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Series GSE105012 Query DataSets for GSE105012
Status Public on Mar 28, 2019
Title Single cell chromatin immunocleavage sequencing (scChIC-Seq) to profile histone modification
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report a single-cell chromatin immunocleavage sequencing (scChIC-seq) methodology for analyzing histone modifications, which involves targeting of the micrococcal nuclease (MNase) by tethering it to an antibody and selective PCR amplification of cleaved target sites. We show that the protocol reliably detects the H3K4me3 and H3K27me3 target sites in single human white blood cells (WBC), resulting data for successful identification of unique blood cell types based on clustering analysis.
Overall design The technique, scChIC-seq, was applied to profile H3K4me3 and H3K27me3 using small number of cells and single cells. By comparing with the Bulk ChIP-seq signal, scChIC-seq was shown to have high specificity. scChIC-seq was applied to profile H3K4me3 using single human white blood cells. The highly co-methylated and highly variable peaks were shown to be related to underlying cellular populations.
Contributor(s) Ku W, Nakamura K, Gao W, Cui K, Hu G, Tang Q, Ni B, Zhao K
Citation(s) 30923384
Submission date Oct 16, 2017
Last update date Jul 25, 2021
Contact name Keji Zhao
Organization name national Institute of Health
Department National Heart, Lung, and Blood Institute
Street address Building 10 Room 7B06A
City Bethesda
State/province MD
ZIP/Postal code 20814
Country USA
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (425)
GSM2814007 ChIPseq mouse LUC/LUC#2-H3K4me3
GSM3475847 mouse 3T3 fixed frozen 3000 cells H3K4me3 Ab-MNase rep 1
GSM3475848 mouse 3T3 fixed frozen 3000 cells IgG Ab-MNase rep 1
BioProject PRJNA414428
SRA SRP120016

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Supplementary file Size Download File type/resource
GSE105012_RAW.tar 1.5 Gb (http)(custom) TAR (of BED, BEDGRAPH, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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