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Series GSE109759 Query DataSets for GSE109759
Status Public on Jul 11, 2019
Title Profiling chromatin state by single-cell itChIP-seq [sonication ChIP]
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 Sonication-based ChIP was the traditional method to profile modification of chromatin. Chromatin was sonicated by Q800R to 200-800 bp fragments. After being pulled down by antibody and Dynabeads protein A beads, fragments were ligated with adaptors by ChIPmentation method. After being amplified, libraries were sequenced on Illumina HiSeq 4000 for paired end 150 bp. Sonication-ChIP data played as the positive control of our itChIP-seq.
Contributor(s) 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 (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (3)
GSM2966501 H3K4me3_1M-sonication-ChIP-ESC_rep1
GSM2966502 H3K4me3_1M-sonication-ChIP-ESC_rep2
GSM2966504 H3K4me3_1M-sonication-input-ESC
This SubSeries is part of SuperSeries:
GSE109762 Profiling chromatin state by single-cell itChIP-seq
BioProject PRJNA431986
SRA SRP131645

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
GSE109759_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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