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| 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
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| 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.
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| 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.
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| Contributor(s) |
Li C, Luo Y, Shi Q, He A |
| Citation(s) |
31481796 |
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| Submission date |
Jan 29, 2018 |
| Last update date |
Oct 10, 2019 |
| Contact name |
Chen Li |
| E-mail(s) |
chenli_imm@pku.edu.cn
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| Organization name |
Peking University
|
| Department |
Institute of Molecular Medicine
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| Lab |
Aibin He Lab
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| Street address |
Yihe Yuan Road No.5
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE109762 |
Profiling chromatin state by single-cell itChIP-seq |
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| Relations |
| BioProject |
PRJNA431986 |
| SRA |
SRP131645 |
