|
| Status |
Public on Apr 19, 2023 |
| Title |
CaSki ChIP Input |
| Sample type |
SRA |
| |
|
| Source name |
CaSki cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CaSki
chip antibody: none
|
| Growth protocol |
Ca Ski were maintained in RPMI-1640 supplemented with 10% fetal bovine serum. SiHa, HeLa and C33A were cultured in DMEM supplemented with 10% fetal bovine serum (10270-106, Gibco, USA). S12 were maintained in DF12 medium according to a previous study5. Raji were maintained in suspension culture in RPMI-1640 supplemented with 10% fetal bovine serum (10270-106, Gibco, USA). All cells were cultured in a humidified 37 °C incubator set at 5% CO2 and passaged 2–3 times weekly as recommended by ATCC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genome DNA were extracted using kit (69,506, Qiagen, Germany). The PCR reaction was conducted using Q5 Hot Start High-Fidelity 2X Master Mix (M0494S, NEW ENGLAND BioLabs, USA).
Cells were cross-linked with formaldehyde and collected with trypsin and the chromatin was extracted. Extracted chromatin was sonicated to an average size of 200‐ 500 bp. Chromatin immunoprecipitation was performed following the Diagenode iDeal histone ChIP‐seq protocol. Finally, pair-end data was generated on an Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CaSki ChIP Input clean read
|
| Data processing |
The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with gene TPM for every gene and every sample
Supplementary_files_format_and_content: H3K4me3 and H3K27Ac peak.txt files for every sample with none antibody ChIP-Seq as control
|
| |
|
| Submission date |
Jan 28, 2022 |
| Last update date |
Apr 19, 2023 |
| Contact name |
yuyan wang |
| E-mail(s) |
wangyy365@mail2.sysu.edu.cn
|
| Organization name |
The First Affiliated Hospital, Sun Yat-sen University
|
| Street address |
Zhongshan 2nd Road, Yuexiu
|
| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE195631 |
HPV integration generates cellular super enhancer and functions as ecDNA to regulate genome-wide transcription |
|
| Relations |
| BioSample |
SAMN25353142 |
| SRA |
SRX13965907 |
