|
| Status |
Public on Jul 26, 2022 |
| Title |
YBX1 |
| Sample type |
SRA |
| |
|
| Source name |
S18
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: nasopharyngeal carcinoma cell
cell line: S18
|
| Treatment protocol |
untreated
|
| Growth protocol |
S18 cells were maintained in DMEM supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, S18 cells were fixed in 1% formaldehyde at room temperature for 10 min and quenched by 1 × glycine solution for 5 min. Afterward, nuclei were isolated, lysed and sonicated to yield chromatin fragments of about 200-1000 bp. The sheared chromatin was incubated with anti-YBX1 (Abcam, ab76149) or negative control IgG at 4℃ overnight, followed by immobilization on ChIP Grade Protein A/G Magnetic Beads. After extensive washing, immunoprecipitated DNA was eluted, de-crosslinked, purified
ChIP and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adaptor ligation with the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified for 15 cycles and sequenced using Illumina NovotSeq 6000 with single-end 2x150 as the sequencing mode.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NextSeq6000. Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length < 35 bp) and low-quality reads. Then FastQC is used to ensure high reads quality.
The clean reads were mapped to the reference genome (assembly GRCh38) using the Bowtie2 (v2.2.6) software.
Peak detection was performed using the MACS (v2.1.1) peak finding algorithm with 0.001 set as the p-value cutoff. Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak
|
| |
|
| Submission date |
Nov 23, 2021 |
| Last update date |
Jul 26, 2022 |
| Contact name |
Yingqin Li |
| E-mail(s) |
liyingq@sysucc.org.cn
|
| Organization name |
Sun Yat-sen University Cancer Center
|
| Lab |
State Key Laboratory of Oncology in South China
|
| Street address |
Room 927, Building 2, No. 651 Road Dong Feng East
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510060 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE189457 |
Genome-wide chromatin binding of YBX1 in nasopharyngeal carcinoma (NPC) cell line S18 (ChIP-Seq) |
| GSE189459 |
CircIPO7 Promotes Nasopharyngeal Carcinoma Metastasis and Cisplatin Chemoresistance by Regulating YBX1 Nuclear Localization |
|
| Relations |
| BioSample |
SAMN23413517 |
| SRA |
SRX13212043 |
