|
| Status |
Public on Oct 01, 2019 |
| Title |
EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
We developed a low input, low sequencing depth method, EpiMethylTag that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA.
|
| |
|
| Overall design |
M-ATAC and CTCF-M-ChIP in mouse embryonic stem cells, M-ATAC and KLF4 M-ChIP in KLF4 KO mESC that reexpress either a WT or mutant version of KLF4 (R462A), and RNAseq
|
| |
|
| Contributor(s) |
Lhoumaud P, Skok J |
| Citation(s) |
31752933 |
| |
| Submission date |
Apr 11, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Priscillia Lhoumaud |
| E-mail(s) |
Priscillia.Lhoumaud@nyumc.org
|
| Phone |
2122630503
|
| Organization name |
NYU Langone Health
|
| Department |
Pathology
|
| Lab |
Jane Skok
|
| Street address |
550 first avenue Smilow 307
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (26)
|
|
| Relations |
| BioProject |
PRJNA532432 |
| SRA |
SRP192109 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE129673_ATAC-BS-GSE131651_WTmerged_R1_bismark_bt2_pe.bedGraph.gz |
61.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE129673_ATAC-BS-GSE131651_WTmerged_R1_bismark_bt2_pe.bismark.cov.gz |
57.8 Mb |
(ftp)(http) |
COV |
| GSE129673_ATAC-BS-MUTmerged_R1_bismark_bt2_pe.bedGraph.gz |
59.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE129673_ATAC-BS-MUTmerged_R1_bismark_bt2_pe.bismark.cov.gz |
57.6 Mb |
(ftp)(http) |
COV |
| GSE129673_M-ATAC-merged.bismark.cov.gz |
57.1 Mb |
(ftp)(http) |
COV |
| GSE129673_M-ATAC-merged.regular_peaks.sort.blacklistfilt.CHR_SORT.TRIM.narrowPeak.gz |
1.9 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE129673_M-ATAC-merged_RPKM.bw |
261.4 Mb |
(ftp)(http) |
BW |
| GSE129673_M-ChIP-CTCF-merged.bismark.cov.gz |
20.2 Mb |
(ftp)(http) |
COV |
| GSE129673_M-ChIP-CTCF-merged.regular_peaks.sort.blacklistfilt.CHR_SORT.TRIM.narrowPeak.gz |
1.0 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE129673_M-ChIP-CTCF-merged_RPKM.bw |
109.6 Mb |
(ftp)(http) |
BW |
| GSE129673_M-ChIP-CTCF-merged_bismark.bedGraph.gz |
22.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE129673_M_ATAC-merged_bismark.bedGraph.gz |
60.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE129673_Mut-Klf4-BC_merged_R1_bismark_bt2_pe.bedGraph.gz |
69.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE129673_Mut-Klf4-BC_merged_R1_bismark_bt2_pe.bismark.cov.gz |
65.0 Mb |
(ftp)(http) |
COV |
| GSE129673_RAW.tar |
3.0 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, BW, COV, NARROWPEAK) |
| GSE129673_RNAseq-mESC-merged.TPM.unstr.txt.gz |
359.6 Kb |
(ftp)(http) |
TXT |
| GSE129673_WT-Klf4-BC_merged_R1_bismark_bt2_pe.bedGraph.gz |
77.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE129673_WT-Klf4-BC_merged_R1_bismark_bt2_pe.bismark.cov.gz |
72.3 Mb |
(ftp)(http) |
COV |
| GSE129673_atac.merged.Peak_atac.merged.Cov_MERGED.tsv.gz |
14.3 Mb |
(ftp)(http) |
TSV |
| GSE129673_ctcf.merged.Peak_ctcf.merged.Cov_MERGED.tsv.gz |
517.6 Kb |
(ftp)(http) |
TSV |
| GSE129673_fimoMA0139_MethylCTCF_PL.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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