|
| Status |
Public on Feb 18, 2019 |
| Title |
ChIP_library_CBL0137treated_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
ChIP_library_CBL0137treated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT1080
tissue source: connective tissue
disease: fibrosarcoma
oncogene: ras +
treatment: CBL0137 for 6hrs
chip antibody: anti-CTCF pAb (ActiveMotif ; Cat. No. 61311, Lot 34614003)
|
| Treatment protocol |
Exposure of cells to CBL0137 (3 μm final concentration in the culture medium) was for 6 h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed in two biological replicates according to Abcam X-ChIP protocol (https://www.abcam.com/protocols/cross-linking-chromatin-immunoprecipitation-x-chip-protocol) with minor changes (see Materials and Methods section).
Each library was sequenced using paired end sequencing on an Illumina NextSeq 550;
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
processed data file:
CBL__PePr_peaks.bed
Diff_intra___PePr_CBL_peaks.bed
|
| Data processing |
Reads for each biological replicate were mapped to the human genome (version hg19) using Bowtie2 (version 2.2.3) with very sensitive preset.
Non-uniquely mapped reads were filtered using 'XS:i' flag. Resulted sam files were sorted,possible PCR and optical duplicates were filtered using Samtools (version 1.5) .
Peaks were called using PePr (https://github.com/shawnzhangyx/PePr, PMID: 24894502) with p-value cutoff 0.05 and sliding window size 100bp.
Differential peak calling was performed using PePr (https://github.com/shawnzhangyx/PePr, PMID: 24894502) with --diff option and intra-group normalization
Bigwig files were generated using deepTools version 2.0, for each biological replicate bigwig file was generated as ratio of ChIP signal to Input, with RPKM normalization and bin size 50bp. Smoothed bigwig files were generated as normal bigwig's but with smoothLength parameter = 3bins.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and bed files (as specified at https://genome.ucsc.edu/FAQ/FAQformat.html#format13)
|
| |
|
| Submission date |
Nov 13, 2018 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Artem Luzhin |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Gene Biology RAS
|
| Street address |
Vavilova 34/5
|
| City |
Moscow |
| ZIP/Postal code |
119334 |
| Country |
Russia |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE122462 |
Anti-cancer drugs curaxins target the 3D genome organization [ChIP-seq] |
| GSE122463 |
Anti-cancer drugs curaxins target the 3D genome organization |
|
| Relations |
| BioSample |
SAMN10414221 |
| SRA |
SRX5001395 |
