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Sample GSM3464562 Query DataSets for GSM3464562
Status Public on Nov 09, 2019
Title 18_WT
Sample type SRA
Source name islets of Langherans isolated from wt mice
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: islets of Langerhans
age: 70 weeks old
Treatment protocol Islets were isolated from 70 week old mice
Growth protocol Mice were housed under a 12-h light/dark cycle and given an ad libitum regular chow diet (A04; Safe)
Extracted molecule genomic DNA
Extraction protocol Total DNA was purified from isolated islets using MasterPureTM Complete DNA and RNA Purification kit
RRBS libraries were prepared with the 'Premium RRBS kit' (Diagenode) according to the manufacturer's instructions.
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2500
Data processing Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
Trim Galore was used to perform adapter trimming and quality control in two subsequent steps. The 2 additional bases that contain a cytosine which was artificially introduced at the end-repair step during the library preparation (--rrbs option) were removed.
The mm9 mouse reference genome was prepared for Bismark using bismark_genome_preparation script. Bismark software (version 0.17.0) from the Babraham Institute was used to align trimmed RRBS reads to the mouse genome.
Then, bismark_methylation_extractor script extracted the methylation call for every single C analysed.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated text file with columns ID, chromosome, start, strand, coverage, frequency methylated, frequency non-methylated
Submission date Nov 09, 2018
Last update date Nov 10, 2019
Contact name Marion de Toledo
Organization name CNRS UMR5535
Department IGMM
Street address 1919 route de Mende
City Montpellier
ZIP/Postal code 34293
Country France
Platform ID GPL17021
Series (2)
GSE122360 β-cell adaptation in mice expressing exclusively lamin C counteracts glucose intolerance associated with aging, obesity and diabetes (LamineA-C_RRBS)
GSE122361 β-cell adaptation in mice expressing exclusively lamin C counteracts glucose intolerance associated with aging, obesity and diabetes
BioSample SAMN10405190
SRA SRX4998196

Supplementary file Size Download File type/resource
GSM3464562_18_CpG_Rawcounts.txt.gz 246.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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