|
| Status |
Public on Mar 08, 2021 |
| Title |
U54-HFF-plate-EGS-HindIII-20190718-R2-T1 |
| Sample type |
SRA |
| |
|
| Source name |
Human Foreskin Fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
protocol: in situ Hi-C
enzyme: HindIII
cell line: HFF
|
| Growth protocol |
4DN Protocols are used to culture the cells. Protocols can be found here: https://data.4dnucleome.org/resources/experimental-resources/cell-lines, https://data.4dnucleome.org/biosources/4DNSRGTEEYSL/?redirected_from=%2F4DNSRGTEEYSL. Hela S3 syncronization protocols are adopted from Abramo et al.2019. Nat Cell Biol.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei was extracted by lyse cells in lysis buffer containing NP40 and protease inhibitor.
DNA library was generated by biotin fill-in followed blunt end ligation. Then removal of biotin from un-ligated ends, sonication, end repair, biotin pull-down, Illumina adaptor ligation and paired end PCR.
Hi-C library generated Hi-C 2.0 protocol. Belaghzal et at.2017.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
In situ Hi-C with HindIII on HFF cells with 1% Formaldehyde and 3mM EGS crosslinking
|
| Data processing |
Distiller (https://github.com/mirnylab/distiller-nf) pipeline is used to process Hi-C and Micro-C datasets.
Sequencing reads were mapped to hg38 using bwa mem with flags-SP.
Mapped reads were parsed and classified using the pairtools package (https://github.com/mirnylab/pairtools ) to get 4DN-compliant pairs files.
PCR and/optical duplicates removed by matching the positions of aligned reads with 2bp flexibility.
Pairs were filtered using mapping quality scores (MAPQ > 30) on each side of aligned chimeric read, binned into multiple resolutions and low coverage bins are removed.
Multiresolution cooler files are created using cooler package (https://github.com/mirnylab/cooler.git)
Genome_build: hg38
Supplementary_files_format_and_content: HDF5, Multiresolution cooler files (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Compartment Calls (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Insulation Boundaries (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Loop Calls (https://github.com/open2c/cooltools)
|
| |
|
| Submission date |
Feb 01, 2021 |
| Last update date |
Mar 08, 2021 |
| Contact name |
Job Dekker |
| E-mail(s) |
Job.Dekker@umassmed.edu
|
| Phone |
508-856-4371
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Systems Biology
|
| Lab |
Dekker Lab
|
| Street address |
368 Plantation Street, AS5-1049
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE163666 |
Systematic evaluation of chromosome conformation capture assays |
| GSE165894 |
Systematic evaluation of chromosome conformation capture assays [Hi-C] |
|
| Relations |
| BioSample |
SAMN17727460 |
| SRA |
SRX9995940 |
