|
| Status |
Public on Nov 04, 2023 |
| Title |
ChIP-Input-Jurkat-gAAVS1_biol_rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat
cell type: T-ALL
chip antibody: none
treatment: gAAVS1 transduction
time: 7 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico instrument (Diagenode).
Sequencing libraries were constructed using ThruPLEX DNA-seq kit (Takara, R400674) according to the manufacturer’s protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Sequencing reads were processed using fastp for adaptor trimming and quality filtering.
The reads were mapped to reference human genome hg38 using Bowtie2 (with the parameter --very-sensitive).
Output files were converted to sorted bam files, proper-paired reads were extracted, and PCR duplicates were removed using SAMtools.
Bam files from replicates were merged, and coverage tracks were generated using deepTools bamCoverage.
Peaks were called using MACS2 (with the parameter -q 1e-10)
Assembly: hg38
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
Sep 12, 2023 |
| Last update date |
Nov 04, 2023 |
| Contact name |
Kosuke Yusa |
| Organization name |
Kyoto University
|
| Department |
Institue for Life and Medical Sciences
|
| Street address |
53 Shogoin Kawaharacho, Sakyo-ku
|
| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL28038 |
| Series (2) |
| GSE227275 |
Characterization of cBAF complex in T-cell acute lymphoblastic leukemia (T-ALL) |
| GSE243007 |
Chromatin binding of RUNX1 in T-cell acute lymphoblastic leukemia (T-ALL) cells with depletion cBAF complex [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN37367427 |
| SRA |
SRX21762919 |
