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Series GSE136578 Query DataSets for GSE136578
Status Public on Apr 07, 2024
Title Super cChIP-seq, a robust and universal epigenetic profiling method using 10 cells
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary ChIP-seq is the standard technique to characterize the genome-wide epigenomic modifications, which requires millions of cells as starting material. Although some methods have recently reported to be suitable for epigenomic profiling with a small number of cells, there are still no methods capable of profiling both histone modifications and DNA methylation with extremely low input. Here, we developed a new method by supplementing carrier materials of chemically modified epigenetic markers and dUPT-containing DNA fragments during ChIP procedures. Using this strategy, we generated high-quality epigenomic profiles of both histone modifications (super cChIP-seq) and DNA methylation (super cMeDIP-seq) with as few as 10 cells. Thus, we provide a robust and straightforward universal approach for epigenomic profiling starting with extremely low input.
 
Overall design Extremely-low input ChIP-seq. Fragmentated chromatin DNA and carrier are enriched with antibody, and followed by library construction.
 
Contributor(s) Hu C, Wu J, Kang Y, Zhao Q, Du W, Wu J, Shao Z, Zhao X
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Submission date Aug 28, 2019
Last update date Apr 08, 2024
Contact name Xiaodong Zhao
E-mail(s) congxiahu0606@sjtu.edu.cn
Organization name Shanghai Jiao Tong University
Lab zxd lab
Street address 800 Dongchuan RD
City Shanghai
ZIP/Postal code 200240
Country China
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (32)
GSM4051759 K562_H3K4me3_1K_cells_super_cChIP-seq_Rep1
GSM4051760 K562_H3K4me3_1K_cells_super_cChIP-seq_Rep2
GSM4051761 K562_H3K4me3_100_cells_super_cChIP-seq_Rep1
Relations
BioProject PRJNA562718
SRA SRP219532

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

Supplementary file Size Download File type/resource
GSE136578_RAW.tar 1.2 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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