|
| Status |
Public on Sep 28, 2022 |
| Title |
HepG2 cells, TFAM KD, H3K4me1 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
disease state: hepatocellular carcinoma
treatment: siRNA TFAM#1 for 72 hours
genotype: TFAM knockdown
chip antibody: anti-Histone H3 (mono methyl K4) antibody - ChIP Grade (ab8895)
|
| Treatment protocol |
For the knockdown experiments, specific siRNAs were introduced to the cells using RNAiMAX reagent (Thermo Fisher Scientific).
|
| Growth protocol |
HepG2 cells were cultured in high glucose (25mM D-glucose) Dulbecco-modified Eagle's Medium (DMEM) (Sigma) supplemented with 10% (v/v) heat-inactivated fetal bovine serum and penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinking and fragmentation were conducted as described for the ChIP-pPCR. Chromatin fragments were incubated at 4 °C overnight with 2 µg of appropriate antibodies and immunoprecipitated with Dynabeads protein A/G (Life Technologies). After decrosslinking, the DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
The ChIP-seq library was prepared using a NEBNext Ultra DNA Library Prep Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HepG2_05
|
| Data processing |
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina)
Sequence data were alignmened onto the human reference genome hg19 using the Burrows-Wheeler alignment algorithm.
Low read/mapping quality reads were trimmed out with Galaxy.
Genome_build: hg19
Supplementary_files_format_and_content: The bigwig files were generated using CONVERTER bam to bigwig (Galaxy).
|
| |
|
| Submission date |
Feb 22, 2022 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Mitsuyoshi Nakao |
| E-mail(s) |
mnakao@gpo.kumamoto-u.ac.jp
|
| Phone |
+81963736800
|
| Organization name |
Kumamoto University
|
| Department |
Institute of Molecular Embryology and Genetics
|
| Lab |
Medical Cell Biology
|
| Street address |
2-2-1 Honjo, Chuo-ku
|
| City |
Kumamoto |
| ZIP/Postal code |
860-0811 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE197242 |
ChIP-seq analysis of H3K4me1 and H3K27ac in TFAM-depleted HepG2 cells |
|
| Relations |
| BioSample |
SAMN26177886 |
| SRA |
SRX14255725 |
