|
| Status |
Public on Apr 18, 2019 |
| Title |
WT ESC |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic Stem Cell
strain: J1
culture: 2i+vitC
genotype: Wild-type
|
| Growth protocol |
ES Cells were either cultured in 2+vitC, or differentiated for seven days into Epiblast-like cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 50,000 cells were washed, but not lysed. Cells were transposed using the Nextera DNA library prep kit (Illumina) for 30 min at 37º. DNA was immediately purified using Qiagen MinElute Kit (Qiagen).
qPCR was used to determine the optimal cycle number for library amplification. The libraries were sequenced on the Illumina HiSeq2500 platform to obtain 2x100 paired-end reads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
2x100bp paired-end reads were aligned onto the Mouse reference genome (mm10) using Bwa mem v0.7.5a with default parameters. Duplicate reads were removed using Picard v1.130 (http://broadinstitute.github.io/picard/). Tracks were created using HOMER software v4.7,
Genome_build: mm10
Supplementary_files_format_and_content: bigWig : coverage
|
| |
|
| Submission date |
Oct 17, 2018 |
| Last update date |
Apr 18, 2019 |
| Contact name |
teissandier aurelie |
| E-mail(s) |
aurelie.teissandier@curie.fr
|
| Organization name |
institut curie
|
| Department |
u934
|
| Lab |
Epigenetic decisions and reproduction in mammals
|
| Street address |
26 rue d'Ulm
|
| City |
paris |
| ZIP/Postal code |
75248 |
| Country |
France |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE121400 |
Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming [ATAC-Seq] |
| GSE121405 |
Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming |
|
| Relations |
| BioSample |
SAMN10252410 |
| SRA |
SRX4899475 |
