|
| Status |
Public on Sep 11, 2018 |
| Title |
ALL-SIL_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
ALL-SIL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ALL-SIL
|
| Growth protocol |
Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed as previously described (Buenrostro et al. 2015) with minor changes. In brief, 50,000 cells were lysed and fragmented using Tn5 transposase (Illumina). Next, the samples were purified using the MinElute kit (Qiagen). The transposased DNA fragments were amplified and purified using the PCR Cleanup kit (Qiagen).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
fastq files were aligned with STARv2.4.2a to GRCh38 with --alignIntronMax 1 --alignMatesGapMax 1000 to avoid splice awareness.
Peak calling was performed with MACS2 using broad setting
Genome_build: GRCh38
Supplementary_files_format_and_content: xls file with MACS2 output
|
| |
|
| Submission date |
Feb 14, 2018 |
| Last update date |
Mar 13, 2019 |
| Contact name |
Karen Verboom |
| E-mail(s) |
karen.verboom@ugent.be
|
| Organization name |
Ghent University
|
| Department |
Pediatrics and Genetics
|
| Lab |
Center for Medical Genetics Ghent
|
| Street address |
De Pintelaan 185
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN08537122 |
| SRA |
SRX3700577 |
