|
| Status |
Public on Aug 04, 2024 |
| Title |
PLC-input |
| Sample type |
SRA |
| |
|
| Source name |
HCC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PLC/PRF/5 cells
cell type: Human liver cancer cells
genotype/variation: ZFP64 overexpression
chip antibody: none (input)
|
| Treatment protocol |
PLC/PRF/5 cells was transfeted with ZFP64 overexpressed lentivirus
|
| Growth protocol |
PLC/PRF/5 cell was cultured in DMEM supplemented with 5% FBS, incubated at 37°C in a humidified chamber containing 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and ZFP64-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (TruSeq® chip DNA LT Sample Prep Kit), including performing end repair, adenylating 3' ends, ligating adapters and enriching DNA Fragments. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
S025_genefund-A_PLC-input_AHKYMFDSXX_S7
|
| Data processing |
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.05 as cutoff
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using Deeptools(3.5.0)
|
| |
|
| Submission date |
Aug 04, 2021 |
| Last update date |
Aug 04, 2024 |
| Contact name |
Chuan Yuan Wei |
| E-mail(s) |
18111210068@fudan.edu.cn
|
| Phone |
13262679886
|
| Organization name |
Zhongshan, Fudan
|
| Department |
Liver cancer institute
|
| Lab |
Jia Fan's Lab
|
| Street address |
fenglin road 180
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE181436 |
The PKCα/ZFP64/CSF1 Axis restricts Tumor Response to Anti-PD1 by driving Macrophage M2 Polarization in Hepatocellular Carcinoma |
|
| Relations |
| BioSample |
SAMN20570042 |
| SRA |
SRX11646013 |
