|
| Status |
Public on Jul 23, 2020 |
| Title |
ATAC-Seq_Jurkat-1 |
| Sample type |
SRA |
| |
|
| Source name |
T lymphocyte
|
| Organism |
Homo sapiens |
| Characteristics |
disease: acute T cell leukemia
germ layer: Mesoderm
|
| Growth protocol |
All cell lines were cultured following the manufacturer’s recommendations
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was carried out as previously described (Buenrostro 2013) and sequenced on an Illumina HiSeq 4000 with 2x100 paired end sequencing.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
we obtained on average 13 ± 7 million paired-end reads
Adaptor sequences were trimmed using cutadapt in paired-end mode (non-default parameters: -q 15 -O 5 -m 30)
Reads were aligned to hg19 using bowtie (version 0.12.8; non-default parameters: -X 2000, -m 1) after which duplicate reads were removed using Picard MarkDuplicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Oct 18, 2019 |
| Last update date |
Jul 23, 2020 |
| Contact name |
Fabian Grubert |
| E-mail(s) |
fabian.grubert@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE134745 |
Landscape of Cohesin-Mediated Chromatin Loops in the Human Genome |
| GSE139099 |
Landscape of Cohesin-Mediated Chromatin Loops in the Human Genome (ATAC-seq) |
|
| Relations |
| BioSample |
SAMN13059002 |
| SRA |
SRX7023018 |
