|
| Status |
Public on Mar 13, 2023 |
| Title |
RPE-1 p53KO LMB2OE + DMSO 3 |
| Sample type |
SRA |
| |
|
| Source name |
Retina (female)
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: female
cell type: hTERT-immortalized retinal pigment epithelial cell line
genotype: p53 KO LMB2OE
treatment: DMSO 10 uL 48 hours before splitting, long-term
cell line: RPE-1
|
| Treatment protocol |
RPE-1 cells were treated with either 1:1000 DMSO (vehicle control) or 0.5 µM reversine for 48 hours, before passaging. This treatment was done long-term until passage #8)
|
| Growth protocol |
RPE-1 cells were grown in DMEM supplemented with 10% FBS and 1X Pen-Strep in 100 mm dish (Corning Corning™ 100 mm TC-Treated Culture Dishes)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction was performed according to Buenrostro et. al. 2015
Library prepared according to Buenrostro et. al. 2015
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RPE-1 p53KO LMB2OE DMSO 3
|
| Data processing |
Reads were mapped to hg38 using bowtie2 with the following parameters: -t -X2000 --no-mixed --no-discordant. Reads were filtered based on -F 1804 -q 30 using samtools and the MarkDuplicates function in Picard tools was used to remove PCR duplicates. Peak calling was done using macs2 callpeak function with the following parameters: -f BAM -g hs --nomodel --shift 37 --extsize 73 --keep-dup all -B --SPMR --call-summits -q 1e-2. Summit of peaks were extended by 250bp and merged across samples. IGVtools count function was used to generate TDF files for visualization.
Genome_build: hg38
Supplementary_files_format_and_content: BED - peak calls from MACS2
Supplementary_files_format_and_content: bigWig files for visualization in IGV
|
| |
|
| Submission date |
Oct 26, 2021 |
| Last update date |
Mar 13, 2023 |
| Contact name |
Albert S Agustinus |
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Street address |
408 East 69th Street, Room 419-G
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE186585 |
Epigenetic dysregulation from chromosomal transit in micronuclei [RPE-1 ATAC-Seq] |
| GSE186589 |
Epigenetic dysregulation from chromosomal transit in micronuclei |
|
| Relations |
| BioSample |
SAMN22569477 |
| SRA |
SRX12776910 |
