|
| Status |
Public on Mar 20, 2021 |
| Title |
M93-Entorhinal Cortex (RRBS) |
| Sample type |
SRA |
| |
|
| Source name |
Entorhinal Cortex
|
| Organism |
Mus musculus |
| Characteristics |
Sex: F
mouse_id: M93
group: 2
tissue: Entorhinal Cortex
|
| Treatment protocol |
Mice were terminally anaesthetized with pentobarbital (intraperitoneal injection) and transcardially perfused with phosphate-buffered saline (PBS). The entorhinal cortex was dissected from the left brain hemisphere on wet ice and snap-frozen on dry ice for subsequent RNA-seq analysis
|
| Growth protocol |
Animals were housed under standard conditions (constant temperature and humidity) with a 12h light/dark cycle in individually ventilated cages, with free access to food (Teklad irradiated global rodent diet (Envigo, United Kingdom)) and water.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from all samples was isolated from the entorhinal cortex using the AllPrep DNA/RNA Mini Kit (Qiagen)
RRBS libraries were prepared using the Premium RRBS kit (Diagenode) with some modifications. Libraries were checked using the High Sensitivity D1000 Screentape and 2200 TapeStation System (Agilent Technologies). Final library pools were distributed across thirty-two HiSeq2500 (Illumina) lanes and subjected to 50 bp single-end sequencing.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing quality was assessed using FastQC (version v0.11.7) with all samples characterized by high quality and thus passing QC
Sequences were trimmed using TrimGalore (version 0.4.4_dev), with a quality score of 20 and an error rate of 0.2 used to remove poor quality bases at the ends of reads
Reads with fewer than 20 base pairs after trimming were then removed
Reads were aligned to the mm10 (GRCm38) mouse genome using Bismark v0.19.0 with default parameters, which implements SAMtools 1.8 and Bowtie2 v2.3.4.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix containing methylation values and read depth
|
| |
|
| Submission date |
Mar 19, 2021 |
| Last update date |
Mar 21, 2021 |
| Contact name |
Emma Walker |
| E-mail(s) |
e.m.walker@exeter.ac.uk
|
| Organization name |
University of Exeter
|
| Street address |
RILD Barrack Rd
|
| City |
Exeter |
| ZIP/Postal code |
EX2 5DW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE169234 |
Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify differences in DNA methylation [RRBS] |
| GSE169235 |
Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify differences in DNA methylation |
|
| Relations |
| BioSample |
SAMN18379126 |
| SRA |
SRX10386701 |
