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Sample GSM2390046 Query DataSets for GSM2390046
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
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)
BioSample SAMN06014814
SRA SRX2345691

Supplementary file Size Download File type/resource
GSM2390046.bedgraph.gz 11.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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