|
| Status |
Public on Jul 29, 2024 |
| Title |
JC73-RK100 RK-582 30 nM Input |
| Sample type |
SRA |
| |
|
| Source name |
JC73-RK100
|
| Organism |
Homo sapiens |
| Characteristics |
cut&run antibody: none
cell line: JC73-RK100
cell type: colorectal cancer patient-derived cells
treatment: 30 nM RK-582 for 120 h
|
| Treatment protocol |
JC73, JC73-RK100 and JC21 cells were treated with the indicated concentration of tankyrase inhibitor RK-582 for 120h.
|
| Growth protocol |
JC73, JC73-RK100 and JC21 cells were maintained in StemProTM hESC SFM supplemented with 10 µM Y-27632 and Antibiotic-Antimycotic Solution in humidified atmosphere with 5% CO2 at 37℃.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
JC73, JC73-RK100 and JC21 cells were treated with 0, 30 nM, 3 µM tankyrase inhibitor RK-582 for 120h. CUT&RUN was performed using CUT&RUN Assay Kit (Cell Signaling Technology) according to the manufacturer’s instructions.
Sequence libraries were constructed with NEBNest UltraⅡ DNA library Prep Kit for Illumina (New England Biolabs, Inc.) according to the manufacture's instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw FASTQ file were checked quality using FastQC (version 0.11.9) and removed adapters using Trimmomatic (version 0.39).
The reads were aligned to hg38 and sacCer3 using STAR (version 2.7.9a).
Normalization using spike-in yeast DNA were performed by bedtools genomecov function.
Peak calling was performed using SEACR (version 1.3) with stringent mode.
Normalized CUT&RUN data was converted to bigwig file format using ucsc-bedgraphtobigwig (version 445).
Assembly: hg38
Supplementary files format and content: Bigwig files
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Jul 31, 2023 |
| Last update date |
Jul 29, 2024 |
| Contact name |
Shun Morino |
| E-mail(s) |
[email protected]
|
| Organization name |
JFCR
|
| Street address |
3-8-31, Ariake, Koto-ku
|
| City |
Tokyo |
| ZIP/Postal code |
135-8550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE239680 |
BET protein-dependent E2F pathway confers bell-shaped type resistance to tankyrase inhibitors in APC-mutated colorectal cancer [CUT&RUN] |
| GSE239683 |
BET protein-dependent E2F pathway confers bell-shaped type resistance to tankyrase inhibitors in APC-mutated colorectal cancer |
|
| Relations |
| BioSample |
SAMN36773254 |
| SRA |
SRX21200328 |
