|
| Status |
Public on Sep 04, 2020 |
| Title |
PeTa_100nM_GSK_d6_R2 [ATACseq] |
| Sample type |
SRA |
| |
|
| Source name |
PeTa_100nM_GSK_d6
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PeTa
cell type: Merkel cell carcinoma cell line
treatment: GSK-LSD1
drug concentration: 100nM
|
| Treatment protocol |
Cells were treated for 6 days with either 100nM GSK-LSD1 or DMSO.
|
| Growth protocol |
Cells were cultured as suspension cells in RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin and 50 mg/mL streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
100,000 viable cells were harvested and nuclei isolated for transposition reaction according to the Omni-ATACseq protocol.
Sequencing libraries were barcoded using Illumina Nextera Indexing
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
ATACseq data was analyzed using the nf-core/ATACseq pipeline (Patel et al, 2019) aligning against the human genome hg38 and calling peaks with MACS2 in narrow- and broad-peak mode. Aligned reads of the individual replicates were merged using samtools v1.9 (Li et al, 2009) and RPGC-normalized tracks were calculated and plotted as composite density plots using deeptools v3.1.2 (Ramírez et al, 2016).
Genome_build: hg38
Supplementary_files_format_and_content: BigWig file format with genome-wide ATACseq profiles.
|
| |
|
| Submission date |
Mar 31, 2020 |
| Last update date |
Sep 05, 2020 |
| Contact name |
Anna Obenauf |
| Organization name |
IMP - Research Institute of Molecular Pathology
|
| Lab |
Anna Obenauf
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE147814 |
Genome-wide chromatin accessibility mapping upon pharmacological LSD1 inhibition in MCC [ATACseq] |
| GSE147817 |
Pharmacological LSD1 inhibition in MCC |
|
| Relations |
| BioSample |
SAMN14501397 |
| SRA |
SRX8036449 |
