|
| Status |
Public on Feb 27, 2018 |
| Title |
WT ZT6_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Cerebral cortex
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
tissue: Cerebral cortex
developmental stage: P120-150
Sex: Male
strain: C57BL/6J
|
| Growth protocol |
Mice were housed in 12 hour light, 12 hour dark conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mice were sacrificed at ZT0, 6, 12, and 16. Genomic DNA was isolated from 5-10mg cortex using the Gentra Puregene kit (Qiagen)
500ng DNA was bisulfite converted using the EZ DNA Methylation-Lightening kit (Zymo). Libraries were prepared with 100ng bisulfite converted DNA using the TruSeq DNA Methylation kit (Illumina) and barcoded using TruSeq DNA Methylation Kit Index PCR Primers (Illumina).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were filtered by Illumina flag
Reads with adapter contamination were trimmed
Reads were aligned to mm10 using BSSeeker2
Trimmed reads and reads with no adapter contamination were combined
SAM files were converted to percent methylation bed files
Percent methylation files from each chromosome were combined
Genome_build: mm10
Supplementary_files_format_and_content: Bed files containing percent methyation values per base
|
| |
|
| Submission date |
Aug 29, 2017 |
| Last update date |
Feb 27, 2018 |
| Contact name |
Rochelle Coulson |
| E-mail(s) |
rlcoulson@ucdavis.edu
|
| Organization name |
University of California, Davis
|
| Street address |
One Shields Ave.
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE103249 |
Snord116-dependent diurnal rhythm of DNA methylation in mouse cortex |
|
| Relations |
| BioSample |
SAMN07572141 |
| SRA |
SRX3144962 |
