|
| Status |
Public on Jun 03, 2024 |
| Title |
HepG2_4_SP2509_H3K4me2_CUTTAG |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: liver
cell line: HepG2
cell type: HCC
cut&tag antibody: H3K4me2 ab32356 Abcam
treatment: SP2509
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The CUT&Tag experiments were performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech Co., Ltd., TD903) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V2 for Illumina kit and PCR amplification
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The sequencing reads obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess the quality of the reads.
Adapter trimming and read filtering were performed using Trim-galore (0.6.5-1).
The filtered reads were then aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6 with parameters.
The aligned reads were processed by MACS2 (v2.2.7.1) to call peaks and transformed to bigwig formatted files by bamCoverage function in Deeptools (v3.5.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag
|
| |
|
| Submission date |
Mar 23, 2023 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Boshi Wang |
| E-mail(s) |
wbs137@126.com
|
| Organization name |
Shanghai Cancer Institute
|
| Street address |
No.800 Dongchuan Road
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE228071 |
Exploring the epigenetic regulatory role of KDM1A inhibition in HCC cells [HepG2_SP2509_CUTTag_seq] |
|
| Relations |
| BioSample |
SAMN33872264 |
| SRA |
SRX19758118 |
