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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
E-mail(s) chenli_imm@pku.edu.cn
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
Relations
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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