|
| Status |
Public on Jan 27, 2014 |
| Title |
SC_shGNMT_2_RRBS |
| Sample type |
SRA |
| |
|
| Source name |
Sciatic nerves
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6J
age: Post natal day 5-8
cell type: Schwann cells
medium: Schwann cell medium
treatment: no treatment
|
| Treatment protocol |
Schwann cells were isolated from scitaic nerves from C57Bl6J mice, and then either treated with SAMe or GNMT silenced by lentiviral vectors.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
(1) After isolation, cultured Schwann cells were scraped, 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 |
| |
|
| 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/)
Genome_build: mm9
Supplementary_files_format_and_content: [Sample].call files contain location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs
Supplementary_files_format_and_content: (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for
Supplementary_files_format_and_content: methylation percentage per base is available at http://code.google.com/p/amp-errbs.
Supplementary_files_format_and_content: Format:
Supplementary_files_format_and_content: <chrBase>
Supplementary_files_format_and_content: <chr (mm9)>
Supplementary_files_format_and_content: <Base>
Supplementary_files_format_and_content: <directon of read/alignment>
Supplementary_files_format_and_content: <coverage>
Supplementary_files_format_and_content: <freqC>
Supplementary_files_format_and_content: <freqT
Supplementary_files_format_and_content: <quality scores for each base in read>
|
| |
|
| Submission date |
Sep 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) |
| GSE45702 |
DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy |
| GSE51031 |
DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy [Bisulfite-Seq2] |
|
| Relations |
| BioSample |
SAMN02360338 |
| SRA |
SRX357066 |
