|
| Status |
Public on Jul 19, 2017 |
| Title |
E14 Np95-/- RRBS |
| Sample type |
SRA |
| |
|
| Source name |
ES-E14
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Np95-/-
cell type: Embryonic stem cell
strain: 129/Ola
|
| Growth protocol |
Embryonic stem cells were cultured under standard feeder-free conditions on gelatinized tissue culture dishes with media containing DMEM (Gibco, 31966021) supplemented with 100 µM 2-mercaptoethanol (Gibco, 31350010), 1 x non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 2 mM L-glutamine (Gibco), 1% penicillin-streptomycin, 15% KnockOut Serum Remplacement (Gibco, 10828028) and 103 U/ml leukemia inhibitory factor (LIF, Millipore) at 37 °C under an atmosphere of 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA with Qiagen All Prep DNA/RNA miniprep, Cat#80204
RRBS protocol as described in Gu et al., 2011 (Nature Protocols) doi:10.1038/nprot.2010.190
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Bisulfited
|
| Data processing |
Sequencing was realized by Integragen genomics on an Illumina HiSeq4000 platform. Image analysis and base calling is performed using Illumina Real Time Analysis ( 2.7.3 ) with default parameters.
Fastq files were first trimmed with trim_galore version 0.4.0 (--phred33 --length 40 --rrbs –non_directional --paired)
Fastq files were mapped to mouse genome (mm9) with bismark (bismark_v0.14.3)
Methylation state analysis has been performed with methylkit R package (version 0.9.5) and R-3.2.0.
CpG methylation was calculated over CpG with a minimum covarage of ten reads and a maximum coverage corresponding to the 99.9 percentil.
Genome_build: NCBI Build 37 – mm9
Supplementary_files_format_and_content: Bedgraph for methylation percentage were generated with methylkit
|
| |
|
| Submission date |
Nov 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Pierre-Antoine Defossez |
| E-mail(s) |
pierre-antoine.defossez@univ-paris-diderot.fr
|
| Organization name |
CNRS-Université Paris Diderot - Sorbonne Paris Cité
|
| Department |
UMR7216 "Epigenetics and Cell Fate"
|
| Lab |
Fonctional Domains of Eukaryotic Genomes
|
| Street address |
35 rue Hélène Brion
|
| City |
Paris |
| ZIP/Postal code |
75205 |
| Country |
France |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE89819 |
A histone mimic within DNA Ligase 1 links DNA replication and DNA remethylation: a revised model for the maintenance of DNA methylation by UHRF (RRBS) |
|
| Relations |
| BioSample |
SAMN06014814 |
| SRA |
SRX2345691 |
