|
| Status |
Public on Sep 28, 2020 |
| Title |
siQ-ChIP: A reverse-engineered quantitative framework for ChIP-sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a key technique for mapping the distribution and relative abundance of histone posttranslational modifications (PTMs) and chromatin-associated factors across genomes. There is a perceived challenge regarding the ability to quantitatively plot ChIP-seq data, and as such, approaches making use of exogenous additives, or “spike-ins” have recently been developed. Relying on the fact that the IP step of ChIP-seq is a competitive binding reaction, we present a quantitative framework for ChIP-seq analysis that circumvents the need to modify standard sample preparation pipelines with spike-in reagents. We also introduce a visualization technique that, when paired with our formal developments, produces a much more rich characterization of sequencing data.
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| |
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| Overall design |
Examination of H3K27me3 in a wild-type cell line and one treated with the EZH2 inhibitor (EPZ6438).
Examination of H3K9me3 in a wild-type cell line.
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| Contributor(s) |
Dickson BM, Tiedemann RL, Chomiak AA, Vaughan RM, Cornett EM, Rothbart SB |
| Citation(s) |
32994221 |
| Submission date |
Jun 18, 2019 |
| Last update date |
Dec 07, 2020 |
| Contact name |
Scott Rothbart |
| E-mail(s) |
scott.rothbart@vai.org
|
| Organization name |
Van Andel Research Institute
|
| Street address |
333 Bostwick Avenue NE
|
| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA549445 |
| SRA |
SRP201748 |
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