title: D6_Ctrl_ETS1_rep1

description:
Library name: Sample 1
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.


title: MM130311

status: Public on Mar 16 2026

type: SRA

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

country: USA

institute: Tulane University

description:
Library name: MM130311
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

tag: cell type

value: monocytes

tag: population

value: European American

tag: Sex

value: male

tag: age

tag: bmi

tag: smoke

tag: alcohol drinking


title: A375_CTC_6

city: Portland

first: Rosalyn

middle: M

last: Fey

state: OR

address: 3181 S.W. Sam Jackson Park Road

institute: Oregon Health & Science University

description: Library name: A375_CTC_6

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with zUMIs.
Assembly: hg38
Supplementary files format and content: merged FASTQ, index and barcode files.
Supplementary files format and content: counts files and gene names file.

molecule: polyA RNA

growth_protocol: 22Rv1 human prostate cancer cells were cultured in RPMI-1640 media/10% FBS. A375 human melanoma cancer cells were cultured in DMEM media/10% FBS.

extract_protocol:
Cells were stored in a lysis buffer containing poly-ethylene glycol, Triton X-100, RNAse inhibitor, a custom oligo strand, dNTPs, and nuclease free water at -80°C until ready for library preparation according to the Smart-seq3 protocol.  The freeze/thaw aided in cell lysis
Libraries were prepared according to the Smart-seq3 protocol (doi: 10.1038/s41587-020-0497-0)

tag: cell line

value: melanoma


title: MM130310

description:
Library name: MM130310
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_ETS1_rep2

city: New York

first: Luis

middle: F

last: Soto-Ugaldi

state: NY

institute: The Rockefeller University

description:
Library name: Sample 4
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.

data_processing:
40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.
Assembly: mm10
Supplementary files format and content: Bigwig files include CPM normalized counts
Library strategy: CUT&Run

organism: Mus musculus

source_name: Skin

extract_protocol:
500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Skin

value: Epidermal Stem Cell

tag: genotype

value: wildtype

tag: treatment

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


title: MM130304

description:
Library name: MM130304
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: A375_CTC_4

description: Library name: A375_CTC_4


title: A375_CTC_3

description: Library name: A375_CTC_3


title: 6h_TPA_Yr1_Ctrl_Rep1

description:
Library name: Sample 1
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.

data_processing:
Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw counts RDS file

extract_protocol:
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads.
PCR amplified library from genomic DNA

value: non-treated


title: MM130308

description:
Library name: MM130308
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: Y1_PIMQ_FOS_TPA_CUT&Run_Rep2

description:
Library name: Sample 43
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.

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


title: MM130306

description:
Library name: MM130306
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: MM130303

description:
Library name: MM130303
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: Lung_Phox2b_011824

city: New Haven

first: I-Uen

last: Hsu

state: Connecticut

address: 100 College Street

department: Neuroscience

institute: Yale University School of Medicine

description:
Library name: E14.5_lung_neuron
10x Genomics

data_processing:
Raw sequencing data were aligned to the mm10-2020-A mouse genome reference using Cell Ranger software v.7.1.0 (10x Genomics).
Assembly: mm10-2020-A mouse genome reference
Supplementary files format and content: Filtered gene expression matrix

source_name: Lung

growth_protocol: For co-culture experiments, cardiac atria and intestines were dissected from E13.5 Phox2b-Flpo;frt-tdTomato embryos and dissociated into single cell suspensions. Neuronal and non-neuronal cells were separated and collected by FACS. Cells were centrifuged at 200 x g for 10 minutes at 4 ˚C and plated for co-culture. Per well, 3,000 tdTomato+ enteric neuronal cells and 6,000 tdTomato-negative cardiac or intestinal cells were mixed and plated into 24-well plates pre-coated with a thin layer of Collagen I/Matrigel (Corning 356237) mixture that contains 0.5 mg /mL of Matrigel and 33 µg/mL Collagen I (Enzo Life Sciences ALX-522-440-0050). Cultures were maintained in Neurobasal Plus Medium (Gibco A3582901) supplemented with 1% FBS (Thermo Scientific 10082147), 2 mM L-Glutamine (Thermo Scientific 25030149), B-27 Plus Supplement (Gibco A3582801), 100 U/mL penicillin, 100 µg/mL streptomycin (Thermo Scientific 15140122), and 100 µg/mL Gentamicin (Thermo Scientific 15710064) at 37 ˚C in 5% CO2 for 4-5 days before harvesting for single-cell RNA sequencing.

extract_protocol:
For scRNA-seq of OINS cells, the heart, lungs, pancreas and intestines were dissected from Wnt1-Cre;lox-tdTomato, Phox2b-Flpo;frt-tdTomato, or Baf53b-Cre;lox-L10GFP mice as indicated at E12.5, E14.5, E16.5, E18.5 and P56 in ice-cold Leibovitz's L-15 Medium (Gibco). For the hearts and lungs, fluorescently labelled OINS regions were isolated by microdissection under a Leica M205FCA fluorescence stereomicroscope. For experiments comparing heart-near and heart-far regions, atrial areas containing Wnt1-Cre;lox-L10GFP labelled ICNS cells were dissected to separate from the atrial areas lacking ICNS. Dissected tissues were cut into 1-3 mm2 pieces and incubated in 0.25% trypsin-EDTA (Gibco) at 37 ˚C for 10 minutes (E12.5, E14.5), 20 minutes (E16.5, E18.5), or 25 minutes (P56) with shaking. After washing with L-15 media containing 10% fetal bovine serum (L15/FBS), tissues were incubated in 2 mg/mL Collagenase A (Sigma-Aldrich) and 2 mg/mL of Dispase II (Sigma-Aldrich) in 1 x HBSS at 37°C for 30 minutes (E12.5, E14.5) or 40 minutes (E16.5, E18.5, P56) with shaking. After washing with L15/FBS, cells were separated into single cells by trituration using three fire-polished Pasteur pipettes of decreasing diameter. Mature ICNS-neurons isolated from Baf53b-Cre;lox-L10GFP hearts at E18.5 and P56 were further purified using 30% and 60% Percoll density gradients. The cell suspension was filtered through a 40 μm cell strainer (Corning). All centrifugation steps were performed at 200 x g at 4°C. After the final centrifugation, the cell pellet was resuspended in 1x HBSS containing 0.04% BSA. Fluorescently labelled cells were sorted on a BD FACS Aria cell sorter at Yale Flow Cytometry Facility and collected in ice-cold 1x HBSS containing 0.04% BSA.  For co-culture experiments, after 4-5 days of culture, media were removed and cells were incubated with 2 mg/mL Collagenase A (Sigma-Aldrich) and 2 mg/mL of Dispase II (Sigma-Aldrich) solutions at 37 ˚C for 10 minutes. The digested cells were collected into ice-cold 10% FBS L-15 media (L15/FBS). This digestion was repeated 3-6 times until the coating layer was completely dissociated. Cells pooled from multiple wells were centrifuged at 200 x g at 4 ˚C for 10 minutes, washed three times with L15/FBS, and treated with Corning Cell Recovery solution (#354253) on ice for 20 minutes to dissolve residual Matrigel. After two additional washes with L15/FBS, cells were gently triturated with a Pasteur pipet, filtered through a 40 μm cell strainer, washed three times, and resuspended in 1x HBSS, 0.04% BSA for scRNA-seq using the 10x Genomics platform.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer’s instructions and sequenced using an Illumina NovaSeq 6000 S4 sequencer at 300 million reads to achieve a sequencing depth of 20,000–300,000 reads per cell.

value: Lung

value: intrapulmonary neurons

value: Phox2b-Flpo; frt-tdTomato


title: A375_CTC_7

description: Library name: A375_CTC_7


title: MM130301

description:
Library name: MM130301
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: 081423_ENSGut

description:
Library name: ENS_intestine_biol rep 2
10x Genomics

source_name: Intestine

value: Intestine

value: Intestinal cells and enteric neurons


title: 6h_TPA_Yr1_PIMQ_Rep1

description:
Library name: Sample 3
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.


title: A375_CTC_2

description: Library name: A375_CTC_2


title: 6h_TPA_Yr1_PIMQ_Rep2

description:
Library name: Sample 4
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.


title: Pancreas_Phox2b_011824

description:
Library name: E14.5_pancreas_neuron
10x Genomics

source_name: Pancreas

value: Pancreas

value: intrapancreatic neurons


title: MM130282

description:
Library name: MM130282
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: 020921ICNE18_5

description:
Library name: E18.5_ICNS
10x Genomics

source_name: Heart

value: Heart

value: Intrinsic cardiac neurons

value: Baf53b-Cre; lox-L10GFP


title: 070623_E14.5_ENS

description:
Library name: E14.5_ENS
10x Genomics

value: Enteric neurons


title: A375_CTC_5

description: Library name: A375_CTC_5

value: melanoma


title: Y1_PIMQ_JUN_CUT&Run_Rep2

description:
Library name: Sample 39
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.

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: MM130295

description:
Library name: MM130295
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

value: male


title: A375_CTC_1

description: Library name: A375_CTC_1


title: 090622ICN_Far_E14_5

description:
Library name: Heart_far
10x Genomics

value: Atrial cells away from ICNS


title: 070623_E14.5_Gut

description:
Library name: E14.5_intestine
10x Genomics

value: Intestine

value: Intestinal cells

value: Phox2b-Flpo; frt-tdTomato


title: Y1_PIMQ_JUN_CUT&Run_Rep1

description:
Library name: Sample 38
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.


title: MM130302

description:
Library name: MM130302
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


title: 22Rv1_CTC_19

description: Library name: 22Rv1_CTC_19

value: prostate


title: 6h_TPA_Yr1_Ctrl_Rep2

description:
Library name: Sample 2
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.

value: non-treated


title: 021320_ICNP56

description:
Library name: P56_ICNS
10x Genomics

value: Heart

value: Intrinsic cardiac neurons

value: Baf53b-Cre; lox-L10GFP


title: MM130274

description:
Library name: MM130274
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: European American


title: 090622ICN_Near_E14_5

description:
Library name: Heart_near
10x Genomics

value: Atrial cells near ICNS


title: 22Rv1_CTC_18

description: Library name: 22Rv1_CTC_18


title: 052721ICNE14_5_1

description:
Library name: E14.5_ICNS_biol rep 2
10x Genomics


title: Y1_Naive_FOS_TPA_CUT&Run_Rep2

description:
Library name: Sample 41
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.

value: Skin

value: Epidermal Stem Cell

value: wildtype

value: non-treated. 6hr TPA treated


title: Y1_PIMQ_FOS_TPA_CUT&Run_Rep1

description:
Library name: Sample 42
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.

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


title: MM130287

description:
Library name: MM130287
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: Y1_Naive_JUN_CUT&Run_Rep1

description:
Library name: Sample 36
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.


title: Y2_PIMQ_ATAC-seq_Rep2

description:
Library name: Sample 19
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

data_processing:
FastQ files were aligned with BWA using mm10 genome reference
Reads were filtered with Samtools -F 1804 -f 2
Peaks were detected using Macs3 using -bed as input format
BigWig files were generated using genomicRanges R package. Score represents CPM normalized values
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigWig files

extract_protocol:
ATAC-seq was performed on 100,000 FACS-purified cells as previously described (Buenrostro et al., 2013). Briefly, cells were lysed in ATAC lysis buffer for five minutes, then treated with Tn5 transposase (Illumina) for 30 minutes. Sequencing libraries were prepared according to manufacturer guidelines (Illumina), with up to eight uniquely-barcoded samples included per sequencing run. Libraries were sequenced on an Illumina NextSeq500 or NovaSeq 6000.
PCR amplified library from genomic DNA

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


title: 22Rv1_CTC_23

description: Library name: 22Rv1_CTC_23


title: 102522ICNE16_5

description:
Library name: E16.5_ICNS
10x Genomics


title: 22Rv1_CTC_22

description: Library name: 22Rv1_CTC_22


title: WT_PBS GEX_B

city: Baltimore

first: Peisong

last: Gao

state: MARYLAND

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins Asthma & Allergy Center

description: Library name: B-GEX

data_processing:
Raw data and the sequencing information of hashtag were passed to Cellranger software (version 7.2) and the reads were aligned to Mus musculus genome m38 which pre-built by 10×.
Assembly: m38
Supplementary files format and content: cellranger output

molecule: total RNA

extract_protocol:
After establishing the asthma mouse model, the right lower lung lobe was harvested to prepare single-cell suspensions. A total of 2 x106 single cells from lung tissues were obtained after filtering through a 40 μm cell filter. The single-cell suspension was labeled with BioLegend TotalSeq™-B antibodies (BioLegend, San Diego, CA) after RBC lyses and cell viability tests. The library preparation was performed following the manufacture’s guidelines of 10× Genomics in the Single Cell & Transcriptomics Core at Johns Hopkins.
After establishing the asthma mouse model, the right lower lung lobe was harvested to prepare single-cell suspensions. A total of 2 x106 single cells from lung tissues were obtained after filtering through a 40 μm cell filter. The single-cell suspension was labeled with BioLegend TotalSeq™-B antibodies (BioLegend, San Diego, CA) after RBC lyses and cell viability tests. The library preparation was performed following the manufacture’s guidelines of 10× Genomics in the Single Cell & Transcriptomics Core at Johns Hopkins.

value: Lung

value: WT

value: PBS

tag: library type

value: mRNA

tag: batch


title: 22Rv1_CTC_20

description: Library name: 22Rv1_CTC_20

value: prostate


title: 101122_ICN_E14_5

description:
Library name: E14.5_ICNS_biol rep 1
10x Genomics

value: Heart


title: 22Rv1_CTC_21

description: Library name: 22Rv1_CTC_21


title: MM130281

description:
Library name: MM130281
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

value: African American


title: Y1_Naive_JUN_CUT&Run_Rep2

description:
Library name: Sample 37
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.

value: non-treated


title: MM130291

description:
Library name: MM130291
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: 22Rv1_CTC_13

description: Library name: 22Rv1_CTC_13


title: MM130277

description:
Library name: MM130277
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: Y2_Naive_ATAC-seq_Rep2

description:
Library name: Sample 17
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

value: Skin


title: 22Rv1_CTC_16

description: Library name: 22Rv1_CTC_16


title: MM130268

description:
Library name: MM130268
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: 062521ICNE12_5

description:
Library name: E12.5_ICNS_biol rep 2
10x Genomics

value: Intrinsic cardiac neurons


title: WT_CRE GEX_A

description: Library name: A-GEX

value: CRE


title: MM130262

description:
Library name: MM130262
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: European American


title: Y2_PIMQ_ATAC-seq_Rep1

description:
Library name: Sample 18
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

value: Epidermal Stem Cell

value: wildtype


title: 22Rv1_CTC_15

description: Library name: 22Rv1_CTC_15


title: MM130261

description:
Library name: MM130261
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: 22Rv1_CTC_14

description: Library name: 22Rv1_CTC_14


title: 061821ICNE12_5

description:
Library name: E12.5_ICNS_biol rep 1
10x Genomics


title: Y2_Naive_ATAC-seq_Rep1

description:
Library name: Sample 16
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).


title: WT_PBS HTO_B

description: Library name: B-HTO

library_source: other

molecule: protein

value: Lung

value: HTO

tag: hto

value: TotalSeq-HashTag Anti-mouse 1 to 8


title: Y1.5_Naive_ATAC-seq_Rep2

description:
Library name: Sample 13
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).


title: S2 mouse tissue, Saline control

city: San Diego

first: Satadeepa

last: Kal

address: 9500 GILMAN Dr

institute: UCSD

description:
Library name: S2
Mus musculus mouse tissue, group S group, Saline control
B16F10_mouse_Tumor.csv

library_source: transcriptomic

data_processing:
Reads were quantified using Salmon, counts imported using tximport, differential expression via DESeq2, and visualization using pHeatmap and pVolcano.
Assembly: Genome assemblies were performed using GRCh38.p14 for human and GRCm39 for mouse.
Supplementary files format and content: normalised count with gene name for each sample

source_name: mouse tissue

extract_protocol:
RNA was extracted using the Qiagen Rneasy column extraction method following the manufacturer's protocol.
Libraries were made using the KAPA mRNA HyperprepKit according to the manufacturer's guidelines.

value: mouse tissue

value: Saline control

value: S group


title: MM130273

description:
Library name: MM130273
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


title: Y1_Naive_FOS_TPA_CUT&Run_Rep1

description:
Library name: Sample 40
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.

value: non-treated. 6hr TPA treated


title: MM130269

description:
Library name: MM130269
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


title: 22Rv1_CTC_12

description: Library name: 22Rv1_CTC_12

value: prostate


title: MM130265

description:
Library name: MM130265
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: S4 mouse tissue, Saline control

description:
Library name: S4
Mus musculus mouse tissue, group S group, Saline control
B16F10_mouse_Tumor.csv


title: 22Rv1_CTC_8

description: Library name: 22Rv1_CTC_8


title: WT_CRE HTO_A

description: Library name: A-HTO

value: WT


title: S3 mouse tissue, Saline control

description:
Library name: S3
Mus musculus mouse tissue, group S group, Saline control
B16F10_mouse_Tumor.csv


title: MM130267

description:
Library name: MM130267
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: MM130256

description:
Library name: MM130256
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: Y1.5_PIMQ_ATAC-seq_Rep1

description:
Library name: Sample 14
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

value: Skin

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


title: C4 mouse tissue, CST treated

description:
Library name: C4
Mus musculus mouse tissue, group C group, CST treated
B16F10_mouse_Tumor.csv

value: CST treated

value: C group


title: 22Rv1_CTC_11

description: Library name: 22Rv1_CTC_11


title: Y1.5_PIMQ_ATAC-seq_Rep2

description:
Library name: Sample 15
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

value: Epidermal Stem Cell

value: wildtype


title: 22Rv1_CTC_17

description: Library name: 22Rv1_CTC_17


title: C2 mouse tissue, CST treated

description:
Library name: C2
Mus musculus mouse tissue, group C group, CST treated
B16F10_mouse_Tumor.csv


title: Y1_PIMQ_ATAC-seq_Rep1

description:
Library name: Sample 8
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).