|
| Status |
Public on Jul 16, 2018 |
| Title |
K562_BG4-ChIP-rep_1_input |
| Sample type |
SRA |
| |
|
| Source name |
K562 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
antibody: none
|
| Treatment protocol |
NA
|
| Growth protocol |
K562 cells were cultured in RPMI-1640 medium supplemented with 10%FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was isolated from K562 cells that were cross-linked using 1% formaldehyde for 10 min at RT and prepared using a ChIP-qPCR Kit (Chromatrap, cat. no. 500117). Chromatin was sonicated using a Bioruptor Plus (Diagenode) to give a fragment distribution of 100-500 bp.
G4 ChIPed DNA was subjected to Nextera library preparation (Illumina, cat. no. FC-121-1030). For further details see methods section in the associated manuscript.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The data was processed as described in the associated manuscript. Details about the analysis can also be found at https://github.com/sblab-bioinformatics/dna-secondary-struct-chrom-lands/blob/master/Methods.md
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at https://github.com/taoliu/MACS/. A tiled data file (TDF) file (.tdf) is a binary file that contains data that has been preprocessed by igvtools for faster display in IGV.
|
| |
|
| Submission date |
Dec 05, 2017 |
| Last update date |
Feb 11, 2020 |
| Contact name |
Avazeh T Ghanbarian |
| Organization name |
University of Cambridge
|
| Department |
Cancer Research UK, Cambridge Inst
|
| Lab |
Balasubramanian
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE107690 |
G-quadruplex structures moulds the DNA methylome |
|
| Relations |
| Reanalyzed by |
GSE145090 |
| BioSample |
SAMN08131881 |
| SRA |
SRX3444808 |
