title: Vibrio_natriegens_Rend_seq_MOPS_comp_3NaCl_25s_frag

description: ribosome protected mRNA

data_processing:
Sequence reads were trimmed for poly A stretches at the 3’ ends.
Trimmed reads were aligned to NC_000913.2 using Bowtie v1.0.1 with options -v 1 -k 2 -m 2. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
CP009977.1
CP009978.1
Base calls performed using Casava version 1.7.
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

value: MOPS complete (Teknova) with full supplement (Neidhart et al., 1974), with added 3% NaCl


title: Caulobacter_crescentus_Rend_seq_PYE_25s_frag

status: Public on Mar 28 2018

type: SRA

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

description: mRNA

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000913.2 using Bowtie v1.0.1 with options -v 1 -k 2 -m 2. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
CP001340.1
Base calls performed using Casava version 1.7.
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

molecule: total RNA

organism: Caulobacter vibrioides

source_name: Bacteria

growth_protocol: Overnight cultures were diluted to OD590 0.0003 in 20 mL fresh media. The culture was kept in a 125 mL flask at 30C with aeration (200 rpm) until OD590 reached 0.3.

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol with 5% phenol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

tag: strain

tag: growth medium

value: PYE


title: Patient_CODE9 - MS

type: RNA

city: Bari

first: Antonio

last: Moschetta

address: Via Orazio Flacco, 65

country: Italy

institute: IRCCS Ospedale Oncologico di Bari

description: 5141769057 F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <100 in more than 1 group were excluded. Data were analyzed with non parametric analysis plus False Discovery Rate, FDR.

label: biotin

organism: Homo sapiens

source_name: PBMCs

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA was extracted using the QIAzol® Lysis Reagent, according to the manufacturer’s instructions. Quality control was performed with Biorad Experion.

tag: disease state

value: Metabolic Syndrome

tag: age

tag: tissue

value: PBMCs


title: Patient_CODE8 - MS

description: 5141769057 D


title: Patient_CODE5 - MS

description: 5141769057 I


title: Patient_CODE6 - MS

description: 5141769057 K


title: Patient_CODE4 - MS

description: 5141769057 G


title: Patient_CODE3 - MS

description: 5141769057 E


title: Patient_CODE2 - MS

description: 5141769057 C


title: Patient_CODE7 - MS

description: 5141769057 B


title: lt-NES_CH1_input_rep1

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

description: CHARGE patient require controlled access. Raw data is being registered at JGA (Japanese Genotype-Phenotype Archive).

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Adaptor was removed and low quality reads were trimmed using Trimmomatic version 0.33.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.1.0 with default settings.
Peaks were called using MACS version 2.1.0.20150731.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using Deeptools version 1.5.1 (bamCoverage) with the following option --binSize 50 --fragmentLength 200.

molecule: genomic DNA

source_name: hiPSC-derived lt-NES

extract_protocol:
For single fixation with formaldehyde, cells were fixed with 1% formaldehyde-containing medium for 10 min. For double fixation, the cells were first fixed with 2 mM EGS for 30 min followed by with 1% formaldehyde-containing medium for 10 min.
Libraries were prepared using KAPA Hyperprep Kit.

value: hiPSC-derived lt-NES

tag: genotype/variation

value: CHARGE patient

tag: chip-antibody


title: Patient_CODE1 - MS

description: 5141769057 A


title: REP-AN J0

status: Public on Mar 27 2018

city: paris

first: veronique

last: PELLOUX

address: 50-52 bld Vincent Auriol

department: UMR 1166 eq 6

country: France

institute: INSERM

data_processing: The data were normalised using quantile normalisation and subtract Background with Genome Studio (Illumina software)

source_name: human adipose tissu (BTA) before VLCD

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

extract_protocol: RNA was extracted 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: subcutaneous adipose tissue

tag: time point

value: before diet


title: heat-damaged MHCC97H treated by HGF at 10ng/ml.

city: Shanghai

first: Rui

last: Zhang

address: Fenglin road of Xuhui district

country: China

institute: Zhongshan hospital of Fudan University

description: Gene expression data from heat-damaged residual MHCC97H treated by HGF at 10 ng/ml

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained using the GeneChip Hybridization Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix, CA, US).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Human HCC Cells

label_protocol: Biotinylated cRNA were labeled using GeneChip 3’IVT PLUS reagent Kit (Affymetrix, CA, US).

growth_protocol: MHCC97H was subjected to sublethal heat stress and then was maintained in 1% FBS DMEM.

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

treatment_protocol: Heat-damaged residual MHCC97H was treated by HGF at 0, 2 ,10ng/ml.

tag: cell

value: Human HCC Cells

tag: treatment

value: HGF at 10 ng/ml


title: NOI-JO S06

source_name: human adipose tissu (BTA) after 6 weeks VLCD

value: after 6 weeks diet


title: MOH-ST S06


title: REP-AN S06


title: MOH-ST J0


title: PAI-AN S06


title: SAL-FR J0


title: heat-damaged MHCC97H treated by HGF at 2ng/ml.

description: Gene expression data from heat-damaged residual MHCC97H treated by HGF at 2 ng/ml

value: HGF at 2 ng/ml


title: heat-damaged MHCC97H treated by HGF at 0 ng/ml

description: Gene expression data from heat-damaged residual MHCC97H treated by HGF at 0 ng/ml

value: HGF at 0 ng/ml


title: REG-KA S06


title: LEP-CH J0


title: LAG-LI J0


title: SAL-FR S06


title: PAI-AN J0


title: REG-KA J0


title: NOI-JO J0


title: LEP-CH S06


title: LAM-PA S06


title: MIL-NI S06


title: MIL-NI J0


title: KAP-FE J0


title: LAM-PA J0


title: KAP-FE S06


title: JOU-DE S06


title: HEN-MU S06


title: JOU-DE J0


title: LAG-LI S06


title: HUR-AN S06


title: HUR-AN J0


title: DZI-ZA J0


title: GAB-AU J0


title: DUR-MO J0


title: DRO-MA S06


title: GAB-AU S06


title: DZI-ZA S06


title: DRO-MA J0


title: DES-NI J0


title: DES-VI S06


title: DUR-MO S06


title: HEN-MU J0


title: DES-VI J0


title: COL-MA J0


title: CHO-OL S06


title: BEL-MA S06


title: CHO-OL J0


title: COL-MA S06


title: BOR-CL J0


title: BAJ-VE J0


title: IMR-90 40_12h

city: Beijing

first: Zhen

last: Zhao

address: Haidian District

department: Department of Automation

institute: Tsinghua University

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 12 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_12h

data_processing:
Sequenced reads were trimmed for adaptor sequence,then mapped to hg19 whole genome using bowtie2 v2.2.3.
Read quality was checked for each sample using FastQC v0.11.5.
High-quality reads were then imported into TopHat v2.0.12 for alignment into BAM files.
The mapped reads were counted for gene using HTSeq v0.6.1.The count data were normalized using DESeq. Gene counts values were log2-transformed after one was added to count values.
If a gene's count value was less than a millionth of the aligned read number, the gene was considered to be low expression. We filtered out genes with low expression in all samples.
Genome_build: hg19, reference sequence is gencode v24(https://www.gencodegenes.org/releases/24lift37.html)
Supplementary_files_format_and_content: ProcessedDataMatrix_Final.txt: tab-delimited text file includes gene count values (for log2-transformed after one was added to count values)

molecule: polyA RNA

source_name: lung

growth_protocol: Human diploid IMR90 fibroblasts were cultured at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium, 10% fetal bovine serum and antibiotics.  The cells were plated at 20000/cm^2.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina was used with 1 ug of total RNA for the construction of sequencing libraries.
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA.The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 20pM hybridization to a 2x125 paired end flow cell.

treatment_protocol: The cells were plated at 20000/cm^2. After two days, the cells were treated with the DNA-damaging agent bleomycin at 0 ug/ml, 2 ug/ml and 40 ug/ml for 2 h. The total RNA was extracted using TRIzol reagent (Invitrogen) at 12 time points (0 h, 2 h, 4 h, 8 h, 12 h, 24 h, 32 h, 2 days, 4 days, 6 days and 8 days) after exposure to bleomycin at 2 ug/ml and 40 ug/ml. The total RNA was extracted at 3 time points (0 h, 4 days and 8 days) after exposure to bleomycin at 0 ug/ml.

tag: cell line

tag: cell type

value: fibroblast

value: 16 weeks gestation

tag: agent

value: bleomycin

tag: dose

value: 40 ug/ml

tag: time


title: IMR-90 40_8h

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 8 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_8h

value: 8 h


title: DES-NI S06


title: BAJ-VE S06


title: IMR-90 40_8d

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 8 days after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_8d

value: 8 days


title: IMR-90 40_24h

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 24 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_24h


title: ANC-TH J0


title: ANC-TH S06


title: AYA-LA J0


title: AYA-LA S06


title: IMR-90 2_36h

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 36 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_36h

value: 2 ug/ml


title: IMR-90 40_4d

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 4 days after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_4d

value: 4 days


title: IMR-90 40_6d

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 6 days after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_6d

value: 6 days


title: IMR-90 40_2d

description:
The sample was treated with the DNA-damaging agent bleomycin at 40 ug/ml for 2 h. The total RNA was extracted at 2 days after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 40_2d

value: 2 days


title: IMR-90 2_8d

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 8 days after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_8d


title: IMR-90 2_4h

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 4 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_4h

value: 4 h


title: IMR-90 2_2h

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 2 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_2h

value: 2 h


title: IMR-90 2_6d

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 6 days after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_6d


title: IMR-90 2_4d

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 4 days after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_4d


title: IMR-90 2_24h

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 24 h after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_24h


title: IMR-90 0_4d

description:
no exposure for 4 days
ProcessedDataMatrix_Final.txt
IMR-90 0_4d

value: control

value: 0 ug/ml


title: IMR-90 0_8d

description:
no exposure for 8 days
ProcessedDataMatrix_Final.txt
IMR-90 0_8d


title: BOR-CL S06

value: subcutaneous adipose tissue

value: after 6 weeks diet


title: TGF beta treatment Pol II S2 ChIPSeq

city: Cambridge

first: zehua

last: chen

state: Massachusetts

address: 55 Cambridge Parkway

country: USA

institute: WuXi NextCODE

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg38 genome assembly using BWA-MEM version 0.7.11 with default parameters
Alignments were filterd for duplicated reads
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deepTools version 2.5.4

growth_protocol: Human aortic smooth muscle cells (#C-007-5C), media (#M231-500), and supplements (SMGS: S-007-25; SMDS: S-008-5) were purchased from Thermofisher Scientific. The cells were grown at 37°C, 5% CO2 in Medium 231 supplemented with smooth muscle growth supplement (SMGS containing 4.9% FBS, 2 ng/ml FGF2, 0.5 ng/ml EGF, 5 ng/ml heparin, 2 ug/ml IGF-1, and 0.2 ug/ml BSA).

extract_protocol:
10x10^6 cells were first cross-linked with 1.5 mM EGS in PBS for 30 mins, followed by 1% paraformaldehyde for 10 minutes at room temperature. Glycine was added at a final concentration of 125 mM for 5 minutes at room temperature in order to quench the crosslinking reaction. The cross-linked material was washed once each with Buffer 1 (0.25% Triton, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH7.5) and Buffer 2 (200 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH7.5) before resuspension in Shearing Buffer (0.1% SDS, 1 mM EDTA, 1 mM Tris-HCl pH7.6) with 1X Complete Protease Inhibitor Cocktail (Roche). Cell pellet was lysed in 130 μl SDS lysis buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS, 50 mM PMSF) and sonicated using an S220 Focused-ultrasonicator (Covaris) to generate 200 to 600 bp fragments. Fragmented chromatin was centrifuged at 10,000 g for 5 minutes and the supernatants were diluted in ChIP dilution buffer (1% Triton, 150 mM NaCl, 20 mM Tris pH 8.0). Immunoprecipition was performed by rotating samples at 4°C with magnetic beads (Dynabeads Protein A or G, Invitrogen) pre-bound with 5 μg of antibody. The beads were washed once each with low salt buffer (50 mM Tris pH 8.0, 150 mM NaCl, 0.1% SDS, 0.5% Deoxycholate, 1% NP40, 1 mM EDTA), high salt buffer (50 mM Tris pH 8.0, 500 mM NaCl, 0.1% SDS, 0.5% Deoxycholate, 1% NP40, 1 mM EDTA), LiCl wash buffer (50 mM Tris pH 8.0, 250 mM LiCl, 0.5% Deoxycholate, 1% NP40, 1 mM EDTA), Morohashi RIPA buffer (50 mM Tris pH7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP40, 0.1% SDS), DOC/Triton Buffer (25 mM Tris pH7.5, 150 mM NaCl, 5 mM EDTA, 1% Triton-X-100, 0.5% DOC), and twice with Tris-EDTA buffer (10 mM Tris pH 8.0, 1 mM EDTA). All washes took place on a rotator for 10 minutes at 4°C. Beads were treated twice with 100μl elution buffer for 15 minutes on a shaker at room temperature, to obtain a total of 200μl eluate. 8 μl of 5M NaCl was added to the eluate and the sample was reverse cross-linked overnight at 55°C. DNA was then purified using the QIAquick PCR Purification Kit (Qiagen).
ChIP DNA samples was used in a 23.3 μl combined end repair and A-tailing reaction using a KAPA Hyper Prep Kit (Kapa Biosciences) for 30 minutes at 20°C followed by 30 minutes at 65°C. 10 μl of ligase buffer, 3.7 μl of Adapters and 3.3 μl ligase (KAPA Hyper Prep Kit) were added and incubated at 20°C for 4 hours. Double-stranded DNA fragments were purified from this reaction using KAPA Pure Beads (Kapa Biosciences) and eluted in 22 μl 10 mM Tris pH8.0. Libraries were generated by PCR and size-selected on a 2% E-Gel EX agarose gel (Invitrogen) and fragments between 150 and 400 bp were extracted using a QIAEX II Gel Extraction Kit (Qiagen) performed at room temperature.

treatment_protocol: For SMC differentiation, HASMC were incubated with Medium 231 containing smooth muscle differentiation supplement (SMDS containing 1% FBS and 30 mg/ml heparin) for different time points. HASMC were treated with TGF beta at 0.5ng/ml daily for 10 days.

value: aortic smooth muscle cells

value: TGF beta treatment

tag: chip antibody

value: RNA pol II CTD phospho Ser2 (active motif 61083)


title: BEL-MA J0

value: before diet


title: TGF beta treatment SMAD ChIPSeq


title: PBS treatment SMAD ChIPSeq

value: PBS treatment


title: IMR-90 2_2d

description:
The sample was treated with the DNA-damaging agent bleomycin at 2 ug/ml for 2 h. The total RNA was extracted at 2 days after exposure to bleomycin.
ProcessedDataMatrix_Final.txt
IMR-90 2_2d

value: fibroblast

value: 16 weeks gestation

value: bleomycin


title: input DNA for PBS treatment samples


title: PBS treatment Pol II S2 ChIPSeq


title: input DNA for TGFbeta treatment samples


title: NFAT3 overexpression experiment-1

city: Chuo

first: Osamu

last: Kaminuma

state: Yamanashi

address: 1110 Shimokato

institute: University of Yamanashi

description: At 48 h after transfection, cells were harvested.

hyb_protocol: 0.825 µg of Cy3 or Cy5-labeled cRNA was fragmented and hybridized to Agilent Human Gene Expression v2 Microarray (G4845A) using Agilent Gene Expression Hybridization Kit. Hybridization was performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

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

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: control vector-transfected cells

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5)-labeled cRNA was prepared from 200 ng of total RNA using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: ASMC were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 1 x MEM non-essential amino acid solution, 100 U/ml penicillin G and 100 U/ml streptomycin.

extract_protocol: Total RNAs were extracted using ReliaPrepTM RNA miniprep system according to the manufacture's protocol.

treatment_protocol: Plasmid or RNAi oligo was transfected into ASMC with LipofectamineTM 2000 following manufacture's instructions.


title: NFAT3 knockdown experiment-1

source_name: control oligo-transfected cells

source_name: NFAT3-specific RNAi oligo-transfected cells


title: colon, medium fat diet (25% energy), age 28 months, rep01

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' (v1.40.1).

organism: Mus musculus

source_name: scraping from colonic mucosa and submucosa, medium fat diet (25% energy), age 28 months

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: The design of the study and experimental procedures have been described in detail previously (PMID: 25504628).  Briefly, male C57BL/6J mice (age: 7 weeks) were purchased from Janvier (Cedex, France) and were housed in pairs of two in the light and temperature (20C)-controlled animal facility of Wageningen University (12-hour light/dark cycle, lights on at 04.00). The mice received standard AIN-93G (Research Diet Services, Wijk bij Duurstede, The Netherlands) for 2 weeks upon arrival. At the age of 9 weeks, mice were individually housed and randomized to different dietary regimens. For the current analyses, we considered mice that were lifelong fed a semi-synthetic control diet consisting of 10E% of fat (C; control), a calorie restriction (CR) diet without malnutrition (30% energy reduction compared to the C diet) or a medium fat (MF) diet consisting of 25E% of fat. All diets, except the CR diet, were fed ad libitum. Mice sacrificed at 6 or 28 months of age were considered in order to differentiate between effects at young and old age. To study the molecular flexibility and dynamics after receiving a strict CR diet for prolonged time, a diet switch was included in this study. A subgroup of mice on CR was switched to the MF diet at the age of 24 months until sacrifice at 28 months.

extract_protocol: Total RNA was isolated from the scrapings using TRIzol Reagent according to the manufacturer’s instructions (Invitrogen, Breda, The Netherlands). Isolated RNA was purified using RNeasy Micro columns (Qiagen, Venlo, The Netherlands) and total RNA yield (Nanodrop ND-1000, Nanodrop Products, Maarssen, The Netherlands) and RNA integrity (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) were assessed. 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: Prior to sacrifice, each mouse was first fasted for 4 hours after which they received an intragastric gavage of 400ul of 0.5% carboxymethyl cellulose, then fasted again for another 6 hours. The animals in CR diet group were fed with half of the portion they normally received 15 min before the first fasting. During the sacrifice, after sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), tissue was snap-frozen and stored at -80C until further analysis.

tag: Sex

value: male

tag: mouseid

tag: diet group

value: MF

tag: diet group (full name)

value: medium fat

tag: age at sacrifice (months)

tag: diet switch at the age of 24m

value: no

value: colon


title: colon, calorie restriction to medium fat diet (25% energy) switch, age 28 months, rep15

source_name: scraping from colonic mucosa and submucosa, switched from calorie restriction diet at age of 24 months to medium fat diet (25% energy), age 28 months

value: CR>MF

value: diet switch (CR>MF)

value: yes

tag: tissue

tag: strain


title: NFAT3 overexpression experiment-2


title: colon, calorie restriction to medium fat diet (25% energy) switch, age 28 months, rep09


title: colon, calorie restriction to medium fat diet (25% energy) switch, age 28 months, rep05


title: colon, calorie restriction to medium fat diet (25% energy) switch, age 28 months, rep03


title: colon, medium fat diet (25% energy), age 28 months, rep05


title: colon, calorie restriction to medium fat diet (25% energy) switch, age 28 months, rep13


title: colon, calorie restriction diet, age 28 months, rep03

source_name: scraping from colonic mucosa and submucosa, calorie restriction diet, age 28 months

value: CR

value: calorie restriction


title: colon, calorie restriction diet, age 28 months, rep01


title: colon, medium fat diet (25% energy), age 28 months, rep15


title: colon, calorie restriction diet, age 28 months, rep13


title: colon, medium fat diet (25% energy), age 28 months, rep07


title: colon, calorie restriction to medium fat diet (25% energy) switch, age 28 months, rep11


title: colon, calorie restriction diet, age 28 months, rep15


title: colon, medium fat diet (25% energy), age 28 months, rep13


title: colon, calorie restriction to medium fat diet (25% energy) switch, age 28 months, rep01


title: colon, medium fat diet (25% energy), age 6 months, rep11

source_name: scraping from colonic mucosa and submucosa, medium fat diet (25% energy), age 6 months


title: colon, medium fat diet (25% energy), age 6 months, rep05


title: colon, calorie restriction diet, age 28 months, rep05


title: colon, medium fat diet (25% energy), age 28 months, rep11


title: colon, calorie restriction diet, age 6 months, rep01

source_name: scraping from colonic mucosa and submucosa, calorie restriction diet, age 6 months


title: colon, medium fat diet (25% energy), age 28 months, rep09


title: colon, medium fat diet (25% energy), age 6 months, rep03


title: colon, medium fat diet (25% energy), age 6 months, rep07


title: colon, calorie restriction diet, age 28 months, rep07


title: colon, medium fat diet (25% energy), age 6 months, rep01


title: colon, calorie restriction diet, age 6 months, rep09


title: colon, calorie restriction diet, age 6 months, rep05


title: colon, calorie restriction diet, age 6 months, rep07


title: colon, calorie restriction diet, age 6 months, rep03


title: colon, calorie restriction diet, age 6 months, rep11


title: PND5 Uteri DES Foxa2 WT2

city: RTP

first: Wendy

last: Jefferson

state: NC

address: 105 T. W. Alexander Drive

institute: NIEHS

description: Gene expression from PND5 Uteri DES Foxa2 WT

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: Day 5 uterus, DES-treated

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Uterine tissue was frozen on dry ice and stored at -80C.  Frozen uterine tissue was pulverized and then total RNA was isolated using Qiagen Rneasy kit along with Dnase I on the column.

tag: gender

value: female

value: uterus

tag: genotype/variation

value: wild type

value: DES-treated


title: PND5 Uteri DES Foxa2 WT4

tag: treatment


title: PND5 Uteri DES Foxo1 WT3

description: Gene expression from PND5 Uteri DES Foxo1 WT


title: PND5 Uteri DES Foxo1 WT2


title: PND5 Uteri DES Foxa2 cKO 3

description: Gene expression from PND5 Uteri DES Foxa2 cKO


title: PND5 Uteri DES Foxa2 cKO 1


title: PND5 Uteri DES Foxo1 WT4


title: PND5 Uteri DES Foxo1 cKO 3

description: Gene expression from PND5 Uteri DES Foxo1 cKO


title: PND5 Uteri DES Foxo1 cKO 2


title: PND5 Uteri DES Foxo1 cKO 1


title: PND5 Uteri DES Foxa2 cKO 4


title: PND5 Uteri DES Esr1 cKO 3

description: Gene expression from PND5 Uteri DES Esr1 cKO


title: PND5 Uteri DES Esr1 WT3

description: Gene expression from PND5 Uteri DES Esr1 WT


title: PND5 Uteri DES Esr1 cKO 1


title: PND5 Uteri DES Foxa2 WT3


title: PND5 Uteri DES Foxo1 cKO 4


title: PND5 Uteri DES Esr1 cKO 4


title: PND5 Uteri DES Foxa2 WT1


title: PND5 Uteri DES Esr1 cKO 2


title: PND5 Uteri DES Foxa2 cKO 2


title: PND5 Uteri DES Esr1 WT4


title: PND5 Co Esr1 cKO 4

description: Gene expression from PND5 Co Esr1 cKO

source_name: Day 5 uterus, vehicle control

value: vehicle control


title: PND5 Co Esr1 cKO 3

description: Gene expression from PND5 Co Esr1 cKO


title: PND5 Uteri DES Esr1 WT1


title: PND5 Uteri DES Esr1 WT2


title: PND5 Uteri DES Foxo1 WT1


title: NFAT3 knockdown experiment-2

value: aortic smooth muscle cells


title: PND5 Co Esr1 cKO 2

description: Gene expression from PND5 Co Esr1 cKO


title: Combination sample 2

city: Southampton

first: Sarah

middle: Louise

last: Buchan

state: Hants

address: Tremona Road

department: Cancer Sciences Unit

country: United Kingdom

institute: University of Southampton

description:
A3214_08
Activated CD8+ T cells

hyb_protocol: Following fragmentation, cDNA samples were hybridized for 16 hours at 45 degrees on an Affy HTA array and washed and stained using the Affymetrix Hyb. Wash and stain kit all by AROS Biotechnology Ltd

scan_protocol: Standard Affymetrix protocol

data_processing: RMA normalization, oligo R package (version 1.38.0).

source_name: pmel1 CD8+ T cells from anti-PD-1/L1 and anti-CD27 treated mice

label_protocol: cDNA was prepared by AROS Biotechnology (Denmark) using 50ng starting RNA material and labelled

extract_protocol: RNA was extracted from isolated CD8+Thy1.1+ T cells using Qiagen RNeasy kits and gDNA eliminator columns

treatment_protocol: Adoptively transferred CD8+ T cells were treated in vivo with peptide and anti-CD27, anti-PD-1/L1 or all three together (with isotype controls to equalize antibody dose across groups).

value: CD8+ T cell

value: anti-PD-1/L1 and anti-CD27


title: Anti-CD27 sample 3

description:
A3214_06
Activated CD8+ T cells

source_name: pmel1 CD8+ T cells from anti-CD27 treated mice


title: Anti-CD27 sample 1

description:
A3214_04
Activated CD8+ T cells


title: PND5 Uteri Co Esr1 WT2

description: Gene expression from PND5 Uteri Co Esr1 WT


title: IMR-90 0_0d

description:
no exposure for 0 day
ProcessedDataMatrix_Final.txt
IMR-90 0_0

tag: cell line

value: fibroblast

tag: age

value: 16 weeks gestation

value: control

value: 0 ug/ml

value: 0 day


title: s1_9A

city: Tianjin

first: jia

middle: jia

last: You

address: 29 13th Street, TEDA

department: College of Biotechnology

institute: Tianjin             University of Science & Technology

data_processing:
Quality control of raw data。
Use SOAPaligner/SOAP2 software to compare with reference sequence
By counting the distribution and coverage of reads on the reference sequence, it is judged whether the comparison result passes the QC of alignment
Differentially expressed genes between samples were screened based on differentially expressed genes.Perform GO function enrichment analysis and pathway significant enrichment analysis
Genome_build: P. aeruginosa PAO1 (NC_002516.2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Pseudomonas aeruginosa

source_name: Bacteria

growth_protocol: Bacterial cultures were routinely incubated in LB medium supplemented with appropriate antibiotics at 37℃

extract_protocol:
The collected cells were treated with RNAprotect Bacteria Reagent (Qiagen) and subjected to snap freezing in liquid nitrogen and delivered to BGI in dry ice for transcriptome resequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: P. aeruginosa PAK-AR2 and 1-9 cells were grown to OD600 of 0.8 before harvesting。

tag: family

value: Pseudomonas

tag: genotype

value: mutants


title: PND5 Co Esr1 cKO 1

description: Gene expression from PND5 Co Esr1 cKO


title: PND5 Uteri Co Esr1 WT4


title: Anti-CD27 sample 2

description:
A3214_05
Activated CD8+ T cells

tag: cell type


title: PND5 Uteri Co Esr1 WT3


title: PND5 Uteri Co Esr1 WT1


title: MLL4 OG86

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

data_processing:
Reads were aligned to human genome hg38 using BWA-MEM (version 0.7.13) (http://bio-bwa.sourceforge.net/, using 16 threads and with -M set to flag shorter split hits as secondary) or Bowtie2 (version 2.2.1) (http://bowtie-bio.sourceforge.net/bowtie2/) using default settings. Reads were then filtered using Samtools (version 0.1.9) (Li et al., 2009) keeping only reads with alignment quality score >= 20. The number of uniquely mapped reads per sample was 50-100 million.
Reads were mapped relative to annotated genes (ENSEMBL v66) using the Annmap database, R and Bioconductor (Gentleman et al., 2004; Yates et al., 2007). MACS2 (Model-based Analysis of ChIP-seq, version 2.1.0) software was used to call peaks (Zhang et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files; browser-ready peak histograms for ChIP seq

source_name: THP1 cells

growth_protocol: THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in RPMI with 10% fetal bovine serum.

extract_protocol:
ChIPs for acetyl-H3K9 (ab4441), acetyl-H3K27 (ab4729)  (both from Abcam) RCOR1 (07-455 from Merck Millipore), SPI1 (2258 from Cell Signaling) and MLL4 (kindly provided by Dr Kai Ge; Wang et al., 2016) were performed using 50-100 million cells and the protocol of Lee et al. (2006).
ChIP DNA samples were prepared for sequencing using the Microplex Library Preparation Kit (Diagenode) and 1ng ChIP DNA. Libraries were size selected with AMPure beads (Beckman Coulter) for 200-800 base pair size range and quantified by Q-PCR using a KAPA Library Quantification Kit. ChIPseq data were generated using the NextSeq platform from Illumina with 2x75bp Mid Output.

tag: disease state

value: AML

tag: antibody


title: Anti-PD-1/L1 sample 2

description:
A3214_02
Activated CD8+ T cells

source_name: pmel1 CD8+ T cells from anti-PD-1/L1 treated mice


title: Combination sample 1

description:
A3214_07
Activated CD8+ T cells


title: Anti-PD-1/L1 sample 3

description:
A3214_03
Activated CD8+ T cells


title: PAK_AR2A


title: WT-DES 3

first: Yin

last: Li

address: 111 TW alexander Drive

description: Gene expression data from WT mouse SV DES group.

hyb_protocol: Five and one half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Expression Console Software (AGCC; Version 1.2) using the RMA algorithm to generate .CHP files.

source_name: WT mouse SVs DES group

label_protocol: Three hundred nanograms (300 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: The SV tissues were collected at week 10 from WT and aERKO mice in the control and DES groups.

treatment_protocol: For neonatal treatment, male pups were treated by subcutaneous injection with DES (Sigma Aldrich), dissolved in corn oil at 2 µg/pup/day on days 1-5 (day of birth = 1) (DES group) or an equal volume of corn oil (control group).

tag: strain/background

value: WT

value: male

value: seminal vesicles

value: DES


title: aERKO-veh 2

description: Gene expression data from αERKO mouse SV control group.

source_name: aERKO mouse SVs control group

value: estrogen receptor-alpha knockout

value: vehicle


title: WT-DES 2


title: WT-veh 3

description: Gene expression data from WT mouse SV control group.

source_name: WT mouse SVs control group


title: aERKO-veh 3


title: MLL4 DMSO

treatment_protocol: THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in RPMI with 10% fetal bovine serum.

value: MLL4 (kindly provided by Dr Kai Ge; Wang et al., 2016)

value: DMSO


title: aERKO-veh 1


title: aERKO-DES 1

description: Gene expression data from αERKO mouse SV DES group.

source_name: aERKO mouse SVs DES group


title: aERKO-DES 3


title: SPI1 OG86

value: SPI1 (2258 from Cell Signaling)


title: WT-DES 1


title: RCOR1 OG86

value: RCOR1 (07-455 from Merck Millipore)


title: WT-veh 1


title: H3K27Ac OG86

value: acetyl-H3K27 (ab4729)


title: aERKO-DES 2


title: H3K27Ac DMSO


title: RCOR1 DMSO


title: H3K9Ac OG86

value: acetyl-H3K9 (ab4441)


title: WT-veh 2


title: HepaRG_Methapyrilene-850uM_72hrs_replicate 3

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

description:
Gene expression in HepaRG cells treated with 850 uM of methapyrilene for 72 hours
HepaRG, Methapyrilene-850uM, 72hrs, replicate 3

hyb_protocol: 600 ng 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 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray (G4858A-072363) 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 (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

source_name: HepaRG, Methapyrilene-850uM, 72hrs

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

growth_protocol: The human liver HepaRG cell line was obtained from Biopredic International (Overland Park, Kansas), and the cells were maintained according to the manufacturer’s recommendations. Briefly, the cells were seeded at a density of 1.3 × 104 cells/cm2 and maintained in William’s E medium supplemented with growth additives for HepaRG cells (Biopredic International) for 14 days. The cells were then differentiated by adding a differentiation supplement (Biopredic International) for an additional 14 days. The medium was changed every other day.

extract_protocol: Total RNA was extracted from HepaRG cells using RNeasy Mini kits (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Twenty-eight days after the initial seeding, the terminally differentiated HepaRG cells were treated with AFB1 at doses 5 and 25 µM and and methapyrilene at doses 650 and 850 µM for 72 hours. Following the treatment, the cells were harvested by mild trypsinization, washed in phosphate-buffered saline, and immediately frozen at −80°C for subsequent analyses.

value: HepaRG cells

value: Female

value: Differentiated cells

tag: agent

value: Methapyrilene

tag: dose


title: Anti-PD-1/L1 sample 1

description:
A3214_01
Activated CD8+ T cells

value: CD8+ T cell


title: HepaRG_Methapyrilene-0uM_72hrs_control_replicate 1

description:
Gene expression in HepaRG cells treated with 0 uM of methapyrilene for 72 hours
HepaRG, Methapyrilene-0uM, 72hrs, control, replicate 1


title: HepaRG_Methapyrilene-650uM_72hrs_replicate 1

description:
Gene expression in HepaRG cells treated with 650 uM of methapyrilene for 72 hours
HepaRG, Methapyrilene-650uM, 72hrs, replicate 1

source_name: HepaRG, Methapyrilene-650uM, 72hrs


title: HepaRG_Methapyrilene-850uM_72hrs_replicate 1

description:
Gene expression in HepaRG cells treated with 850 uM of methapyrilene for 72 hours
HepaRG, Methapyrilene-850uM, 72hrs, replicate 1


title: HepaRG_Methapyrilene-650uM_72hrs_replicate 2

description:
Gene expression in HepaRG cells treated with 650 uM of methapyrilene for 72 hours
HepaRG, Methapyrilene-650uM, 72hrs, replicate 2


title: HepaRG_Methapyrilene-0uM_72hrs_control_replicate 2

description:
Gene expression in HepaRG cells treated with 0 uM of methapyrilene for 72 hours
HepaRG, Methapyrilene-0uM, 72hrs, control, replicate 2


title: HepaRG_Methapyrilene-850uM_72hrs_replicate 2

description:
Gene expression in HepaRG cells treated with 850 uM of methapyrilene for 72 hours
HepaRG, Methapyrilene-850uM, 72hrs, replicate 2


title: HepaRG_Methapyrilene-0uM_72hrs_control_replicate 3

description:
Gene expression in HepaRG cells treated with 0 uM of methapyrilene for 72 hours
HepaRG, Methapyrilene-0uM, 72hrs, control, replicate 3


title: WT_Input_1

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description: whole bacterial cells

data_processing:
Adapter removal and filtering were performed using cutadapt 1.15. Quality threshold for trimming was set to 20. Reads that after adapter removal and quality trimming we shorter than 36 bp were removed.
ChIP-seq reads were aligned to the Pseudomonas aeruginosa PAO1 (NC_2516.2) genome assembly using Bowtie2 version NC_2516.2 using default option for paired-end reads.
Coverage files were generated using bamCoverage 2.5.0 with normaliztion to 1x sequencing depth (RPGC). Effective genome size was set to 6264404 bp. Scores represent coverage of individual basepairs in the genome, without smoothing.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: Processed files in bigwig format represent normalized coverages of individual basepairs in the P. aeruginosa PAO1 genome.

growth_protocol: P. aeruginosa strains were taken from a deep-frozen stock (WT, parS1-4, parS2+, parSnull and parBnull) spread on L agar plates and grown overnight at 37oC. To obtain ParB overproducing cells (ParBplus), WT cells were transformed with pKGB9 (araC-araBADp-parB) [Kawalek et al., 2017] and cells containing the plasmid were selected on L agar plates supplemented with 150 μg ml-1 chloramfenicol. Four independent overnight cultures for each strain inoculated from single colonies were diluted 1:100 in fresh L -broth (50 ml media in 250ml flask closed with a cotton plug) and grown with at 37oC with shaking (200 rpm). PAO1161/pKGB9 transformats were grown in medium supplemented with 75 μg ml-1 chloramphenicol and 0.02% arabinose to induce the expression of parB. Bacteria were grown in L-broth until exponential phase (OD600 =0.5). Two cultures with most similar OD600 were combined and used as one biological replicate.

extract_protocol:
Cells were fixed with formaldehyde washed and resuspended in lysis buffer, followed by sonication to obtain DNA fragments with an average fragment lengthsize 250-350. Cleared lysates were incubated with affinity purified polyclonal rabbit anti-ParB antibodies, followed by recovery of antibody-ParB-DNA conjugates using protein A coupled with magnetic beads. Complexes were decrosslinked and  the ChIP DNA was purified using a MinElute PCR purification kit.
Libraries were prepared according to NEB instructions accompanying the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB, E7370S). The libraries were sequenced using HiSeq4000 (Illumina) in the PE100 mode.

tag: growth phase

value: exponential

tag: chip antibody

value: rabbit polyclonal anti-ParB [Bartosik et al., 2004]


title: parBnull_ChIP_2

description: whole bacterial cells

source_name: cells with parB disruption, mock-IP control

value: PAO1161 parBnull


title: HepaRG_AFB1-25uM_72hrs_replicate 2

description:
Gene expression in HepaRG cells treated with 25 uM of AFB1 for 72 hours
HepaRG, AFB1-25uM, 72hrs, replicate 2

source_name: HepaRG, AFB1-25uM, 72hrs


title: parBnull_ChIP_1

description: whole bacterial cells


title: HepaRG_AFB1-25uM_72hrs_replicate 1

description:
Gene expression in HepaRG cells treated with 25 uM of AFB1 for 72 hours
HepaRG, AFB1-25uM, 72hrs, replicate 1


title: parSnull_ChIP_2

description: whole bacterial cells

source_name: cells with 10 modified parS sequences

value: PAO1161 parSnull


title: parSnull_ChIP_1

description: whole bacterial cells


title: parS1-4_ChIP_2

description: whole bacterial cells

source_name: cells with modified parS1 - parS4 sequences

value: PAO1161 parSmut15


title: HepaRG_AFB1-5uM_72hrs_replicate 3

description:
Gene expression in HepaRG cells treated with 5 uM of AFB1 for 72 hours
HepaRG, AFB1-5uM, 72hrs, replicate 3

source_name: HepaRG, AFB1-5uM, 72hrs


title: parS2plus_ChIP_2

description: whole bacterial cells

source_name: cells with 9 modified parS sequences; unmodified parS2

value: PAO1161 parSmut28


title: parS1-4_ChIP_1

description: whole bacterial cells


title: HepaRG_AFB1-0uM_72hrs_control_replicate 4

description:
Gene expression in HepaRG cells treated with 0 uM of AFB1 for 72 hours
HepaRG, AFB1-0uM, 72hrs, control, replicate 4

source_name: HepaRG, AFB1-0uM, 72hrs, control


title: M2 macrophages,miR1246 inhib., biological rep2

city: Bethesda

first: Ana

middle: I

last: Robles

state: MD

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

description: Gene expression data from macrophages transfected with miR-1246 inhibitor

hyb_protocol: Four replicates of each group were hybridized to Affymetrix mouse (human) Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.

scan_protocol: Wash and stain were performed on Affymetrix Fluidics Station 450 and scanned on Affymetrix GeneChip scanner 3000.

data_processing: The data were analyzed with BRBarrayTools settings with RMA normalization and general background correction.

label: total RNA

source_name: macrophages

label_protocol: Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: Blood was obtained from healthy donors. PBMCs from buffy coats were isolated. Subsequently, PBMCs underwent negative selection for CD14 Monocytes. Selected monocytes were then seeded in M2-activation medium . After 6 days additional boost of fresh media were added together with  IL-4 (50ng/ml) . After 3 more days (day 9) media were replaced and cytokines were added as in day 6.

extract_protocol: RNA was isolated using the miRNeasy Micro Kit (QIagen) according to manufactures protocol. RNA was quantified using a Nanodrop ND-1000 (Thermo Fischer Scientific) and Bioanalyser (Agilent).

treatment_protocol: Mature M2 macrophages were transfected with either mimic or inhibitor using the Lipofectamin RNAiMAX reagent according to manufacturer instructions.

tag: tissue

value: M2 macrophages

tag: polarization state

value: M2 like


title: M2 macrophages,miR1246 mimic, biological rep2

description: Gene expression data from macrophages transfected with miR-1246 mimic


title: M2 macrophages, control, biological rep2

description: Gene expression data from macrophages transfected with scramble control


title: HepaRG_AFB1-5uM_72hrs_replicate 2

description:
Gene expression in HepaRG cells treated with 5 uM of AFB1 for 72 hours
HepaRG, AFB1-5uM, 72hrs, replicate 2

tag: gender


title: HepaRG_AFB1-0uM_72hrs_control_replicate 3

description:
Gene expression in HepaRG cells treated with 0 uM of AFB1 for 72 hours
HepaRG, AFB1-0uM, 72hrs, control, replicate 3


title: M2 macrophages,miR1246 mimic, biological rep1


title: M2 macrophages,miR1246 inhib., biological rep1


title: M2 macrophages, control, biological rep1


title: HepaRG_AFB1-0uM_72hrs_control_replicate 2

description:
Gene expression in HepaRG cells treated with 0 uM of AFB1 for 72 hours
HepaRG, AFB1-0uM, 72hrs, control, replicate 2


title: parS2plus_ChIP_1

description: whole bacterial cells

tag: strain


title: HepaRG_AFB1-0uM_72hrs_control_replicate 1

description:
Gene expression in HepaRG cells treated with 0 uM of AFB1 for 72 hours
HepaRG, AFB1-0uM, 72hrs, control, replicate 1


title: ParBplus_ChIP_2

description: whole bacterial cells

source_name: ParB overproducing cells

value: PAO1161 pKGB9 (araBADp_parB)


title: Placenta_stressed_Pool#2

city: Munich

first: Mira

middle: Alexandra

last: Jakovcevski

state: Bavaria

address: Kraepelin Str. 2-10

department: Stress Neurobiology and Neurogentics

country: Germany

institute: Max Planck Institute of Psychiatry

hyb_protocol: According to instructions

scan_protocol: Slides were scanned directly after washing

data_processing: The bioinformatic analysis was performed using the Limma (Liniar Models for MicroArray Data) package which is part of the Bioconductor software (http://bioconductor.org). We corrected the background with the Normexp method, used the Loess method for the within arrays normalization and the Aquantile for between arrays normalization. A linear model was applied in order to find the differentially expressed genes (a simple Bayesian model).

source_name: placenta stressed mother 2

label_protocol: Cy3 according to instructions

growth_protocol: Samples were collected on GD17.5 by cesarian section

extract_protocol: Purification of total RNA containing miRNAs done using Tri Reagent (MRC Inc., Cincinnati, OH) according to the manufacturer’s recommendations. gDNA was removed using Turbo DNAse digestion in solution, followed by heat deactivation (#AM2238, Thermo Fisher Scientific).

treatment_protocol: From gestation day (GD) 1.5 until GD16.5, pregnant females were exposed to a chronic variable mild stress protocol, including 2 short manipulations during the dark phase and a further overnight (ON) manipulation during the light phase. The chosen stressors did not induce pain and did not directly influence maternal food intake or weight gain and were repeated on a weekly basis. The short stressors included multiple cage changes, cage tilt, white noise, water in cage or no bedding for 2 periods of 2 hours, immobilization in a tube or elevated platform for 30 minutes and swim stress in warm water for 15min. Overnight manipulations included illumination, saturated bedding (with water), novel object (marbles) and overcrowding.

value: placenta

tag: condition

value: stressed

value: female (mother and pups)


title: Placenta_stressed_Pool#4

source_name: placenta stressed mother 4


title: Placenta_stressed_Pool#3

source_name: placenta stressed mother 3


title: Placenta_stressed_Pool#1

source_name: placenta stressed mother 1


title: Placenta_control_Pool#4

source_name: placenta control mother 4

value: control


title: ParBplus_ChIP_1

description: whole bacterial cells


title: WT_ChIP_2

description: whole bacterial cells

source_name: WT cells


title: Combination sample 3

description:
A3214_09
Activated CD8+ T cells

source_name: pmel1 CD8+ T cells from anti-PD-1/L1 and anti-CD27 treated mice

tag: treatment

value: anti-PD-1/L1 and anti-CD27


title: WT_ChIP_1

description: whole bacterial cells


title: Placenta_control_Pool#2

source_name: placenta control mother 2


title: Placenta_control_Pool#1

source_name: placenta control mother 1


title: Placenta_control_Pool#3

source_name: placenta control mother 3


title: Hoxd4-Liver_WT-Batch3-ZT20-WT-S229

status: Public on Mar 26 2018

city: Lausanne

first: Felix

last: Naef

address: AAB 040 Station 15

department: Bioengineering

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description:
4CSeq of Liver_WT of mice
processed_4Cseq_log10_counts_around_the_clock.txt.gz

data_processing:
Library strategy: 4C-Seq
mm9
Mapping was done using HTS station (http://htsstation.epfl.ch). See Supplemental methods of paper for detailed processing methods. In brief, read counts were normalized by total counts on the cis chromosome. For each fragment, we fit a weighted linear model with a Gaussian window of 2.5kb in order to incorporate signal from neighboring fragments.
Log10 4CSeq signal (value A with variance Avar). Processed formats show fragments within +/- 2MB of the bait. Zscore and p-value represent differential contacts between liver and kidney

source_name: Crosslinked genomic DNA

extract_protocol: Liver and kidney nuclei were prepared as previously described (Ripperger and Schibler 2006) with some minor changes.         In brief, liver and kidneys from individual animals were homogenized and fixed in 4ml of PBS including 1.5percent formaldehyde for 10 minutes at room temperature.         Cross-linking reaction was stopped by adding 25 ml of ice-cold stop reaction buffer (2.2 M sucrose; 150 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         to the homogenates and kept 5 minutes on ice. Homogenates were then loaded on top of 10 ml cushion buffer (2.05 M sucrose; 10 % glycerol; 125 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         and centrifuged for 45 minutes at 105g at  4degC. Nuclei were washed twice in PBS and immediately frozen.

tag: feeding

value: Ad libitum

tag: age

value: post-natal 8-12 weeks

value: WT


title: Hoxd4-Liver_WT-Batch3-ZT12-WT-S225

tag: genotype


title: Hoxd4-Liver_WT-Batch3-ZT0-WT-S231


title: Hoxd4-Liver_WT-Batch3-ZT0-WT-S210


title: Gys2_TSS-Liver_WT-Batch3-ZT4-WT-S512


title: Hoxd4-Liver_WT-Batch3-ZT8-WT-S235


title: Gys2_TSS-Liver_WT-Batch3-ZT8-WT-S507


title: Hoxd4-Liver_WT-Batch3-ZT20-WT-S241


title: Hoxd4-Liver_WT-Batch3-ZT0-WT-S219


title: Gys2_TSS-Liver_WT-Batch3-ZT8-WT-S502


title: Hoxd4-Liver_WT-Batch3-ZT8-WT-S223


title: Hoxd4-Liver_WT-Batch3-ZT16-WT-S215


title: Hoxd4-Liver_WT-Batch3-ZT12-WT-S237


title: Hoxd4-Liver_WT-Batch3-ZT4-WT-S221


title: Hoxd4-Liver_WT-Batch3-ZT16-WT-S227


title: Hoxd4-Liver_WT-Batch3-ZT4-WT-S233


title: Gys2_TSS-Liver_WT-Batch3-ZT8-WT-S513


title: Gys2_TSS-Liver_WT-Batch3-ZT4-WT-S506


title: Hoxd4-Liver_WT-Batch3-ZT8-WT-S213


title: Gys2_TSS-Liver_WT-Batch3-ZT20-WT-S516


title: Hoxd4-Liver_WT-Batch3-ZT16-WT-S239


title: Hoxd4-Liver_WT-Batch3-ZT20-WT-S217


title: Gys2_TSS-Liver_WT-Batch3-ZT20-WT-S510


title: Gys2_TSS-Liver_WT-Batch3-ZT20-WT-S504


title: Gys2_TSS-Liver_WT-Batch3-ZT0-WT-S505


title: Gys2_Exon8-Liver_WT-Batch3-ZT20-WT-S520


title: Gys2_TSS-Liver_WT-Batch3-ZT12-WT-S508


title: Gys2_Exon8-Liver_WT-Batch3-ZT4-WT-S522


title: Gys2_TSS-Liver_WT-Batch3-ZT12-WT-S514


title: Gys2_Exon8-Liver_WT-Batch3-ZT12-WT-S524


title: Gys2_Exon8-Liver_WT-Batch3-ZT8-WT-S523


title: Gys2_TSS-Liver_WT-Batch3-ZT0-WT-S501


title: Gys2_Exon8-Liver_WT-Batch3-ZT8-WT-S518


title: Gys2_Exon8-Liver_WT-Batch3-ZT16-WT-S531


title: Gys2_Exon8-Liver_WT-Batch3-ZT4-WT-S528


title: Gys2_Exon8-Liver_WT-Batch3-ZT20-WT-S532


title: Gys2_Exon8-Liver_WT-Batch3-ZT20-WT-S526


title: Gys2_TSS-Liver_WT-Batch3-ZT0-WT-S511


title: Gys2_Exon8-Liver_WT-Batch3-ZT0-WT-S517


title: Cry1_UP-Liver_WT-Batch3-ZT8-WT-S414


title: Gys2_Exon8-Liver_WT-Batch3-ZT0-WT-S521


title: Gys2_Exon8-Liver_WT-Batch3-ZT0-WT-S527


title: Gys2_TSS-Liver_WT-Batch3-ZT16-WT-S515


title: Cry1_UP-Liver_WT-Batch3-ZT8-WT-S426


title: Gys2_TSS-Liver_WT-Batch3-ZT16-WT-S503


title: Gys2_Exon8-Liver_WT-Batch3-ZT16-WT-S519


title: Gys2_Exon8-Liver_WT-Batch3-ZT16-WT-S525


title: Gys2_Exon8-Liver_WT-Batch3-ZT12-WT-S530


title: Gys2_TSS-Liver_WT-Batch3-ZT16-WT-S509


title: Gys2_Exon8-Liver_WT-Batch3-ZT8-WT-S529


title: Cry1_UP-Liver_WT-Batch3-ZT4-WT-S424


title: Cry1_UP-Liver_WT-Batch3-ZT8-WT-S404


title: Cry1_UP-Liver_WT-Batch3-ZT20-WT-S408


title: Cry1_UP-Liver_WT-Batch3-ZT12-WT-S416


title: Cry1_UP-Liver_WT-Batch3-ZT4-WT-S412


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S415

description:
4CSeq of Liver_Cry1intronKO of mice
processed_4Cseq_log10_counts_around_the_clock.txt.gz


title: Cry1_UP-Liver_WT-Batch3-ZT16-WT-S418


title: Cry1_UP-Liver_WT-Batch3-ZT20-WT-S432


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S427


title: Cry1_UP-Liver_WT-Batch3-ZT16-WT-S406


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S405


title: Cry1_UP-Liver_WT-Batch3-ZT0-WT-S410


title: Cry1_UP-Liver_WT-Batch3-ZT0-WT-S422


title: Cry1_UP-Liver_WT-Batch3-ZT20-WT-S420


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S403


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S413


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S425


title: Cry1_UP-Liver_WT-Batch3-ZT16-WT-S430


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S433


title: Cry1_UP-Liver_WT-Batch3-ZT0-WT-S401


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S409


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S419


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S431


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S421


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S407


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S429


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S423


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S411


title: Cry1_TSS-Liver_WT-Batch3-ZT8-WT-S326


title: Cry1_TSS-Liver_WT-Batch3-ZT8-WT-S304


title: Cry1_TSS-Liver_WT-Batch3-ZT4-WT-S324


title: Cry1_TSS-Liver_WT-Batch3-ZT4-WT-S312


title: Cry1_TSS-Liver_WT-Batch3-ZT8-WT-S314


title: H3K9Ac DMSO

source_name: THP1 cells

value: AML

value: acetyl-H3K9 (ab4441)

value: DMSO


title: Cry1_TSS-Liver_WT-Batch3-ZT20-WT-S308


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S402


title: HepaRG_AFB1-5uM_72hrs_replicate 1

description:
Gene expression in HepaRG cells treated with 5 uM of AFB1 for 72 hours
HepaRG, AFB1-5uM, 72hrs, replicate 1

source_name: HepaRG, AFB1-5uM, 72hrs

tag: cell line

value: HepaRG cells

value: Female

value: Differentiated cells


title: Cry1_TSS-Liver_WT-Batch3-ZT20-WT-S320


title: Cry1_TSS-Liver_WT-Batch3-ZT16-WT-S318


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S327


title: Cry1_TSS-Liver_WT-Batch3-ZT16-WT-S306


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S305


title: Cry1_TSS-Liver_WT-Batch3-ZT12-WT-S316


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S325


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S313


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT8-Cry1intronKO-S315


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT4-Cry1intronKO-S303


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S333


title: Cry1_UP-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S417


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S309


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT20-Cry1intronKO-S321


title: Cry1_TSS-Liver_WT-Batch3-ZT20-WT-S332


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S319


title: HepaRG_AFB1-25uM_72hrs_replicate 3

description:
Gene expression in HepaRG cells treated with 25 uM of AFB1 for 72 hours
HepaRG, AFB1-25uM, 72hrs, replicate 3

source_name: HepaRG, AFB1-25uM, 72hrs


title: Cry1_TSS-Liver_WT-Batch3-ZT12-WT-S328


title: Cry1_TSS-Liver_WT-Batch3-ZT16-WT-S330


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S307


title: Rep1_vehicle_ATACSeq

city: Baltimore

first: Hyun Jun

last: Jung

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Adapter sequences were trimmed for both forward and reverse reads using cutadapt (-q 30 --minimum-length 36 --paired-output) and aligned on mouse reference genome mm10 using bowtie2 (-q -X 2000 --no-mixed --no-discordant).
Convert format from Sam to Bam and index the files using Samtools: Samtools view –bhS sample.sam > sample.bam, samtools sort sample.bam sample.sorted; samtools index sample.sorted.bam.
Duplicates were removed from mapped reads using Picard.
Bam files were converted to Bed files using Bedtools. Reads were shifted 4 bp for the forward reads and 5 bp for the reverse reads. Peaks were identified using MACS2 (-q 0.01 --nomodel --shift -37 --extsize 73 --keep-dup -SPMR).
BigWig files for UCSC browser tracks were generated using UCSC bedClip and bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files and bed files including MACS2 peaks

source_name: mpkCCD cells

growth_protocol: Cultured mouse mpkCCD (clone 11) cells were grown and maintained in complete medium, DMEM/F12 containing 2% dialyzed serum and supplements (5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin), as previously described (Yu MJ, Proc Natl Acad Sci U S A 106:2441-2446, 2009).

extract_protocol:
ATAC-Seq was performed following a method published by Buenrostro et al. (Nat Methods. 2013, PMID: 24097267). Briefly, a homogenous single cell suspension was prepared by harvesting cells using a cell scraper and a cell strainer in cold PBS buffer. 50,000 cells were centrifuged at 500×g for 5 min, 4°C and washed with 50 μl of cold PBS buffer. The plasma membrane was lysed in 50 μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and centrifuged immediately at 500×g for 10 min, 4°C to obtain nuclei.
The nuclear pellets were reacted in the transposition reaction mixture of 1X Tagment DNA Buffer (FC-121-1030, Illumina) and Tn5 transposase (FC-121-1030, Illumina) for 30 min at 37°C. DNA was purified using a Qiagen MinElute PCR Purification Kit (QIAGEN). The transposed DNA fragments were amplified in the PCR mixture containing a specific index adapter (Illumina standard index adapter) for each sample by PCR. Amplified libraries were purified using a AMPure beads (1:1.8 ratio, BECKMAN COULTER). Libraries were quantified using a Qubit® dsDNA High-Sensitivity Assay Kit (Q32854, Life Technologies). Fragment size distribution was tested on E-Gel (2%, Invtrogen). DNA libraries were sequenced on an Illumina HiSeq 3000 platform (50 bp, Paired-end) by the NHLBI DNA Sequencing and Genomics Core, NHLBI.

treatment_protocol: For dDAVP treatment, cells were transferred to permeable supports (24mm, 0.4um pore, Corning #3450), and grown until confluency as documented transepithelial resistance measurements (Epithelial Volt ohmmeter; WPI). At that point, the complet medium was changed to serum- and hormone-free medium. Cells were incubated with the V2 receptor-selective vasopressin analog dDAVP (0.1 nM) or its vehicle and harvested after 30 minutes.

tag: cell type

value: cultured mouse cortical collecting duct cells (mpkCCD)

tag: passages

value: Kidney

value: vehicle


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S329


title: HumanOmni2.5 NPF3

type: genomic

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Copy numbers were estimated using circular binary segmentation (CBS) [PMID: 15475419] to translate intensity measurements into regions of equal copy number. The raw array data was processed using crlmm (v1.25.1) [PMID: 19661241] for background correction and normalization, accounting for batch effects.The resulting log R ratios were then smoothed to remove outliers prior to segmentation (R package DNAcopy). All analyses were carried out in R3.1.2 (www.r-project.org).
Tab delimited text files - LogR ratio (LRR), B allele frequency (BAF) and genotype calls (1=AA, 2=AB, 3=BB)

source_name: NPF

growth_protocol: Prostate tissue was chopped into small pieces, approximately 2 mm3, and digested overnight at 37°C in RPMI containing 10% fetal calf serum (FCS), 25 mM HEPES, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.5 mg/mL fungizone, 100 mg/mL gentamicin, 225 U/mL Collagenase Type I and 125 U/mL Hyaluronidase Type II (Sigma Aldrich) as previously described [PMID: 23558784]. Cell suspensions were seeded in RPMI containing 5% FCS, penicillin/streptomycin, 1 nM testosterone (Sigma Aldrich) and 10 ng/mL bFGF (Millipore), a medium that selects for fibroblasts compared to other prostatic cell types. Cells were grown at 37°C in a humidified incubator with 5% O2 and 5% CO2. The first passage of cells typically reached confluency within 2 weeks. The cells were used between passages 2-6.

extract_protocol: DNA was extracted from CAF and NPF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Eluates were precipitated with 0.1 volume sodium acetate and 2.5 volumes ethanol and then resuspended in nuclease-free water. DNA was quantified using a NanoDrop 2000.  200ng of DNA was quantified using the Illumina HumanOmni2.5-8 Beadchip (Illumina, CA, USA)

treatment_protocol: Cells were cultured in standard media to approximately 80% confluency before being trypsinised, resuspended in media and then centrifuged to create cell pellets. Cells were stored at -80°C until DNA extraction.

tag: patient

value: Male

value: Prostate

value: Normal Prostate Fibroblast


title: Rep2_dDAVP_ATACSeq

tag: agent

value: dDAVP


title: HumanOmni2.5 CAF3

source_name: CAF

value: Cancer Associated Fibroblast


title: HumanOmni2.5 CAF4


title: Rep1_dDAVP_ATACSeq


title: HumanOmni2.5 CAF1


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT12-Cry1intronKO-S317

value: Ad libitum


title: HumanOmni2.5 NPF1


title: HumanOmni2.5 NPF4


title: Rep2_vehicle_ATACSeq


title: HumanOmni2.5 NPF2


title: HumanOmni2.5 CAF2


title: HuGene-1.0_NPF7

hyb_protocol: Standard Affymetrix protocol

data_processing: Data was divided into 2 datasets and processed separately: dataset 1 containing data from patients 1,2,3 and 5, and dataset 2 containing data from patients 4,6 and 7. CEL files were RMA normalized using Oligo (version 1.30.0) [PMID: 20688976] and probeset mappings to Ensembl Gene IDs were obtained from BioMart (ENSEMBL version 74) [PMID: 22083790].

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase I digestion. RNA concentration and integrity was assessed on an Agilent Bioanalyzer 2100 using the Eukaryote Total RNA Nano Chip (Agilent).  RNA (500 ng) was quantified using the Affymetrix Human Gene 1.0 ST Array

treatment_protocol: Cells were cultured in standard media to approximately 80% confluency before being trypsinised, resuspended in media and then centifuged to create cell pellets. Cells were stored at -80°C until RNA extraction.


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT16-Cry1intronKO-S331

value: post-natal 8-12 weeks


title: HuGene-1.0_NPF3


title: HuGene-1.0_NPF6


title: HuGene-1.0_NPF4


title: SPI1 DMSO

tag: disease state

tag: antibody

value: SPI1 (2258 from Cell Signaling)


title: HuGene-1.0_CAF6


title: HuGene-1.0_CAF7


title: HuGene-1.0_NPF5


title: HuGene-1.0_CAF3


title: HuGene-1.0_NPF1


title: HuGene-1.0_CAF4


title: HuGene-1.0_CAF2


title: B276

status: Public on Mar 25 2018

city: Los Angeles

first: Alice

last: Mouton

state: CA

address: 610 Charles E. Young Dr. East

department: Ecology and Evolutionary Biology

institute: UCLA

description:
regressed_normalized_counts.txt
normalizedcounts.txt
rawcounts_genelength_gccontent.txt

data_processing:
Filtering and quality:  Raw sequences were processed using Trim Galore! 0.3.1 to remove Illumina adapters and filter out sequences that did not meet the quality thresholds (q > 20, length > 25 bp).
Alignment : Alignment of reads was performed on TOPHAT2 2.1.0  using the domestic cat (Felis catus) as a reference genome (Ensembl release 85.62; ftp://ftp.ensembl.org/pub/release-82/fasta/felis_catus/dna/Felis_catus.Felis_catus_6.2.dna.toplevel.fa.gz) . To maximize the number of unique reads mapped to the reference genome, we used the following parameters: read mismatches 10, max-insertion-length 12, read-edit-dist 22.
Counts: Aligned reads were converted to raw counts using HTSEQ (Anders  et al., 2014) with the “union” mode, resulting in alignment to 21,890 genes.
Normalization: After removal of three globin-related genes (ENSFCAG00000030531, ENSFCAG00000031043,ENSFCAG00000022139) with high expression levels prior to normalization, values for the remaining 21,887 genes were normalized using the trimmed mean of M-values (TMM) method in the edgeR package (Robinson & Oshlack, 2010) in R and adjusted for gene length and GC content using custom Python scripts and the package CQN in R (Hansen et al., 2012).
Differential expression: We performed principal components analysis to identify and remove technical factors from the expression data (Figure S3). Gene by gene linear mixed models were used to identify differentially expressed genes in AR-positive bobcats using the limma package in R (Ritchie et al., 2015). We adjusted our significance values to account for multiple hypothesis testing using the false discovery rate (FDR) method as implemented in the qvalue package in R (Storey  et al., 2015) and selected genes falling below Q < 0.05
Genome_build: Felis catus (Ensembl release 85.62)
Supplementary_files_format_and_content: Tab-delimited text file including the regressed normalized counts on 12333 genes.
normalizedcounts.txt
rawcounts_genelength_gccontent.txt

organism: Lynx rufus

source_name: Blood sample

extract_protocol:
Total RNA was extracted from 0.5 mL whole blood using the Ambion Mouse RiboPure Blood extraction kit, followed by globin removal using the Ambion GlobinClear Mouse kit (Life Technologies, Inc). RNA was quantified on the Agilent bioanalyzer (Agilent Technologies, USA).
Each sample was uniquely tagged with custom index sequences developed at UCLA (Faircloth et al., 2014) comparable to Illumina TruSeq tags.  Individual sample libraries were then pooled in equimolar ratios, with 13 or 14 samples per pool and each pool sequenced on two lanes of an Illumina HiSeq 2500 or HiSeq 4000 sequencer

tag: ar detection (0=neg;1=pos)

value: blood


title: B273

tag: tissue


title: HuGene-1.0_CAF5


title: B270


title: B271


title: B269


title: B281


title: B267


title: B266


title: HuGene-1.0_CAF1


title: B265


title: B261


title: B264


title: B253


title: B252


title: B263


title: B251


title: B259


title: B260


title: B250


title: B249


title: B244


title: B243


title: HM450 CAF4

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: Raw intensity data (IDAT) files were imported into R using the minfi package (version 1.12.0) [PMID: 24478339]. Data was divided into 2 datasets: dataset 1 containing data from patients 1-4, and dataset 2 containing data from patients 5-7. The datasets were processed separately in minfi using functional normalisation (preprocessFunnorm) with background and dye bias correction [PMID: 25599564].  Poor quality probes with a detection p-value >0.05 or bead count <3 in at least one sample were removed.  To reduce the risk of false discoveries we removed probes that mapped to multiple locations or repeat regions as identified by Naeem and colleagues [PMID: 24447442]. The resulting datasets comprised 409,693 CpG sites and 410,970 CpG sites, for datasets 1 and 2 respectively. β values were calculated from unmethylated (U) and methylated (M) signal [M/(U + M + 100)] and ranged from 0 to 1 (0 to 100% methylation).

label: Cy5 and Cy3

extract_protocol: DNA was extracted from CAF and NPF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Eluates were precipitated with 0.1 volume sodium acetate and 2.5 volumes ethanol and then resuspended in nuclease-free water. DNA was quantified using a NanoDrop 2000.

treatment_protocol: Cells were cultured in standard media to approximately 80% confluency before being trypsinised, resuspended in media and then centifuged to create cell pellets. Cells were stored at -80°C until DNA extraction.


title: B242B


title: B241B


title: B228


title: B232


title: B236


title: B224


title: B226


title: B237


title: B220


title: HM450 CAF3


title: HM450 NPF6


title: HM450 CAF5


title: HM450 CAF7


title: B218


title: HM450 NPF7


title: B217


title: B216


title: B215


title: HM450 NPF2


title: B240


title: B214


title: B238


title: B282


title: B272


title: B222


title: B298


title: B233


title: B206


title: B219


title: B268


title: B208


title: RASC0509 48h pre-ctr

city: Nagasaki

first: Naoki

last: Iwamoto

state: Nagasaki

address: 1-7-1 Sakamoto

department: Immunology and Rheumatology

institute: Nagasaki University

description: fibroblast cells, rheumatoid arthritis, obtained at the time of orthopedic surgery

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/μg cRNA) was fragmented at 60 °C for 30 min in a reaction volume of 25 μL containing 1X Agilent fragmentation buffer and 2X Agilent blocking agent following the manufacturers’ instructions. On completion of the fragmentation reaction, 25 μL of 2X Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray Kit (G4851B) for 17 h at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 min at room temperature with GE Wash Buffer 1 (Agilent Technologies, Santa Clara, CA) and 1 min with 37 °C GE Wash buffer 2 (Agilent Technologies, Santa Clara, CA).

scan_protocol: slides were scanned on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61 × 21 mm, Scan resolution 3 μm, Dye channel set to Green and Green PMT set to 100 %).

data_processing: The data were analyzed by GeneSpring software version 12.6.1(Agilent Technologies, Santa Clara, CA). The raw signals were log transformed and normalized using the Percentile shift normalization method, the value was set at 75th percentile.

source_name: fibroblast-like synovial cells from rheumatoid arthritis

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, and then purified by RNeasy Mini Kit (Qiagen, Valencia, CA) purification. Dye incorporation and cRNA yield were checked with the Nanodrop 1000 (Thermo Fisher Scientific, Waltham, MA).

extract_protocol: A mirVana miRNA Isolation kit was used for isolation of total RNA (Ambion/Applied Biosystems).

treatment_protocol: Transfection with synthetic precursor miR-218 (sample2), with inhibitors of miR-218 (sample4), or with scrambled controls (Pre-miR (sample1)/Anti-miR Negative Control #1(sample3); Ambion/Applied Biosystems, Foster City, CA) at a final concentration of 100 nM with the use of Lipofectamine 2000 reagent (Invitrogen, Carlsbad, CA, USA).

value: fibroblast cells

value: rheumatoid arthritis

value: scrambled control


title: B204


title: HM450 NPF4


title: RASC0509 48h pre-218

value: synthetic precursor miR-218


title: RASC0509 48h anti-218

value: inhibitors of miR-218


title: RASC0509 48h anti-ctr

value: Anti-miR Negative Control


title: HM450 NPF1


title: HM450 CAF2


title: HM450 CAF6


title: HM450 CAF1


title: B200


title: HM450 NPF5


title: B194


title: B191


title: B193


title: B201


title: Sp-OR flies 1

status: Public on Mar 24 2018

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

institute: University of Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt v.1.8. Reads matching to rRNA sequences were removed with fastq_screen v. 0.9.3. Remaining reads were further filtered for low complexity with reaper v. 15-065.
Reads were aligned against the Spiroplasma poulsonii MSRO (v2) genome using STAR v. 2.5.2b
The number of read counts per gene locus was summarized with htseq-count v. 0.6.1 using Spiroplasma poulsonii MSRO (v2) gene annotation.
Genome_build: Spiroplasma poulsonii MSRO (accession: JTLV02000000)
Supplementary_files_format_and_content: Tab-delimited text files include htseq gene counts for each sample.

organism: Spiroplasma poulsonii

source_name: In host Spiroplasma

extract_protocol:
RNA was extracted from (i) the hemolymph of 30 1-week-old infected flies and (ii) 20 ml of 4-month-old in vitro culture pelleted by 30 min of centrifugation at 16,000 X g by the TRIzol method following the manufacturer’s instructions. Three independent replicates were prepared for each condition.
RNA quality was assessed on a Fragment Analyzer (Advanced Analytical Technologies, Inc., Ankeny, IA, USA. RNA-seq libraries were prepared using 25 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) without the polyA selection step.

value: MSRO

tag: host age

value: 1 week

value: hemolymph


title: Sp-OR flies 2


title: Sp-OR flies 3


title: HuGene-1.0_NPF2

tag: gender

value: Male

value: Prostate


title: AKBA rep1

city: Shanghai

first: Jing

last: Bai

state: Shanghai

address: 280# South Chongqing Road

department: School of Medicine

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.8
Adapter sequences were removed by using SeqPrep, and then poor quality reads filtered by sickle(version 1.200) for quality control
Quality filtered reads were then mapped to GRCm38 using Hiast2(v2.1.0)
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
GO functional enrichment and KEGG pathway analysis were carried out by Goatools  and KOBAS
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file of expression analysis result of  EdgeR and annotation

source_name: mouse epidermis

extract_protocol:
Epidermis was separated from dermis with Dispase II (BD Biosciences). Total RNA was extracted using TRIzol® Reagent (Invitrogen).
RNA libraries were prepared for sequencing using TruSeq RNA library Prep Kit (Illumina) according to the protocol.

value: AKBA gel

value: epidermis of mouse skin

tag: strain background

value: wild type


title: AKBA rep2


title: AKBA rep3


title: Control rep1

value: Control gel


title: Control rep2


title: Vitamine D depletion diet, biological replicate #1

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rat GE 4*44K V3 Microarray  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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters .  Data treatment was performed with bioconductor and Limma library. Background substraction was performed using the Normexp correction with offset =50. Quantile normalization was then applied.  Features flagged in Feature Extraction as control, as Feature Non-uniform outliers, saturating or too weak were excluded.

organism: Rattus norvegicus

source_name: plantaris skeletal muscle

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

extract_protocol: RNA was extracted with Trizol (Life Technologies) 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).

tag: strain

value: Wistar

tag: diet

value: depletion and repletion of vitamin D in the diet


title: Vitamine D depletion followed by repletion diet, biological replicate #3


title: Control diet, biological replicate #4

value: control diet (1000UI/Kg vit D)


title: Vitamine D depletion followed by repletion diet, biological replicate #1


title: Vitamine D depletion diet, biological replicate #2

value: Vitamin D depletion diet


title: Culture 3

source_name: In vitro cultured Spiroplasma


title: Vitamine D depletion diet, biological replicate #3


title: Vitamine D depletion diet, biological replicate #4


title: Vitamine D depletion followed by repletion diet, biological replicate #2


title: Control diet, biological replicate #3


title: Culture 2


title: Vitamine D depletion followed by repletion diet, biological replicate #4


title: liver-Refed 3-rep 3

city: Guangzhou

first: jirong

last: jia

address: No.135 Xingang West Road

institute: Sun Yat-sen university

hyb_protocol: Each Slide was hybridized with 1.65μg 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.

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).

organism: Danio rerio

source_name: liver, refed for 15 days

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).

growth_protocol: Female zebrafish that approximately 3 months old were bought from the local aquarium market, randomly allocated to tanks (24 L capacity) with stocking density of 30 individuals per tank. The tanks were supplied with flow-through water at 28 ± 1°C and a photoperiod maintained at constant 12 h/day (8 a.m.-8 p.m.). Zebrafish were fed twice daily for 2 weeks as acclimation.

extract_protocol: Total liver RNA was prepared with TRIzol according to the manufacturer’s protocol (Life Technologies, USA).RNA quantity and purification was determined by optical density measurements (OD260/280) and RNA integrity by using the bioanalyzer 2100 (Agilent technologies, USA).

treatment_protocol: zebrafish were starved for 3 weeks. When the fasting ended, food was re-supplied twice daily.

value: liver

value: female

value: 3 month old

tag: treatment

value: refed for 15 days


title: liver-Refed 3-rep 2

tag: age


title: liver-Refed 2-rep 2

source_name: liver, refed for 10 days

value: refed for 10 days


title: liver-Refed 2-rep 3


title: Control diet, biological replicate #2


title: liver-Refed 3-rep 1


title: Control rep3

tag: genotype


title: Control diet, biological replicate #1


title: NCP2

city: Yichang

last: Yang

address: Jijin Road

institute: China Three Gorges Corporation

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt[1]（version 1.9.1）to be high quality clean data.
With the the unigene sequence file as a reference gene file, RSEM[3](v1.2.6) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq[4] Bioconductor package, a model based on the negative binomial distribution.
GO-TermFinder was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05.
We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Acipenser sinensis

source_name: Palate tissue

extract_protocol:
Palates were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Palate

value: 4 months

tag: population

value: Artificial population


title: Vitamine D depletion diet, biological replicate #5


title: Culture 1

value: MSRO


title: NCP1


title: NCP3


title: CP3


title: liver-Refed 2-rep 1


title: Vitamine D depletion diet, biological replicate #6


title: liver-Refed1-rep 1

source_name: liver, refed for 3 days

value: refed for 3 days


title: CP2


title: liver-Refed1-rep 2


title: liver-fasted-rep 2

source_name: liver, fasted for 3 weeks

value: fasted for 3 weeks


title: pMH9783

status: Public on Mar 23 2018

city: Cambridge

first: Shristi

last: Pandey

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

data_processing:
Reads were aligned to a reference genome (Zv10 ensembl) using Tophat v2.0.10
Expression levels were quantified using RSEM v1.2.28 (inferred counts and tpm values)
Genome_build: Zv10
Supplementary_files_format_and_content: text file with tab delimiters

source_name: Danio Rerio, 10days post fertilization

extract_protocol:
Dissociated brains were FAC sorted into 96 well plates(single cells) containing lysis buffer
Smart-seq2 (Picelli et al., Nature Methods, 2014)

value: brain

tag: cell type

value: 10days post fertilization habenula


title: pMH9784


title: CP1


title: liver-control-rep 4

source_name: liver, continuously fed

value: continuously fed


title: pMH9779


title: pMH9780


title: liver-fasted-rep 3


title: liver-Refed1-rep 3


title: pMH9776


title: pMH9781


title: pMH9777


title: liver-control-rep 3


title: liver-fasted-rep 1


title: pMH9773


title: pMH9772


title: pMH9774


title: pMH9775


title: liver-control-rep 2


title: pMH9782


title: pMH9768


title: liver-control-rep 1


title: pMH9771


title: pMH9770


title: pMH9769


title: pMH9766


title: pMH9778


title: pMH9763


title: pMH9765


title: pMH9764


title: pMH9761


title: pMH9762


title: pMH9760


title: pMH9759


title: pMH9757


title: pMH9758


title: pMH9756


title: pMH9755


title: pMH9753


title: pMH9754


title: pMH9767


title: pMH9752


title: pMH9750


title: pMH9748


title: pMH9749


title: pMH9743


title: pMH9746


title: pMH9742


title: pMH9745


title: pMH9744


title: pMH9747


title: pMH9740


title: pMH9738


title: pMH9739


title: pMH9737


title: pMH9732


title: pMH9733


title: pMH9734


title: pMH9736


title: pMH9735


title: pMH9730


title: pMH9731


title: pMH9728


title: pMH9751


title: pMH9727


title: pMH9726


title: pMH9725


title: pMH9724


title: pMH9723


title: pMH9741


title: pMH9722


title: pMH9719


title: pMH9721


title: pMH9717


title: pMH9716


title: pMH9713


title: pMH9715


title: pMH9712


title: pMH9711


title: pMH9714


title: pMH9710


title: pMH9709


title: pMH9706


title: pMH9707


title: pMH9729


title: pMH9704


title: pMH9703


title: pMH9705


title: pMH9702


title: pMH9701


title: pMH9698


title: pMH9718


title: pMH9700


title: pMH9696


title: pMH9695


title: pMH9720


title: pMH9694


title: pMH9692


title: pMH9691


title: pMH9697


title: pMH9690


title: pMH9708


title: pMH9693


title: pMH9688


title: pMH9687


title: pMH9686


title: pMH9683


title: pMH9682


title: pMH9684


title: pMH9679


title: pMH9681


title: pMH9680


title: pMH9677


title: pMH9676


title: pMH9699


title: pMH9678


title: pMH9675


title: pMH9674


title: pMH9670


title: pMH9672


title: pMH9669


title: pMH9666


title: pMH9668


title: pMH9689


title: pMH9673


title: pMH9664


title: pMH9662


title: pMH9665


title: pMH9685


title: pMH9663


title: pMH9661


title: pMH9660


title: pMH9657


title: pMH9656


title: pMH9655


title: pMH9653


title: pMH9652


title: pMH9651


title: pMH9654


title: pMH9650


title: pMH9648


title: pMH9671


title: pMH9667


title: pMH9647


title: pMH9645


title: pMH9642


title: pMH9646


title: pMH9639


title: pMH9641


title: pMH9643


title: pMH9644


title: pMH9640


title: pMH9659


title: pMH9635


title: pMH9637


title: pMH9633


title: pMH9632


title: pMH9636


title: pMH9658


title: pMH9626


title: pMH9631


title: pMH9629


title: pMH9630


title: pMH9627


title: pMH9649


title: pMH9625


title: pMH9624


title: pMH9623


title: pMH9622


title: HM450 NPF3

value: Male

value: Prostate

value: Normal Prostate Fibroblast


title: pMH9638


title: pMH9621


title: pMH9634


title: pMH9618


title: pMH9619


title: pMH9617


title: pMH9611


title: pMH9615


title: pMH9612


title: pMH9628


title: pMH9614


title: pMH9616


title: pMH9620


title: pMH9613


title: pMH9608


title: pMH9609


title: pMH9604


title: pMH9605


title: pMH9610


title: pMH9602


title: pMH9599


title: pMH9601


title: pMH9600


title: pMH9598


title: pMH9603


title: pMH9597


title: pMH9606


title: pMH9607


title: pMH9596


title: pMH9595


title: pMH9594


title: pMH9593


title: pMH9592


title: pMH9590


title: pMH9591


title: pMH9588


title: pMH9589


title: pMH9587


title: pMH9586


title: pMH9585


title: pMH9584


title: pMH9583


title: pMH9580


title: pMH9581


title: pMH9582


title: pMH9579


title: pMH9575


title: pMH9574


title: pMH9576


title: pMH9573


title: pMH9571


title: pMH9570


title: pMH9567


title: pMH9572


title: pMH9568


title: pMH9569


title: pMH9566


title: pMH9564


title: pMH9565


title: pMH9563


title: pMH9562


title: pMH9561


title: pMH9559


title: pMH9558


title: pMH9560


title: pMH9556


title: pMH9553


title: pMH9554


title: pMH9578


title: pMH9577


title: pMH9550


title: pMH9549


title: pMH9555


title: pMH9546


title: pMH9548


title: pMH9551


title: pMH9545


title: pMH9547


title: pMH9542


title: pMH9544


title: pMH9540


title: pMH9539


title: pMH9541


title: pMH9538


title: pMH9543


title: pMH9557


title: pMH9537


title: pMH9533


title: pMH9531


title: pMH9532


title: pMH9530


title: pMH9534


title: pMH9552


title: pMH9536


title: pMH9529


title: pMH9526


title: pMH9525


title: pMH9523


title: pMH9524


title: pMH9528


title: pMH9522


title: pMH9520


title: pMH9527


title: pMH9518


title: pMH9517


title: pMH9521


title: pMH9512


title: pMH9516


title: pMH9519


title: pMH9513


title: pMH9514


title: pMH9515


title: pMH9511


title: pMH9508


title: pMH9535


title: pMH9510


title: pMH9509


title: pMH9506


title: pMH9505


title: pMH9503


title: pMH9502


title: pMH9504


title: pMH9500


title: pMH9501


title: pMH9498


title: pMH9497


title: pMH9494


title: pMH9499


title: pMH9492


title: pMH9487


title: pMH9484


title: pMH9495


title: pMH9490


title: pMH9488


title: pMH9485


title: pMH9483


title: pMH9482


title: pMH9507


title: pMH9478


title: pMH9479


title: pMH9480


title: pMH9481


title: pMH9475


title: pMH9476


title: pMH9486


title: pMH9474


title: pMH9496


title: pMH9489


title: pMH9493


title: pMH9471


title: pMH9473


title: pMH9472


title: pMH9470


title: pMH9468


title: pMH9467


title: pMH9491


title: pMH9466


title: pMH9465


title: pMH9464


title: pMH9463


title: pMH9461


title: pMH9462


title: pMH9460


title: pMH9459


title: pMH9457


title: pMH9458


title: pMH9456


title: pMH9455


title: pMH9477


title: pMH9453


title: pMH9452


title: pMH9451


title: pMH9469


title: pMH9449


title: pMH9448


title: pMH9447


title: pMH9454


title: pMH9443


title: pMH9446


title: pMH9442


title: pMH9450


title: pMH9445


title: pMH9440


title: pMH9439


title: pMH9438


title: pMH9437


title: pMH9444


title: pMH9441


title: pMH9434


title: pMH9436


title: pMH9435


title: pMH9433


title: pMH9432


title: pMH9430


title: pMH9429


title: pMH9428


title: pMH9427


title: pMH9426


title: pMH9424


title: pMH9425


title: pMH9420


title: pMH9421


title: pMH9423


title: pMH9422


title: pMH9417


title: pMH9418


title: pMH9416


title: pMH9414


title: pMH9410


title: pMH9411


title: pMH9412


title: pMH9407


title: pMH9409


title: pMH9415


title: pMH9431


title: pMH9405


title: pMH9404


title: pMH9406


title: gng_p9_h9

description: HHKCVBGXY.RSEM.genes


title: pMH9403


title: pMH9402


title: gng_p9_h8

description: HHKCVBGXY.RSEM.genes


title: pMH9401


title: gng_p9_h6

description: HHKCVBGXY.RSEM.genes


title: pMH9419


title: gng_p9_h5

description: HHKCVBGXY.RSEM.genes


title: gng_p9_h4

description: HHKCVBGXY.RSEM.genes


title: pMH9413


title: gng_p9_h2

description: HHKCVBGXY.RSEM.genes


title: gng_p9_h3

description: HHKCVBGXY.RSEM.genes


title: gng_p9_h12

description: HHKCVBGXY.RSEM.genes


title: gng_p9_h10

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g8

description: HHKCVBGXY.RSEM.genes


title: gng_p9_h11

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g9

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g6

description: HHKCVBGXY.RSEM.genes


title: pMH9408


title: gng_p9_g5

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g2

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g3

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f6

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f5

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f3

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g12

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g1

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f4

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g11

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f7

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f11

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f2

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e8

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e5

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e6

description: HHKCVBGXY.RSEM.genes


title: gng_p9_h1

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g7

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g4

description: HHKCVBGXY.RSEM.genes


title: gng_p9_g10

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f9

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e9

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e4

description: HHKCVBGXY.RSEM.genes


title: gng_p9_h7

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f10

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e2

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f12

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f1

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e3

description: HHKCVBGXY.RSEM.genes


title: gng_p9_f8

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e1

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e11

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e7

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d8

description: HHKCVBGXY.RSEM.genes