|
| Status |
Public on Jan 24, 2018 |
| Title |
ATACseq in AtT-20 expressing ER-Pax7 (72 hours) 50k cells (rep1) |
| Sample type |
SRA |
| |
|
| Source name |
AtT-20 cells expressing 3x flag-ER-Pax7
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pituitary corticotroph cell
passages: 10-20
cell line: AtT-20 cells
treatment: 72 hours of 4-hydroxy-Tamoxifen treatment
|
| Treatment protocol |
(if applicable) Treatment was added directly in the media of the cultured cells and left for the mentioned amount of time
|
| Growth protocol |
AtT-20 cells were plated on adherent culture dishes to obtain about 70% confluence after 3 days. They are cultured in DMEM + 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Transposase reaction was performed on 100 000 nuclei using Nextera enzyme
Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequence reads were trimmed for adapter sequences.
The resulting reads were trimmed to obtain high quality reads and then mapped to the mm10 mouse genome build using Bowtie with the following parameter: -t -p 4 --trim5 1 --best mm10 –S
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads
|
| |
|
| Submission date |
Jan 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
ALEXANDRE MAYRAN |
| E-mail(s) |
alexandre.mayran@epfl.ch
|
| Organization name |
EPFL
|
| Street address |
Station 19
|
| City |
LAUSANNE |
| State/province |
Waadt |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE87178 |
ATACseq in Pax7-reprogrammed corticotropes AtT-20 cells |
| GSE87185 |
Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate |
|
| Relations |
| BioSample |
SAMN06203071 |
| SRA |
SRX2463195 |
