|
| Status |
Public on Jan 24, 2018 |
| Title |
WGBS in AtT-20 expressing Neo |
| Sample type |
SRA |
| |
|
| Source name |
AtT-20 cells expressing 3x flag-Neo
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pituitary corticotroph cell
passages: 10-20
cell line: AtT-20 cells
treatment: non treated
: Bisulfite conversion
|
| 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 |
Genomic DNA was extracted from 1,000,000 cells and bisulfite conversion was performed with the Zymo Research EZ DNA Methylation- Lightning Kit.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 100bp paired end reads.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequence reads were trimmed for adapter sequences.
The resulting 100bp reads were mapped to thebisulfite converted reference genome GRCm38 with bismarck. After alignement, we removed duplicate reads.
Genome_build: mm10
Supplementary_files_format_and_content: Differential methylation analsysis was performed using methylkit
|
| |
|
| Submission date |
Sep 21, 2016 |
| 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) |
| GSE87184 |
Whole Genome Bisulfite Sequencing in Pax7-reprogrammed corticotropes AtT-20 cells |
| GSE87185 |
Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate |
|
| Relations |
| BioSample |
SAMN05799349 |
| SRA |
SRX2183005 |
