|
| Status |
Public on Jan 01, 2024 |
| Title |
Lung, de novo SCLC, chromatin, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
genotype: PNEC-RPMT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Established Omni-ATAC extraction protocol
Established Omni-ATAC library construction protocol
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Bulk ATAC-seq raw reads were processed using the standard nf-core ATAC-seq pipeline. Library quality was assessed using the nf-core quality-control report unique mapped reads, GC-content, and peak annotation. Loess normalization was used for differential accessibility testing to minimize technical batch effects.
Assembly: mm10
Supplementary files format and content: .txt: comma separated text file. This contains the consensus peak annotations for ATAC chromatin peaks across all replicates.
|
| |
|
| Submission date |
Nov 19, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Ashley M Laughney |
| E-mail(s) |
ashley.laughney@gmail.com
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Physiology, Biophysics, and Systems Biology
|
| Lab |
Laughney Lab
|
| Street address |
413 East 69th Street
|
| City |
NEW YORK |
| State/province |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE248206 |
Lineage-specific intolerance to oncogenic drivers restricts histological transformation [ATAC-Seq] |
| GSE248207 |
Lineage-specific intolerance to oncogenic drivers restricts histological transformation |
|
| Relations |
| BioSample |
SAMN38320971 |
| SRA |
SRX22573287 |
