|
| Status |
Public on Jun 19, 2024 |
| Title |
B16_TdgTrp53_DKO1 ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cell line
cell line: B16
cell type: Melanoma
genotype: Tdg Trp53 DKO
|
| Growth protocol |
B16 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A total of 5 × 104 B16 cells were collected and washed with ice-cold PBS, followed by suspending in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) to isolate nucleis.
Isolated nuclei were then tagmented with Tn5 transposase and libraries were constructed using TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme TD501). Amplified libraries were purified using MinElute columns and quantified with a Bioanalyzer using high-sensitivity DNA chips (Agilent 2100). ATAC-seq libraries were pooled and sequenced using an Illumina NovaSeq 6000 platform with paired-end reads of 150 bases.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For data analysis, raw data were trimmed by Trim Galore with default settings. Then, the clean data were mapped to mouse reference genome mm10 using bowtie2 with the parameters --no-unal --no-mixed --no-discordant -X 2000. Duplicates were removed using Picard. Bedgraph files were generated following MACS2 callpeak with the parameters --nomodel --shift -100 --extsize 200 --p 0.00001 -B -g mm. Metaplot and heatmap were generated using deepTools.
Assembly: mm10
Supplementary files format and content: bigwig files for ATAC-seq signals
|
| |
|
| Submission date |
Jul 06, 2023 |
| Last update date |
Jun 19, 2024 |
| Contact name |
Zhenyu Shao |
| Organization name |
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
|
| Department |
Center for Excellence in Molecular Cell Science
|
| Street address |
Yueyang Road 320
|
| City |
shanghai |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE236717 |
Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [ATAC-seq] |
| GSE236728 |
Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer |
|
| Relations |
| BioSample |
SAMN36344164 |
| SRA |
SRX20927615 |
