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Series GSE109760 Query DataSets for GSE109760
Status Public on Jul 11, 2019
Title Profiling chromatin state by single-cell itChIP-seq [ATAC-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 ATAC-seq was processed with 50K mouse embryonic cells as previously described. Tn5-MEA/B was used to tagment the native chromatin.
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 (2)
GSM2966529 ATAC-50K-ESC_rep1
GSM2966530 ATAC-50K-ESC_rep2
This SubSeries is part of SuperSeries:
GSE109762 Profiling chromatin state by single-cell itChIP-seq
BioProject PRJNA431984
SRA SRP131646

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
GSE109760_RAW.tar 183.7 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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