title: SpColCtrl_rep2a1297


title: SpColCtrl_rep2a1298

status: Public on Feb 14 2018

type: SRA

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

molecule: total RNA

organism: Mus musculus

source_name: spleen

growth_protocol: Live cells were sorted by flow cytometry from the spleen and colon lamina propria of mice (carrying a Foxp3 reporter gene).

extract_protocol:
Spleen were mechanically dissociated and colon were digested with collagenase/dispase to single cell suspensions. Tregs were sorted by flow cytometry as DAPI- TCRb+ CD4+ GFP+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: tissue

value: spleen

tag: library name

tag: sample type

tag: strain

tag: Sex

value: male

tag: age (months)

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


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title: SpColCtrl_rep2a16


title: SpColCtrl_rep2a32


title: SpColCtrl_rep2a13


title: SpColCtrl_rep2a14


title: SpColCtrl_rep2a10


title: SpColCtrl_rep2a12


title: SpColCtrl_rep2a8


title: SpColCtrl_rep2a9


title: SpColCtrl_rep2a27


title: SpColCtrl_rep2a7


title: SpColCtrl_rep2a5


title: SpColCtrl_rep2a6


title: SpColCtrl_rep2a4


title: SpColCtrl_rep2a21


title: SpColCtrl_rep2a2


title: SpColCtrl_rep2a1


title: SpColCtrl_819

value: B6 Foxp3-Ires-Gfp


title: SpColCtrl_820


title: SpColCtrl_816


title: SpColCtrl_814


title: SpColCtrl_rep2a15


title: SpColCtrl_810


title: SpColCtrl_811


title: SpColCtrl_rep2a11


title: SpColCtrl_812


title: SpColCtrl_813


title: SpColCtrl_806


title: SpColCtrl_807


title: SpColCtrl_809


title: SpColCtrl_805


title: SpColCtrl_797


title: SpColCtrl_801


title: SpColCtrl_795


title: SpColCtrl_791


title: SpColCtrl_rep2a3


title: SpColCtrl_790


title: SpColCtrl_796


title: SpColCtrl_798


title: SpColCtrl_794


title: SpColCtrl_817


title: SpColCtrl_789


title: SpColCtrl_787


title: SpColCtrl_815


title: SpColCtrl_784


title: SpColCtrl_785


title: SpColCtrl_804


title: SpColCtrl_782


title: SpColCtrl_788


title: SpColCtrl_775


title: SpColCtrl_799


title: SpColCtrl_774


title: SpColCtrl_808


title: SpColCtrl_783


title: SpColCtrl_776


title: SpColCtrl_777


title: SpColCtrl_773


title: SpColCtrl_780


title: SpColCtrl_769


title: SpColCtrl_771


title: SpColCtrl_768


title: SpColCtrl_767


title: SpColCtrl_772


title: SpColCtrl_765


title: SpColCtrl_786


title: SpColCtrl_764


title: SpColCtrl_762


title: SpColCtrl_759


title: SpColCtrl_758


title: SpColCtrl_761


title: SpColCtrl_763


title: SpColCtrl_753


title: SpColCtrl_757


title: SpColCtrl_755


title: SpColCtrl_754


title: SpColCtrl_752


title: SpColCtrl_746


title: SpColCtrl_751


title: SpColCtrl_744


title: SpColCtrl_749


title: SpColCtrl_735


title: SpColCtrl_741


title: SpColCtrl_739


title: SpColCtrl_740


title: SpColCtrl_738


title: SpColCtrl_737


title: SpColCtrl_733


title: SpColCtrl_732


title: SpColCtrl_729


title: SpColCtrl_727


title: SpColCtrl_723


title: SpColCtrl_725


title: SpColCtrl_726


title: SpColCtrl_718


title: SpColCtrl_717


title: SpColCtrl_711


title: SpColCtrl_745


title: SpColCtrl_742


title: SpColCtrl_709


title: SpColCtrl_716


title: SpColCtrl_706


title: SpColCtrl_701


title: SpColCtrl_721


title: SpColCtrl_708


title: SpColCtrl_730


title: SpColCtrl_702


title: SpColCtrl_705


title: SpColCtrl_704


title: SpColCtrl_703


title: SpColCtrl_700


title: SpColCtrl_699


title: SpColCtrl_710


title: SpColCtrl_697


title: SpColCtrl_698


title: SpColCtrl_694


title: SpColCtrl_695


title: SpColCtrl_687


title: SpColCtrl_707


title: SpColCtrl_692


title: SpColCtrl_686


title: SpColCtrl_685


title: SpColCtrl_681


title: SpColCtrl_682


title: SpColCtrl_679


title: SpColCtrl_680


title: SpColCtrl_675


title: SpColCtrl_674


title: SpColCtrl_678


title: SpColCtrl_677


title: SpColCtrl_672


title: SpColCtrl_673


title: SpColCtrl_670


title: SpColCtrl_667


title: CRC-703-BR

type: RNA

city: Dunedin

first: Sunali

last: Mehta

state: Otago

address: 56 Hanover Street, Dunedin

country: New Zealand

institute: University of Otago

hyb_protocol: Hybridization was performed using 5 µg of biotinylated target, which was incubated with the GeneChip® Human Exon 1.0 ST array at 45°C for 16 h. Following hybridization, arrays were washed and stained using a Fluidics Station 450 and the Affymetrix wash and stain kit following the manufacturer's instructions using Affymetrix fluidics protocol FS450_0001.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G

data_processing: Raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package. After the microarrays were scanned, quality checks were performed using the Affymetrix Expression Console™ Software, the intensity data was subjected to quantile normalisation and summarisation using the RMA algorithm

label: biotin

organism: Homo sapiens

source_name: Tumour

label_protocol: Sense Target Labelling and Control Reagents kit as described by the manufacturer. The sense cDNA was then fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip® WT Terminal labelling kit.

extract_protocol: All samples were frozen at -80°C. rRNA removal procedure was performed with the RiboMinus Human/Mouse Transcriptome Isolation Kit, followed by cDNA synthesis using the GeneChip® WT (Whole Transcript)

tag: disease free survival (months)

tag: disease free status

value: No-Recurrence

tag: ajcc stage

value: II

value: Colorectal cancer, fresh frozen, biopsy


title: CRC-666-BR

value: Recurrence


title: CRC-655-BNR


title: CRC-604-BR


title: CRC-678-BR


title: CRC-651-BNR


title: SpColCtrl_666


title: PA14 PA4496 mutant LB 7 h 37C biofilm cell

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from biofilm cells of P. aeruginosa PA4496 mutant after 7 hours of growth in LB with glasswool at 37ºC

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix P. aeruginosa Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa

source_name: PA4496 mutant biofilm cell

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 7 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

tag: genotype/variation

value: PA4496 mutant

tag: temp

tag: time

value: 7 h

tag: cell type

value: biofilm


title: SpColCtrl_665


title: CRC-627-BNR


title: PA14 w/t LB 7 h 37C biofilm cell

description: RNA extracted from biofilm cells of P. aeruginosa wild type after 7 hours of growth in LB with glasswool at 37ºC

source_name: wild type biofilm cell

value: wild type


title: SpColCtrl_661


title: CRC-674-BR

value: IV


title: CRC-599-BNR

value: I


title: CRC-576-BR


title: SpColCtrl_660


title: CRC-535-BNRa


title: CRC-500-BR


title: CRC-556-BRa


title: CRC-548-BNRa


title: SpColCtrl_662


title: CRC-532-BNR


title: CRC-517-BR


title: SpColCtrl_658


title: CRC-488-BNR


title: CRC-612-BNR


title: SpColCtrl_657


title: SpColCtrl_654


title: SpColCtrl_655


title: SpColCtrl_653


title: SpColCtrl_651


title: CRC-459-BNR


title: CRC-467-BNR

value: III


title: CRC-470-BR


title: CRC-435-BNR


title: CRC-446-BR


title: SpColCtrl_650


title: CRC-380-BNR


title: SpColCtrl_646


title: CRC-402-BNR


title: CRC-474-BNR


title: SpColCtrl_648


title: CRC-391-BNR


title: SpColCtrl_649


title: SpColCtrl_644


title: SpColCtrl_642


title: SpColCtrl_647


title: SpColCtrl_645


title: SpColCtrl_643


title: SpColCtrl_641


title: CRC-377-BNRa


title: SpColCtrl_637


title: SpColCtrl_639


title: SpColCtrl_640


title: SpColCtrl_635


title: CRC-348-BNR


title: CRC-350-BNR


title: CRC-357-BNR


title: CRC-370-BR


title: SpColCtrl_631


title: SpColCtrl_632


title: CRC-328-BR


title: SpColCtrl_630


title: SpColCtrl_629


title: CRC-334-BR


title: SpColCtrl_628


title: CRC-356-BNR


title: SpColCtrl_627


title: SpColCtrl_626


title: SpColCtrl_625


title: SpColCtrl_622


title: SpColCtrl_621


title: SpColCtrl_623


title: SpColCtrl_633


title: SpColCtrl_619


title: SpColCtrl_618


title: SpColCtrl_613


title: SpColCtrl_614


title: SpColCtrl_612


title: SpColCtrl_615


title: SpColCtrl_608


title: SpColCtrl_624


title: SpColCtrl_620


title: SpColCtrl_610


title: SpColCtrl_606


title: SpColCtrl_611


title: SpColCtrl_609


title: SpColCtrl_605


title: SpColCtrl_604


title: Mammary carcinoma, #12

type: genomic

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

hyb_protocol: Labeled DNAs (3.5 µg) were combined and mixed with rat Cot-1 DNA (10 mM final concentration; Applied Genetics Laboratories, Melbourne, FL, USA), the Agilent Blocking Agent, de-ionized formamide, and the Agilent Hybridization Buffer at 67 °C for 40 hours.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1) and analyzed with Agilent Genomic Workbench standard Edition 6.5 software for methylation analysis.
Probe log ratio signals were Lowess normalized and transformed into Z-scores according to their melting temperatures.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Mammary carcinoma induced by radiation

label_protocol: Labeling reactions with Cyanine 5-UTP and Cyanine 3-UTP were performed according to the Agilent Genomic DNA Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Rats were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (CE-2; Clea Japan, Tokyo, Japan) and sterilized water ad libitum.

extract_protocol: Genomic DNA was isolated by proteinase K digestion, followed by phenol/chloroform extraction.

treatment_protocol: Rats were left untreated or were subjected to whole-body 137Cs gamma-irradiation (4 Gy, 0.5 Gy/min) at 7 weeks of age.

tag: strain/background

value: F1 hybrid of Sprague-Dawley and Copenhagen

value: mammary carcinoma

tag: gender

value: female

tag: isolation of methylated dna

value: methyl-CpG binding domain-based protein


title: Mammary carcinoma, #15

tag: tissue


title: Mammary carcinoma, #8


title: SpColCtrl_603

value: spleen

tag: library name

tag: sample type

tag: strain

value: male


title: Mammary carcinoma, #10


title: Mammary carcinoma, #16


title: Mammary carcinoma, #7


title: Mammary carcinoma, #3


title: Mammary carcinoma, #9


title: Normal mammary gland, #4

source_name: Normal mammary gland

value: normal mammary gland


title: Mammary carcinoma, #11


title: SpColCtrl_602

value: B6 Foxp3-Ires-Gfp

tag: Sex

tag: age (months)

tag: total number of reads


title: Mammary carcinoma, #1


title: SpColCtrl_599

tag: number of mapped reads

tag: number of unique reads (umi)


title: Mammary carcinoma, #14


title: SpColCtrl_597


title: Mammary carcinoma, #6


title: SpColCtrl_594


title: Mammary carcinoma, #2


title: SpColCtrl_601


title: SpColCtrl_598


title: Mammary carcinoma, #13


title: Normal mammary gland, #3


title: Mammary carcinoma, #5


title: SpColCtrl_589


title: SpColCtrl_588


title: Normal mammary gland, #2


title: SpColCtrl_593


title: SpColCtrl_587


title: SpColCtrl_600


title: Mammary carcinoma, #4


title: P49

city: Glasgow

first: Chiara

last: Braconi

address: Switchback road

department: Wolfson Wohl Cancer Research Centre

country: United Kingdom

institute: University of Glasgow

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files, log transfromed, normalized using quantile method
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.

source_name: adjacent Padova cohort

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was processed following the NanoString manufacturer's protocol

extract_protocol: RNA was isolated from FFPE tissue

value: adjacent tissue - biliary tract cancer

tag: disease state

value: biliary tract cancer


title: SpColCtrl_592


title: Normal mammary gland, #1


title: SpColCtrl_584


title: SpColCtrl_582


title: SpColCtrl_583


title: SpColCtrl_580


title: SpColCtrl_579


title: SpColCtrl_578


title: SpColCtrl_574


title: P46


title: P40


title: P44


title: P37


title: SpColCtrl_571


title: SpColCtrl_568


title: P38


title: SpColCtrl_575


title: P35


title: P36


title: P34


title: SpColCtrl_572


title: SpColCtrl_566


title: P33


title: SpColCtrl_585


title: P30


title: P20


title: P47


title: P19


title: SpColCtrl_565


title: P39


title: SpColCtrl_564


title: P17


title: SpColCtrl_563


title: P15


title: SpColCtrl_559


title: SpColCtrl_561


title: P12


title: SpColCtrl_557


title: SpColCtrl_560


title: P13


title: SpColCtrl_558


title: SpColCtrl_556


title: P14


title: P11


title: P09


title: SpColCtrl_555


title: SpColCtrl_554


title: P08


title: P07


title: Zebrafish_melanoma_rep4

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

hyb_protocol: standard protocol

scan_protocol: GenePix4000B scannerusing standard operating protocol

data_processing: .pair raw file was used for quantile normalization and background correction with robust multichip average (RMA) analysis ( nimbleScan v2.5 Software).

organism: Danio rerio

source_name: melanoma

label_protocol: Cy3 labelling

growth_protocol: Unpigmented EGFP-positive melanocytes and melanoma cells were isolated by FACS

extract_protocol: RNA was harvested from cells using Trizol reagent.

value: melanoma

tag: phenotype

value: tumor


title: SpColCtrl_562


title: P06


title: Zebrafish_melanoma_rep2


title: Zebrafish_melanocyte_rep1

source_name: melanocyte

value: melanocyte

value: normal


title: Zebrafish_melanoma_rep3


title: Zebrafish_melanoma_rep1


title: Zebrafish_melanocyte_rep2


title: Zebrafish_melanocyte_rep3


title: Zebrafish_melanoma_rep5


title: P10


title: SpColCtrl_548


title: SpColCtrl_547


title: SpColCtrl_550


title: P05


title: SpColCtrl_545


title: P01


title: SpColCtrl_544


title: X30468N [II]

source_name: adjacent Humanitas cohort


title: SpColCtrl_543


title: X3517N [II]


title: SpColCtrl_553


title: X1924N [II]


title: SpColCtrl_542


title: P03


title: X18159N [II]


title: P02


title: SpColCtrl_540


title: X102N [II]


title: X7842N [II]


title: SpColCtrl_539


title: SpColCtrl_541


title: X7201N [II]


title: X11616N [II]


title: SpColCtrl_538


title: 64.during mastectomy (C; 4 weeks)

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

source_name: breast tumor_during mastectomy (C; 4 weeks)

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

extract_protocol: mRNA from i) diagnosis (A), ii) intra-operative at OvX (B; 2 weeks), and iii) during mastectomy (C; 4 weeks) tumour biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: subject status

value: premenopausal women with ER+ breast cancer

value: breast tumour

tag: timepoint

value: during mastectomy (C; 4 weeks)

value: negative


title: SGC7901-rhSTIP1

city: Guangzhou

first: Lin

middle: Lin

last: Huang

address: 58 Zhongshan 2nd Road

department: Department of Gastroenterology

country: China

institute: the First Affiliated Hospital of Sun Yat-sen University

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using average normalization GenomeStudio 2011.1, Gene Expression version 1.9.

source_name: Gastric cancer cell line

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

growth_protocol: Under normal circumstances, the cells were grown in 10% fetal bovine serum (FBS) in RPMI-1640 medium.

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

treatment_protocol: The cells were grown to 80%, washed with PBS three times, added with 1% FBS in RPMI-1640 medium overnight, added with 1% FBS in RPMI-1640 medium containing rhSTIP1 (50 ng / ml) or Ig-G for 24 hours, then collected total RNA.

tag: cell line

tag: cell type

value: Gastric cancer cell line

tag: treatment

value: rhSTIP1 24h


title: 71.diagnosis (A)

source_name: breast tumor_diagnosis (A)

value: diagnosis (A)

value: positive


title: 48.intra-operative at OvX (B; 2 weeks)

source_name: breast tumor_intra-operative at OvX (B; 2 weeks)

value: intra-operative at OvX (B; 2 weeks)


title: SpColCtrl_537

value: spleen

value: male


title: SGC7901-IgG

value: IgG 24h


title: 98.during mastectomy (C; 4 weeks)


title: H1-TKO mES cells 1

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

country: Spain

institute: CBMSO(CSIC/UAM)

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K mouse microarray (SurePrint G3mouse CGH Microarray Kit, 4x180K, AGILENT Technologies, genome reference mm9) that covers the whole genome with one probe every 13 Kb (11 KB in RefSeq sequences).

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 3 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the Agilent Genomic Workbench 5.0 software.

source_name: neosynthetized DNA in early S phase

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA, so whole genome amplification was conducted (WGA, Sigma) to obtain sufficient specific immunoprecipited DNA. To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: mES cells were grown at 37ºC and 5% CO2 in DMEM supplemented with 10% fetal calf serum, 1x non-essential  aminoacids, 2 mM L-glutamine, 50 mM b-mercaptoethanol, 1 mM sodium piruvate, 100 U/ml penicillin,  100 μg/ml streptomycin  and 10E3 U/ml LIF.

extract_protocol: Cells were incubated with BrdU (50µM) for one hour, then collected, washed three times in DPBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in DPBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 100,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipited by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) as described by Hiratani et al 2008. To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with Pou5f1 oligonucleotides (early control) and with Akt3 oligonucleotides (late control).

value: Embryonic stem cells

tag: genotype/variation

value: triple-KO for three somatic histone H1 genes

source_name: neosynthetized DNA in late S phase


title: 89.diagnosis (A)

tag: tissue


title: 71.during mastectomy (C; 4 weeks)


title: X20019N [II]

value: adjacent tissue - biliary tract cancer

value: biliary tract cancer


title: 101.diagnosis (A)


title: 82.during mastectomy (C; 4 weeks)


title: X5419N [II]


title: 71.intra-operative at OvX (B; 2 weeks)


title: WT mES cells 2

value: WT


title: H1-TKO mES cells 2


title: 55.diagnosis (A)

value: premenopausal women with ER+ breast cancer


title: WT mES cells 1


title: X18935N [II]


title: SpColCtrl_533

tag: library name

value: B6 Foxp3-Ires-Gfp


title: SpColCtrl_536

tag: sample type


title: P48


title: X10507N [II]


title: SpColCtrl_532

tag: strain


title: 78.during mastectomy (C; 4 weeks)

value: breast tumour

value: during mastectomy (C; 4 weeks)


title: X8810N [II]


title: 62.diagnosis (A)

value: negative


title: SpColCtrl_534

tag: Sex


title: 32.during mastectomy (C; 4 weeks)


title: 20.intra-operative at OvX (B; 2 weeks)


title: 82.diagnosis (A)


title: 62.intra-operative at OvX (B; 2 weeks)


title: 13.intra-operative at OvX (B; 2 weeks)


title: X7999N [II]


title: SpColCtrl_531

tag: age (months)


title: 81.diagnosis (A)


title: X7907N [II]


title: X6775N [II]


title: SpColCtrl_529

tag: total number of reads


title: SpColCtrl_528

tag: number of mapped reads


title: 82.intra-operative at OvX (B; 2 weeks)


title: SpColCtrl_526

tag: number of unique reads (umi)


title: 64.diagnosis (A)


title: X15148N [II]

tag: disease state


title: SpColCtrl_525


title: 63.diagnosis (A)


title: 19.diagnosis (A)


title: 96.diagnosis (A)


title: 37.diagnosis (A)


title: 78.intra-operative at OvX (B; 2 weeks)


title: X5610N [II]


title: 107.intra-operative at OvX (B; 2 weeks)


title: SpColCtrl_523


title: 92.during mastectomy (C; 4 weeks)


title: SpColCtrl_522


title: X16420N [II]


title: SpColCtrl_517


title: X25584N [II]


title: SpColCtrl_520


title: X12132N [II]


title: 96.intra-operative at OvX (B; 2 weeks)


title: X12822N [II]


title: 81.during mastectomy (C; 4 weeks)


title: X3517T

source_name: tumour tissue - biliary tract cancer

value: tumour tissue - biliary tract cancer


title: 81.intra-operative at OvX (B; 2 weeks)


title: 79.during mastectomy (C; 4 weeks)


title: 37.during mastectomy (C; 4 weeks)


title: 107.diagnosis (A)

value: diagnosis (A)


title: 96.during mastectomy (C; 4 weeks)


title: 66.intra-operative at OvX (B; 2 weeks)


title: 111.intra-operative at OvX (B; 2 weeks)

value: positive


title: 103.intra-operative at OvX (B; 2 weeks)

value: intra-operative at OvX (B; 2 weeks)


title: SpColCtrl_516

source_name: spleen

value: spleen


title: X30468N

source_name: adjacent tissue - biliary tract cancer


title: X3517N


title: SpColCtrl_515

value: male


title: 56.intra-operative at OvX (B; 2 weeks)


title: 54.diagnosis (A)


title: 56.diagnosis (A)


title: X1924N


title: SpColCtrl_514


title: 98.diagnosis (A)


title: X30468T


title: 92.diagnosis (A)


title: 103.during mastectomy (C; 4 weeks)


title: 66.during mastectomy (C; 4 weeks)


title: X1924T


title: SpColCtrl_507


title: 20.during mastectomy (C; 4 weeks)


title: SpColCtrl_512


title: 88.during mastectomy (C; 4 weeks)


title: 53.during mastectomy (C; 4 weeks)


title: 54.intra-operative at OvX (B; 2 weeks)


title: SpColCtrl_513


title: SpColCtrl_510


title: SpColCtrl_511


title: SpColCtrl_506


title: 92.intra-operative at OvX (B; 2 weeks)


title: X18159N


title: X102N


title: 53.diagnosis (A)


title: X18159T


title: 88.diagnosis (A)


title: X102T


title: 86.intra-operative at OvX (B; 2 weeks)


title: X11616T


title: 13.during mastectomy (C; 4 weeks)


title: 103.diagnosis (A)


title: 66.diagnosis (A)


title: 86.diagnosis (A)


title: SpColCtrl_501


title: X11616N


title: SpColCtrl_504


title: X7842N


title: 111.diagnosis (A)


title: SpColCtrl_503


title: SpColCtrl_502


title: X7201T


title: 27.diagnosis (A)


title: 86.during mastectomy (C; 4 weeks)


title: SpColCtrl_499


title: SpColCtrl_497


title: X7842T


title: SpColCtrl_494


title: X7201N


title: X5419N


title: SpColCtrl_496


title: SpColCtrl_493


title: X5419T


title: 98.intra-operative at OvX (B; 2 weeks)


title: 48.diagnosis (A)


title: 53.intra-operative at OvX (B; 2 weeks)


title: SpColCtrl_492


title: 101.during mastectomy (C; 4 weeks)


title: 89.intra-operative at OvX (B; 2 weeks)


title: SpColCtrl_498


title: 72.during mastectomy (C; 4 weeks)


title: 88.intra-operative at OvX (B; 2 weeks)


title: 64.intra-operative at OvX (B; 2 weeks)


title: 32.intra-operative at OvX (B; 2 weeks)


title: 48.during mastectomy (C; 4 weeks)


title: X18935T


title: 37.intra-operative at OvX (B; 2 weeks)


title: X20019T


title: SpColCtrl_491


title: 55.intra-operative at OvX (B; 2 weeks)


title: 62.during mastectomy (C; 4 weeks)


title: SpColCtrl_489


title: 27.during mastectomy (C; 4 weeks)


title: 19.during mastectomy (C; 4 weeks)


title: X20019N


title: 79.diagnosis (A)


title: 78.diagnosis (A)


title: 56.during mastectomy (C; 4 weeks)


title: SpColCtrl_488


title: 13.diagnosis (A)


title: X18935N


title: 55.during mastectomy (C; 4 weeks)


title: 14.intra-operative at OvX (B; 2 weeks)


title: SpColCtrl_485


title: X10507T


title: X10507N


title: X8810T


title: 79.intra-operative at OvX (B; 2 weeks)


title: 54.during mastectomy (C; 4 weeks)


title: X8810N


title: SpColCtrl_481


title: SpColCtrl_483


title: 72.diagnosis (A)


title: SpColCtrl_484


title: 107.during mastectomy (C; 4 weeks)


title: 14.during mastectomy (C; 4 weeks)


title: 89.during mastectomy (C; 4 weeks)


title: X7999T


title: 63.during mastectomy (C; 4 weeks)


title: X7907T


title: 111.during mastectomy (C; 4 weeks)


title: SpColCtrl_482


title: X7999N


title: X7907N


title: SpColCtrl_480


title: X6775T


title: SpColCtrl_476


title: X6775N


title: germ-free, female, untreated, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.40.2).

source_name: terminal ileum, from a germ-free female mouse, untreated

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Young (7-10 weeks) or old (17 months) C57BL/6JRccHsd conventional female mice were purchased from a commercial supplier (Envigo, Horst, the Netherlands). Female germ-free mice of 12-14 weeks were obtained from a breeding colony at the animal facility of Radboud University Nijmegen Medical Centre (Nijmegen, the Netherlands). All animals were put on an autoclaved Rat/mouse maintenance V153X R/M-H diet (Ssniff, Soest, Germany) directly after weaning in the case of germ-free mice, or directly after arrival in the case of conventional mice. The mice were kept on this diet throughout the experiment. Conventional mice were housed in IVC cages and germ-free mice were housed in germ-free isolators.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Each experimental group consisted of 10 mice per group, except the control group of germ-free mice, which consisted of 5 mice per group. After an acclimatization period of at least 4 weeks, feces were freshly collected from the conventional mice. Feces from the same group was pooled and mixed in PBS. Next, 200 μl of 100 mg/ml of this mixture was given by oral gavage to germ-free mice of 12-14 weeks old. After transfer, recipient mice were individually housed in IVC cages for another 4 weeks. Mice were then killed, and part of the terminal ileum was collected, snap-frozen and stored at -80 until gene expression profiling.

value: terminal ileum

value: female

tag: initial microbiome status

value: germ-free raised

value: untreated


title: SpColCtrl_475


title: germ-free, female, untreated, replicate 4


title: X15148T

value: biliary tract cancer


title: germ-free, male, untreated, replicate 3

source_name: terminal ileum, from a germ-free male mouse, untreated


title: germ-free, female, received microbiota from conventional young females, replicate 2

source_name: terminal ileum, from a germ-free female mouse, 4 wks treated with microbiota from conventionally raised young female mice

value: microbiota from conventional young females for 4 weeks


title: germ-free, female, received microbiota from conventional young females, replicate 4


title: SpColCtrl_477


title: germ-free, male, received microbiota from conventional young females, replicate 3

source_name: terminal ileum, from a germ-free male mouse, 4 wks treated with microbiota from conventionally raised young female mice


title: germ-free, male, received microbiota from conventional young females, replicate 1


title: SpColCtrl_474


title: germ-free, male, untreated, replicate 4


title: germ-free, male, received microbiota from conventional young females, replicate 5


title: X15148N

value: adjacent tissue - biliary tract cancer


title: germ-free, female, received microbiota from conventional males, replicate 1

source_name: terminal ileum, from a germ-free female mouse, 4 wks treated with microbiota from conventionally raised male mice

value: microbiota from conventional males for 4 weeks


title: germ-free, female, received microbiota from conventional old females, replicate 1

source_name: terminal ileum, from a germ-free female mouse, 4 wks treated with microbiota from conventionally raised old female mice

value: microbiota from conventional old females for 4 weeks


title: germ-free, female, received microbiota from conventional males, replicate 4


title: germ-free, female, received microbiota from conventional old females, replicate 2


title: germ-free, female, received microbiota from conventional old females, replicate 4


title: germ-free, male, received microbiota from conventional males, replicate 2

source_name: terminal ileum, from a germ-free male mouse, 4 wks treated with microbiota from conventionally raised male mice


title: SpColCtrl_479

value: B6 Foxp3-Ires-Gfp


title: germ-free, male, received microbiota from conventional males, replicate 4


title: SpColCtrl_473


title: conventional, young female,  untreated,  replicate 5

source_name: terminal ileum, from a young female mouse, conventionally raised, untreated

value: conventionally raised


title: X12132N


title: conventional, old female, untreated, replicate5

source_name: terminal ileum, from an old female mouse, conventionally raised, untreated


title: SpColCtrl_470


title: SpColCtrl_468


title: SpColCtrl_466


title: X5610T

value: tumour tissue - biliary tract cancer


title: X5610N


title: X25584T


title: SpColCtrl_472


title: conventional, old female, untreated, replicate2


title: X25584N


title: conventional, young female,  untreated,  replicate 3


title: conventional, old female, untreated, replicate1


title: germ-free, male, received microbiota from conventional males, replicate 3


title: conventional, male, untreated, replicate4

source_name: terminal ileum, from a male mouse, conventionally raised, untreated


title: germ-free, female, untreated, replicate 1


title: germ-free, female, untreated, replicate 2


title: germ-free, male, untreated, replicate 1


title: germ-free, male, untreated, replicate 2


title: germ-free, female, received microbiota from conventional young females, replicate 5


title: germ-free, female, received microbiota from conventional young females, replicate 1


title: conventional, male, untreated, replicate3


title: SpColCtrl_463


title: SpColCtrl_465


title: SpColCtrl_467


title: X16420T


title: SpColCtrl_464


title: germ-free, female, received microbiota from conventional young females, replicate 3


title: X16420N


title: X12822T


title: SpColCtrl_458


title: SpColCtrl_462


title: germ-free, female, received microbiota from conventional old females, replicate 3


title: germ-free, female, received microbiota from conventional males, replicate 2


title: germ-free, male, received microbiota from conventional young females, replicate 4


title: germ-free, male, received microbiota from conventional young females, replicate 2


title: SpColCtrl_457


title: SpColCtrl_460


title: X12822N


title: SpColCtrl_459


title: germ-free, female, received microbiota from conventional males, replicate 5


title: germ-free, female, received microbiota from conventional males, replicate 3


title: germ-free, female, received microbiota from conventional old females, replicate 5


title: SpColCtrl_454


title: conventional, young female,  untreated,  replicate 1


title: germ-free, male, received microbiota from conventional males, replicate 5


title: conventional, male, untreated, replicate1


title: conventional, young female,  untreated,  replicate 4


title: conventional, male, untreated, replicate2


title: conventional, old female, untreated, replicate4


title: germ-free, male, received microbiota from conventional males, replicate 1


title: SpColCtrl_453


title: conventional, male, untreated, replicate5


title: SpColCtrl_456


title: SpColCtrl_452


title: SpColCtrl_450


title: SpColCtrl_449


title: SpColCtrl_448


title: conventional, old female, untreated, replicate3


title: SpColCtrl_447


title: A375-siFAH-72h-rep3

city: Wuhan

first: chao

middle: zhi

last: gu

state: Hubei

address: Liberation Road No. 1095

department: Department of Dermatology, Tongji Hospital

institute: Huazhong University of Science and Technology

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's specifications (Affymetrix Inc., Santa Clara, CA, USA)

scan_protocol: Arrays were scanned in a GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA)

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization, then normalized to median of all samples.

source_name: melanoma cells, siRNA, 72h

label_protocol: The Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix) is used to create biotin – labeled sense -strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.

extract_protocol: RNA was extracted using RNeasy Fibrous Tissue kit (Qiagen) according to the manufacturer’s instructions.

tag: transfection

value: siFAH for 72 hours


title: conventional, young female,  untreated,  replicate 2


title: SpColCtrl_445


title: SpColCtrl_444


title: SpColCtrl_441


title: SpColCtrl_442


title: A375-siFAH-72h-rep2


title: X12132T


title: A375-siFAH-72h-rep1


title: SpColCtrl_440


title: SpColCtrl_439


title: A375-NC-72h-rep3

value: negative control siRNA


title: MF.IFNa.2hr.PC_4

hyb_protocol: Affymetrix Mouse Gene 1.0 ST Array.

scan_protocol: Affymetrix GeneChip Scanner.

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: Peritoneal Cavity

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit.

extract_protocol: TriZol

tag: genetic background

value: Male

tag: age

value: 6 Weeks

value: 10000 U IFNa

value: Peritoneal cavity macrophages

tag: phenotype markers

tag: separation method

value: FACSAria


title: MF.IFNg.2hr.PC_1

tag: treatment

value: 8000 U IFNg

tag: cell type


title: MF.IFNa.2hr.PC_3


title: MF.PC.SPF_3

value: No treatment


title: A375-NC-72h-rep2

tag: cell line


title: MF.IFNg.2hr.PC_2


title: MF.PC.SPF_1


title: A375-NC-72h-rep1


title: SpColCtrl_438

tag: tissue

value: spleen

tag: library name

tag: sample type

value: male


title: MF.IFNa.2hr.PC_1

tag: Sex


title: SpColCtrl_443

tag: strain

tag: age (months)

tag: total number of reads


title: SpColCtrl_437

tag: number of mapped reads

tag: number of unique reads (umi)


title: MF.PC.SPF_2


title: SpColCtrl_436


title: M.TB–specific antigens stimulated PBMCs_healthy control_sample 2

city: Beijing

first: Liping

last: Pan

address: 97 Machang Road, Tongzhou District

institute: Beijing Chest Hospital, Capital Medical Universtiy.

hyb_protocol: Each slide was hybridized with 1.65μg/600 ng 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=5μm, PMT 100%, 10%, 16bit/3μm, PMT 100%, 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, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, healthy control, sample 2

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 from PBMCs using miRneasy® Mini kit (Cat.# 217004, QIAGEN, Germany) according to the protocols recommended by the manufacturer. RNase-free DNase I (Cat.# 79254, QIAGEN, Germany) was used to remove the genomic DNA contamination. The integrity and quality of RNA was evaluated by Agilent 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA, US). RNA with a 2100 RIN (RNA integrity number) ≥ 7.0 and 28S/18S > 0.7 was used for the microarray study and qPCR validation.

treatment_protocol: Peripheral blood samples (6ml) were collected in heparin-containing vacutainer tubes from each subject. PBMCs were separated by density gradient using Lympholyte Cell Separation Media (Cat.#HY2015, Tianjin Haoyang Biological Manufacture Co., Ltd, China) within 6 hours of blood collection. The number of live cells were counted using Muse Cell Analyer (Cat.#MCH600103, Merck & Millipore, Germany). PBMCs were cultured with AIM-V (Cat.#0870112-DK, Invitrogen Life Technology, USA) containing 2mM L-glutamine, 50ug/ml streptomycin sulfate, 10ug/ml gentamicin sulfate, and stimulated with10ug/ml M.TB-specific antigens ESAT-6/CFP-10 for 24h at 37 ºC in a humidified incubator with 5% CO2.

tag: cell

value: peripheral blood mononuclear cells

tag: gender

value: Female


title: M.TB–specific antigens stimulated PBMCs_healthy control_sample 3

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, healthy control, sample 3

tag: age


title: M.TB–specific antigens stimulated PBMCs_healthy control_sample 4

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, healthy control, sample 4


title: M.TB–specific antigens stimulated PBMCs_LTBI individual_sample 4

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, LTBI individual, sample 4


title: M.TB–specific antigens stimulated PBMCs_healthy control_sample 1

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, healthy control, sample 1


title: M.TB–specific antigens stimulated PBMCs_LTBI individual_sample 3

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, LTBI individual, sample 3


title: SpColCtrl_433

source_name: spleen


title: SpColCtrl_428


title: SpColCtrl_430


title: SpColCtrl_431


title: liver_V_rep6.

city: Saint-Pée sur Nivelle

first: Viviana

last: Lazzarotto

address: Quartier Ibarron

country: France

institute: INRA

description: hepatic gene expression

hyb_protocol: Cy3-labelled cRNA sample yields (> 0.825µg cRNA) and specific activity (> 6pmol of Cy3/µg of cRNA) were verified using a NanoDrop ND-1000: 600ng of Cy3-cRNA were fragmented and hybridized on a sub-array, following the LIQA kit instructions. The hybridization reactions were allowed to continue for 17 hours in a rotating hybridization oven (65°C), prior to washing according to the manufacturer’s instructions.

scan_protocol: Slides were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm – 20 bits).

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.1.1), according to the appropriate GE protocol (GE1_107_Sep09). Data were analysed using GeneSpring software (v. 12.6).

organism: Oncorhynchus mykiss

source_name: liver, 48h after last meal, V replicate 6

label_protocol: Cy3-labelled experimental cRNA samples were generated using the Agilent “One-Color Microarray-based Gene Expression Analysis” (Low Input Quick Amp Labeling-LIQA) kit, according to manufacturer’s instructions. The method uses T7 RNA Polymerase Blend, which simultaneously amplifies target material and incorporates Cyanine 3-CTP (Cy3). For each sample 150ng of total RNA were used to generate fluorescent cRNA. Agilent Spike-In was included in each reaction. After the denaturation step (10 min in circulating bath at 65°C) and cRNA synthesis step (2hr at 40°C), the reactions were incubated at 70°C for 15 min to inactivate the AffinityScript enzyme. To perform the labelling reaction, cRNA samples were each mixed with 6µL of Transcription Master Mix cocktail, containing Cy3-dye, and then incubated at 40°C for two hours. Purification was performed using Quiagen RNeasy mini spin columns, eluting in 30uL of RNase-free water.

extract_protocol: Total RNA was extracted from intestine (mid gut) and liver of rainbow trout juveniles (10g fish) using the TRIZOL reagent method.

value: liver


title: M.TB–specific antigens stimulated PBMCs_TB patient_sample 4

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, TB patient, sample 4


title: MF.IFNa.2hr.PC_2

tag: genetic background

tag: phenotype markers


title: SpColCtrl_426

value: B6 Foxp3-Ires-Gfp


title: liver_V_rep7.

description: hepatic gene expression

source_name: liver, 48h after last meal, V replicate 7


title: CD27+ -2

city: Lisbon

first: Francisco

middle: J.

last: Enguita

address: Av. Professor Egas Moniz

department: Instituto de Medicina Molecular

country: Portugal

institute: Faculdade de Medicina, Universidade de Lisboa

description: CD27+1 sorted from 4 mice pooled lymh node and spleen

hyb_protocol: miRCURY LNA microRNA Array, 6th generation - miRBase 16.0 (GPL19997)

scan_protocol: The hybridization was performed according to the miRCURY LNA™ microRNA Array instruction manual using a Tecan HS 4800™ hybridization station (Tecan, Austria)

data_processing: GenEX Exiqon software for microarray analysis

source_name: lymph node and spleen

label_protocol: miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™

extract_protocol: RNA was isolated from FACS-sorted cell populations using High Pure miRNA Isolation kit (Roche) for small RNA


title: CD27- CCR6+

description: CD27- CCR6+ sorted from 8 mice pooled lymph node and spleen


title: liver_V_rep5.

description: hepatic gene expression

source_name: liver, 48h after last meal, V replicate 5


title: SpColCtrl_425


title: M.TB–specific antigens stimulated PBMCs_LTBI individual_sample 2

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, LTBI individual, sample 2


title: M.TB–specific antigens stimulated PBMCs_TB patient_sample 1

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, TB patient, sample 1


title: liver_V_rep4.

description: hepatic gene expression

source_name: liver, 48h after last meal, V replicate 4


title: SpColCtrl_427


title: liver_V_rep2.

description: hepatic gene expression

source_name: liver, 48h after last meal, V replicate 2


title: liver_V_rep3.

description: hepatic gene expression

source_name: liver, 48h after last meal, V replicate 3


title: SpColCtrl_423


title: CD27+ -1


title: M.TB–specific antigens stimulated PBMCs_TB patient_sample 3

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, TB patient, sample 3


title: SpColCtrl_422


title: liver_C_rep8.

description: hepatic gene expression

source_name: liver, 48h after last meal, C replicate 8


title: M.TB–specific antigens stimulated PBMCs_LTBI individual_sample 1

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, LTBI individual, sample 1


title: SMKY104_arrested

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description: Non-replicating control sample

library_source: genomic

data_processing:
Sequence reads were mapped to the sacCer3 using Bowtie2 (version 2.2.5).
Sequence reads mapping to a single genomic location were summed in 1 kb bins, using Samtools (version 1.3.1) and Bedtools (version 2.26.0).
Relative copy numbers were generated by dividing the sequence read counts from the replicating sample by counts from the non-replicating (alpha factor arrested) sample processed in parallel, and by normalising for differences in read coverage, using R.
The resulting ratios were normalised to the percentage of replicated DNA at that timepoint, using R. The percentage of replicated DNA was calculated using flow cytometry data generated from the same biological samples.
Genome_build: sacCer3

organism: Saccharomyces cerevisiae

source_name: Total genomic DNA from cell cycle synchronised yeast

growth_protocol: Cells were arrested in G1 with alpha-factor, then released into S-phase and harvested at various timepoints.

extract_protocol:
DNA was purified by phenol chloroform extraction.
Library preparation was carried out according to NEBUltra II instructions. Sequencing was carried out using Illumina instructions.

tag: relevant genotype

value: ARS607::URA3, ARS609::LEU2, ARS610::hphNT1, ARS608::kanMX

tag: time point

value: 0 min


title: SMKY104_65min

description: Late S phase sample

value: rif1-delta::NAT, ARS607::URA3, ARS609::LEU2, ARS610::hphNT1, ARS608::kanMX

value: 65 min


title: liver_V_rep1.

description: hepatic gene expression

source_name: liver, 48h after last meal, V replicate 1


title: SMKY101_65

description: Late S phase sample


title: SpColCtrl_432


title: liver_C_rep6.

description: hepatic gene expression

source_name: liver, 48h after last meal, C replicate 6


title: liver_V_rep8.

description: hepatic gene expression

source_name: liver, 48h after last meal, V replicate 8


title: liver_C_rep5.

description: hepatic gene expression

source_name: liver, 48h after last meal, C replicate 5


title: M.TB–specific antigens stimulated PBMCs_TB patient_sample 2

source_name: M.TB–specific antigens stimulated peripheral blood mononuclear cells, TB patient, sample 2


title: liver_C_rep7.

description: hepatic gene expression

source_name: liver, 48h after last meal, C replicate 7


title: SpColCtrl_419

source_name: spleen


title: HE61_75

description: Late S phase sample

value: 75 min


title: liver_C_rep4.

description: hepatic gene expression

source_name: liver, 48h after last meal, C replicate 4


title: SpColCtrl_418


title: GA1459_75

description: Late S phase sample

value: background genotype


title: liver_C_rep3.

description: hepatic gene expression

source_name: liver, 48h after last meal, C replicate 3


title: SpColCtrl_414


title: GA1459_0

description: Non-replicating control sample


title: SpColCtrl_415


title: SpColCtrl_413


title: SpColCtrl_412


title: liver_C_rep2.

description: hepatic gene expression

source_name: liver, 48h after last meal, C replicate 2


title: SpColCtrl_411


title: SpColCtrl_410


title: SpColCtrl_409


title: SpColCtrl_408


title: SpColCtrl_406


title: SpColCtrl_405


title: SpColCtrl_404


title: 24hr_AF+BCNU.1

city: Camperdown, Sydney

first: Rima

last: Chaudhuri

state: NSW

address: D17 Johns Hopkins Drive

department: Charles Perkins Center

country: Australia

institute: University of Sydney

hyb_protocol: Performed as part of the 'gene array service' by the Ramaciotti Centre for Genomics, The University of New South Wales, Sydney, Australia.

data_processing: Initial data analysis files were generated using the Affymetrix GeneChip Command Console software (Thermo Fisher Scientific). Data was pre-processed using RMA algorithm

source_name: 3T3-L1 adipocyte

growth_protocol: 3T3-L1 were cultured and differentiated in Dulbecco's modified Eagle's medium, supplemented with 10% (v/v) foetal bovine serum and 2 mM GlutaMAX (Life Technologies).

extract_protocol: RNA was extracted by TRI reagent and 1-bromo-3-chloropropane (Sigma-Aldrich), analysed for purity prior to microarray analysis.

treatment_protocol: 3T3-L1 adipocytes were treated with or without 100 µM 1,3-bis-(2-chloroethyl)-1-nitrosourea (BCNU) and/or 1 µM auranofin for 2-24 h.

tag: treatment

value: 24hr AF+BCNU

tag: cell line


title: liver_M_rep5.

description: hepatic gene expression

source_name: liver, 48h after last meal, M replicate 5

tag: tissue


title: liver_M_rep3.

description: hepatic gene expression

source_name: liver, 48h after last meal, M replicate 3


title: liver_M_rep7.

description: hepatic gene expression

source_name: liver, 48h after last meal, M replicate 7


title: 24hr_BCNU.1

scan_protocol: Performed as part of the 'gene array service' by the Ramaciotti Centre for Genomics, The University of New South Wales, Sydney, Australia.

value: 24hr BCNU


title: liver_C_rep1.

description: hepatic gene expression

source_name: liver, 48h after last meal, C replicate 1


title: 24hr_AF.1

label_protocol: Performed as part of the 'gene array service' by the Ramaciotti Centre for Genomics, The University of New South Wales, Sydney, Australia.

value: 24hr AF


title: 24hr_AF+BCNU.2


title: liver_M_rep6.

description: hepatic gene expression

source_name: liver, 48h after last meal, M replicate 6


title: liver_M_rep4.

description: hepatic gene expression

source_name: liver, 48h after last meal, M replicate 4


title: SpColCtrl_402

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

extract_protocol:
Spleen were mechanically dissociated and colon were digested with collagenase/dispase to single cell suspensions. Tregs were sorted by flow cytometry as DAPI- TCRb+ CD4+ GFP+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: library name

tag: sample type


title: intestine_V_rep5.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, V replicate 5

value: intestine (mid gut)


title: SpColCtrl_403

tag: strain

tag: Sex


title: 24hr_Control.1

value: 24hr Control


title: 24hr_BCNU.2


title: 24hr_Control.2


title: liver_M_rep8.

description: hepatic gene expression

source_name: liver, 48h after last meal, M replicate 8


title: 8hr_AF+BCNU.2

value: 8hr AF+BCNU


title: 8hr_AF+BCNU.1


title: 24hr_AF.2


title: liver_M_rep2.

description: hepatic gene expression

source_name: liver, 48h after last meal, M replicate 2


title: intestine_V_rep7.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, V replicate 7


title: SpColCtrl_401

value: spleen

value: male

tag: age (months)

tag: total number of reads


title: liver_M_rep1.

description: hepatic gene expression

source_name: liver, 48h after last meal, M replicate 1


title: intestine_V_rep8.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, V replicate 8


title: intestine_V_rep6.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, V replicate 6


title: SpColCtrl_399

source_name: spleen

tag: number of mapped reads

tag: number of unique reads (umi)


title: SpColCtrl_400


title: SpColCtrl_397


title: SpColCtrl_398


title: SpColCtrl_396


title: SpColCtrl_394


title: 8hr_BCNU.2

value: 8hr BCNU


title: SpColCtrl_390


title: 8hr_BCNU.1


title: intestine_V_rep2.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, V replicate 2


title: intestine_V_rep4.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, V replicate 4


title: intestine_V_rep3.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, V replicate 3


title: 8hr_AF.2

source_name: 3T3-L1 adipocyte

value: 8hr AF


title: intestine_C_rep7.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, C replicate 7


title: 8hr_Control.2

value: 8hr Control


title: intestine_V_rep1.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, V replicate 1


title: 8hr_AF.1


title: intestine_C_rep8.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, C replicate 8


title: intestine_C_rep6.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, C replicate 6


title: 8hr_Control.1


title: intestine_C_rep5.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, C replicate 5


title: SpColCtrl_393

value: B6 Foxp3-Ires-Gfp


title: SpColCtrl_388


title: SpColCtrl_387


title: SpColCtrl_389


title: intestine_C_rep3.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, C replicate 3


title: 4hr_BCNU.2

value: 4hr BCNU


title: SpColCtrl_386


title: intestine_C_rep4.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, C replicate 4


title: 4hr_AF+BCNU.1

value: 4hr AF+BCNU


title: 4hr_AF.2

value: 4hr AF


title: SpColCtrl_385


title: SpColCtrl_420


title: 4hr_AF+BCNU.2


title: SpColCtrl_384


title: intestine_C_rep2.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, C replicate 2


title: 4hr_BCNU.1


title: blood_Sham operated_2 (mRNA)

city: Bunkyo-ku

first: Ayako

last: Takuma

state: Tokyo

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

hyb_protocol: cRNA 15µg were flagmentated, and hybridized for 16hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized using the statistical software R, and the DFW method.

source_name: blood extracted from Sham treated rats

label_protocol: Biotin-labeled cRNA was synthesized from 100ng total RNA according to the manufacture's protocol.

growth_protocol: The rats had free access to food and water, and were kept in a 12 hour light/dark cycle.

extract_protocol: Total RNA was extracted according to the manufacture's protocol. The extracted total RNA was cleaned up with RNeasy Mini Kit (QIAGEN).

treatment_protocol: The rats were subjected to operation, and blood was extracted from the heart 24hr after the reperfusion.  The blood was mixtured with TRIzol LS Reagent(Thermo Fisher Scientific) and Nuclease-free water, according to the manufacture's protocol.

tag: gender

value: 8 weeks old

tag: stress

value: Sham

value: blood


title: intestine_C_rep1.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, C replicate 1


title: blood_MCAO operated_3 (mRNA)

source_name: blood extracted from MCAO treated rats

tag: age

value: Middle Cerebral Artery Occlusion


title: 4hr_Control.2

value: 4hr Control


title: blood_Sham operated_1 (mRNA)


title: 4hr_AF.1


title: SpColCtrl_380

city: Boston

first: CBDM

last: Lab

institute: Harvard Medical School


title: blood_Sham operated_3 (mRNA)


title: intestine_M_rep8.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, M replicate 8

value: intestine (mid gut)


title: SpColCtrl_379

source_name: spleen


title: 2hr_AF+BCNU.2

value: 2hr AF+BCNU


title: blood_MCAO operated_2 (mRNA)


title: intestine_M_rep7.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, M replicate 7


title: SpColCtrl_378


title: 2hr_AF+BCNU.1


title: SpColCtrl_376


title: SpColCtrl_375


title: SpColCtrl_374


title: SpColCtrl_373


title: intestine_M_rep5.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, M replicate 5


title: 4hr_Control.1


title: intestine_M_rep6.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, M replicate 6


title: SpColCtrl_372


title: intestine_M_rep4.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, M replicate 4


title: 2hr_AF.2

source_name: 3T3-L1 adipocyte

value: 2hr AF


title: 2hr_BCNU.2

value: 2hr BCNU


title: SpColCtrl_371

value: spleen

value: male


title: intestine_M_rep3.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, M replicate 3


title: blood_MCAO operated_1 (mRNA)


title: 2hr_BCNU.1


title: 0hr_No_Treatment.2

value: 0hr No Treatment


title: intestine_M_rep2.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, M replicate 2


title: 2hr_AF.1


title: intestine_M_rep1.

description: Intestinal gene expression

source_name: mid gut, 48h after last meal, M replicate 1


title: SpColCtrl_368


title: SpColCtrl_369


title: SpColCtrl_366


title: 0hr_No_Treatment.1


title: Testis_PND90_DOS300_rep4

city: Montreal

first: Oceane

last: Albert

state: Quebec

address: 3655 Promenade Sir William Osler, McIntyre Medical Sciences Bldg, Room 107

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

description: Gene expression after exposure to 300 mg/kg/day DOS from gestational day 8 to post-natal day 21

hyb_protocol: … hybridized on arrays using the SurePrint G3 Rat Gene Expression 8x60K microarray kit (Agilent Technologies) as per manufacturer’s instructions

scan_protocol: Arrays were read on an Agilent SureScan Microarray Scanner G2600D.

data_processing: The resulting data were analyzed using GeneSpring version 14.9 (Agilent Technologies). Data were normalized using percentile shift normalization to the 75th percentile.

source_name: Testis RNA, 90 days, 300 mg/kg/day DOS, replicate 4

label_protocol: RNA (100 ng) was labeled with Cy3 using the Agilent One Color Low Input Quick Amp kit and …

extract_protocol: RNA was extracted from entire testes using the Qiagen RNEasy® Mini Kit (Qiagen, Toronto, ON). Briefly, frozen testes were pulverized to a thin powder using a chilled mortar and pestle. Approximately 30 mg of powder were placed in 1 mL of RLT buffer supplemented with ß-mercaptoethanol and mechanically disrupted using a rotor-stator homogenizer (Polytron PT10-35GT, Kinematica Inc) at 20 000 rpm for 20 s. Homogenates were further processed with a QIAshredder column (Qiagen), and RNA was isolated as per the manufacturer's instructions. RNA quality was measured using a NanoDrop 2000 Spectrophotometer (Thermo Fisher), with 260/280 and 260/230 absorbance ratios comprised between 1.9-2.1 and 2.0-2.2, respectively.

treatment_protocol: Sprague-Dawley dams were gavaged from gestational day 8 to post-natal day 21 with corn oil, or 30 or 300 mg/kg/day DEHP, DINCH, BDB or DOS. Male offspring were kept and necropsied at post-natal day 90.

value: Sprague-Dawley

value: Male

value: Testis

value: 90 days


title: WT NASH liver, biological rep2

city: Ann Arbor

first: Jiandie

last: Lin

state: Michigan

address: 210 Washtenaw Avenue

department: Life Sciences Institute and Department of Cell & Developmental Biology

institute: University of Michigan

description: Gene expression data from wild type liver, pool 2

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592)

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical language version 3.3.0. RMA was used to fit log2 transformed expression values

source_name: Wild type mouse liver

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Wild type and Neuregulin 4 (Nrg4) knockout mice were fed NASH diet (Research Diets D09100301) starting at 3 months of age for twenty weeks.

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

treatment_protocol: Liver tissues were harvested under random fed condition.

value: liver

tag: genotype

value: wild type

tag: feeding

value: NASH diet fed


title: SpColCtrl_365

address: 77 Avenue Louis Pasteur

value: B6 Foxp3-Ires-Gfp


title: Testis_PND90_DOS300_rep3

source_name: Testis RNA, 90 days, 300 mg/kg/day DOS, replicate 3


title: WT NASH liver, biological rep1

description: Gene expression data from wild type liver, pool 1


title: Testis_PND90_DOS300_rep6

source_name: Testis RNA, 90 days, 300 mg/kg/day DOS, replicate 6


title: KO NASH liver, biological rep2

description: Gene expression data from Nrg4 knockout liver, pool 2

source_name: Nrg4 KO mouse liver

value: Nrg4 knockout


title: Testis_PND90_DOS300_rep5

source_name: Testis RNA, 90 days, 300 mg/kg/day DOS, replicate 5


title: Testis_PND90_DOS30_rep5

description: Gene expression after exposure to 30 mg/kg/day DOS from gestational day 8 to post-natal day 21

source_name: Testis RNA, 90 days, 30 mg/kg/day DOS, replicate 5


title: KO NASH liver, biological rep1

description: Gene expression data from Nrg4 knockout liver, pool 1


title: SpColCtrl_370


title: Testis_PND90_DOS30_rep6

source_name: Testis RNA, 90 days, 30 mg/kg/day DOS, replicate 6


title: SpColCtrl_364

source_name: spleen


title: SpColCtrl_359


title: SpColCtrl_362


title: SpColCtrl_361


title: SpColCtrl_358


title: SpColCtrl_360


title: SpColCtrl_363


title: SpColCtrl_356


title: SpColCtrl_355


title: Testis_PND90_BDB300_rep5

description: Gene expression after exposure to 300 mg/kg/day BDB from gestational day 8 to post-natal day 21

source_name: Testis RNA, 90 days, 300 mg/kg/day BDB, replicate 5


title: Testis_PND90_DOS30_rep3

source_name: Testis RNA, 90 days, 30 mg/kg/day DOS, replicate 3


title: Testis_PND90_BDB300_rep3

source_name: Testis RNA, 90 days, 300 mg/kg/day BDB, replicate 3


title: SpColCtrl_352


title: Testis_PND90_BDB300_rep6

source_name: Testis RNA, 90 days, 300 mg/kg/day BDB, replicate 6


title: SpColCtrl_354


title: Testis_PND90_BDB300_rep2

source_name: Testis RNA, 90 days, 300 mg/kg/day BDB, replicate 2


title: Testis_PND90_DOS300_rep1

source_name: Testis RNA, 90 days, 300 mg/kg/day DOS, replicate 1


title: Testis_PND90_DOS30_rep2

source_name: Testis RNA, 90 days, 30 mg/kg/day DOS, replicate 2


title: SpColCtrl_351


title: Testis_PND90_DOS30_rep1

source_name: Testis RNA, 90 days, 30 mg/kg/day DOS, replicate 1


title: Testis_PND90_DOS30_rep4

source_name: Testis RNA, 90 days, 30 mg/kg/day DOS, replicate 4


title: Testis_PND90_BDB300_rep4

source_name: Testis RNA, 90 days, 300 mg/kg/day BDB, replicate 4


title: SpColCtrl_348


title: SpColCtrl_346


title: SpColCtrl_345


title: SpColCtrl_343


title: SpColCtrl_344


title: SpColCtrl_342


title: SpColCtrl_341


title: Testis_PND90_BDB30_rep4

description: Gene expression after exposure to 30 mg/kg/day BDB from gestational day 8 to post-natal day 21

source_name: Testis RNA, 90 days, 30 mg/kg/day BDB, replicate 4


title: Testis_PND90_DINCH300_rep5

description: Gene expression after exposure to 300 mg/kg/day DINCH from gestational day 8 to post-natal day 21

source_name: Testis RNA, 90 days, 300 mg/kg/day DINCH, replicate 5


title: Testis_PND90_BDB30_rep6

source_name: Testis RNA, 90 days, 30 mg/kg/day BDB, replicate 6


title: Testis_PND90_BDB300_rep1

source_name: Testis RNA, 90 days, 300 mg/kg/day BDB, replicate 1


title: Testis_PND90_BDB30_rep5

source_name: Testis RNA, 90 days, 30 mg/kg/day BDB, replicate 5


title: Testis_PND90_DINCH300_rep6

source_name: Testis RNA, 90 days, 300 mg/kg/day DINCH, replicate 6


title: Testis_PND90_BDB30_rep2

source_name: Testis RNA, 90 days, 30 mg/kg/day BDB, replicate 2


title: Testis_PND90_BDB30_rep3

source_name: Testis RNA, 90 days, 30 mg/kg/day BDB, replicate 3


title: Testis_PND90_DINCH300_rep4

source_name: Testis RNA, 90 days, 300 mg/kg/day DINCH, replicate 4


title: Testis_PND90_BDB30_rep1

source_name: Testis RNA, 90 days, 30 mg/kg/day BDB, replicate 1


title: Testis_PND90_DINCH300_rep2

source_name: Testis RNA, 90 days, 300 mg/kg/day DINCH, replicate 2


title: Testis_PND90_DINCH300_rep3

source_name: Testis RNA, 90 days, 300 mg/kg/day DINCH, replicate 3


title: high glucose, biological rep1

city: Chicago

first: Xiaofeng

last: Zhou

state: Illinois

address: 801 S Paulina Street

institute: University of Illinois at Chicago

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The scanned array images were processed with GeneChip Operating software (GCOS). The microarray data were pre-processed using Robust Multi-array Analysis (RMA).

source_name: UM1 cell line, 16.7 mM glucose

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: standard protocol and conditions

extract_protocol: Qiagen RNAeasy kit

treatment_protocol: cultured in 5.6 or 16.7 mM glucose for 7 days

tag: cell type

value: oral tongue cancer


title: SpColCtrl_334

source_name: spleen


title: SpColCtrl_337


title: SpColCtrl_339


title: SpColCtrl_333


title: SpColCtrl_338


title: low glucose, biological rep2

source_name: UM1 cell line, 5.6 mM glucose


title: high glucose, biological rep2


title: low glucose, biological rep1


title: SpColCtrl_332


title: SpColCtrl_330


title: SpColCtrl_331


title: SpColCtrl_329


title: Testis_PND90_DINCH30_rep6

description: Gene expression after exposure to 30 mg/kg/day DINCH from gestational day 8 to post-natal day 21

source_name: Testis RNA, 90 days, 30 mg/kg/day DINCH, replicate 6


title: Testis_PND90_DINCH30_rep3

source_name: Testis RNA, 90 days, 30 mg/kg/day DINCH, replicate 3


title: SpColCtrl_327


title: Testis_PND90_DINCH300_rep1

source_name: Testis RNA, 90 days, 300 mg/kg/day DINCH, replicate 1


title: dkfz_BT183_pGF1

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: ETMR cell line'

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

value: ETMR cell line BT183 labeld by pGF1


title: Testis_PND90_DINCH30_rep5

source_name: Testis RNA, 90 days, 30 mg/kg/day DINCH, replicate 5


title: Testis_PND90_DINCH30_rep4

source_name: Testis RNA, 90 days, 30 mg/kg/day DINCH, replicate 4


title: SpColCtrl_326


title: Testis_PND90_DOS300_rep2

source_name: Testis RNA, 90 days, 300 mg/kg/day DOS, replicate 2


title: SpColCtrl_324


title: Testis_PND90_DINCH30_rep1

source_name: Testis RNA, 90 days, 30 mg/kg/day DINCH, replicate 1


title: SpColCtrl_323


title: SpColCtrl_367


title: SpColCtrl_325


title: dkfz_BT183_xeno

source_name: ETMR xenograft

value: orthotopic xenograft of BT183_pGF1


title: SpColCtrl_319


title: SpColCtrl_320


title: dkfz_BT183

source_name: ETMR cell line

value: ETMR cell line BT183


title: Testis_PND90_DEHP300_rep3

description: Gene expression after exposure to 300 mg/kg/day DEHP from gestational day 8 to post-natal day 21

source_name: Testis RNA, 90 days, 300 mg/kg/day DEHP, replicate 3


title: Testis_PND90_DEHP300_rep2

source_name: Testis RNA, 90 days, 300 mg/kg/day DEHP, replicate 2


title: SpColCtrl_317


title: SpColCtrl_322


title: SpColCtrl_316


title: Testis_PND90_DEHP300_rep5

source_name: Testis RNA, 90 days, 300 mg/kg/day DEHP, replicate 5


title: Testis_PND90_DEHP300_rep4

source_name: Testis RNA, 90 days, 300 mg/kg/day DEHP, replicate 4


title: SpColCtrl_315


title: SpColCtrl_321


title: Testis_PND90_DEHP300_rep6

source_name: Testis RNA, 90 days, 300 mg/kg/day DEHP, replicate 6


title: SpColCtrl_314

source_name: spleen


title: SpColCtrl_313


title: SpColCtrl_312


title: Testis_PND90_DEHP30_rep4

description: Gene expression after exposure to 30 mg/kg/day DEHP from gestational day 8 to post-natal day 21

source_name: Testis RNA, 90 days, 30 mg/kg/day DEHP, replicate 4


title: SpColCtrl_310


title: Testis_PND90_DEHP30_rep5

source_name: Testis RNA, 90 days, 30 mg/kg/day DEHP, replicate 5


title: Testis_PND90_DEHP30_rep1

source_name: Testis RNA, 90 days, 30 mg/kg/day DEHP, replicate 1


title: Testis_PND90_DEHP30_rep6

source_name: Testis RNA, 90 days, 30 mg/kg/day DEHP, replicate 6


title: Testis_PND90_DEHP300_rep1

source_name: Testis RNA, 90 days, 300 mg/kg/day DEHP, replicate 1


title: Testis_PND90_DEHP30_rep2

source_name: Testis RNA, 90 days, 30 mg/kg/day DEHP, replicate 2


title: SpColCtrl_309


title: Testis_PND90_DEHP30_rep3

source_name: Testis RNA, 90 days, 30 mg/kg/day DEHP, replicate 3


title: Caprine Endometrial Epithelial Cells PPRV24h 1

city: Yangling

first: Bo

last: Yang

address: 22 Xinong Rd, College of Veterinary Medicine 4316

department: College of Veterinary Medicine,

institute: Northwest A&F University

description: Gene expression infection of PPRV

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 019921_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Capra hircus

source_name: EECs  PPRV 24h

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

extract_protocol: Each group of samples was added by 1ml RNAiso Plus(TAKARA).RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Sheep Genome Oligo Microarray (8x15K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

treatment_protocol: PPRV with multiplicity of infection (MOI) of 2 was absorbed into the cells at 4 °C for 1 h. After fully adsorption, the cells were allowed to proceed at 37 °C for 1h. To determine the rate of virus internalization, a parallel set of cultures was processed under the same conditions, except that PPRV was replaced by culture medium.

value: endometrial epithelial cells

tag: infection duration


title: Caprine Endometrial Epithelial Cells PPRV24h 2

description: Gene expression infection of PPRV


title: Caprine Endometrial Epithelial Cells control2

description: Gene expression of control

source_name: EECs  PPRV 0h


title: Testis_PND90_CORNOIL_rep6

description: Gene expression after exposure to corn oil from gestational day 8 to post-natal day 21

source_name: Testis RNA, 90 days, corn oil, replicate 6


title: Testis_PND90_CORNOIL_rep5

source_name: Testis RNA, 90 days, corn oil, replicate 5


title: Caprine Endometrial Epithelial Cells control3

description: Gene expression of control


title: Testis_PND90_CORNOIL_rep4

source_name: Testis RNA, 90 days, corn oil, replicate 4


title: Caprine Endometrial Epithelial Cells PPRV1h 3

description: Gene expression infection of PPRV

source_name: EECs  PPRV 1h


title: SpColCtrl_308

value: spleen


title: Testis_PND90_CORNOIL_rep1

source_name: Testis RNA, 90 days, corn oil, replicate 1


title: Testis_PND90_CORNOIL_rep3

source_name: Testis RNA, 90 days, corn oil, replicate 3


title: Caprine Endometrial Epithelial Cells control1

description: Gene expression of control


title: Caprine Endometrial Epithelial Cells PPRV1h 2

description: Gene expression infection of PPRV


title: Testis_PND90_CORNOIL_rep2

source_name: Testis RNA, 90 days, corn oil, replicate 2