|
| Status |
Public on Mar 13, 2023 |
| Title |
4T1 Sorted intact micronuclei rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
4T1 Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
cell type: 4T1 TNBC Breast Cancer Cells
treatment: Reversine 0.5 uM 48 hours
|
| Treatment protocol |
4T1 cells were treated with 0.5 µM Reversine for 48 hours before micronuclei isolation (Toufektchan E and Maciejowski J, STAR Protoc. 2021)
|
| Growth protocol |
4T1 cells were grown in RPMI media supplemented with 10% FBS and 1X Pen-Strep in 245x245 mm dish (Corning Corning™ TC-Treated Culture Dishes)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
According to Toufektchan E and Maciejowski J, STAR Protoc. 2021
Library prepared according to Buenrostro et. al. 2015 (Micronuclei adjusted to 20x of nuclei)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample_MNI_2_IGO_12086_4
|
| Data processing |
Reads were mapped to mm10 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: mm10
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 |
GPL19057 |
| Series (2) |
| GSE186584 |
Epigenetic dysregulation from chromosomal transit in micronuclei [4T1 MN ATAC-Seq] |
| GSE186589 |
Epigenetic dysregulation from chromosomal transit in micronuclei |
|
| Relations |
| BioSample |
SAMN22569238 |
| SRA |
SRX12776878 |
