|
| Status |
Public on Jan 24, 2018 |
| Title |
ATAC in Pax7 KO replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
neuro-lntermediate lobe
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 129/sv
cell type: pituitary
genotype/variation: Pax7 KO
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We performed the ATACseq on dissected neuro-intermediate lobe from Pax7 WT and Pax7 KO mice. Transposase reaction was performed on 50 000 nuclei.
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 |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| 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 |
GPL9185 |
| Series (2) |
| GSE87179 |
ATACseq in primary pituitary cells |
| GSE87185 |
Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate |
|
| Relations |
| BioSample |
SAMN07278714 |
| SRA |
SRX2957342 |
