|
| Status |
Public on Nov 09, 2019 |
| Title |
19_KIN-KIN |
| Sample type |
SRA |
| |
|
| Source name |
islets of Langherans isolated from lmna LCS 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 |
| E-mail(s) |
marion.detoledo@igmm.cnrs.fr
|
| 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 |
|
| Relations |
| BioSample |
SAMN10405189 |
| SRA |
SRX4998197 |
