|
| Status |
Public on Apr 29, 2023 |
| Title |
HiC for patient 5676 |
| Sample type |
SRA |
| |
|
| Source name |
Patient
|
| Organism |
Homo sapiens |
| Characteristics |
ctcf status: Deleted
deep sequenced: No
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HiC was performed according to Rao et al. Cell, 2014. In short chromatin was crosslinked using formaldehyde, digested using MboI. Subsequently, ends were filled in using biotin labelled nucleotides and ligation was performed in situ. DNA was then extracted from the nuclei and purified. The DNA template was then sheared and a streptavidin pulldown was performed to enrich for DNA concatemers containing a ligation junction.
Illumina library prep was performed using custom adapters identical to those used in the illumina truseq kit and PCR amplified using adapter-overhang PCR.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Mapping was done using BWA mem
Duplicates were removed using HICUP v0.5.10
Interaction matrices were generated using Juicer
Insulation scores were calculated using HiCExplorer
Genome_build: CRCh37
Supplementary_files_format_and_content: Hic file
|
| |
|
| Submission date |
Aug 17, 2021 |
| Last update date |
Apr 29, 2023 |
| Contact name |
Rico Hagelaar |
| E-mail(s) |
[email protected]
|
| Organization name |
Princess Maxima Center
|
| Street address |
Heidelberglaan 25
|
| City |
Utrecht |
| ZIP/Postal code |
3584CS |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE182316 |
Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia [HiC] |
| GSE182317 |
Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia |
|
| Relations |
| BioSample |
SAMN20840956 |
| SRA |
SRX11805070 |
