: time of treatment


title: 211At_cortex_7.5kBq_6h_#1

tag: strain

tag: injected activity

tag: time point

tag: nuclide


title: 211At_cortex_1.7kBq_7d_#1

value: 1.7 kBq


title: Systemic-control-w12-1

value: vehicle control

value: systemic

tag: sampling time point

tag: experiment type


title: Topical-bari-w0-1

value: baricitinib

value: after disease establishment


title: Systemic-control-w0-1

value: week 0

value: systemic treatment


title: 211At_cortex_1.7kBq_6h_#1

source_name: Mouse kidney cortex, 1.7 kBq, 6h

value: female


title: 27_Dorper sheep DNA

value: blood

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: 78_Dorper sheep DNA

tag: gender

tag: tissue

tag: birth weight (kg)

tag: weaning weight (kg)

tag: height at withers (cm)

tag: daily weight gain (kg)


title: Systemic-bari-w12-3

source_name: skin, systemic baricitinib after disease establishment, week 12

tag: strain/background

tag: treatment

tag: administered form

tag: time of treatment

value: week 12


title: 82_Dorper sheep DNA

tag: 6-month weight (kg)


title: 211At_cortex_0kBq_#3

tag: strain

value: Balb/c

tag: injected activity

value: 0 kBq

tag: time point

tag: nuclide


title: Topical-bari-w12-1

value: topical

tag: sampling time point

tag: experiment type

value: topical treatment


title: Systemic-bari-w12-1


title: 211At_cortex_1.7kBq_7d_#2

tag: gender

value: kidney cortex


title: 73_Dorper sheep DNA

tag: tissue

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: Systemic-bari-w12-2

tag: strain/background

value: C3H/HeJ grafted model of alopecia areata

tag: treatment

tag: administered form


title: 211At_cortex_1.7kBq_6h_#2

tag: strain


title: 211At_cortex_1.7kBq_6h_#3

tag: injected activity


title: 211At_cortex_105kBq_1h_#2

source_name: Mouse kidney cortex, 105 kBq, 1h

value: 105 kBq

tag: time point


title: 94_Dorper sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: height at withers (cm)

tag: daily weight gain (kg)


title: Systemic-bari-w0-3

source_name: skin, systemic baricitinib after disease establishment, week 0

tag: tissue

value: skin

tag: time of treatment

tag: sampling time point

tag: experiment type


title: 66_Dorper sheep DNA

tag: gender

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)


title: 211At_cortex_105kBq_1h_#1

tag: strain

tag: injected activity

tag: nuclide


title: 521_German Mutton sheep DNA

source_name: German Mutton sheep

tag: birth weight (kg)

tag: weaning weight (kg)

tag: post-weaning gain (kg)


title: 522_German Mutton sheep DNA

tag: 6-month weight (kg)

tag: height at withers (cm)

tag: daily weight gain (kg)


title: 211At_cortex_1.7kBq_1h_#3

source_name: Mouse kidney cortex, 1.7 kBq, 1h

tag: tissue

value: 1.7 kBq

tag: time point


title: PZQ treatment_Female Paired_replicate 2

city: São Paulo

first: Giulliana

middle: Tessarin

last: Almeida

state: SP

address: Av Prof Lineu Prestes, 748

department: Departamento de Bioquímica

country: Brazil

institute: University of São Paulo - Instituto de Química

description: Replicate 2 of 2. PZQ treated paired females  vs. untreated paired females.

hyb_protocol: Agilent Gene Expression Hybridization Kit were used and samples were applied to microarrays enclosed in Agilent  Microarray Hybridization Chamber. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent High-Resolution Microarray scanner . Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1).

data_processing: Low intensity data were eliminated according to Feature Extraction software criteria. Locally weighted linear regression (LOWESS) algorithm was used to correct systematic labeling/detection dye biases. For a gene that was represented in the array by multiple probes, we chose a single representative probe by selecting the probe with the smallest coefficient of variation (CV) of probe intensity among the different probes for the same Smp gene on the array, when analyzing the replicas of essentially all previously published experiments using this array; the selected probes (marked "YES, to be used in expression analysis")

organism: Schistosoma mansoni

source_name: Female Paired Control

label_protocol: 300 ng of DNAse-treated total RNA aliquots were amplified and labeled using Agilent Low RNA Input Fluorescent Linear Amplification Kit  following manufacturer's instructions

growth_protocol: S. mansoni (LE strain) was maintained at Centro de Pesquisas René Rachou, Fiocruz (Brazil) by routine passage through Biomphalaria glabrata snails and female Swiss mice (mean weight 25 g), which were infected by subcutaneous route with 100 ± 10 cercariae. Seven weeks after the infection, adult worms were recovered by perfusion of portal-mesenteric system with 0.85% saline solution and 1% heparin.

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

value: LE

tag: Sex

value: paired

source_name: Female  Paired PZQ


title: PZQ treatment_Female Paired_replicate 2_swap

description: Replicate 2 of 2 (dye-swap). PZQ treated paired females  vs. untreated paired females.

source_name: Female Paired PZQ


title: PZQ treatment_Female Unpaired_replicate 2_swap

description: Replicate 2 of 2 (dye-swap). PZQ treated unpaired females  vs. untreated unpaired females.

source_name: Female  Unpaired PZQ

value: unpaired

source_name: Female Unpaired Control


title: Systemic-bari-w0-1

tag: strain/background

tag: treatment

value: baricitinib

tag: administered form

value: systemic

tag: time of treatment

value: after disease establishment

tag: sampling time point

value: week 0

tag: experiment type


title: 520_German Mutton sheep DNA

tag: gender

value: female

value: blood

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)


title: Prevention-control-5

source_name: skin, vehicle control at time of grafting, week 12

extract_protocol: miRNeasy Mini Kit (Qiagen) with on-column DNase treatment (Qiagen) of skin biopsy samples taken after 12 weeks.

treatment_protocol: Baricitinib was administered to mice in systemic form at the time of grafting.

value: vehicle control

value: time of grafting

value: week 12

value: prevention


title: 211At_cortex_1.7kBq_1h_#1

tag: strain

value: Balb/c

value: kidney cortex

tag: injected activity

tag: nuclide


title: Systemic-bari-w0-2

value: C3H/HeJ grafted model of alopecia areata

tag: tissue

value: skin

value: systemic treatment


title: 211At_cortex_1.7kBq_1h_#2

value: 1.7 kBq

tag: time point


title: PZQ treatment_Female Unpaired_replicate 2

description: Replicate 2 of 2. PZQ treated unpaired females  vs. untreated unpaired females.

value: LE

tag: Sex

value: unpaired


title: PZQ treatment_Male Paired_replicate 2

description: Replicate 2 of 2. PZQ treated paired males  vs. untreated paired males.

source_name: Male Paired Control

value: male

value: paired

source_name: Male  Paired PZQ


title: Prevention-control-4

tag: strain/background

tag: treatment

value: systemic


title: PZQ treatment_Male Paired_replicate 2_swap

description: Replicate 2 of 2 (dye-swap). PZQ treated paired males  vs. untreated paired males.

source_name: Male Paired PZQ


title: Prevention-control-3

tag: administered form

tag: time of treatment


title: 513_German Mutton sheep DNA

value: female

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: height at withers (cm)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 510_German Mutton sheep DNA

tag: gender

value: blood

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)


title: Prevention-control-1

tag: tissue

value: vehicle control

tag: sampling time point

tag: experiment type


title: 514_German Mutton sheep DNA


title: 511_German Mutton sheep DNA


title: 512_German Mutton sheep DNA


title: PZQ treatment_Female Unpaired_replicate 1_swap

description: Replicate 1 of 2 (dye-swap). PZQ treated paired females  vs. untreated paired females.

tag: strain

tag: Sex


title: PZQ treatment_Female Unpaired_replicate 1

description: Replicate 1 of 2. PZQ treated paired females  vs. untreated paired females.


title: 516_German Mutton sheep DNA

tag: birth weight (kg)


title: PZQ treatment_Female Paired_replicate 1

description: Replicate 1 of 2. PZQ treated unpaired females  vs. untreated unpaired females.


title: PZQ treatment_Female Paired_replicate 1_swap

description: Replicate 1 of 2 (dye-swap). PZQ treated unpaired females  vs. untreated unpaired females.


title: PZQ treatment_Male Paired_replicate 1_swap

description: Replicate 1 of 2 (dye-swap). PZQ treated paired males  vs. untreated paired males.


title: PZQ treatment_Male Paired_replicate 1

description: Replicate 1 of 2. PZQ treated paired males  vs. untreated paired males.


title: Prevention-control-2

tag: strain/background

tag: treatment

tag: administered form

tag: time of treatment

value: time of grafting


title: Prevention-bari-4

source_name: skin, systemic baricitinib at time of grafting, week 12

value: baricitinib

value: week 12


title: 494_German Mutton sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: height at withers (cm)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 509_German Mutton sheep DNA

tag: gender

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)


title: 506_German Mutton sheep DNA

tag: tissue

tag: pre-weaning gain(kg)


title: Prevention-bari-3

tag: sampling time point

tag: experiment type

value: prevention


title: 491_German Mutton sheep DNA

tag: birth weight (kg)


title: Prevention-bari-2

tag: strain/background

tag: treatment

tag: administered form


title: 493_German Mutton sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)


title: Prevention-bari-1

tag: time of treatment


title: 507_German Mutton sheep DNA

tag: height at withers (cm)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: Follicles_12h_50AMH_rep3

description: Gene expression data from follicles after 24 h AMH (50 ng/mL) stimulation

source_name: Ovary follicles, 12hours, 50ng/mL AMH

growth_protocol: For each experiment follicles from seven mice were pooled to obtain one biological sample with sufficient number of follicles. From this sample follicles were allocated to single drop cultures with 0 (control), 50 or 200 ng/mL recombinant Anti-Müllerian hormone (R&D). The culture medium also contained gonadotropins; 80 IU/L FSH (Merch Serono, UK) and 10 IU/L LH (Sigma-Aldrich). The same procedure was done for 12 and 24 hours experiment.

extract_protocol: RNA was purified using RNeasy micro kit. Concentration and quality of total RNA was checked using Bioanalyzer 2100.

tag: strain

value: preantral/small antral follicle

tag: age

value: six to eight weeks


title: Follicles_12h_200AMH_rep3

description: Gene expression data from follicles after 24 h AMH (200 ng/mL) stimulation

source_name: Ovary follicles, 12hours, 200ng/mL AMH


title: Follicles_12h_0AMH_rep3

description: Gene expression data from follicles cultured with vehicle

source_name: Ovary follicles, 12hours, control


title: 490_German Mutton sheep DNA

extract_protocol: Genomic DNA was extracted from blood samples using the TIANamp Blood DNA Kit (Tiangen Biotech Co,Ltd., Beijing, China).

tag: gender

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)


title: 488_German Mutton sheep DNA

tag: tissue

tag: birth weight (kg)

tag: pre-weaning gain(kg)


title: 487_German Mutton sheep DNA


title: 489_German Mutton sheep DNA


title: Follicles_24h_50AMH_rep3

source_name: Ovary follicles, 24hours, 50ng/mL AMH


title: Follicles_24h_200AMH_rep3

source_name: Ovary follicles, 24hours, 200ng/mL AMH


title: Follicles_24h_0AMH_rep3

source_name: Ovary follicles, 24hours, control


title: SW-13-BRG1+IFNI

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized using Average Nornalization with processed use Beadstudio software

label_protocol: Biotinylated cRNA were prepared with the RNA Amplification Kit (Life Technologies) for Illumina arrays

extract_protocol: Standard Trizol extraction according to Invitrogen insert

tag: cell line


title: SW-13-GFP+IFNIII


title: 483_German Mutton sheep DNA

source_name: German Mutton sheep

tag: weaning weight (kg)


title: Follicles_12h_50AMH_rep2


title: Follicles_12h_200AMH_rep2


title: SW-13-BRG1+IFNII


title: 482_German Mutton sheep DNA

tag: 6-month weight (kg)


title: 481_German Mutton sheep DNA


title: Caffeine_-

description: test

source_name: Caffeine

source_name: Control


title: Follicles_12h_0AMH_rep2


title: Caffeine_+

description: test


title: Follicles_24h_50AMH_rep2


title: SW-13-BRG1-IFNI


title: Tunicamycin_+

description: training

source_name: Tunicamycin


title: SW-13-BRG1-IFNIII


title: Follicles_24h_200AMH_rep2


title: SW-13-GFP+IFNII


title: Follicles_12h_200AMH_rep1


title: Follicles_24h_0AMH_rep2


title: 485_German Mutton sheep DNA


title: Tunicamycin_-

description: training


title: Thapsigargin_+

description: training

source_name: Thapsigargin


title: Follicles_24h_200AMH_rep1


title: RMKN28 exp.2

city: Sendai

first: yuriko

last: saiki

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Molecular Pathology

country: Japan

institute: Tohoku University School of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: RMKN28 GEM resistant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp labeling kit one color (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: Cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Studio City, 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).

treatment_protocol: For establishment of gemcitabine resistant cells, the cells were exposed to the concentration showing IC50, for more than one month. After that, the concentrations were increased in stepwise (10 fold) to 10,000 ng / ml finally.

tag: cell type

value: Gastric cancer cell line


title: 486_German Mutton sheep DNA

data_processing: Genomic DNA extracted from sheep blood was genotyped using OvineSNP50 Beadchip (Illumina). Genome wide association studies (GWAS) software TASSEL 3.0 (http://www.maizegenetics.net) and Plink software (v1.07,http://pngu.mgh.harvard.edu/~purcell/plink) were used for data analysis and quality control.

tag: height at withers (cm)


title: Follicles_12h_50AMH_rep1

data_processing: The readings from the quantitative scanning were MAS5 normalized using the Affymetrix Gene Expression Analysis Software.


title: Follicles_24h_50AMH_rep1


title: Thapsigargin_-

description: training


title: SW-13-BRG1+IFNIII


title: 479_German Mutton sheep DNA

tag: post-weaning gain (kg)


title: SW-13-GFP+IFNI


title: 480_German Mutton sheep DNA

tag: daily weight gain (kg)


title: Prevention-bari-5

tag: strain/background

value: C3H/HeJ grafted model of alopecia areata

value: skin

tag: treatment

tag: administered form

tag: time of treatment

tag: sampling time point

tag: experiment type


title: 471_German Mutton sheep DNA

tag: gender

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)


title: Follicles_12h_0AMH_rep1

tag: strain

tag: tissue

tag: age


title: 469_German Mutton sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: height at withers (cm)

tag: pre-weaning gain(kg)


title: SW-13-GFP-IFNIII

tag: cell line


title: Follicles_24h_0AMH_rep1


title: SW-13-BRG1-IFNII


title: 475_German Mutton sheep DNA

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 476_German Mutton sheep DNA


title: RMKN28 exp.1

tag: cell type


title: SW-13-GFP-IFNII


title: MMS_+

description: training

source_name: MMS


title: MKN28 exp.2

source_name: MKN28 parental


title: 473_German Mutton sheep DNA

tag: gender


title: 468_German Mutton sheep DNA

tag: fat thickness (cm)


title: SW-13-GFP-IFNI


title: MMS_-

description: training


title: 477_German Mutton sheep DNA

tag: eye muscle area (cm2)


title: MKN28 exp.1


title: 474_German Mutton sheep DNA

tag: chest girth (cm)


title: x-Ray_+

description: training

source_name: x-Ray


title: 466_German Mutton sheep DNA

tag: shin circumference (cm)


title: 467_German Mutton sheep DNA


title: x-Ray_-

description: training


title: Hydroxyurea_+

description: training

source_name: Hydroxyurea


title: Hydrogen Peroxide_+

description: training

source_name: Hydrogen Peroxide


title: patDp/+ replicate-3

city: Wako

first: Xiaoxi

last: Liu

state: Saitama

address: Hirosawa 2-1

department: Brain Science Institute

institute: RIKEN

description: patDp/+

hyb_protocol: Amplified and Cy3 labeled RNA were fragmentated and hybridized onto mouse GE 4x44K microarrays (G4122F)

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2505B)

data_processing: The raw singal intensities were acquired by Feature Extraction Software 9.5 (Agilent) and analyzed by Limma package (3.18.2) under the R environment. The signal intensities were corrected by backgroundCorrect function of the Limma package and the between arrays normalization was performed by using the quantile method. Differentially expressed genes (DEGs) were ranked using a moderated t-statistic.

source_name: epididymal white adipose tissue (WAT), wild type mouse, early stage, replicate 1

label_protocol: 200 ng of total RNA was used for further procedure including Cy3 labeling with T7 RNA polymerase amplification method according to manufacturer's instruction (Low Input Quick Amp Labeling Kit for one color; Agilent)

extract_protocol: Total RNA from WAT of young adult stage (9-10 weeks old) was extracted using TRIzol (Life Technologies) followed by column purification with DNase treatment (Promega). The concentration of RNA was estimated by using the NanoDrop spectrometer (Thermo) and the quality of total RNA was evaluated with Agilent 2100 Bioanalyzer (Agilent)

value: epididymal white adipose tissue

value: 9-10 weeks

tag: genotype

value: patDp/+

tag: genetic background


title: Heat shock_+

description: training

source_name: Heat shock


title: Hydroxyurea_-

description: training


title: Hydrogen Peroxide_-

description: training


title: Heat shock_-

description: training


title: Etoposide_+

description: training

source_name: Etoposide


title: Etoposide_-

description: training


title: patDp/+ replicate-1

description: patDp/+

tag: tissue

value: male

tag: age


title: Wild type replicate -2

description: Wild type

value: Wild type


title: Wild type replicate -1

description: Wild type


title: Control 12H Biological Replicate 2 Technical Replicate 1

city: Fort Collins

first: Kathleen

last: Yeater

state: CO

address: 2150 Centre Avenue

institute: USDA-ARS

hyb_protocol: 2ug aRNA probe labeled with either Cy3 or Cy5.  The slides were pre-hybridized in 5X SSC, 0.1% SDS, and 0.1 mg/ml BSA (Fraction V) at 42oC for 45 minutes and then submerged in 0.1X SSC for 5 minutes 3X, followed by final submersion in ddH20 for 30 seconds.  The slides were dried by centrifugation at 1000 X g for 5 minutes. The probe hybridization buffer consisted of 35% formamide, 5X SSC, 0.1% SDS, and 0.1 mg/ml sheared fish testes DNA. All hybridizations were carried out at 42oC for 16 hours in a Genetix 10-slide Hybridization Chamber (Genetix, New Milton, England). Following hybridization, slides were washed in 2X SSC, 0.1% SDS at 42oC for 5 minutes, then washed twice in 1X SSC at room temperature for 3 minutes, then washed twice in 0.1X SSC at room temperature for 2 minutes, and finally washed once in 0.05X SSC for 30 seconds. After drying by centrifugation, the slides were treated with DyeSaver2 (Genisphere Inc., Hatfield, PA, USA) as per the manufacturer’s protocol to prevent ozone-mediated degradation of the Cy5 dye.

scan_protocol: Slides were scanned in a GenePix 4000B microarray scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) at 10mm resolution using the GenePix Pro 6.0 software package.

data_processing: Data quality was evaluated using data distribution and ratio analysis tools.  The data was normalized within and across arrays using Loess normalization (Dudoit et al., 2002; Wolfinger et al., 2001). The normalized expression levels were further evaluated for quality using correlation and principal components analyses. The normalized expression levels were then analyzed in individual gene-specific models. The gene-specific models were fit in JMP® Genomics 3.2 using mixed models analysis (Wolfinger et al., 2001). The hormone treatment, treatment time, the interaction between treatment and time, and dye channel were the fixed effects. The array effect was considered as a random effect.

organism: Gossypium hirsutum

source_name: unfertilized cotton ovule untreated for 12H

label_protocol: RNA amplification and labeling using the Amino Allyl MessageAmp(TM) aRNA Amplification Kit (Ambion, Austin, TX) as per manufacturer's protocol.  1000ng of total RNA used for starting material of each amplification reaction.  The in vitro transcription reaction for synthesizing amplified RNA (aRNA) performed for 12 hours.

growth_protocol: Cotton ovaries harvested from the cotton squares (-1 DPA) were surface-sterilized and dissected under sterile conditions. The unfertilized ovules were transferred  to a liquid basal medium and incubated at 32oC in a 5% CO2 atmosphere.

extract_protocol: Total RNA extracted using Sigma Spectrum ™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO) with DNase1 digestion according to manufacturer's protocol.

treatment_protocol: The unfertilized ovules were placed in a liquid basal medium in the presence or absence of 5μM indole-3-acetic acid (IAA) and 1μM GA. Cotton ovules were incubated for 1, 3, 6, and 12 and harvested for RNA extraction.

tag: germplasm line

value: Texes Marker-1 (TM-1)

tag: developmental stage

value: -1 day of antheis (DOA)

tag: plant growth conditions

value: field

value: unfertilized ovule

tag: treatment


title: 459_German Mutton sheep DNA

city: Beijing

first: Li

last: Zhang

address: Yuanmingyuan Street

institute: CAAS

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

value: female

value: blood

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: height at withers (cm)

tag: pre-weaning gain(kg)


title: 464_German Mutton sheep DNA

tag: gender

tag: fat thickness (cm)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: Treated 12H Biological Replicate 2 Technical Replicate 2

source_name: unfertilized cotton ovule treated with phytohormones for 12H

value: 5μM IAA and 1μM GA


title: Control 1H Biological Replicate 2 Technical Replicate 2

source_name: unfertilized cotton ovule untreated for 1H


title: 456_German Mutton sheep DNA

source_name: German Mutton sheep

tag: eye muscle area (cm2)

tag: chest girth (cm)

tag: shin circumference (cm)


title: 458_German Mutton sheep DNA

tag: tissue


title: patDp/+ replicate-2

description: patDp/+

tag: age

tag: genotype

tag: genetic background


title: Cisplatin_-

description: training

source_name: Cisplatin

tag: cell line


title: Wild type replicate -3

description: Wild type


title: Treated 6H Biological Replicate 1 Technical Replicate 1

source_name: unfertilized cotton ovule treated with phytohormones for 6H

tag: germplasm line

tag: developmental stage

tag: plant growth conditions

tag: treatment


title: 455_German Mutton sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: height at withers (cm)

tag: pre-weaning gain(kg)


title: 463_German Mutton sheep DNA

tag: gender

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 460_German Mutton sheep DNA

tag: tissue

tag: chest girth (cm)

tag: shin circumference (cm)


title: Chromate_+

description: training

source_name: Control

tag: cell line

source_name: Chromate


title: 454_German Mutton sheep DNA


title: Cisplatin_+

description: training


title: Treated 6H Biological Replicate 2 Technical Replicate 1

tag: germplasm line

tag: developmental stage


title: Control 12H Biological Replicate 2 Technical Replicate 2

tag: plant growth conditions

tag: treatment


title: 457_German Mutton sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: Chromate_-

description: training


title: 453_German Mutton sheep DNA

tag: 6-month weight (kg)

tag: height at withers (cm)


title: 451_German Mutton sheep DNA

tag: gender

tag: pre-weaning gain(kg)


title: Camptothecin_+

description: training

source_name: Camptothecin


title: Camptothecin_-

description: training


title: Cadmium_+

description: training

source_name: Cadmium


title: Cadmium_-

description: training


title: Bleomycin_+

description: training

source_name: Bleomycin


title: Bleomycin_-

description: training


title: 450_German Mutton sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: Arsenite_+

description: training

source_name: Arsenite


title: Treated 1H Biological Replicate 2 Technical Replicate 1

source_name: unfertilized cotton ovule treated with phytohormones for 1H


title: 452_German Mutton sheep DNA

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: Treated 12H Biological Replicate 1 Technical Replicate 2

tag: tissue


title: Treated 3H Biological Replicate 2 Technical Replicate 2

source_name: unfertilized cotton ovule treated with phytohormones for 3H


title: Control 3H Biological Replicate 2 Technical Replicate 1

source_name: unfertilized cotton ovule untreated for 3H


title: 449_German Mutton sheep DNA

tag: chest girth (cm)

tag: shin circumference (cm)


title: Treated 3H Biological Replicate 1 Technical Replicate 2

tag: germplasm line


title: Treated 0H Biological Replicate 2 Technical Replicate 2

source_name: unfertilized cotton ovule treated with phytohormones for 0H

tag: developmental stage


title: 444_German Mutton sheep DNA


title: Control 12H Biological Replicate 1 Technical Replicate 1

tag: plant growth conditions


title: 443_German Mutton sheep DNA


title: 447_German Mutton sheep DNA


title: 442_German Mutton sheep DNA


title: AraC_+

description: training

tag: cell line

source_name: AraC


title: Arsenite_-

description: training


title: Control 3H Biological Replicate 1 Technical Replicate 1

tag: treatment


title: 441_German Mutton sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: Control 12H Biological Replicate 1 Technical Replicate 2

source_name: unfertilized cotton ovule untreated for 12H


title: AraC_-

description: training


title: Treated 0H Biological Replicate 2 Technical Replicate 1


title: 440_German Mutton sheep DNA

tag: 6-month weight (kg)

tag: height at withers (cm)


title: Antimycin_+

description: training

source_name: Antimycin


title: Antimycin_-

description: training


title: SW-13-siCtrl siBRM+IFNIII

source_name: SW-13-siCtrl siBRM+IFNIII

extract_protocol: Used Trizol


title: 439_German Mutton sheep DNA

source_name: German Mutton sheep

tag: gender

tag: pre-weaning gain(kg)


title: 446_German Mutton sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: Control 0H Biological Replicate 2 Technical Replicate 2

source_name: unfertilized cotton ovule untreated for 0H


title: Control 6H Biological Replicate 2 Technical Replicate 1

source_name: unfertilized cotton ovule untreated for 6H


title: 2-Deoxyglucose_+

description: training

source_name: Control


title: SW-13-siSUZ+IFNIII


title: 438_German Mutton sheep DNA

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: Control 1H Biological Replicate 1 Technical Replicate 2

source_name: unfertilized cotton ovule untreated for 1H

tag: tissue


title: Control 6H Biological Replicate 2 Technical Replicate 2


title: SW-13-siCtrl siBRM-IFNIII

source_name: SW-13-siCtrl siBRM-IFNIII


title: 436_German Mutton sheep DNA

tag: chest girth (cm)

tag: shin circumference (cm)


title: 437_German Mutton sheep DNA


title: SW-13-siSUZ siBRM+IFNII

source_name: SW-13-siSUZ siBRM+IFNII


title: 2-Deoxyglucose_-

description: training


title: Treated 12H Biological Replicate 2 Technical Replicate 1

source_name: unfertilized cotton ovule treated with phytohormones for 12H

tag: germplasm line

tag: developmental stage


title: Treated 3H Biological Replicate 2 Technical Replicate 1

tag: plant growth conditions


title: Control 0H Biological Replicate 2 Technical Replicate 1

tag: treatment


title: 434_German Mutton sheep DNA

tag: birth weight (kg)


title: SW-13-siCtrl-IFNIII

tag: cell line


title: SW-13-siCtrl+IFNIII


title: SW-13-siCtrl siBRM+IFNII

source_name: SW-13-siCtrl siBRM+IFNII


title: SW-13-siSUZ siBRM-IFNIII

source_name: SW-13-siSUZ siBRM-IFNIII


title: SW-13-siSUZ-IFNIII


title: 435_German Mutton sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)


title: Control 6H Biological Replicate 1 Technical Replicate 2


title: SW-13-siSUZ+IFNII


title: Treated 3H Biological Replicate 1 Technical Replicate 1

source_name: unfertilized cotton ovule treated with phytohormones for 3H


title: 36-N2-Pa

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: RMA by software Partek

organism: Caenorhabditis elegans

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

growth_protocol: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

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

treatment_protocol: C. elegans  were maintained in a pathogen-free facility  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

tag: genotype

value: P. aeruginosa

value: L4-exposed worms


title: 433_German Mutton sheep DNA

tag: gender

tag: height at withers (cm)

tag: pre-weaning gain(kg)


title: 432_German Mutton sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: post-weaning gain (kg)


title: Treated 6H Biological Replicate 1 Technical Replicate 2

source_name: unfertilized cotton ovule treated with phytohormones for 6H

tag: tissue


title: SW-13-siCtrl+IFNII


title: 430_German Mutton sheep DNA

tag: chest girth (cm)

tag: shin circumference (cm)

tag: daily weight gain (kg)


title: 431_German Mutton sheep DNA


title: 34-N2-Pa

tag: developmental stage


title: 35-N2-Pa

tag: treatment


title: Control 3H Biological Replicate 2 Technical Replicate 2

source_name: unfertilized cotton ovule untreated for 3H

tag: germplasm line

tag: plant growth conditions


title: 429_German Mutton sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: SW-13-siSUZ-IFNII

tag: cell line


title: 33-ok1207-Pa

tag: genotype


title: Control 6H Biological Replicate 1 Technical Replicate 1


title: 31-ok1207-Pa


title: 32-ok1207-Pa


title: 428_German Mutton sheep DNA

tag: gender

tag: 6-month weight (kg)

tag: height at withers (cm)


title: SW-13-siCtrl-IFNII


title: 426_German Mutton sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: pre-weaning gain(kg)


title: SW-13-siSUZ siBRM+IFNI

source_name: SW-13-siSUZ siBRM+IFNI


title: SW-13-siSUZ siBRM-IFNII

source_name: SW-13-siSUZ siBRM-IFNII


title: Treated 0H Biological Replicate 1 Technical Replicate 1

source_name: unfertilized cotton ovule treated with phytohormones for 0H

tag: tissue


title: Treated 0H Biological Replicate 1 Technical Replicate 2


title: 425_German Mutton sheep DNA

tag: chest girth (cm)

tag: shin circumference (cm)

tag: post-weaning gain (kg)


title: 29-ok1474-Pa

tag: treatment

tag: developmental stage


title: Control 1H Biological Replicate 2 Technical Replicate 1

tag: germplasm line

tag: plant growth conditions


title: 427_German Mutton sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)

tag: daily weight gain (kg)


title: Treated 6H Biological Replicate 2 Technical Replicate 2


title: 30-ok1474-Pa

tag: genotype


title: 27-km25-Pa


title: SW-13-siSUZ+IFNI

tag: cell line


title: 26-km25-Pa


title: 423_German Mutton sheep DNA

tag: gender

tag: 6-month weight (kg)

tag: height at withers (cm)


title: Control 0H Biological Replicate 1 Technical Replicate 2


title: SW-13-siCtrl siBRM-IFNII

source_name: SW-13-siCtrl siBRM-IFNII


title: Treated 1H Biological Replicate 1 Technical Replicate 1

source_name: unfertilized cotton ovule treated with phytohormones for 1H


title: 28-ok1474-Pa


title: SW-13-siCtrl siBRM+IFNI

source_name: SW-13-siCtrl siBRM+IFNI


title: SW-13-siCtrl siBRM-IFNI

source_name: SW-13-siCtrl siBRM-IFNI


title: 424_German Mutton sheep DNA

source_name: German Mutton sheep

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: pre-weaning gain(kg)


title: 421_German Mutton sheep DNA

tag: tissue

tag: chest girth (cm)

tag: shin circumference (cm)


title: 420_German Mutton sheep DNA

tag: post-weaning gain (kg)


title: Treated 12H Biological Replicate 1 Technical Replicate 1

tag: germplasm line

tag: developmental stage

tag: treatment


title: 418_German Mutton sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: 24-N2-Sa

tag: genotype

value: S. aureus


title: 25-km25-Pa


title: SW-13-siCtrl+IFNI

tag: cell line


title: Control 1H Biological Replicate 1 Technical Replicate 1

source_name: unfertilized cotton ovule untreated for 1H

tag: plant growth conditions


title: SW-13-siCtrl-IFNI


title: Treated 1H Biological Replicate 1 Technical Replicate 2


title: SW-13-siSUZ siBRM-IFNI

source_name: SW-13-siSUZ siBRM-IFNI


title: Control 3H Biological Replicate 1 Technical Replicate 2


title: 22-N2-Sa


title: 19-0k1207-Sa


title: 20-0k1207-Sa


title: 23-N2-Sa


title: 413_German Mutton sheep DNA

tag: gender

tag: 6-month weight (kg)

tag: daily weight gain (kg)


title: SW-13-siSUZ-IFNI


title: 18-0k1474-Sa


title: 415_German Mutton sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: 21-0k1207-Sa


title: 411_German Mutton sheep DNA

tag: tissue

tag: chest girth (cm)

tag: pre-weaning gain(kg)


title: MCF7_shMEL_rep2

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, Hanyang University

description:
Sample name: shMel_K
MCF7 cells infected with lentiviral MEL-18 shRNA

hyb_protocol: Standard lllumina hybridization protocol

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader following the standard Illumina scanning protocol.

data_processing: Standard Illumina GenomeStudio processing of images plus quantile normalization of all samples. Background subtracted.

source_name: Breast cancer cell line

label_protocol: Biotinylated cRNAs were prepared with the Illumina TotalPrep™ RNA amplification kit for Illumina arrays.

growth_protocol: Cells were cultured in phenol-red free DMEM supplemented with 10% FBS

extract_protocol: RNA was extracted with Trizol reagent following the manufacturer's instructions. Quality control was peformed with Agilent Bioanalyzer.

treatment_protocol: MCF7 cells were infected with lentiviruses encoding either control or MEL-18 shRNA

value: MEL-18 shRNA


title: Control 0H Biological Replicate 1 Technical Replicate 1

source_name: unfertilized cotton ovule untreated for 0H

tag: germplasm line


title: MCF7_shCon_rep1

description:
Sample name: shcon_A
MCF7 cells infected with lentiviral control shRNA

value: control shRNA


title: 445_German Mutton sheep DNA

tag: shin circumference (cm)

tag: post-weaning gain (kg)


title: MCF7_shCon_rep2

description:
Sample name: shcon_C
MCF7 cells infected with lentiviral control shRNA

tag: treatment


title: 409_German Mutton sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: 410_German Mutton sheep DNA


title: SW-13-siSUZ siBRM+IFNIII

source_name: SW-13-siSUZ siBRM+IFNIII

tag: cell line


title: 15-km25-Sa

tag: genotype

tag: developmental stage


title: 16-0k1474-Sa


title: treated with both 7.5mM JQ1 and 12.5nM rapamycin, rep1

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: Gene expression data from MNNG/HOS cell line

data_processing: The data were background subtracted and normalized using cross correlation.  The trimmed mean target intensity of each array was set to 20 based on detection p value.

source_name: cells from MNNG/HOS cell line

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

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

value: MNNG/HOS

tag: cell type

value: osteosarcoma


title: 13-km25-Sa


title: treated with both 7.5mM JQ1 and 12.5nM rapamycin, rep2


title: 14-km25-Sa


title: MCF7_shMEL_rep1

description:
Sample name: shMel_I
MCF7 cells infected with lentiviral MEL-18 shRNA


title: 10-N2-OP50

value: E. coli


title: treated with 12.5nM rapamycin, rep2


title: 406_German Mutton sheep DNA

tag: gender

tag: 6-month weight (kg)

tag: daily weight gain (kg)


title: 12-N2-OP50


title: 404_German Mutton sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: treated with 7.5mM JQ1 rep2


title: 11-N2-OP50


title: 17-0k1474-Sa


title: 402_German Mutton sheep DNA

tag: tissue

tag: chest girth (cm)

tag: pre-weaning gain(kg)


title: treated with DMSO (control) rep2


title: treated with 12.5nM rapamycin, rep1


title: 302_German Mutton sheep DNA

value: male

tag: shin circumference (cm)

tag: post-weaning gain (kg)


title: 401_German Mutton sheep DNA

tag: birth weight (kg)


title: treated with 7.5mM JQ1 rep1


title: 305_German Mutton sheep DNA

tag: weaning weight (kg)


title: 405_German Mutton sheep DNA


title: treated with DMSO (control) rep1

tag: cell line


title: 408_German Mutton sheep DNA


title: Treated 1H Biological Replicate 2 Technical Replicate 2

tag: germplasm line

tag: plant growth conditions

tag: treatment


title: 7-ok1207-OP50

tag: genotype

tag: developmental stage


title: 9-ok1207-OP50


title: 290_German Mutton sheep DNA

tag: gender

tag: 6-month weight (kg)

tag: daily weight gain (kg)


title: 5-ok1474-OP50


title: 8-ok1207-OP50


title: 1-km25-OP50


title: 3-km25-OP50


title: 285_German Mutton sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)