|
| Status |
Public on Jan 27, 2014 |
| Title |
GNMT_KO1_B_RRBS |
| Sample type |
SRA |
| |
|
| Source name |
Sciatic nerves
|
| Organism |
Mus musculus |
| Characteristics |
genotype: GNMT KO
age: Post natal day 90
strain: C57Bl6J
|
| Growth protocol |
Sciatic nerves from C57Bl6J, GNMT (wt and KO) and (db/+ or db/db) mice of either sex, were dissected and pooled together at different developmental stages.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After isolation, nerves were desheathed and flash-frozen in liquid nitrogen, before pooling together for genomic DNA extraction using PureLINK Genomic Extraction kit from Invitrogen.
RRBS/MspI followed by a modified TruSeq DNA sample preparation kit (Illumina Inc.). Samples were multiplexed according to Illumina's recommendations and experimental design.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
G_K_1.call
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were filtered from the adapter sequences and their quality score using trim_galore software (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and only are retained those with at least 20 phred quality score.
Reads were mapped to mm9 (Mus musculus) reference genome using the BSMAP (http://rrbsmap.computational-epigenetics.org/) with the following parameters -s 12 -D C-CGG .
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 5X coverage. We use methylKit to compute methylation ratios and differential methylation analysis (http://code.google.com/p/methylkit/)
[Sample].call files contain location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs.
Genome_build: mm9
Supplementary_files_format_and_content: Format: <chrBase> <chr (mm9)> <Base> <directon of read/alignment> <coverage> <freqC> <freqT>
|
| |
|
| Submission date |
Mar 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose Luis Lavin |
| E-mail(s) |
joluito@gmail.com
|
| Organization name |
CIC bioGUNE
|
| Street address |
Parque Tecnológico de Bizkaia Building 502, Floor 0
|
| City |
Derio |
| State/province |
Bizkaia |
| ZIP/Postal code |
48160 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16173 |
| Series (2) |
| GSE45343 |
DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy [Bisulfite-Seq] |
| GSE45702 |
DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy |
|
| Relations |
| SRA |
SRX252587 |
| BioSample |
SAMN01984885 |
