|
| Status |
Public on Aug 11, 2023 |
| Title |
INPUT-SCARB2cas9_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2 cells
cell type: hepatocyte
tissue: liver
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~150 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina bcl2fq software was used for basecalling.
Low-quality reads (Q≤19 bases over 50%), Ns reads (N%>5%) and adapter polluted reads (adapter bases>5 bp) are filtered out.
ChIP-seq reads were aligned to the human genome assembly using Bowtie2.
Peaks were called using MACS2.
Genome_build: Homo_sapiens.GRCh38.89.chr
|
| |
|
| Submission date |
Oct 13, 2021 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Yang Gao |
| E-mail(s) |
yxgyang@126.com
|
| Phone |
18238837867
|
| Organization name |
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College
|
| Street address |
Dongcheng District, Tiantan Xili
|
| City |
Beijing |
| ZIP/Postal code |
100050 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE185838 |
Genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells. |
| GSE185844 |
Scavenger Receptor SCARB2 Drives Hepatic Carcinoma Initiation by Enhancing MYC Transcriptional Activity and Supporting Cancer Stem Cell Traits. |
|
| Relations |
| BioSample |
SAMN22246853 |
| SRA |
SRX12592705 |
