|
| Status |
Public on Feb 27, 2018 |
| Title |
THP-1(BglII) |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood monocyte cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood monocyte cells
cell line: THP-1
|
| Treatment protocol |
Without treatment
|
| Growth protocol |
K562 (ATCC, CCL-243) and THP-1 (ATCC, TIB-202) cells were grown in RPMI-1640 with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Follow DLO Hi-C library construction protocol. Cells were double cross-linked with EGS and formaldehyde and then digested with a restriction enzyme. The digested chromatins were divided into two tubes, ligated with different 20-bp half linkers by the simultaneous digestion and ligation, and subsequently mixed for in-gel proximity ligation. The ligated DNA was purified and digested by MmeI, which released specific 80-bp DLO Hi-C DNA fragments. These DLO Hi-C DNA fragments were ligated with Illumina adapters and subjected to high-throughput sequencing
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
THP-1 cell lines DLO Hi-C data (Constuct by BglII)
|
| Data processing |
ChIA-PET Tool used for linker filtering
Two end of interacted fragments were seperated by the command awk
Two end of interacted fragments were separately mapped to hg19 by bwa v0.7.12-r1039 with the parameter -n 0, and then unique mapping reads were conserved
Samtools v1.2 was used to transfer the sam format to bed format
Two end bed format files were combined to bedpe file by a perl script
Redundancies and same fragment interactions were discard by perl scripts
The bedpe format file sorted by the command sort
The sorted file transferred to matrix by a python script
The matrix normalized by ICE
Locations of topologically associated domains (TADs) were computed using the scripts provided by Dixon et al. 2012 (PMID: 22495300)
Genome_build: hg19
Supplementary_files_format_and_content: The THP-1_HindIII.TADs.bed, THP-1_BglII.TADs.bed and THP-1_MseI.TADs.bed contain the coordinates of TADs
|
| |
|
| Submission date |
Nov 08, 2016 |
| Last update date |
Feb 27, 2018 |
| Contact name |
Ping Hong |
| Organization name |
Huazhong Agricultural University
|
| Department |
college of informatics
|
| Lab |
Guoliang's Lab
|
| Street address |
No.1,Shizishan Street
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE89663 |
Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture |
|
| Relations |
| BioSample |
SAMN06005748 |
| SRA |
SRX2336881 |
