|
| Status |
Public on Jan 24, 2018 |
| Title |
H3K9me3 ChIPseq in AtT-20 expressing Neo |
| Sample type |
SRA |
| |
|
| Source name |
AtT-20 cells expressing 3x flag-Neo
|
| Organism |
Mus musculus |
| Characteristics |
cell line: AtT-20 cells
cell type: pituitary corticotroph cell
passages: 10-20
genotype/variation: expressing 3x flag-Neo
chip antibody: H3K9me3 millipore 07-442
|
| 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 |
| |
|
| 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 |
Jun 26, 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 |
SAMN07278732 |
| SRA |
SRX2957353 |
