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Series GSE109757 Query DataSets for GSE109757
Status Public on Jul 11, 2019
Title Profiling chromatin state by single-cell itChIP-seq [itChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We present a low-cost, generalizable ChIP-seq (itChIP), compatible to both low-input and single cells for profiling chromatin states. This method combines chromatin opening, simultaneous cellular indexing and chromatin tagmentation in a single tube. Single-cell itChIP data yield ~ 5000 unique reads per cell, sufficiently defining cell identifies and subpopulations of a given cell type. Our results demonstrate that itChIP is a generalizable technology for single-cell chromatin profiling of samples limited to ultra-low number of cells.
Overall design Based on Tn5 transposition of chromatin, the generalizable itChIP combines chromatin opening, simultaneous cellular indexing and chromatin tagmentation in a single tube.
Contributor(s) Ai S, Xiong H, Li C, Luo Y, Shi Q, He A
Citation(s) 31481796
Submission date Jan 29, 2018
Last update date Oct 10, 2019
Contact name Chen Li
Organization name Peking University
Department Institute of Molecular Medicine
Lab Aibin He Lab
Street address Yihe Yuan Road No.5
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (43)
GSM3609634 H3K4me3_1M_it_rep1_ESC
GSM3609635 H3K4me3_1M_it_rep2_ESC
GSM3609636 H3K4me3_10K_it_EpiLC
This SubSeries is part of SuperSeries:
GSE109762 Profiling chromatin state by single-cell itChIP-seq
BioProject PRJNA431987
SRA SRP131644

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
GSE109757_RAW.tar 2.4 Gb (http)(custom) TAR (of BW)
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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