|
| Status |
Public on Jan 24, 2018 |
| Title |
Pax7 ChIPseq in AtT-20 expressing ERPax7 (72h) (exo-like protocol) |
| Sample type |
SRA |
| |
|
| Source name |
AtT-20 cells cells expressing 3x flag-ER-Pax12
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pituitary corticotroph cell
passages: 10-20
cell line: AtT-20 cells
treatment: 72 hours of 4-hydroxy-tamoxifen
chip antibody: FlagM2 Sigma F1365
|
| 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 |
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-400bp were kept for library preparation
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
AtT-20 cells cells expressing 3x flag-ER-Pax12
|
| Data processing |
Sequence reads were trimmed for adapter sequences.
The resulting 50bp 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) |
| GSE87180 |
ChIPseq in Pax7-reprogrammed corticotropes AtT-20 cells |
| GSE87185 |
Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate |
|
| Relations |
| BioSample |
SAMN06203090 |
| SRA |
SRX2463205 |
