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Series GSE179266 Query DataSets for GSE179266
Status Public on Oct 20, 2021
Title CUT&Tag-BS: an efficient and low-cost method for simultaneous profiling of histone modification and DNA methylation
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary It remains a challenge to decipher the complex relationship between DNA methylation, histone modification, and the underlying DNA sequence with limited input material. Here, we developed an efficient, low-input, and low-cost method for simultaneous profiling of genomic binding sites of histone modification and methylation status of the underlying DNA at single-base resolution from the same cells in a single experiment by integrating CUT&Tag with tagmentation-based bisulfite sequencing (CUT&Tag-BS). We demonstrated the validity of our method for both active and repressive histone modifications using 250,000 mouse ESCs. CUT&Tag-BS showed similar enrichment patterns of histone modification to those observed in non-bisulfite-treated control; it further revealed that H3K4me1-marked regions are mostly CpG-poor, lack of methylation concordance, and exhibit prevalent DNA methylation heterogeneity among the cells. We anticipate that CUT&Tag-BS will be widely applied to directly address the genomic relationship between DNA methylation and histone modification, especially in low-input scenario with precious biological samples.
Overall design CUT&Tag-BS was performed for H3K4me1, H3K9me3, and H3K27me3 using 250,000 (or fewer) mouse E14 embryonic stem cells. The resulting libraries were sequenced with either paired-end 35-bp (run1) or 75-bp reads (run2). To benchmark our method, we also prepared corresponding non-bisulfite-treated CUT&Tag libraries as controls.
Contributor(s) Li R, Grimm SA
Citation(s) 35028637
Submission date Jul 01, 2021
Last update date Jan 20, 2022
Contact name ruifang li
Organization name NIEHS
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
Platforms (1)
GPL21626 NextSeq 550 (Mus musculus)
Samples (11)
GSM5412769 CnT-BS-H3K4me1.run1
GSM5412770 CnT-BS-H3K4me1.run2
GSM5412771 CnT-BS-H3K9me3.run1
BioProject PRJNA743025
SRA SRP326502

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE179266_CnT-BS.CpG_counts_table.txt.gz 174.1 Mb (ftp)(http) TXT
GSE179266_RAW.tar 667.5 Mb (http)(custom) TAR (of BED, BIGWIG)
GSE179266_unified-H3K27me3.peaks.bed.gz 158.9 Kb (ftp)(http) BED
GSE179266_unified-H3K4me1.peaks.bed.gz 305.7 Kb (ftp)(http) BED
GSE179266_unified-H3K9me3.peaks.bed.gz 186.1 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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