|
| Status |
Public on Mar 06, 2019 |
| Title |
WGBS_mm_dLGN_Math5KO_P23 |
| Sample type |
SRA |
| |
|
| Source name |
dLGN from P23 Math5-KO mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6J.129-Atoh7tm1Gla/Mmucd
developmental stage: P23
tissue: brain
cell type: dLGN (dorsolateral geniculate nucleus)
genotype: Math5-KO
gender: male
|
| Growth protocol |
Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee, Virginia Polytechnic Institute and State University
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from mouse dLGN tissues using DNeasy mini Kit (Qiagen) according to the manufacturer’s instructions. One microgram genomic DNA per sample was used for library construction following the standard Whole Genome Bisulfite Sequencing (WGBS) method.
One microgram mouse genomic DNA was spiked with 0.02% unmethylated cl857 Sam7 Lambda DNA (Promega) and sonicated to 200-bp fragments with Covaris M2 (AB). After end repair, dA tailing, the DNA fragments were ligated with cytosine-methylated Illumina TruSeq DNA adapters using T4 DNA ligase (NEB) overnight. After purification, Adapter-ligated DNA fragments were subject to bisulfite conversion using the EpiTect Bisulfite Kit (Qiagen). After bisulfite conversion, the single-stranded uracil-containing DNA was subjected to 12 cycles of PCR reaction with Illumina TruSeq PCR primers and 2.5 U Pfu TurboCx Hotstart DNA polymerase (Agilent) to recover enough DNA for sequencing. The recovered libraries were sequenced on Hiseq 4000 platform (Illumina).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequecing adapters and low quality sequences were removed by Trim Galore (v0.4.1) with parameters: -q 28 --length 30. Trimmed reads were mapped to mm10 by Bismark (v0.16.3) with Bowtie2 (v2.2.9). PCR duplicates were removed by bismark deduplication script in paired end mode.
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH (.bdg)
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Mar 06, 2019 |
| Contact name |
Xiguang Xu |
| E-mail(s) |
xiguang@vt.edu
|
| Organization name |
Virginia Tech
|
| Department |
Department of Biomedical Sciences and Pathobiology
|
| Lab |
Epigenomics and Computational Biology Laboratory
|
| Street address |
1015 Life Science Circle
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24060 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE119525 |
WGBS (Whole Genome Bisulfite Sequencing) of Wild-type and Math5-/- mouse dLGN (dorsolateral geniculate nucleus) at postnatal day 6 and postnatal day 23 |
| GSE125482 |
Wild-type and Math5-/- mouse dLGN (dorsolateral geniculate nucleus) at postnatal day time points |
|
| Relations |
| BioSample |
SAMN09980245 |
| SRA |
SRX4644282 |
