|
| Status |
Public on Jun 29, 2022 |
| Title |
A375-Top5 |
| Sample type |
SRA |
| |
|
| Source name |
Skin
|
| Organism |
Homo sapiens |
| Characteristics |
strain: A375
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-Seq samples were prepared as previously described in Buenrostro et al., 2015
ATAC-Seq libraries were prepared as previously described in Buenrostro et al., 2015.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Adapters and reads with a quality score less than 20 were trimmed from the final libraries using Skewer/0.2.2
Trimmed reads were aligned to the hg19 genome using bowtie2 with default parameters
Peaks were called using MACS2 with the following parameters: --nomodel --extsize 300 -g hs --keep-dup all.
Genome_build: hg19
|
| |
|
| Submission date |
Jan 14, 2020 |
| Last update date |
Jun 29, 2022 |
| Contact name |
Rosela Golloshi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Tennessee Knoxville
|
| Department |
Department of Biochemistry & Cellular and Molecular Biology
|
| Lab |
Rachel Patton McCord Lab
|
| Street address |
1311 Cumberland Avenue
|
| City |
Knoxville |
| State/province |
TN |
| ZIP/Postal code |
37996 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE143674 |
Consticted migration is associated with stable 3D genome structure differences in cancer cells (ATAC-Seq) |
| GSE143678 |
Consticted migration is associated with stable 3D genome structure differences in cancer cells |
|
| Relations |
| BioSample |
SAMN13863747 |
| SRA |
SRX7562963 |
