 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 16, 2022 |
| Title |
HiCuT: an efficient and low input method to identify protein-centric chromatin interactions |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
Protein-DNA interactions regulate gene expression, and some interactions occur over large distances, such that they are nearby in 3-D space but are separated by many nucleotides in the linear genome. These long-range chromatin loops are essential for gene regulation but remain difficult to interrogate. Methods to capture these chromatin interactions mediated by a specific protein factor include Hi-C sequencing coupled with chromatin immunoprecipitation-sequencing (ChIP-seq), chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), proximity ligation-assisted ChIP-seq (PLAC-seq), and HiChIP. These methods all require high amounts of starting material (0.5M – 100M cells) , which limits their general use. Here, we describe Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT), an enzyme-based tagmentation strategy that provides efficient and high-resolution protein-centric chromatin mapping from as few as 5,000 cells. Thus, HiCuT will permit protein-centric 3-D genome binding assessment in rare cell populations that were previously not testable, including primary cells, human tissue samples, and personalized epigenomics.
|
| |
|
| Overall design |
HiCuT assay on GM12878 and primary Keratinocytes
|
| |
|
| Contributor(s) |
Sati S, Jones P, Kim HS, Zhou LA, Leung T |
| Citation(s) |
35320278 |
| |
| Submission date |
Oct 15, 2021 |
| Last update date |
Apr 19, 2022 |
| Contact name |
Satish Sati |
| E-mail(s) |
satisatish16@gmail.com
|
| Phone |
+12675863881
|
| Organization name |
University of Pennsylvania
|
| Department |
Dermatology
|
| Lab |
Thomas Leung
|
| Street address |
421 Curie Blvd, BRB 1039
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA771696 |
| SRA |
SRP341623 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE186011_RAW.tar |
555.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...