title: CNE2 cells, cshcontrol rep3

status: Public on Sep 30 2023

type: SRA

city: Nantong

first: Siyu

last: Zhang

address: Xisi Road 20

country: China

institute: Affiliated Hospital of Nantong University

library_source: transcriptomic

data_processing:
The process of transcriptome sequencing experiments includes RNA extraction, RNA sample quality testing by Agilent bioanalyzer 2100, library construction, library purification by Beckman Agencourt AMPure XP beads, library detection, library quantification by Agilent bioanalyzer 2100& Qubit, sequencing cluster generation, and machine sequencing.
Supplementary files format and content: tab-delimited text file includes RPKM values for each Samples; FPKM_Sample1 = cshcontrol; FPKM_Sample2 = 31shHAX-1.

molecule: total RNA

organism: Homo sapiens

source_name: nasopharyngeal tissue

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, USA) .
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

tag: tissue

value: nasopharyngeal tissue

tag: cell line

tag: cell type

value: nasopharyngeal carcinoma


title: CNE2 cells, 31shHAX-1 rep2


title: CNE2 cells, 31shHAX-1 rep3


title: MUTZ3 - RNA-seq  - Empty vector Rep1

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 with the settings --no-eamss --mismatches 1
Transcript abundance was quantified using Salmon v0.3.1 for pseudoalignment against RefSeq gene transcripts of the hg38 human reference build
Assembly: hg38
Supplementary files format and content: quant.sf contain transcript abundance and transcripts per million (TPM) quantified by Salmon

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: MUTZ3 cells were cultured in αMEM with 20% FCS and 20% conditioned 5637 medium

extract_protocol:
Total RNA was isolated by phenol chloroform extraction followed by DNase digestion. The SuperScript II Reverse Transcriptase kit (Invitrogen) was used for synthesis of cDNA.
The cDNA was sheared with the Covaris device and further processed according to the TruSeq RNA Sample Preparation v2 Guide (Illumina)

treatment_protocol: Samples were transduced with a retroviral construct containg either of these three: a) PLDLS peptide that inhibits interaction between EVI1 and CTBP proteins, a PLASS peptide that has no such effect, an empty vector.

value: Bone marrow

value: acute myelomonocytic leukemia

tag: genotype

tag: treatment

tag: timepoint

tag: replicate


title: MUTZ3 - RNA-seq  - PLASS control Rep2


title: CNE2 cells, cshcontrol rep2


title: CNE2 cells, cshcontrol rep1


title: HeLa S3 PCIF1 siRNA#2_rep1

type: RNA

city: Toyama

first: Yutaka

last: Hirose

state: Toyama

address: 2630 Sugitani

department: Graduate School of Medicine and Pharmaceutical Sciences

country: Japan

institute: University of Toyama

description: HeLa S3 cells transfected with PCIF1 siRNA#2

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

label: biotin

source_name: human cervical cancer cell line HeLa S3

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: HeLa S3 cells were cultured in DMEM medium supplemented with 10% calf serum at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted using a NucleoSpin column kit (TAKARA) and treated with DNase I (Promega) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.5 and 10.

treatment_protocol: HeLa S3 cells were seeded on 6-well plates at 1.0 × 105 cell/well and cultured at 37°C 24 h before transfection. Cells were transfected with either negative control siRNA or two different siRNAs specific to human PCIF1 gene using Lipofectamine RNAi MAX (ThermoFisher) and further cultured for 72 h at 37°C.

value: HeLa S3

tag: transfection

value: PCIF1 siRNA#2


title: CNE2 cells, 31shHAX-1 rep1


title: MUTZ3 - RNA-seq  - Empty vector Rep2


title: HeLa S3 PCIF1 siRNA#2_rep2


title: HeLa S3 PCIF1 siRNA#1_rep1

description: HeLa S3 cells transfected with PCIF1 siRNA#1

value: PCIF1 siRNA#1


title: Liver biopsy, EN3 and EN4

city: Shanghai

first: Xiaoqi

last: YU

address: No.197 Ruijin 2nd Road

institute: Ruijin Hospital

description: Fresh frozen spatial transcriptome sequencing

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the 10xGenomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to human hg38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

source_name: Liver biopsy

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit acccording to manufacturer's construction

value: Liver biopsy

tag: disease state

value: HBeAg-negative CHB (EN3 and EN4)

tag: antiviral treatment

value: Untreated (EN2 and EN4)


title: Liver biopsy, EP2 and SL2

value: HBeAg-positive CHB (EP2) and HBsAg loss (SL2)

value: Untreated (EP2) and on-treatment (SL2)


title: MUTZ3 - RNA-seq  - PLDLS treated Rep2

value: PLDLS


title: LHSAR, RNA-Seq, rep1

city: Badalona

first: François

middle: José

last: Serra

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Institut de Recerca Contra la Leucèmia Josep Carreras-IJC

description: Data generated for: https://pubmed.ncbi.nlm.nih.gov/33785741/

data_processing:
HiChIP reads were mapped with Bowtie2
HiChIP loops called with FitHiChIP version 5.1
HiChIP loops were filtered considering only those overlapping H3K27ac ChIP-seq peaks in both loop-ends
HiChIP loops were prioritized using ad-hoc processing (see methods)
RNA-seq data were processed using the VIPER pipeline. Reads were aligned with STAR. FPKM values were calculated with Cufflinks for 20,114 RefSEQ genes included in the VIPER repository. Differential expression analysis was performed with the DESeq2 R package
Chip-seq data was aligned with BWA.
Chip-seq peaks were called with MACS2
Assembly: GRCh37
Supplementary files format and content: HiChIP-loop files contain, in tsv format, the coordinates of the promoter anchor, the coordinates of the enhancer anchor, and the gene name corresponding to the promoter anchor

source_name: prostate

growth_protocol: Hormone-depleted LNCaP cells (ATCC CRL-1740) were grown in phenol red free RPMI (#11835030, GIBCO) with 10% charcoal stripped FBS (#100-119, GemBio) for 3 day.

extract_protocol:
RNA from 5 million cells was extracted using the miRNeasy Micro Kit (#217084, Qiagen) coupled with on-column DNAse I treatment (#79254, Qiagen). RNA sample concentration and its trace were evaluated using a Bioanalyzer RNA 6000 Nano kit (#5067-1511, Agilent) to submit them to Novogene RNA seq dept which prepped RNA library.
The library was for RNA seq sequenced to a target depth of 40 M reads on an Illumina platform HiSeq® 2500 with pair-end 150 bp reads. Read alignment, quality control and data analyses were performed using VIPER 57.

value: prostate

value: LHSAR

value: prostate epithelial cells


title: HeLa S3 PCIF1 siRNA#1_rep2


title: MUTZ3 - RNA-seq  - PLASS control Rep1


title: LHSAR, RNA-Seq, rep2


title: MUTZ3 - RNA-seq  - PLDLS treated Rep1


title: Liver biopsy, OT3 and OT4

value: HBeAg-positive CHB (OT3) and HBeAg-negative CHB (OT4)

value: On-treatment (OT3 and OT4)


title: Liver biopsy, OT5 and OT6

value: HBeAg-positive CHB (OT6) and HBeAg-negative CHB (OT5)

value: On-treatment (OT5 and OT6)


title: LHSAR, H3K27ac, ChIP-Seq, rep2

library_source: genomic

molecule: genomic DNA

extract_protocol:
12 million cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched. Cells were collected in lysis buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS and protease inhibitor [#11873580001, Roche] in PBS).43 Chromatin was sonicated to 300–800 bp with Covaris E220 sonicator (140PIP, 5% duty cycle, 200 cycle burst). H3K27ac antibody (C15410196, Diagenode, 1:600 ratio) was incubated with 40 μL of Dynabeads protein A/G (Invitrogen) for at least 6 h before immunoprecipitation with the sonicated chromatin overnight. Chromatin was washed with LiCl wash buffer (100 mM Tris [pH 7.5], 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) six times for 10 min each time.
Eluted sample DNA was prepared as the sequencing libraries with the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced with 150-base pair end reads on the Illumina platform HiSeq® 2500 at Novogene.


title: LNCaP, RNA-Seq, rep2

value: LNCaP

value: Human prostate adenocarcinoma


title: HeLa S3 negative control siRNA_rep1

description: HeLa S3 cells transfected with negative control siRNA

value: HeLa S3

value: negative control siRNA


title: HeLa S3 negative control siRNA_rep2


title: Liver biopsy, EP4 and SL3

value: Liver biopsy

value: HBeAg-positive CHB (EP4) and HBsAg loss (SL3)

value: Untreated (EP4 and SL3)


title: Liver biopsy, OT1 and OT2

value: HBeAg-positive CHB (OT1) and HBeAg-negative CHB (OT2)

value: On-treatment (OT1 and OT2)


title: Liver biopsy, EP1 and EN1

value: HBeAg-positive (EP1) and HBeAg-negative chronic HBV infection(EN1)

value: Untreated (EP1 and EN1)


title: Liver biopsy, EN2 and SL1

value: HBeAg-negative CHB (EN2) and HBsAg loss (SL1)

value: Untreated (EN2) and on-treatment (SL1)


title: Liver biopsy, EP3 and EN5

value: HBeAg-positive CHB (EP3) and HBeAg-negative CHB (EN5)

value: Untreated (EP3 and EN5)


title: LHSAR, H3K27ac ,HiChIP, rep3

data_processing:
HiChIP reads were mapped with Bowtie2
HiChIP loops called with FitHiChIP version 5.1
HiChIP loops were filtered considering only those overlapping H3K27ac ChIP-seq peaks in both loop-ends
HiChIP loops were prioritized using ad-hoc processing (see methods)
RNA-seq data were processed using the VIPER pipeline. Reads were aligned with STAR. FPKM values were calculated with Cufflinks for 20,114 RefSEQ genes included in the VIPER repository. Differential expression analysis was performed with the DESeq2 R package
Chip-seq data was aligned with BWA.
Chip-seq peaks were called with MACS2
Assembly: GRCh37
Supplementary files format and content: HiChIP-loop files contain, in tsv format, the coordinates of the promoter anchor, the coordinates of the enhancer anchor, and the gene name corresponding to the promoter anchor
Library strategy: HiChIP

extract_protocol:
Trypsinized 10 million cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched. Sample was lysed in HiChIP lysis buffer and digested with MboI (NEB) for 4 h. After 1 h of biotin incorporation with biotin dATP, the sample was ligated with T4 DNA ligase for 4 h and chipped with H3K27ac antibody (DiAGenode, C1541019) after chromatin. Reverse-crossed IP sample was pulled down with streptavidin C1 beads (Life Technologies) treated with Transposase (Illumina).
Library was amplified with reasonable cycle numbers based on the qPCR with 5-cycle pre-amplified library. Library was sequenced with 150-base pair end reads on the Illumina platform HiSeq® 2500 (Novogene).

value: prostate

value: LHSAR

value: prostate epithelial cells


title: LNCaP, H3K27ac ,HiChIP, rep5

description: data generated for: https://pubmed.ncbi.nlm.nih.gov/34822763/

value: LNCaP

value: Human prostate adenocarcinoma


title: LNCaP, RNA-Seq, rep1


title: LHSAR, H3K27ac ,HiChIP, rep4


title: LNCaP, H3K27ac, ChIP-Seq, rep1

extract_protocol:
10 million cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched. Cells were collected in lysis buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS and protease inhibitor [#11873580001, Roche] in PBS).43 Chromatin was sonicated to 300–800 bp with Covaris E220 sonicator (140PIP, 5% duty cycle, 200 cycle burst). H3K27ac antibody (C15410196, Diagenode, 1:600 ratio) was incubated with 40 μL of Dynabeads protein A/G (Invitrogen) for at least 6 h before immunoprecipitation with the sonicated chromatin overnight. Chromatin was washed with LiCl wash buffer (100 mM Tris [pH 7.5], 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) six times for 10 min each time.
Eluted sample DNA was prepared as the sequencing libraries with the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced with 150-base pair end reads on the Illumina platform HiSeq® 2500 at Novogene.


title: LHSAR, H3K27ac ,HiChIP, rep1


title: LNCaP, H3K27ac ,HiChIP, rep2


title: LNCaP, H3K27ac ,HiChIP, rep3


title: HeLa-P22077

city: Chungju-si

first: Ji-Hong

last: Lim

state: Chungcheongbuk-do

address: 268 Chungwon-daero

country: South Korea

institute: Konkuk University

data_processing:
Raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Homo sapiens using HISAT v2.1.0.
The reference genome sequence and annotation data were downloaded from the NCBI
Transcript assembly of known transcripts was processed by StringTie v2.1.3b
Expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample
Assembly: GRCh38
Supplementary files format and content: Excel file includes FPKM for each sample

source_name: Cervix

growth_protocol: Cells were cultured in DMEM containing 10% fetal bovine serum and penicillin/streptomycin, 20% O2 and 5% CO2

extract_protocol:
Total RNA was extracted by using TRIzol(Invitrogen) and 10ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO or P22077 20uM for 3h in 10%FBS containing DMEM

value: Cervix

value: HeLa

value: Cervix Epithelial cells

value: WT


title: HeLa-DMSO

value: DMSO 3h


title: LNCaP, H3K27ac ,HiChIP, rep1


title: H1299-DMSO

source_name: Lung

value: Lung

value: Lung Adenocarcinoma cells


title: H1299-P22077


title: LHSAR, H3K27ac ,HiChIP, rep2


title: 61

city: Beijing

first: Liu

middle: xue

last: ting

address: Dongzhimen

institute: China Academy of Chinese Medical Science

data_processing:
Use fastp software to clean and filter the original offline data to obtain high-quality sequences (Clean Reads)
Use Hisat2 software to compare Clean Reads with reference genes (the reference genome version is GRnor_6.0.100)
Stringtie 1.3.3b software was used to compare the results and quantify the transcriptome expression; Normalize with TMM (trimmed mean of M values) algorithm, and finally calculate FPKM (Fragments PerKilobase Million) value of each gene
Differential analysis of gene expression between samples/groups using edgeR 3.30.3 software package
Assembly: GRnor_6.0.100
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: synovium

extract_protocol:
RNA was harvested using RNeasy Mini Kit （250） Qiagen#74106.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: synovium

tag: strain

value: Lewis

value: NC


title: 6

value: AIA


title: 59


title: 56


title: 27

value: TZG


title: 30


title: 4


title: 10


title: NC rep 3

city: Guangzhou

first: jinfeng

last: fu

state: Guangdong

address: Wushan Street

department: School of Food Science and Engineering

institute: South China University of Technology

data_processing:
Illumina Casava 1.7 software used for baswcalling
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or loe-quality sequence, the mapped to mm8 whole genome using bowtie V0.12.2 with parameters
reads per kilobase of exon per megabase of library size (RPKM) wrer calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, Exons from all isoforms
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: kidney

extract_protocol:
kidney was removed, flash-frozen in liquid nitrogen, and stored at -80 ° C,A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® following the manufacturer’s recommendations

value: kidney

value: male

value: 23weeks old

value: health

value: the normal control, fed with water


title: MP rep 2

value: diabetic

value: the treatment group, fed with the medium doses of plantain flour


title: LNCaP, H3K27ac ,HiChIP, rep4

value: prostate

value: LNCaP

value: Human prostate adenocarcinoma


title: NH rep 3

value: the normal control, fed with the high doses of plantain flour


title: NC rep 2


title: NH rep 1


title: LHSAR, H3K27ac, ChIP-Seq, rep1

extract_protocol:
11 million cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched. Cells were collected in lysis buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS and protease inhibitor [#11873580001, Roche] in PBS).43 Chromatin was sonicated to 300–800 bp with Covaris E220 sonicator (140PIP, 5% duty cycle, 200 cycle burst). H3K27ac antibody (C15410196, Diagenode, 1:600 ratio) was incubated with 40 μL of Dynabeads protein A/G (Invitrogen) for at least 6 h before immunoprecipitation with the sonicated chromatin overnight. Chromatin was washed with LiCl wash buffer (100 mM Tris [pH 7.5], 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) six times for 10 min each time.
Eluted sample DNA was prepared as the sequencing libraries with the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced with 150-base pair end reads on the Illumina platform HiSeq® 2500 at Novogene.

value: LHSAR

value: prostate epithelial cells


title: MP rep 1


title: NH rep 2


title: LP rep 3

value: the treatment group, fed with the low doses of plantain flour


title: 23

value: synovium

value: Lewis


title: LP rep 2


title: NC rep 1


title: MP rep 3


title: HP rep 1

value: the treatment group, fed with the high doses of plantain flour


title: DM rep 3

value: kidney

value: the diabetic control, fed with water


title: HP rep 2

value: male

value: 23weeks old


title: DM rep 2


title: DM rep 1


title: atac-seq_bat_control_male_8w_biological_rep4_vial_90237016904

city: Stanford

first: Euan

last: Ashley

state: CA

address: 870 Quarry Road

country: USA

institute: Stanford University

description: motrpac_pass1b-06_t69-brown-adipose_epigen-atac-seq_counts.txt.gz

data_processing:
Pooled libraries were sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) to a target depth of 35 million read pairs (70 million paired-end reads) per sample using a paired-end 50 base-pair run configuration
Reads were demultiplexed with bcl2fastq2 (v2.20.0) (Illumina, San Diego, CA, USA)
Data was processed with the ENCODE ATAC-seq pipeline (v1.7.0) (https://github.com/ENCODE-DCC/atac-seq-pipeline)
Samples from a single sex and training time point, e.g., males trained for 2 weeks, were analyzed together as biological replicates in a single workflow
Briefly, adapters were trimmed with cutadapt v2.5 and aligned to release 96 of the Ensembl Rattus norvegicus (rn6) genome with Bowtie 2 v2.3.4.3
Duplicate reads and reads mapping to the mitochondrial chromosome were removed
12 Signal files and peak calls were generated using MACS2 v2.2.4, both from reads from each sample and pooled reads from all biological replicates
Pooled peaks were compared with the peaks called for each replicate individually using Irreproducibility Discovery Rate and thresholded to generate an optimal set of peaks
The cloud implementation of the ENCODE ATAC-seq pipeline and source code for the post-processing steps are available at https://github.com/MoTrPAC/motrpac-atac-seq-pipeline
Optimal peaks (overlap.optimal_peak.narrowPeak.bed.gz) from all workflows were concatenated, trimmed to 200 base pairs around the summit, and sorted and merged with bedtools v2.29.0 to generate a master peak list
This peak list was intersected with the filtered alignments from each sample using bedtools coverage with options -nonamecheck and -counts to generate a peak by sample matrix of raw counts.
Assembly: rn6
Supplementary files format and content: Raw read counts matrix of the number of reads aligning to the genomic region per merged consensus ATAC-seq peak per tissue/phase.

source_name: ATAC-seq of Rat Male Brown Adipose Powder Control - 8 weeks

extract_protocol:
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed at Stanford University and the Icahn School of Medicine at Mount Sinai. Only Stanford ATAC-seq data were used in this manuscript. Nuclei from aliquoted tissue samples (30 mg for white adipose, 15 mg for brown adipose, 10 mg for hippocampus, kidney, lung, gastrocnemius, heart, and liver tissues) were extracted using the Omni-ATAC protocol with modifications. Two tissue-specific consortium reference standards were included for sample processing QC. The white adipose, brown adipose, and hippocampus tissues were processed using no-douncing nuclei extraction to prevent fat droplets from interfering with the subsequent transposition steps. Tissue powder was incubated in the homogenization buffer for 10 min at 4C. The tube was inverted every 2-3 minutes. The heart, liver, kidney, lung, and gastrocnemius tissues were processed using the Omni-ATAC protocol with modifications. Tissue powder was incubated in the homogenization buffer for 5 minutes on ice and dounced 10 times using pestle A and 20 times with pestle B. For both protocols, the homogenate passed through a 40 µm cell strainer to collect nuclei. Nuclei were stained with DAPI and counted using an automated cell counter. 50,000 nuclei (or max. 500 µl nuclei) were added to 1 ml ATAC-RSB buffer and spun at 1000 g for 10 minutes, and the supernatant was removed. The nuclei pellet was resuspended in 50 µl of transposition mixture and incubated at 37C for 30 minutes with 1000 rpm shaking. The transposed DNA was purified using Qiagen MinElute Purification kits (Qiagen # 28006).
The DNA product was amplified using NEBnext High-Fidelity 2x PCR Master Mix (NEB, M0541L) and custom indexed primers. 1.8x SPRIselect beads were used to clean the PCR reaction and obtain the ATAC-seq library for sequencing.

value: Brown Adipose Powder

value: Control - 8 weeks


title: atac-seq_bat_training_male_8w_biological_rep2_vial_90222016904

source_name: ATAC-seq of Rat Male Brown Adipose Powder Training - 8 weeks

value: Training - 8 weeks


title: atac-seq_bat_training_male_8w_biological_rep1_vial_90218016904


title: atac-seq_bat_training_male_8w_biological_rep4_vial_90225016904


title: atac-seq_bat_control_male_8w_biological_rep3_vial_90232016904


title: atac-seq_bat_training_male_8w_biological_rep3_vial_90223016904


title: atac-seq_bat_control_female_8w_biological_rep1_vial_90245016904

source_name: ATAC-seq of Rat Female Brown Adipose Powder Control - 8 weeks


title: atac-seq_bat_control_male_8w_biological_rep5_vial_90239016904


title: atac-seq_bat_control_male_8w_biological_rep2_vial_90229016904


title: atac-seq_bat_training_male_8w_biological_rep5_vial_90227016904


title: LP rep 1

value: diabetic


title: atac-seq_wat_training_female_2w_biological_rep4_vial_90585017011

description: motrpac_pass1b-06_t70-white-adipose_epigen-atac-seq_counts.txt.gz

source_name: ATAC-seq of Rat Female White Adipose Powder Training - 2 weeks

value: White Adipose Powder

value: Training - 2 weeks


title: atac-seq_wat_training_female_2w_biological_rep3_vial_90581017011


title: atac-seq_wat_training_female_2w_biological_rep5_vial_90587017011


title: atac-seq_wat_training_female_1w_biological_rep1_vial_90559017011

source_name: ATAC-seq of Rat Female White Adipose Powder Training - 1 week

value: Training - 1 week


title: HP rep 3


title: atac-seq_wat_training_female_1w_biological_rep5_vial_90571017011


title: atac-seq_wat_training_female_2w_biological_rep2_vial_90578017011


title: atac-seq_wat_training_female_1w_biological_rep4_vial_90567017011


title: atac-seq_wat_training_female_2w_biological_rep1_vial_90576017011


title: atac-seq_wat_training_female_1w_biological_rep3_vial_90564017011


title: atac-seq_wat_training_male_2w_biological_rep1_vial_90439017011

source_name: ATAC-seq of Rat Male White Adipose Powder Training - 2 weeks


title: atac-seq_wat_training_male_2w_biological_rep2_vial_90441017011


title: atac-seq_wat_training_male_2w_biological_rep3_vial_90444017011


title: atac-seq_wat_training_male_1w_biological_rep5_vial_90430017011

source_name: ATAC-seq of Rat Male White Adipose Powder Training - 1 week


title: atac-seq_wat_training_female_1w_biological_rep2_vial_90560017011


title: atac-seq_wat_training_male_1w_biological_rep3_vial_90423017011


title: atac-seq_wat_training_male_4w_biological_rep5_vial_90292017011

source_name: ATAC-seq of Rat Male White Adipose Powder Training - 4 weeks

value: Training - 4 weeks


title: atac-seq_wat_training_male_1w_biological_rep1_vial_90421017011


title: atac-seq_wat_training_female_4w_biological_rep2_vial_90410017011

source_name: ATAC-seq of Rat Female White Adipose Powder Training - 4 weeks


title: atac-seq_wat_training_female_4w_biological_rep5_vial_90420017011


title: atac-seq_wat_training_male_2w_biological_rep4_vial_90449017011


title: atac-seq_wat_training_male_1w_biological_rep2_vial_90422017011


title: atac-seq_wat_training_female_4w_biological_rep3_vial_90412017011


title: atac-seq_wat_training_female_4w_biological_rep4_vial_90416017011


title: atac-seq_wat_training_male_4w_biological_rep2_vial_90281017011


title: atac-seq_wat_training_female_4w_biological_rep1_vial_90406017011


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title: atac-seq_heart_training_male_1w_biological_rep1_vial_90421015802


title: atac-seq_kidney_control_female_8w_biological_rep5_vial_90266015904


title: atac-seq_heart_training_female_4w_biological_rep4_vial_90416015802

source_name: ATAC-seq of Rat Female Heart Powder Training - 4 weeks


title: atac-seq_heart_training_female_4w_biological_rep5_vial_90420015802


title: atac-seq_heart_training_female_4w_biological_rep1_vial_90406015802


title: atac-seq_heart_training_male_4w_biological_rep4_vial_90289015802

source_name: ATAC-seq of Rat Male Heart Powder Training - 4 weeks


title: atac-seq_heart_training_male_4w_biological_rep5_vial_90292015802


title: atac-seq_kidney_training_female_8w_biological_rep4_vial_90259015904


title: atac-seq_kidney_training_female_8w_biological_rep2_vial_90254015904


title: atac-seq_kidney_training_female_8w_biological_rep1_vial_90251015904


title: atac-seq_kidney_control_female_8w_biological_rep2_vial_90248015904


title: atac-seq_kidney_control_female_8w_biological_rep1_vial_90245015904


title: atac-seq_kidney_control_male_8w_biological_rep1_vial_90217015904


title: atac-seq_kidney_training_male_8w_biological_rep2_vial_90222015904


title: atac-seq_kidney_training_male_8w_biological_rep1_vial_90218015904


title: atac-seq_heart_control_female_8w_biological_rep5_vial_90266015802

source_name: ATAC-seq of Rat Female Heart Powder Control - 8 weeks


title: atac-seq_heart_training_female_2w_biological_rep4_vial_90585015802


title: atac-seq_heart_training_female_2w_biological_rep5_vial_90587015802


title: atac-seq_heart_control_female_8w_biological_rep4_vial_90265015802


title: atac-seq_heart_training_female_2w_biological_rep2_vial_90578015802


title: atac-seq_heart_training_female_1w_biological_rep3_vial_90564015802


title: atac-seq_heart_training_female_2w_biological_rep1_vial_90576015802


title: atac-seq_heart_training_male_4w_biological_rep3_vial_90283015802


title: atac-seq_heart_control_female_8w_biological_rep2_vial_90248015802


title: atac-seq_heart_training_female_8w_biological_rep4_vial_90259015802

source_name: ATAC-seq of Rat Female Heart Powder Training - 8 weeks


title: atac-seq_heart_control_male_8w_biological_rep5_vial_90239015802

source_name: ATAC-seq of Rat Male Heart Powder Control - 8 weeks


title: atac-seq_heart_training_male_2w_biological_rep1_vial_90439015802


title: atac-seq_heart_training_male_1w_biological_rep4_vial_90426015802


title: atac-seq_heart_control_male_8w_biological_rep3_vial_90232015802


title: atac-seq_heart_training_male_1w_biological_rep2_vial_90422015802


title: atac-seq_heart_training_female_4w_biological_rep3_vial_90412015802


title: atac-seq_heart_training_female_4w_biological_rep2_vial_90410015802


title: atac-seq_heart_training_male_4w_biological_rep2_vial_90281015802


title: atac-seq_heart_training_male_4w_biological_rep1_vial_90280015802


title: atac-seq_heart_training_male_8w_biological_rep5_vial_90227015802

source_name: ATAC-seq of Rat Male Heart Powder Training - 8 weeks


title: atac-seq_heart_training_male_8w_biological_rep4_vial_90225015802


title: atac-seq_heart_training_female_8w_biological_rep5_vial_90267015802


title: atac-seq_heart_training_female_8w_biological_rep1_vial_90251015802


title: atac-seq_heart_control_female_8w_biological_rep3_vial_90252015802


title: atac-seq_heart_control_female_8w_biological_rep1_vial_90245015802


title: atac-seq_heart_training_female_8w_biological_rep2_vial_90254015802


title: atac-seq_heart_control_male_8w_biological_rep4_vial_90237015802


title: atac-seq_heart_training_female_8w_biological_rep3_vial_90258015802


title: atac-seq_skm-gn_training_female_2w_biological_rep4_vial_90585015505

description: motrpac_pass1b-06_t55-gastrocnemius_epigen-atac-seq_counts.txt.gz

source_name: ATAC-seq of Rat Female Gastrocnemius Powder Training - 2 weeks

value: Gastrocnemius Powder


title: atac-seq_skm-gn_training_female_1w_biological_rep5_vial_90571015505

source_name: ATAC-seq of Rat Female Gastrocnemius Powder Training - 1 week


title: atac-seq_skm-gn_training_female_1w_biological_rep4_vial_90567015505


title: atac-seq_skm-gn_training_female_2w_biological_rep2_vial_90578015505


title: atac-seq_skm-gn_training_female_1w_biological_rep3_vial_90564015505


title: atac-seq_heart_control_male_8w_biological_rep2_vial_90229015802


title: atac-seq_heart_training_male_8w_biological_rep3_vial_90223015802


title: atac-seq_skm-gn_training_male_2w_biological_rep5_vial_90450015505

source_name: ATAC-seq of Rat Male Gastrocnemius Powder Training - 2 weeks


title: atac-seq_skm-gn_training_male_2w_biological_rep4_vial_90449015505


title: atac-seq_heart_training_male_8w_biological_rep2_vial_90222015802


title: atac-seq_skm-gn_training_female_2w_biological_rep3_vial_90581015505


title: atac-seq_skm-gn_training_female_2w_biological_rep1_vial_90576015505


title: atac-seq_skm-gn_training_female_1w_biological_rep2_vial_90560015505


title: atac-seq_skm-gn_training_female_2w_biological_rep5_vial_90587015505


title: atac-seq_skm-gn_training_male_1w_biological_rep3_vial_90423015505

source_name: ATAC-seq of Rat Male Gastrocnemius Powder Training - 1 week


title: atac-seq_skm-gn_training_female_1w_biological_rep1_vial_90559015505


title: atac-seq_skm-gn_training_male_2w_biological_rep3_vial_90444015505


title: atac-seq_skm-gn_training_male_1w_biological_rep2_vial_90422015505


title: atac-seq_heart_training_male_8w_biological_rep1_vial_90218015802


title: atac-seq_skm-gn_training_male_2w_biological_rep2_vial_90441015505


title: atac-seq_skm-gn_training_female_4w_biological_rep1_vial_90406015505

source_name: ATAC-seq of Rat Female Gastrocnemius Powder Training - 4 weeks


title: atac-seq_skm-gn_training_male_2w_biological_rep1_vial_90439015505


title: atac-seq_skm-gn_training_female_4w_biological_rep2_vial_90410015505


title: atac-seq_skm-gn_training_male_4w_biological_rep5_vial_90292015505

source_name: ATAC-seq of Rat Male Gastrocnemius Powder Training - 4 weeks


title: atac-seq_skm-gn_training_male_1w_biological_rep5_vial_90430015505


title: atac-seq_skm-gn_training_male_1w_biological_rep4_vial_90426015505


title: atac-seq_skm-gn_training_female_8w_biological_rep4_vial_90259015505

source_name: ATAC-seq of Rat Female Gastrocnemius Powder Training - 8 weeks


title: atac-seq_skm-gn_training_male_1w_biological_rep1_vial_90421015505


title: atac-seq_skm-gn_training_female_4w_biological_rep4_vial_90416015505


title: atac-seq_skm-gn_training_female_4w_biological_rep3_vial_90412015505


title: atac-seq_skm-gn_training_male_4w_biological_rep4_vial_90289015505


title: atac-seq_skm-gn_training_male_4w_biological_rep3_vial_90283015505


title: atac-seq_skm-gn_training_male_4w_biological_rep2_vial_90281015505


title: atac-seq_skm-gn_training_female_8w_biological_rep1_vial_90251015505


title: atac-seq_skm-gn_control_female_8w_biological_rep1_vial_90245015505

source_name: ATAC-seq of Rat Female Gastrocnemius Powder Control - 8 weeks


title: atac-seq_skm-gn_training_male_4w_biological_rep1_vial_90280015505


title: atac-seq_skm-gn_training_female_8w_biological_rep5_vial_90267015505


title: atac-seq_skm-gn_control_male_8w_biological_rep4_vial_90237015505

source_name: ATAC-seq of Rat Male Gastrocnemius Powder Control - 8 weeks


title: atac-seq_skm-gn_control_female_8w_biological_rep4_vial_90265015505


title: atac-seq_skm-gn_control_male_8w_biological_rep2_vial_90229015505


title: atac-seq_heart_control_male_8w_biological_rep1_vial_90217015802


title: atac-seq_skm-gn_training_female_8w_biological_rep3_vial_90258015505


title: atac-seq_skm-gn_control_female_8w_biological_rep5_vial_90266015505


title: atac-seq_skm-gn_training_male_8w_biological_rep4_vial_90225015505

source_name: ATAC-seq of Rat Male Gastrocnemius Powder Training - 8 weeks


title: atac-seq_skm-gn_training_male_8w_biological_rep2_vial_90222015505


title: atac-seq_skm-gn_training_male_8w_biological_rep3_vial_90223015505


title: atac-seq_skm-gn_training_female_8w_biological_rep2_vial_90254015505


title: atac-seq_skm-gn_control_female_8w_biological_rep2_vial_90248015505


title: atac-seq_skm-gn_control_male_8w_biological_rep1_vial_90217015505


title: atac-seq_skm-gn_control_male_8w_biological_rep5_vial_90239015505


title: atac-seq_skm-gn_control_female_8w_biological_rep3_vial_90252015505


title: atac-seq_skm-gn_training_female_4w_biological_rep5_vial_90420015505


title: atac-seq_skm-gn_training_male_8w_biological_rep5_vial_90227015505


title: atac-seq_hippoc_training_female_1w_biological_rep4_vial_90567015204

description: motrpac_pass1b-06_t52-hippocampus_epigen-atac-seq_counts.txt.gz

source_name: ATAC-seq of Rat Female Hippocampus Powder Training - 1 week

value: Hippocampus Powder


title: atac-seq_hippoc_training_female_1w_biological_rep2_vial_90560015204


title: atac-seq_skm-gn_control_male_8w_biological_rep3_vial_90232015505


title: atac-seq_hippoc_training_female_1w_biological_rep3_vial_90564015204


title: atac-seq_hippoc_training_female_2w_biological_rep2_vial_90578015204

source_name: ATAC-seq of Rat Female Hippocampus Powder Training - 2 weeks


title: atac-seq_hippoc_training_male_2w_biological_rep4_vial_90449015204

source_name: ATAC-seq of Rat Male Hippocampus Powder Training - 2 weeks


title: atac-seq_hippoc_training_female_2w_biological_rep5_vial_90587015204


title: atac-seq_hippoc_training_female_2w_biological_rep1_vial_90576015204


title: atac-seq_hippoc_training_male_2w_biological_rep1_vial_90439015204


title: atac-seq_hippoc_training_male_1w_biological_rep5_vial_90430015204

source_name: ATAC-seq of Rat Male Hippocampus Powder Training - 1 week


title: atac-seq_skm-gn_training_male_8w_biological_rep1_vial_90218015505


title: atac-seq_hippoc_training_male_2w_biological_rep2_vial_90441015204


title: atac-seq_hippoc_training_male_1w_biological_rep3_vial_90423015204


title: atac-seq_hippoc_training_male_1w_biological_rep2_vial_90422015204


title: atac-seq_hippoc_training_male_1w_biological_rep1_vial_90421015204


title: atac-seq_hippoc_training_female_2w_biological_rep4_vial_90585015204


title: atac-seq_hippoc_training_male_1w_biological_rep4_vial_90426015204


title: atac-seq_hippoc_training_female_4w_biological_rep2_vial_90410015204

source_name: ATAC-seq of Rat Female Hippocampus Powder Training - 4 weeks


title: atac-seq_hippoc_training_male_4w_biological_rep5_vial_90292015204

source_name: ATAC-seq of Rat Male Hippocampus Powder Training - 4 weeks


title: atac-seq_hippoc_training_male_4w_biological_rep4_vial_90289015204


title: atac-seq_hippoc_training_female_2w_biological_rep3_vial_90581015204


title: atac-seq_hippoc_training_female_1w_biological_rep5_vial_90571015204


title: atac-seq_hippoc_training_female_1w_biological_rep1_vial_90559015204


title: atac-seq_hippoc_training_female_4w_biological_rep1_vial_90406015204


title: atac-seq_hippoc_training_male_4w_biological_rep3_vial_90283015204


title: atac-seq_hippoc_training_male_2w_biological_rep5_vial_90450015204


title: atac-seq_hippoc_training_female_8w_biological_rep5_vial_90267015204

source_name: ATAC-seq of Rat Female Hippocampus Powder Training - 8 weeks


title: atac-seq_hippoc_training_female_8w_biological_rep4_vial_90259015204


title: atac-seq_hippoc_training_male_4w_biological_rep1_vial_90280015204


title: atac-seq_hippoc_training_male_2w_biological_rep3_vial_90444015204


title: atac-seq_hippoc_training_female_8w_biological_rep3_vial_90258015204


title: atac-seq_hippoc_control_female_8w_biological_rep5_vial_90266015204

source_name: ATAC-seq of Rat Female Hippocampus Powder Control - 8 weeks


title: atac-seq_hippoc_control_female_8w_biological_rep3_vial_90252015204


title: atac-seq_hippoc_training_female_8w_biological_rep2_vial_90254015204


title: atac-seq_hippoc_training_female_4w_biological_rep4_vial_90416015204


title: atac-seq_hippoc_training_female_4w_biological_rep3_vial_90412015204


title: atac-seq_hippoc_training_female_4w_biological_rep5_vial_90420015204


title: atac-seq_hippoc_training_female_8w_biological_rep1_vial_90251015204


title: atac-seq_hippoc_control_female_8w_biological_rep2_vial_90248015204


title: atac-seq_hippoc_training_male_8w_biological_rep5_vial_90227015204

source_name: ATAC-seq of Rat Male Hippocampus Powder Training - 8 weeks


title: atac-seq_hippoc_training_male_8w_biological_rep3_vial_90223015204


title: atac-seq_hippoc_training_male_8w_biological_rep2_vial_90222015204


title: atac-seq_hippoc_training_male_8w_biological_rep1_vial_90218015204


title: atac-seq_hippoc_control_male_8w_biological_rep1_vial_90217015204

source_name: ATAC-seq of Rat Male Hippocampus Powder Control - 8 weeks


title: atac-seq_hippoc_control_female_8w_biological_rep1_vial_90245015204


title: atac-seq_hippoc_control_male_8w_biological_rep5_vial_90239015204


title: atac-seq_hippoc_training_male_4w_biological_rep2_vial_90281015204


title: atac-seq_hippoc_control_female_8w_biological_rep4_vial_90265015204


title: atac-seq_wat_male_reference_8_vial_80004887039

source_name: ATAC-seq of Rat Male White Adipose Powder Reference

value: Reference


title: atac-seq_hippoc_control_male_8w_biological_rep2_vial_90229015204


title: atac-seq_liver_male_reference_6_vial_80002886822

source_name: ATAC-seq of Rat Male Liver Powder Reference


title: atac-seq_bat_female_reference_7_vial_80031996925

source_name: ATAC-seq of Rat Female Brown Adipose Powder Reference


title: atac-seq_wat_female_reference_8_vial_80005997039

source_name: ATAC-seq of Rat Female White Adipose Powder Reference


title: atac-seq_hippoc_control_male_8w_biological_rep4_vial_90237015204


title: atac-seq_hippoc_control_male_8w_biological_rep3_vial_90232015204


title: atac-seq_kidney_female_reference_4_vial_80029995927

source_name: ATAC-seq of Rat Female Kidney Powder Reference


title: atac-seq_liver_female_reference_6_vial_80003996822

source_name: ATAC-seq of Rat Female Liver Powder Reference


title: atac-seq_lung_male_reference_5_vial_80026886627

source_name: ATAC-seq of Rat Male Lung Powder Reference


title: atac-seq_bat_male_reference_7_vial_80030886921

source_name: ATAC-seq of Rat Male Brown Adipose Powder Reference


title: atac-seq_kidney_male_reference_4_vial_80028885927

source_name: ATAC-seq of Rat Male Kidney Powder Reference


title: atac-seq_skm-gn_male_reference_2_vial_80000885530

source_name: ATAC-seq of Rat Male Gastrocnemius Powder Reference


title: atac-seq_heart_male_reference_3_vial_80032885820

source_name: ATAC-seq of Rat Male Heart Powder Reference


title: atac-seq_skm-gn_female_reference_2_vial_80001995541

source_name: ATAC-seq of Rat Female Gastrocnemius Powder Reference


title: atac-seq_hippoc_female_reference_1_vial_80035995233

source_name: ATAC-seq of Rat Female Hippocampus Powder Reference


title: atac-seq_hippoc_training_male_8w_biological_rep4_vial_90225015204


title: rrbs_wat_training_female_2w_biological_rep4_vial_90585017004

data_processing:
Reads were demultiplexed with bcl2fastq (version 2.20) using options --use-bases-mask Y*,I8Y*,I*,Y* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0 (Illumina, San Diego, CA, USA), and UMIs in the index FASTQ files were attached to the read FASTQ files
The regular 5-prime and 3-prime adapters were trimmed with TrimGalore (v1.18), and the diversity adapter that is about 0 to 3 bases of RDD (R={A or G} and D={A, G, or T}) that is added before YGG (Y={C or T} depending on the methylation) from the YGG MspI cut signature was trimmed with the NuGEN script trimRRBSdiversityAdaptCustomers.py (https://github.com/nugentechnologies/NuMetRRBS)
FastQC (v0.11.8) was used to generate pre-alignment QC metrics3
Bismark (v0.20.0) was used to index and align reads to release 96 of the Ensembl Rattus norvegicus (rn6) genome and gene annotation
As the lambda genome was spiked into each sample to determine the bisulfite conversion efficiency, the lambda genome (GenBank: J02459.1) was also indexed
Default parameters were used for Bismark's  bismark_genome_preparation in the alignment step
Bismark output BAM files were first formatted using a custom script; Bismark's deduplicate_bismark with -p --barcode options was used to remove PCR duplicates from the bam files; and Bismark's bismark_methylation_extractor --comprehensive --bedgraph was used to quantify methylated and unmethylated coverages for all the CpG sites
Bowtie 2 (v2.3.4.3) was used to index and align reads to globin, rRNA, and phix sequences in order to quantify the percent of reads that mapped to these contaminants and spike-ins
SAMtools (v1.3.1) was used to compute mapping percentages to different chromosomes
UMIs were used to accurately quantify PCR duplicates with NuGEN's nodup.py script (https://github.com/tecangenomics/nudup)
QC metrics from every stage of the quantification pipeline were compiled, in part with multiQC (v1.6)
The openWDL-based implementation of the RRBS pipeline on Google Cloud Platform is available on GitHub (https://github.com/MoTrPAC/motrpac-rrbs-pipeline).
Assembly: rn6
Supplementary files format and content: Methylated and unmethylated coverages across all CpG sites for the species aligned sample. One file per sample/tissue. Available through command-line only. Table format : <chr> <start> <end><methylation percentage> <count methylated> <count unmethylated>

source_name: RRBS of Rat Female White Adipose Powder Training - 2 weeks

extract_protocol:
Reduced representation bisulfite sequencing (RRBS)2 was performed at the Icahn School of Medicine at Mount Sinai. Rat tissues (10-30 mg of white adipose tissue) were disrupted in GenFind v2 lysis buffer (Beckman Coulter, Indianapolis, IN) using a tissue ruptor (Omni International, Kennesaw, GA) and the genomic DNA was extracted in a BiomekFx automation workstation (Beckman Coulter, Chaska, Minnesota), according to the manufacturerΓÇÖs instructions. Two tissue-specific consortium reference standards were included to monitor the sample processing QC. DNA samples were quantified by Qubit assay (dsDNA HR assay, Thermo Fisher Scientific), and the quality was determined by the Nanodrop A260/280 and A260/230 ratios.
The Ovation RRBS Methyl-Seq kit from Tecan Genomics (Baldwin Park, CA) was used to generate the RRBS libraries according to the manufacturer's instructions. All library preparations were carried out in an automated workstation (Biomek Fx, Beckman Coulter). Briefly, purified genomic DNA (100 ng) was digested by the methylation-insensitive restriction enzyme MspI to generate short fragments that contain CpG dinucleotides at the ends. After end-repair, A-tailing, and ligation to methylated Illumina adapters, the CpG-rich DNA fragments (40-220 base pairs) were size-selected and subjected to bisulfite conversion according to the manufacturer's instructions. The single-stranded uracil-containing DNA was purified after desulfonation using the magnetic beads provided in the kit, and eluted DNA was converted to double-stranded DNA by PCR with the following cycling parameters: 95C for 2 minutes, followed by the optimal number of cycles of 95C for 15 seconds, 60C for 1 minute, and 72C for 30 seconds, and a final step at 72C for 10 minutes. The optimal number of cycles for the enrichment PCR was calculated based on qPCR values. A final clean-up step was performed by 1x AMPure XP beads. The quantity of the libraries was measured by Qubit High Sensitivity assays (ThermoFisher Scientific), and the quality was evaluated using Bioanalyzer High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). The libraries were pooled and 10 sequenced in a MiSeq Nano flow cell to determine the sequencing quality of the libraries. Unmethylated lambda DNA (Promega, D1521) was spiked (0.05%) in each sample to monitor bisulfite conversion. Jurkat genomic DNA (ThermoFisher, SD1111) and CpG Methylated Jurkat genomic DNA (ThermoFisher, SD1121) were used as positive controls with each batch.


title: rrbs_liver_training_female_2w_biological_rep1_vial_90576016804

source_name: RRBS of Rat Female Liver Powder Training - 2 weeks


title: rrbs_wat_training_female_2w_biological_rep2_vial_90578017004


title: rrbs_wat_training_female_1w_biological_rep4_vial_90567017004

source_name: RRBS of Rat Female White Adipose Powder Training - 1 week


title: rrbs_wat_training_female_1w_biological_rep5_vial_90571017004


title: rrbs_wat_training_female_1w_biological_rep3_vial_90564017004


title: rrbs_wat_training_female_1w_biological_rep1_vial_90559017004


title: rrbs_wat_training_male_2w_biological_rep5_vial_90450017004

source_name: RRBS of Rat Male White Adipose Powder Training - 2 weeks


title: atac-seq_heart_female_reference_3_vial_80033995820

source_name: ATAC-seq of Rat Female Heart Powder Reference


title: rrbs_wat_training_male_2w_biological_rep2_vial_90441017004


title: rrbs_wat_training_male_1w_biological_rep3_vial_90423017004

source_name: RRBS of Rat Male White Adipose Powder Training - 1 week


title: rrbs_liver_training_female_2w_biological_rep2_vial_90578016804


title: rrbs_wat_training_male_1w_biological_rep4_vial_90426017004


title: atac-seq_lung_female_reference_5_vial_80027996627

source_name: ATAC-seq of Rat Female Lung Powder Reference


title: rrbs_wat_training_female_2w_biological_rep5_vial_90587017004


title: rrbs_wat_training_female_2w_biological_rep3_vial_90581017004


title: rrbs_wat_training_female_4w_biological_rep5_vial_90420017004

source_name: RRBS of Rat Female White Adipose Powder Training - 4 weeks


title: rrbs_wat_training_male_2w_biological_rep4_vial_90449017004


title: rrbs_wat_training_male_2w_biological_rep3_vial_90444017004


title: rrbs_wat_training_female_4w_biological_rep2_vial_90410017004


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source_name: ATAC-seq of Rat Male Hippocampus Powder Reference


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source_name: RRBS of Rat Female White Adipose Powder Training - 8 weeks


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source_name: RRBS of Rat Male White Adipose Powder Training - 4 weeks


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source_name: RRBS of Rat Female White Adipose Powder Control - 8 weeks


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source_name: RRBS of Rat Male White Adipose Powder Control - 8 weeks


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source_name: RRBS of Rat Male White Adipose Powder Training - 8 weeks


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source_name: RRBS of Rat Female Brown Adipose Powder Training - 2 weeks


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source_name: RRBS of Rat Female Brown Adipose Powder Training - 1 week


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source_name: RRBS of Rat Male Brown Adipose Powder Training - 2 weeks


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source_name: RRBS of Rat Female Brown Adipose Powder Training - 8 weeks


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source_name: RRBS of Rat Female Brown Adipose Powder Control - 8 weeks


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title: rrbs_liver_training_female_2w_biological_rep4_vial_90585016804

source_name: RRBS of Rat Female Liver Powder Training - 2 weeks


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source_name: RRBS of Rat Female Liver Powder Training - 1 week


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source_name: RRBS of Rat Male Liver Powder Training - 2 weeks


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source_name: RRBS of Rat Male Liver Powder Training - 1 week


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source_name: RRBS of Rat Female Liver Powder Training - 4 weeks


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source_name: RRBS of Rat Male Liver Powder Training - 4 weeks


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source_name: RRBS of Rat Female Liver Powder Training - 8 weeks


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source_name: RRBS of Rat Male Lung Powder Training - 1 week


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source_name: RRBS of Rat Female Kidney Powder Training - 2 weeks


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source_name: RRBS of Rat Female Heart Powder Training - 2 weeks


title: rrbs_heart_training_female_2w_biological_rep5_vial_90587015804


title: rrbs_heart_training_female_2w_biological_rep1_vial_90576015804


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title: rrbs_heart_training_female_1w_biological_rep3_vial_90564015804

source_name: RRBS of Rat Female Heart Powder Training - 1 week


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title: rrbs_kidney_training_female_8w_biological_rep4_vial_90259015903


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source_name: RRBS of Rat Male Heart Powder Training - 2 weeks


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source_name: RRBS of Rat Male Heart Powder Training - 1 week


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title: rrbs_heart_training_female_4w_biological_rep5_vial_90420015804

source_name: RRBS of Rat Female Heart Powder Training - 4 weeks


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source_name: RRBS of Rat Male Heart Powder Training - 4 weeks


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title: rrbs_heart_training_female_8w_biological_rep5_vial_90267015804

source_name: RRBS of Rat Female Heart Powder Training - 8 weeks


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source_name: RRBS of Rat Female Heart Powder Control - 8 weeks


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source_name: RRBS of Rat Male Heart Powder Control - 8 weeks


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source_name: RRBS of Rat Male Heart Powder Training - 8 weeks


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source_name: RRBS of Rat Female Gastrocnemius Powder Training - 2 weeks


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source_name: RRBS of Rat Female Gastrocnemius Powder Training - 1 week


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source_name: RRBS of Rat Male Gastrocnemius Powder Training - 2 weeks


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source_name: RRBS of Rat Male Gastrocnemius Powder Training - 1 week


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source_name: RRBS of Rat Female Gastrocnemius Powder Training - 4 weeks


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source_name: RRBS of Rat Male Gastrocnemius Powder Training - 4 weeks


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source_name: RRBS of Rat Female Gastrocnemius Powder Control - 8 weeks


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source_name: RRBS of Rat Female Gastrocnemius Powder Training - 8 weeks


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source_name: RRBS of Rat Male Gastrocnemius Powder Control - 8 weeks


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source_name: RRBS of Rat Male Gastrocnemius Powder Training - 8 weeks


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source_name: RRBS of Rat Female Hippocampus Powder Training - 2 weeks


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source_name: RRBS of Rat Female Hippocampus Powder Training - 1 week


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source_name: RRBS of Rat Male Hippocampus Powder Training - 2 weeks


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source_name: RRBS of Rat Male Hippocampus Powder Training - 1 week


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source_name: RRBS of Rat Female Hippocampus Powder Training - 4 weeks


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source_name: RRBS of Rat Female Hippocampus Powder Training - 8 weeks


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source_name: RRBS of Rat Female Hippocampus Powder Control - 8 weeks


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source_name: RRBS of Rat Male Hippocampus Powder Control - 8 weeks


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