title: Y1.5_PIMQ_WGBS_Rep2

description:
Library name: Sample 20
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: chromatin-associated RNA in LbetaT2 gonadotropes sample 2

status: Public on Mar 16 2026

type: SRA

city: Haifa

first: Philippa

last: Melamed

address: Technion City

country: Israel

institute: Technion-Israel Institute ofTechnology

description: Library name: Sample_crom_2

library_source: transcriptomic

data_processing:
FASTQ, cutadapt, Tophat2, HTseq-count
Assembly: mm10
Supplementary files format and content: Bam

molecule: nuclear RNA

organism: Mus musculus

growth_protocol: high glucose DMEM with 10% FCS, incubated at 37C under 5% CO2

extract_protocol:
Separation according to Conrad and Ørom (10.1007/978-1-4939-4035-6_1) - RNA extracted using Trizol and cleaned with RNA clean & concentrator kit, Zymo.
RNA libraries were prepared using SMARTer stranded total RNA-seq kit v2, following manufacturer's instructions.

tag: cell line

tag: cell type

value: gonadotrope


title: MM130151

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

country: USA

institute: Tulane University

description:
Library name: MM130151
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

library_source: genomic

data_processing:
Sequencing reads were quality-filtered and aligned to the human reference genome using BSMAP. Methylation levels at CpG sites were calculated as the ratio of methylated reads to total reads covering each site. CpG sites overlapping known SNPs were removed. Rank-based inverse normal transformation was applied for normalization. Reads with >10% unknown bases or >10% of bases with quality scores <20 were further excluded to obtain high-quality data. The cleaned reads were aligned to the GRCh37/hg19 human reference genome using BSMAP, then converted to GRCh38/hg38 using the UCSC LiftOver tool (https://genome.ucsc.edu/cgi-bin/hgLiftOver).
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data files contain tab-delimited matrices of CpG-level DNA methylation beta values. Rows represent CpG loci with genomic coordinates, and columns represent individual samples. Chromosome-specific methylation matrices are provided in compressed format.

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Genomic DNA was extracted from purified peripheral blood monocytes using the QIAamp DNA Mini Kit (Qiagen) following the manufacturer’s protocol. DNA concentration and purity were evaluated using NanoDrop spectrophotometry and agarose gel electrophoresis.
Monocytes were isolated from peripheral blood mononuclear cells using negative selection. Genomic DNA was extracted and fragmented. Libraries were prepared following bisulfite conversion using the EZ DNA Methylation-Gold kit and sequenced on the Illumina HiSeq 4000 platform.

tag: tissue

value: peripheral blood

value: monocytes

tag: population

value: European American

tag: Sex

value: male

tag: age

tag: bmi

tag: smoke

tag: alcohol drinking


title: 3222401L13Rik knockdown 4

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
Library name: Sample 10
column name in exonCount.txt: 3222401L13Rik knockdown 4

data_processing:
bcl2fastq
sequencing reads were mapped to GrCM38/mm10 genome
sequencing reads were counted using FeaturesCount
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each sample

molecule: total RNA

source_name: primary microglia

growth_protocol: primary microglia were maintained in DMEM medium supplemented with 10% FBS and antibiotics in a humidified chamber at 37°C

extract_protocol:
RNA was isolated using the Zymo RNA clean & Concentrator-5 Kit.
RNA-seq libraries were prepared using  SMARTer® Stranded Total RNA-Seq Kit v2 -Pico Input kit (Takara).

treatment_protocol: Primary microglia were treated with either control gapmers or 3222401L13Rik targeting gapmers

value: primary microglia

tag: genotype

value: WT

tag: treatment

value: 3222401L13Rik knockdown


title: Y1.5_PIMQ_WGBS_Rep1

city: New York

first: Luis

middle: F

last: Soto-Ugaldi

state: NY

institute: The Rockefeller University

description:
Library name: Sample 19
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region
Assembly: GRCm38 (mm10)
Supplementary files format and content: Bigwig

source_name: Skin

extract_protocol:
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines
Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads.

value: Skin

value: Epidermal Stem Cell

value: wildtype

value: 2-3 postnatal day 60  murine backskin was treated with Imiquimod for 6 consecutive days


title: Y1_Naive_WGBS_Rep2

description:
Library name: Sample 14
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: Untreated P60 mouse back-skin control


title: MM130146

description:
Library name: MM130146
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: African American


title: MM130138

description:
Library name: MM130138
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: Y1_PIMQ_WGBS_Rep1

description:
Library name: Sample 15
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: MM130141

description:
Library name: MM130141
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: A498 ELOVL2 and ELOVL5 double knockdown replicate 1

city: Tsukuba

first: Shotaro

last: Sakka

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description:
Library name: A498_siELOVL2_5_rep1
A498 renal cancer cells, ELOVL2 and ELOVL5 double knockdown, biological replicate 1

data_processing:
Raw sequencing reads were processed and quantified using the CLC Genomics Workbench pipeline.
Gene-level expression values were obtained for all samples.
Normalized expression values were generated and used for downstream comparative analyses among control, ELOVL2 knockdown, ELOVL5 knockdown, and double knockdown groups.
Differential expression-related statistical analyses, including ANOVA-based comparisons, were performed on the processed expression matrix.
Assembly: Homo sapiens reference genome.
Supplementary files format and content: The processed data file contains a gene-by-sample expression matrix including normalized expression values for all 12 samples. Rows correspond to genes/features, and columns correspond to individual samples.
Supplementary files format and content: Additional processed data include statistical analysis results derived from the normalized expression matrix.

growth_protocol: A498 renal cancer cells were maintained under standard cell culture conditions until siRNA transfection.

extract_protocol:
Total RNA was extracted from A498 renal cancer cells after siRNA transfection. RNA quality and quantity were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA obtained from A498 renal cancer cells transfected with control siRNA or siRNAs targeting ELOVL2, ELOVL5, or both genes. Libraries were validated using a Bioanalyzer (Agilent Technologies) to determine size distribution and concentration. Validated libraries were sequenced on an Illumina NextSeq 500 platform using the paired-end 36-base read option.

treatment_protocol: Cells were transfected with control siRNA or siRNAs targeting ELOVL2, ELOVL5, or both genes and harvested for RNA extraction.

value: ELOVL2 and ELOVL5 double knockdown

tag: batch


title: Brain Organoid, DEAB, Day 60, scRNAseq, biol rep1

city: Shanghai City

first: Yali

last: Li

address: No.320, Yueyang Avenue

country: China

institute: Center for Excellence in Molecular Cell Science

description: GEXSCOPE

library_source: other

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1 contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCh38
Supplementary files format and content: matrix files

molecule: other

extract_protocol:
Organoids were stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a Novaseq6000 platform (Illumina, San Diego, USA)

treatment_protocol: The medium with the addition of DMSO or 18.5 μM MTK or 10 μM DEAB was refreshed every day from day 20 to day 60.

value: Human embryonic stem cells

value: cerebral differentiation with DEAB treatment

tag: time

value: Day 60


title: Y1_Naive_WGBS_Rep1

description:
Library name: Sample 13
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: Brain Organoid, DMSO, Day 60, scRNAseq, biol rep3

description: GEXSCOPE

value: cerebral differentiation with DMSO treatment


title: A498 ELOVL2 knockdown replicate 2

description:
Library name: A498_siELOVL2_rep2
A498 renal cancer cells, ELOVL2 knockdown, biological replicate 2

value: ELOVL2 knockdown


title: Y1.5_Naive_WGBS_Rep1

description:
Library name: Sample 17
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: MM130145

description:
Library name: MM130145
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood

value: monocytes

value: European American


title: Brain Organoid, DMSO, Day 60, scRNAseq, biol rep2

description: GEXSCOPE

value: WT


title: MM130128

description:
Library name: MM130128
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: male


title: A498 ELOVL5 knockdown replicate 2

description:
Library name: A498_siELOVL5_rep2
A498 renal cancer cells, ELOVL5 knockdown, biological replicate 2

value: ELOVL5 knockdown


title: 3222401L13Rik knockdown 5

description:
Library name: Sample 11
column name in exonCount.txt: 3222401L13Rik knockdown 5

value: primary microglia

value: 3222401L13Rik knockdown


title: MM130130

description:
Library name: MM130130
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: A498 ELOVL2 knockdown replicate 1

description:
Library name: A498_siELOVL2_rep1
A498 renal cancer cells, ELOVL2 knockdown, biological replicate 1


title: D180_Naive_WGBS_Rep1

description:
Library name: Sample 9
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: Skin

value: Epidermal Stem Cell

value: wildtype


title: Control 5

description:
Library name: Sample 5
column name in exonCount.txt: Control 5

value: Control


title: 3222401L13Rik knockdown 1

description:
Library name: Sample 7
column name in exonCount.txt: 3222401L13Rik knockdown 1


title: Control 3

description:
Library name: Sample 3
column name in exonCount.txt: Control 3


title: NT rep2

city: Paris

first: Chun-Long

last: CHEN

state: Ile-de-France

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
Library name: Sample 2
Okazaki fragment sequencing ReAmp

data_processing:
Cutadapt 1.15 (adapter trimming)
FastQC v0.11.5 (quality control)
BWA 0.6.2-r126 (mapping) then merge the original BAM with re-amplificated BAM together by samtools
Picard 2.22.5 (deduplication)
OKseqHMM toolkit for replication fork direction (RFD) and initiation zone (IZ) termination zone (TZ) calling
Assembly: hg19
Supplementary files format and content: bigwig file for RFD profile and bed file for the initiation and termination zones
Library strategy: Ok-seq

source_name: JEFF cells

growth_protocol: JEFF cells were maintained in RPMI 1640 medium supplemented with 5% FBS, 100 U mL⁻¹ penicillin and 100 µg mL⁻¹ streptomycin.

extract_protocol:
Okazaki fragments were separated from bulk gDNA by sucrose gradient centrifugation, followed by streptavidin affinity capture of biotinylated, EdU-labelled DNA.
Purified fragments were treated to remove 5′ RNA primers, phosphorylated at the 5′ termini, ligated to sequencing adapters on both ends, and amplified with indexed primers.

treatment_protocol: At a density of 0.7–0.8 × 10⁶ cells mL⁻¹, cells were pulse-labelled with 20 µM 5-ethynyl-2′-deoxyuridine (EdU) for 2 min. Cells were lysed in 1% SDS buffer (50 mM Tris–HCl pH 8.0, 10 mM EDTA, 150 mM NaCl, and 0.1 µg mL⁻¹ proteinase K), and genomic DNA (gDNA) was purified by phenol–chloroform–isoamyl alcohol (25:24:1) extraction.

value: JEFF cells

value: Epstein-Barr-virus-immortalized human B lymphocytes

value: Untreated


title: MM130127

description:
Library name: MM130127
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: African American


title: A498 ELOVL5 knockdown replicate 1

description:
Library name: A498_siELOVL5_rep1
A498 renal cancer cells, ELOVL5 knockdown, biological replicate 1


title: D30_PIMQ_WGBS_Rep1

description:
Library name: Sample 7
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: 2-3 postnatal day 60  murine backskin was treated with Imiquimod for 6 consecutive days


title: MM130137

description:
Library name: MM130137
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood


title: A498 ELOVL2 knockdown replicate 3

description:
Library name: A498_siELOVL2_rep3
A498 renal cancer cells, ELOVL2 knockdown, biological replicate 3

value: ELOVL2 knockdown


title: 3222401L13Rik knockdown 2

description:
Library name: Sample 8
column name in exonCount.txt: 3222401L13Rik knockdown 2


title: 3222401L13Rik knockdown 3

description:
Library name: Sample 9
column name in exonCount.txt: 3222401L13Rik knockdown 3


title: MM130135

description:
Library name: MM130135
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: monocytes

value: European American


title: MM130123

description:
Library name: MM130123
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: male


title: MM130131

description:
Library name: MM130131
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: D180_PIMQ_WGBS_Rep1

description:
Library name: Sample 11
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: NT rep1 G1/S1

description:
Library name: Sample 29
Enrichement of BrdU labelled DNA (Replicate 1)

data_processing:
Demultiplexing: bcl2fastq2 (v2.15.0, v2.18.12).
Adapter trimming: Cutadapt (v1.3-v1.9), read length ≥ 10 nt.
Mapping: bwa-mem2 (v2.2.1).
PCR duplicates were removed with Picard (http://broadinstitute.github.io/picard, v3.3).
Only proper paired-end reads with MAPQ ≥ 6 were kept.
The read densities for each sample were computed within 10 kb non-overlapping windows using R package bamsignals v1.30, and normalized to the sample with the lowest number of reads with custom scripts.
Peak calling: local maxima were identified by convoluting the normalized Repli-seq signal with a first derivative of a Gaussian (sigma 3 over ± 90 kb). The points of inflection were identified by convoluting the normalized Repli-seq signal with a kernel containing the second derivative of a Gaussian (sigma 3 over ± 90 kb). Peaks were called as a local maximum between two inflection points with opposite inclination. The peaks identified on the “consensus” sample (called consensus peaks) with a mean replication timing value (S50) less than 0.4 are named ATRAP peaks.
Differential analysis: to define the early constitutive origins with increased G1/S Repli-seq signal in ATR-depleted cells treated with Aph, a genome-wide differential analysis has been performed on the raw read density of each 10 kb adjacent window between non-treated (n=4) and ATRAP-seq samples (n=6) with the R package DESeq2 v.1.36 (fitType = local).
Over-activated early constitutive origins are defined as ATRAP peaks overlapping with windows significantly enriched in ATRAP-seq samples compared to NT (Wald test p < 0.05, log2(FC) > 0.45). The same differential analysis has been performed using different control samples i.e., 4 APH vs. 6 ATRAP and 3 ATRi vs. 6 ATRAP
Assembly: hg19
Supplementary files format and content: BigWigs files were obtained from raw counts with MAPQ ≥ 6 in 1kb non-overlapping windows, normalized to 15 million total read counts and smoothed with a rolling mean (+/- 25 kb, 1 kb step).
Supplementary files format and content: The "Consensus" bigwig file represent the average read densities of the 6 ATRAP-seq samples (3 replicates with Aph 0.3 µM and 3 with Aph 0.6 µM).
Supplementary files format and content: Bigwig files indicated with "average" correspond to the average read densities of the G1-S1 fractions of the corresponding conditions. The average for untreated cells (NT) is the average of the bigwig deposited here as well as 3 other NT samples available under GEO IDs: GSM3963958, GSM3963964 and GSM5610009
Library strategy: Repli-seq

growth_protocol: Lymphoblasts were grown in RPMI 1640 + GlutaMAX-I medium (61870-010, ThermoFisher scientific) supplemented with 10% foetal calf serum (CVFSVF00-0T, Eurobio) and 100 µg/mL of penicillin and streptomycin (151140-122, ThermoFisher scientific) at 37°C in a humid atmosphere containing 5% CO2.

extract_protocol:
Cells were incubated overnight in lysis buffer (50 mM Tris-HCl pH8, 10 mM EDTA, 0.1% SDS, 50 ug/mL RNAse A, 100 ug/mL Proteinase K). DNA was purified from the lysates by phenol extraction.
Four µg of genomic DNA was fragmented to a mean size of 500 bp on a Covaris S220 intrument (peak power: 140, duty factor: 10%, cycle/burst: 200, time: 80 seconds). Fragmented DNA was treated with the End-Repair module (New England BioLabs, E6050) and the A-Tailing module (New England BioLabs, E6053), according to the manufacturer recommendations. Illumina Truseq indexed adapters were ligated on the resulting fragments, using the Quick Ligation module (New England BioLabs, E6056), according to the manufacturer recommendations. Following heat denaturation, BrdU-DNA was isolated by immunoprecipitation using an anti-BrdU monoclonal antibody (BD Biosciences, 347580). Immunoprecipitated fragments were amplified for 10 cycles using the KAPA Hifi DNA polymerase (KAPABiosystems, KK2502) and the resulting libraries were purified with AMPure XP beads (Beckman Coulter, A63881). Illumina libraries were pooled and sequenced on a NextSeq500 instrument on Paired-end 2x43 bp runs, using a NextSeq 500/550 High Output Kit v2 (75 cycles) kit.

treatment_protocol: Exponentially growing lymphoblastoid cells (~200x106), were pulse-labelled with 50 µM BrdU (Merck, B-5002) prior to recovery. Untreated cells were pulse labeled for 1 h, while all the other conditions were labeled for the last 3 h. Cells were then fixed in 70% ethanol and incubated overnight at 4°C in the presence of 15 µg/ml Hoescht 33342 (ThermoFisher Scientific, H3570). Cells were re-suspended in 1X PBS and sorted in six fractions at a time by flow cytometry based on their DNA content using a BD Biosciences INFLUX cell sorter. The first fraction contains cells in the second half of the G1 phase plus very early S (called G1/S1); the rest of the S phase was divided into four fractions (S2 to S5); and the last fraction contains cells in very late S, G2 and M phases (S6/G2/M). Aphidicolin (A0781) was obtained from Sigma-Aldrich.


title: β-catenin-/-ESCs cultured untreated control replicate 3

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

description: Library name: ESC_Control_rep3

data_processing:
Raw reads were trimmed to remove adapter sequences and low quality bases.
Trimmed reads were aligned to mm10 mouse genome
Feature counts were performed using RSEM
Differential gene expression were done using DESeq2
Assembly: mm10
Supplementary files format and content: txt file with genes in rows and sample in columns

molecule: polyA RNA

source_name: ESCs

growth_protocol: The β-catenin-/-ESCs were cultured on feeder treated dishes at 37°C in a 5% CO2 atmosphere. DMEM/F12-N2 medium was prepared by adding 1 ml of N2 (Gibco) 100× stock solution to 100 ml of DMEM/F12. For Neurobasal/B27 medium, 2 ml of B27 (Gibco) and 2 mM L-glutamine were added to 100 ml of Neurobasal medium. N2B27 medium was prepared by mixing DMEM/F12-N2 medium with Neurobasal/B27 medium at a 1:1 ratio, followed by the addition of 0.1 mM β-mercaptoethanol (Sigma). To expand naive-state ESC, 3 µM CHIR-99021 (Selleckchem), 1 µM PD03 (Selleckchem), and 40 ng/ml LIF (Peprotech) (2iL) were added to the DMEM/FBS or N2B27 medium.

extract_protocol:
Total RNA was extracted using the Qiagen RNA purification kit. For RNA-seq library preparation, 1 g total RNA was used to prepare the RNA-seq library with the Truseq RNA Library Prep Kit V2 with RiboZero (Illumina).
For RNA-seq library preparation, 1 g total RNA was used to prepare the RNA-seq library with the Truseq RNA Library Prep Kit V2 with RiboZero (Illumina).

treatment_protocol: Change the culture medium to N2B27 overnight before RNA extraction, then treat with Ctr, BRD0705, or CHIR for 30 minutes respectively.

value: ESCs

value: beta-catenin-/-


title: D180_Naive_WGBS_Rep2

description:
Library name: Sample 10
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: Untreated P60 mouse back-skin control


title: β-catenin-/-ESCs cultured untreated control replicate 2

description: Library name: ESC_Control_rep2


title: Control 1

description:
Library name: Sample 1
column name in exonCount.txt: Control 1

value: primary microglia

value: WT


title: A498 control replicate 3

description:
Library name: A498_control_rep3
A498 renal cancer cells, control siRNA, biological replicate 3

value: control siRNA


title: A498 control replicate 2

description:
Library name: A498_control_rep2
A498 renal cancer cells, control siRNA, biological replicate 2


title: Control 4

description:
Library name: Sample 4
column name in exonCount.txt: Control 4

value: Control


title: A498 control replicate 1

description:
Library name: A498_control_rep1
A498 renal cancer cells, control siRNA, biological replicate 1


title: D180_PIMQ_WGBS_Rep2

description:
Library name: Sample 12
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: Skin

value: Epidermal Stem Cell

value: wildtype


title: D30_PIMQ_WGBS_Rep2

description:
Library name: Sample 8
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: MM130106

description:
Library name: MM130106
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Control 2

description:
Library name: Sample 2
column name in exonCount.txt: Control 2


title: D30_Naive_WGBS_Rep1

description:
Library name: Sample 5
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: MM130124

description:
Library name: MM130124
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: African American


title: D30_Naive_WGBS_Rep2

description:
Library name: Sample 6
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: MM130101

description:
Library name: MM130101
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: D6_IMQ_WGBS_Rep2

description:
Library name: Sample 4
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: 2-3 postnatal day 60  murine backskin was treated with Imiquimod for 6 consecutive days


title: β-catenin-/-ESCs cultured with CHIR replicates 3

description: Library name: ESC_CHIR_rep3

value: CHIR


title: D6_Naive_WGBS_Rep2

description:
Library name: Sample 2
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: NT rep1

description:
Library name: Sample 1
Okazaki fragment sequencing

value: JEFF cells

value: Epstein-Barr-virus-immortalized human B lymphocytes

value: Untreated


title: MM130118

description:
Library name: MM130118
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood

value: monocytes

value: European American

value: male


title: ATRi+Aph03 rep3 G1/S1

description:
Library name: Sample 23
Enrichement of BrdU labelled DNA (Replicate 3)
Consensus.bw
ATRi-Aph03_G1-S1_average.bw

value: ATRi 100nM 16h + Aph 300nM 4h


title: D30_Y1_scRNA_GEX

description:
Library name: Sample 52
scRNA-seq was performed for epidermal stem cells collected at D30 naïve, D30 PIMQ, Y1 Control and Y1 PIMQ. Two replicates per biological condition. FastQ files were aligned with Cellranger v7.1.0 the transcriptome refdata-gex-mm10-2020-A using the command cellranger  count indicating the feature references the eight sequences for the different antibody capture (ACCCACCAGTAAGAC, GGTCGAGAGCATTCA, CTTGCCGCATGTCAT, AAAGCATTCTTCACG, CTTTGTCTTTGTGAG,  TATGCTGCCACGGTA, GAGTCTGCCAGTATC, TATAGAACGCCAGGC). We used CellBender v.0.3.0 to remove ambient RNA from the raw count matrix (raw_feature_bc_matrix.h5) with a false positive rate of 0.01, 150 epoch and using the full model. Output CellBender  and CellRanger matrices were read using the load_anndata_from_input_and_output function. This anndata was filtered to include cells annotated with a predicted cell probability > 0.5 and pre-processed with Scanpy v1.10. 0.

library_source: transcriptomic single cell

data_processing:
scRNA-seq was performed for epidermal stem cells collected at D30 naïve, D30 PIMQ, Y1 Control and Y1 PIMQ. Two replicates per biological condition. FastQ files were aligned with Cellranger v7.1.0 the transcriptome refdata-gex-mm10-2020-A using the command cellranger  count indicating the feature references the eight sequences for the different antibody capture (ACCCACCAGTAAGAC, GGTCGAGAGCATTCA, CTTGCCGCATGTCAT, AAAGCATTCTTCACG, CTTTGTCTTTGTGAG,  TATGCTGCCACGGTA, GAGTCTGCCAGTATC, TATAGAACGCCAGGC). We used CellBender v.0.3.0 to remove ambient RNA from the raw count matrix (raw_feature_bc_matrix.h5) with a false positive rate of 0.01, 150 epoch and using the full model. Output CellBender   and CellRanger matrices were read using the load_anndata_from_input_and_output function. This anndata was filtered to include cells annotated with a predicted cell probability > 0.5 and pre-processed with Scanpy v1.10.0.
Assembly: GRCm38 (mm10)
Supplementary files format and content: csvs files

extract_protocol:
EpdSCs (CD49f+, Sca-1+, CD29+, CD34-, CD45-, CD117-, CD140a-, CD31-) were FACS isolated and nuclei extracted using 10x protocol for nuclei extraction. Following nuclei extraction downstream processing was performed by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center where single cell ATAC-seq was performed.
Single-cell ATAC-seq libraries were prepared using the 10x Genomics Chromium Single Cell ATAC Solution (v1.1) according to the manufacturer’s protocol. Briefly, nuclei were isolated from fresh/frozen tissue, tagmented with a Tn5 transposase loaded with sequencing adapters, and then encapsulated into Gel Bead-In Emulsions (GEMs) for barcoding. Following barcoding, libraries were PCR-amplified and purified. Final libraries were quantified and sequenced on an Illumina platform using paired-end sequencing.

value: D30 naïve, D30 post-inflamed, Y1 naïve and Y1 post-inflamed (multiplexed single-cell suspension); 2 replicates per condition; P60 murine back-skin treated with Imiquimod for 6 days


title: APH03 rep2 G1/S1

description:
Library name: Sample 27
Enrichement of BrdU labelled DNA (Replicate 2)
Aph_G1-S1_average.bw

value: APH 300nM 4h


title: APH06 rep2 G1/S1

description:
Library name: Sample 28
Enrichement of BrdU labelled DNA (Replicate 2)
Aph_G1-S1_average.bw

value: APH 600nM 4h


title: ATRi+Aph03 rep1 G1/S1

description:
Library name: Sample 21
Enrichement of BrdU labelled DNA (Replicate 1)
Consensus.bw
ATRi-Aph03_G1-S1_average.bw


title: β-catenin-/-ESCs cultured untreated control replicate 1

description: Library name: ESC_Control_rep1

value: ESCs

value: beta-catenin-/-


title: β-catenin-/-ESCs cultured with BRD0705 replicates 1

description: Library name: ESC_BRD0705_rep1


title: BDL_2, scRNA-seq

city: Changchun

first: Lin

last: Lei

address: 5333 Xi’an Road, Changchun, Jilin, China

department: State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Veterinary Medicine

institute: Jilin University

description:
Library name: Sample 5
10X Genomics

data_processing:
Raw base-call files were demultiplexed and converted into FASTQ format using bcl2fastq software v2.20 (Illumina). Only confidently mapped, non-PCR duplicates with valid barcodes and unique molecular identifiers were utilized in generating the gene-barcode matrix, by using the CellRanger software v7.0.0 (10X Genomics) with standard settings and aligned to mm10/GRCm38 reference genome (Ensembl 105). Subsequent analysis was performed in R v4.1.3 using the generated count matrices generated by CellRanger.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Mice subjected BDL and Sham operation were first anesthetized. After cannulation of the inferior vena cava, Hanks' balanced salt solution (HBSS) without Ca2+ and Mg2+ containing 1% EDTA was used to perfuse the liver in situ retrograde perfusion through the portal vein for 5 min at 37°C. Then, NCD mice received a retrograde stepwise perfusion of HBSS with Ca2+ and Mg2+ containing 0.5 mg/mL collagenase Ⅳfor 10 min at 37°C, while CDAHFD mice and BDL mice received the same perfusion solution with a higher concentration of collagenase Ⅳ at 1 mg/mL. After perfusion, the liver was rapidly collected and carefully dispersed into ice-cold HBSS without Ca2+ and Mg2+. After removing as much liver parenchyma as possible, the minced bilio-vascular tree fragments were incubated in low glucose DMEM containing 0.075 mg/mL collagenase P, 0.02 mg/mL DNase, 3% FBS, 1% Hepes and 1% Penicillin-Streptomycin at 37°C for 15 min under agitation. The bilio-vascular fragments were then filtered and collected using a 350-mesh (40 µm) cell sieve. Following centrifugation at 1,250 rpm for 5 min at 4°C, the cell pellet was resuspended and incubated with 0.05% Trypsin-EDTA containing 0.02 mg/mL DNase for 15 min at 37°C under agitation. Next, the dissociated cells were gently and repeatedly pipetted and filtered three times through a 500-mesh (25 µm) cell sieve to obtain single-cell suspensions. Finally, the dead cells were removed from single-cell suspensions with the Dead Cell Removal kit according to the manufacturer’s protocol. Cell viability (> 95%) was determined using trypan blue staining.
10X Genomics Chromium Single-Cell 3’kits (V3) were used to prepare barcoded scRNA-seq libraries according to the manufacturer’s protocol. Single-cell suspensions were loaded onto 10X Chromium Single-Cell Controller Instrument to generated single cell gel beads in emulsions (GEMs), aiming to capture a total of 2,000-4,000 cells per library for Control samples (Sham mice), and 8,000-10,000 cells per library for BDL samples. After GEMs generation, DNA amplification and library construction were performed, and the libraries were sequenced on a Novaseq 6000 (Illumina) platform (paired-end multiplexing run,150 bp).

value: Liver

value: single-cell suspension from bilio-vascular tree fragments

value: C57BL/6, WT

value: BDL-induced mouse cholestasis model


title: MM130085

description:
Library name: MM130085
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130104

description:
Library name: MM130104
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: APH03 rep1 G1/S1

description:
Library name: Sample 26
Enrichement of BrdU labelled DNA (Replicate 1)
Aph_G1-S1_average.bw

value: JEFF cells


title: D6_IMQ_WGBS_Rep1

description:
Library name: Sample 3
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: Skin

value: Epidermal Stem Cell

value: wildtype

value: 2-3 postnatal day 60  murine backskin was treated with Imiquimod for 6 consecutive days


title: β-catenin-/-ESCs cultured with CHIR replicates 2

description: Library name: ESC_CHIR_rep2

value: CHIR


title: MM130100

description:
Library name: MM130100
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood

value: monocytes

value: European American

value: male


title: ATRi rep2 G1/S1

description:
Library name: Sample 24
Enrichement of BrdU labelled DNA (Replicate 2)
ATRi_G1-S1_average.bw

value: Epstein-Barr-virus-immortalized human B lymphocytes

value: ATRi 100nM 16h


title: D6_Naive_WGBS_Rep1

description:
Library name: Sample 1
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: Untreated P60 mouse back-skin control


title: Sham_3, scRNA-seq

description:
Library name: Sample 3
10X Genomics

value: Liver

value: Sham operation


title: MM130089

description:
Library name: MM130089
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: African American


title: ATRi rep3 G1/S1

description:
Library name: Sample 25
Enrichement of BrdU labelled DNA (Replicate 3)
ATRi_G1-S1_average.bw


title: D30_Y1_scRNA_HTO

description:
Library name: Sample 53
Hashtag-oligo (HTO) feature-barcode library sequenced in parallel; eight TotalSeq-C tags supplied via feature_reference.csv (ACCCACCAGTAAGAC, GGTCGAGAGCATTCA, CTTGCCGCATGTCAT, AAAGCATTCTTCACG, CTTTGTCTTTGTGAG,  TATGCTGCCACGGTA, GAGTCTGCCAGTATC, TATAGAACGCCAGGC); aligned with Cell Ranger v7.1.0 to generate HTO count matrix.

molecule: protein

value: D30 naïve, D30 post-inflamed, Y1 naïve and Y1 post-inflamed (multiplexed single-cell suspension); 2 replicates per condition; P60 murine back-skin treated with Imiquimod for 6 days


title: β-catenin-/-ESCs cultured with CHIR replicates 1

description: Library name: ESC_CHIR_rep1

value: ESCs

value: beta-catenin-/-


title: ATRi+Aph06 rep1 S5

description:
Library name: Sample 17
Enrichement of BrdU labelled DNA (Replicate 1)
Consensus.bw
ATRi-Aph06_G1-S1_average.bw

value: JEFF cells

value: ATRi 100nM 16h + Aph 600nM 4h


title: β-catenin-/-ESCs cultured with BRD0705 replicates 3

description: Library name: ESC_BRD0705_rep3


title: ATRi+Aph03 rep2 G1/S1

description:
Library name: Sample 22
Enrichement of BrdU labelled DNA (Replicate 2)
Consensus.bw
ATRi-Aph03_G1-S1_average.bw

value: ATRi 100nM 16h + Aph 300nM 4h


title: β-catenin-/-ESCs cultured with BRD0705 replicates 2

description: Library name: ESC_BRD0705_rep2


title: MM130060

description:
Library name: MM130060
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: MM130086

description:
Library name: MM130086
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130087

description:
Library name: MM130087
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: ATRi+Aph06 rep3 G1/S1

description:
Library name: Sample 20
Enrichement of BrdU labelled DNA (Replicate 3)
Consensus.bw
ATRi-Aph06_G1-S1_average.bw


title: MM130088

description:
Library name: MM130088
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: BDL_3, scRNA-seq

description:
Library name: Sample 6
10X Genomics

value: single-cell suspension from bilio-vascular tree fragments

value: C57BL/6, WT

value: BDL-induced mouse cholestasis model


title: ATRi+Aph06 rep1 S3

description:
Library name: Sample 15
Enrichement of BrdU labelled DNA (Replicate 1)
Consensus.bw
ATRi-Aph06_G1-S1_average.bw


title: ATRi+Aph06 rep2 G1/S1

description:
Library name: Sample 19
Enrichement of BrdU labelled DNA (Replicate 2)
Consensus.bw
ATRi-Aph06_G1-S1_average.bw


title: BDL_1, scRNA-seq

description:
Library name: Sample 4
10X Genomics


title: MM130080

description:
Library name: MM130080
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: peripheral blood

value: monocytes


title: 1mM_NaVA_28h_after_HS_rep3

type: RNA

city: Warsaw

first: Olaf

last: Geyderowicz

state: Masovian Voivodeship

address: Ilji Miecznikowa 1

department: Faculty of Biology

country: Poland

institute: University of Warsaw

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto medium supplemented with 1 mM NaVA, treated with 43.5°C for 4 h and collected 24 h after the end of the temperature treatment.

hyb_protocol: Samples were hybridized with GeneChip® Arabidopsis Gene 1.1 ST Array Strips

scan_protocol: Arrays were scanned in Gene Atlas Imaging Station (Affymetrix)

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) v4.0.3 with default settings

label: biotin

organism: Arabidopsis thaliana

source_name: 14-day-old Arabidopsis seedlings kept for additional 72h on medium with 1 mM NaVA before 4 h of heat shock at 43.5°C. Sampling 24 after the end of HS.

label_protocol: Total RNA was treated according to manufacturers protocol for GeneChip™ WT PLUS Reagent Kit (ThermoFisher Scientific, Waltham, MA, USA)

growth_protocol: Surface-sterilised Arabidopsis thaliana Col-0 seeds were sown on half-strenght and germinated for 14 days under 200 µmol/m2/s under 16 h photoperiod at 22°C.

extract_protocol: RNA was isolated using E.Z.N.A® Plant RNA Kit (Omega Bio-tek)

treatment_protocol: 14-day-old A.thaliana Col-0  seedlings grown on half-strength MS media were transferred onto fresh media with  1 mM sodium valerate (NaVA) or devoid of the inhibitor as control (C). After 72 h of growth on the new media, the plates with plants were transferred to an incubator set at 43.5°C for 4 h (HS). Immediately after the end of heat shock, the plants were returned to the growth chamber for regeneration. Plants were sampled at timepoints indicated in the SAMPLES section. In each case, 3 plantlets were pooled for each sample.

tag: sampling point


title: 1mM_NaVA_28h_after_HS_rep2


title: ATRi+Aph06 rep1 G1/S1

description:
Library name: Sample 13
Enrichement of BrdU labelled DNA (Replicate 1)
Consensus.bw
ATRi-Aph06_G1-S1_average.bw

value: Epstein-Barr-virus-immortalized human B lymphocytes