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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
E-mail(s) lir4@niehs.nih.gov
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
Relations
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
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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