|
| Status |
Public on Nov 15, 2017 |
| Title |
BG4-ChIP-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HaCaT cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HaCaT
|
| Treatment protocol |
NA
|
| Growth protocol |
HaCaT cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was isolated from HaCaT 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. For further details see methods section in the associated manuscript.
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 following paper https://doi.org/10.1038/ng.3662. 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/.
|
| |
|
| Submission date |
May 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Giovanni Marsico |
| E-mail(s) |
persego@gmail.com
|
| Organization name |
CRUK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE99205 |
Chromatin immunoprecipitation for genome-wide mapping of endogenous G-quadruplex DNA structures |
|
| Relations |
| BioSample |
SAMN07157022 |
| SRA |
SRX2844871 |
