|
| Status |
Public on Apr 19, 2023 |
| Title |
HEK293T ChIP-seq H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
treatment: H3K27ac antibody
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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 |
| |
|
| Data processing |
RNA-seq: 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.
ChIP-seq: 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.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports
|
| |
|
| Submission date |
Oct 19, 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 |
SAMN31370307 |
| SRA |
SRX17960348 |
