|
| Status |
Public on Apr 18, 2019 |
| Title |
WT (E14) ESC Rep 2_pLiz VP |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic Stem Cell
strain: E14TG2a
culture: 2i+vitC
genotype: Wild-type
|
| Treatment protocol |
Cells were cross-linked, digested and ligated twice to make high resolution circular DNA
|
| 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 |
Inverse primers with illumina adapter sequences amplified the circular DNA prior to sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: 4C-seq
Reverse primer sequences were removed in 3' end of the reads using Cutadapt v1.12. Reads shorter than 15bp were discarded.
Cleaned sequences were aligned onto the Mouse reference genome (mm10) using Bowtie2 v2.1.0 allowing one mismatch in the seed (22bp) and an end to end alignment.
Following steps were performed using the FourCSeq R package (v1.12.0). Mouse reference genome was in-silico digested using the two restriction enzymes. Restriction fragments that do not contain a cutting site of the second restriction enzyme or are smaller than 20bp were filtered out. Fragments 2.5 kb up- and downstream from the viewpoint were excluded during the procedure. Intrachromosomal contacts were kept. Valid fragments were quantified. The fragment counts were then normalized per one million reads. Data were smoothed using a running mean function with 5 informative fragments.
Genome_build: mm10
|
| |
|
| 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) |
| GSE121399 |
Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming [4C-Seq] |
| GSE121405 |
Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming |
|
| Relations |
| BioSample |
SAMN10252400 |
| SRA |
SRX4899436 |
