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Sample GSM2746935

Query DataSets for GSM2746935

Status

Public on Dec 02, 2019

Title

netrin-1 rep2 [RRBS]

Sample type

SRA

Source name

mouse embryonic stem cells

Organism

Mus musculus

Characteristics

cell type: CGR8 mESC
transfection: empty ppy-cagg-netrin-ires-puro vector expressing the netrin-1 transgene

Treatment protocol

mESC are stably transfected with ppy-cagg-ires-puro vector epty or encoding a netrin-1 transgene.

Growth protocol

mESC are grown in serum/LIF conditions

Extracted molecule

genomic DNA

Extraction protocol

genomic DNA is extracted on colums
RRBS libraries prepared by inegragen: Msp1 enzymatic digestion, gel selection of DNA fragments, adaptor ligation, bisulfite conversion, libraries preparation, paired end sequencing 2x75bp on illumina hiseq4000

Library strategy

Bisulfite-Seq

Library source

genomic

Library selection

RANDOM

Instrument model

Illumina HiSeq 4000

Data processing

read quality: Quality of reads was assessed for each sample using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
sequence alignment: We used BS-Seeker21 to map RRBS data to the mouse genome mm10/GRCm38 and retrieve the number of methylated and unmethylated cytosines at each covered CpG site.
methylation rates analysis: Methylation rates were then integrated across CpG island (CGI)-based and gene-based features. CGI-based features were defined as follows: CpG islands (from UCSC database GRCm38/mm10), shores (2 kb on each side of the island) and shelves (2 kb on each side of the shores). DNA methylation outside CpG islands was analyzed by grouping CpG sites not located in CGI-based features every 100kb window. Gene-based features were defined based on Ensembl Mus musculus GRCm38.78 assembly. We calculated for each gene the methylation rate across the promoter region (TSS +/- 500bp) and the gene body.
Supplementary_files_format_and_content: xls files. Integrated DNA methylation values across genomic features are provided as Excel tables. The DNA_methylation_by_gene_features.xlsx table contains DNA methylation values in gene features (TSS, body), the DNA_methylation_by_CGI_features.xlsx table contains DNA methylation values in CGI features (islands, shores, shelves) and the DNA_methylation_by_100kb_windows.xlsx table contains DNA methylation values in 100kb-windows. For each feature, the number of values considered, the number of individual CpG sites and the average methylation value are indicated for each sample.

Submission date

Aug 18, 2017

Last update date

Dec 02, 2019

Contact name

Fabrice Lavial

Organization name

CRCL

Street address

28 rue Laennec

City

Lyon