|
| Status |
Public on Aug 31, 2016 |
| Title |
HiChIP: Efficient and sensitive analysis of protein-directed genome architecture |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
|
| Summary |
Three-dimensional genome structure is central to gene control, but current technologies are often impractical for many biological questions due to cell and read number requirements. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the fraction of conformation-informative reads by over 10-fold and lowers input requirement greater than 100-fold to 1 million cells. HiChIP of cohesin reveals multi-scale genome architecture with greater signal to noise than in situ Hi-C. Thus, HiChIP will enable insight into the genome’s three-dimensional structure and regulation in once-inaccessible biological systems.
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| Overall design |
[HiChIP cohesin] GM and mESC 25m (25 million cell input): 2 biological with 2 technical replicates, mESC 10m, 5m, and 1m: 2 technical replicates
[HiChIP oct4] mESC 25m (25 million cell input): 2 biological with 2 technical replicates
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| |
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| Contributor(s) |
Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY |
| Citation(s) |
27643841 |
| Submission date |
Apr 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Alexander Flynn |
| E-mail(s) |
raflynn@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
380 Roth Way, Room 265
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
|
| Samples (18)
|
| GSM2138324 |
HiChIP GM biological replicate 1 technical replicate 1 |
| GSM2138325 |
HiChIP GM biological replicate 1 technical replicate 2 |
| GSM2138326 |
HiChIP GM biological replicate 2 technical replicate 1 |
| GSM2138327 |
HiChIP GM biological replicate 2 technical replicate 2 |
| GSM2138328 |
HiChIP v6.5 biological replicate 1 technical replicate 1 |
| GSM2138329 |
HiChIP v6.5 biological replicate 1 technical replicate 2 |
| GSM2138330 |
HiChIP v6.5 biological replicate 2 technical replicate 1 |
| GSM2138331 |
HiChIP v6.5 biological replicate 2 technical replicate 2 |
| GSM2138332 |
HiChIP v6.5 10m technical replicate 1 |
| GSM2138333 |
HiChIP v6.5 10m technical replicate 2 |
| GSM2138334 |
HiChIP v6.5 5m technical replicate 1 |
| GSM2138335 |
HiChIP v6.5 5m technical replicate 2 |
| GSM2138336 |
HiChIP v6.5 1m technical replicate 1 |
| GSM2138337 |
HiChIP v6.5 1m technical replicate 2 |
| GSM2238504 |
HiChIP oct4 v6.5 biological replicate 1 technical replicate 1 |
| GSM2238508 |
HiChIP oct4 v6.5 biological replicate 1 technical replicate 2 |
| GSM2238510 |
HiChIP oct4 v6.5 biological replicate 2 technical replicate 1 |
| GSM2238512 |
HiChIP oct4 v6.5 biological replicate 2 technical replicate 2 |
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| Relations |
| BioProject |
PRJNA320090 |
| SRA |
SRP074188 |
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