|
| Status |
Public on May 08, 2024 |
| Title |
K562 H3K27me3 HiChIP |
| Sample type |
SRA |
| |
|
| Source name |
K562 wild type cells
|
| Organism |
Homo sapiens |
| Characteristics |
hichip antibody: H3K27me3 (C36B11, Cell Signaling Technologies)
treatment: untreated
cell line: K562
|
| Treatment protocol |
none
|
| Growth protocol |
K562 cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin. All cultures were maintained at 37 °C, 5% CO2 in a humidified incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Five million cells was fixed and used for HiChIP experiment using Dovetail HiChIP MNase kit (Dovetail Genomics) according to the manufacturer’s protocol. Briefly, 1ul MNase enzyme mix and 1250ng H3K27me3 antibody were used for HiChIP experiment.
Libraries were prepared using the Dovetail Primer Set for Illumina and Dovetail Library Module for Illumina kits, according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Library strategy: HiChIP
HiChip analysis was done by following the documentation of Dovetail (https://hichip.readthedocs.io/en/latest/index.html) step by step. Paired-end reads were aligned to hg19 using BWA mem (0.7.17-r1188) with parameter “-5SP -T0” to get mapped reads in sam file format. Next, the mapped reads were processed by pairtools (0.3.0) to perform valid ligation recording, sorting, removing PCR duplicates, and splitting. After this step, pairs and bam were obtained from pairtools. Bam file was then sorted and produced index file using samtools for downstream analysis. Before the further process, the quality of HiChip library and the enrichment of HiChIP reads at H3K27me3 binding sites were evaluated by the QC report generated from get_qc.py and enrichment_stats.sh scripts in HiChIP.
After Pasing the QC assessment, pairs file from pairtools was converted into contact matrix in hic format by Juicer Tools and HiChip loops were called by FitHiChIP (9.0) in 25kb bin size.
Genome_build: hg19
Supplementary_files_format_and_content: *.bed
Supplementary_files_format_and_content: *.hic
|
| |
|
| Submission date |
Jan 11, 2022 |
| Last update date |
May 08, 2024 |
| Contact name |
KAIJING CHEN |
| E-mail(s) |
KAIJING001@e.ntu.edu.sg
|
| Phone |
98667053
|
| Organization name |
Nanyang Technological University
|
| Department |
school of biological science
|
| Lab |
Melissa Fullwood
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE193484 |
Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [HiChIP] |
| GSE193489 |
Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth |
|
| Relations |
| BioSample |
SAMN24849028 |
| SRA |
SRX13731845 |
