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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 23, 2018 |
| Title |
BL05 |
| Sample type |
SRA |
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| Source name |
BL-Hi-C experiment of 500 K cells, rep2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
restriction enzyme: HaeIII
proximity ligation: two-step ligation
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| Growth protocol |
K562 cell line was cultured according to manufacturer's instructions.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
BL-Hi-C: cells were cross-linked with formaldehyde and then nucleuses were isolated for lysis. Then the chromatin was fragmented with restriction enzymes (HaeIII, MboI or HindIII) and the proximal ends were ligated (one-step or two-step) with biotin-labeled bridge linker in situ. A whole genome chromatin was extracted and sheared into 300-500 bp. Then the biotinylated junctions were captured by M-280 streptavidin magnetic beads.
The BL-Hi-C libraries were prepared according to the standard Illumina library construction protocol and sequenced on the HiSeq2500/HiSeq X Ten.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Library strategy: BL-Hi-C
We used software ChIA-PET2 to process BL-Hi-C sequencing data, including linker trimming, reads alignment (BWA), paired-end tags formation and duplicates removal (two-step ligation parameters: -m 1 -k 2 -e 1 -A ACGCGATATCTTATC -B AGTCAGATAAGATAT; one-step ligation parameters: -m 2 -k 2-e 1 -A AGCTGAGGGATCCCTCAGCT -B AGCTGAGGGATCCCTCAGCT ).
genome build: GRCh37/hg19
processed data files format and content: bedpe format: Chromosome 1, Start 1, End 1, Chromosome 2, Start 2, End 2, ID, ., Strand 1, Strand 2
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| Submission date |
Jan 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhengyu LIANG |
| E-mail(s) |
zyliang.cn@gmail.com
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| Organization name |
Southern University of Science and Technology
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| Department |
Department of Biology
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| Lab |
Zhengyu Liang
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| Street address |
1088 Xueyuan Avenue
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| City |
Shenzhen |
| State/province |
Guangzhou |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE93921 |
BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions |
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| Relations |
| BioSample |
SAMN06250178 |
| SRA |
SRX2510778 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2465026_BL05.bedpe.gz |
1.5 Gb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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