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Series GSE139857 Query DataSets for GSE139857
Status Public on Dec 14, 2020
Title Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Recently, multiple single cell assays were developed for detecting histone marks at the single cell levels. These techniques are either limited by the low cell throughput or sparse reads which limit their applications. To address these problems, we introduce indexing single-cell immunocleavage sequencing (iscChIC-seq), a multiplex indexing method based on TdT terminal transferase and T4 DNA ligase mediated barcoding strategy and single-cell ChIC-seq, which is capable of readily analyzing histone modifications across tens of thousands of single cells in one experiment. Application of iscChIC-seq to profiling H3K4me3 and H3K27me3 in human white blood cells (WBCs) enabled successful detection of more than 10,000 single cells for each histone modification with 11K and 45K non-redundant reads per cell, respectively. Cluster analysis of these data allowed identification of monocytes, T cells, B cells, and NK cells from WBCs. The cell types annotated from H3K4me3 single cell data are specifically correlated with the cell types annotated from H3K27me3 single cell data. Our data indicate that iscChIC-seq is a reliable technique for profiling histone modifications in a large number of single cells, which may find broad applications in studying cellular heterogeneity and differentiation status in complex developmental and disease systems.
Overall design Profiling genome-wide H3K4me3 with multiplex indexing tecnique at the single cell level

Please note that processed data have been updated on Feb 26, 2021.
Contributor(s) Ku WL, Pan L, Zhao K
Citation(s) 33853847
Submission date Nov 01, 2019
Last update date Oct 13, 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 (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (960)
GSM4147373 human WBC GB930101
GSM4147374 human WBC GB930102
GSM4147375 human WBC GB930103
BioProject PRJNA587152
SRA SRP227999

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
GSE139857_K4_K27_bivalent_domain.txt.gz 181.4 Kb (ftp)(http) TXT
GSE139857_barcode_96.txt.gz 366 b (ftp)(http) TXT
GSE139857_combined_sicer_E100_peaks.sort.merge.txt.gz 517.6 Kb (ftp)(http) TXT
GSE139857_peakname3.txt.gz 362.8 Kb (ftp)(http) TXT
GSE139857_scH3K4me3_7798_cell_counts_at_WBCpeaks.txt.gz 23.3 Mb (ftp)(http) TXT
GSE139857_scK27_4lanes_rc_at_25951_bipeaks.txt.gz 28.7 Mb (ftp)(http) TXT
GSE139857_scK27_4lanes_rc_at_79100peaks_width10k.txt.gz 113.4 Mb (ftp)(http) TXT
GSE139857_scK4_rc_at_25951_bipeaks.txt.gz 12.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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