|
| Status |
Public on Mar 11, 2024 |
| Title |
Male 2017, selected line, warm temp, fish 08 |
| Sample type |
SRA |
| |
|
| Source name |
milt/sperm
|
| Organism |
Salvelinus fontinalis |
| Characteristics |
tissue: milt/sperm
Sex: Male
treatment: selected line, warm temp
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a salt-precipitation based protocol (Aljanabi and Martinez 1997, NAR. doi:10.1093/nar/25.22.4692).
Whole-genome bisulfite sequencing libraries were prepared using the NEB Ultra II library prep protocol.
Libraries were pooled and sequenced across 20 lanes on the HiSeq X platform with between two and four samples per lane and an expected total sequencing effort of one half lane per sample.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Five |
| |
|
| Data processing |
Raw reads were adaptor trimmed and filtered using fastp
Trimmed reads were mapped with bwa-meth
Duplicates were removed using MarkDuplicates from the Piacrd Tools suite
Methylation pileups were generated using methylDackel
Assembly: SaNama_1.0 (RefSeq: GCF_016432855.1)
Supplementary files format and content: bedGraph files with methylated and non-methylated base coverage counts
|
| |
|
| Submission date |
Mar 14, 2023 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Kyle Wellband |
| E-mail(s) |
kyle.wellband@gmail.com
|
| Organization name |
Université Laval
|
| Department |
Institut de biologie intégrative et des systèmes
|
| Street address |
1030 avenue de la Médecine
|
| City |
Québec |
| State/province |
QC |
| ZIP/Postal code |
G1V 0A6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL33246 |
| Series (1) |
| GSE227271 |
Selection and simulated climate-warming effects on Brook Charr sperm DNA methylation |
|
| Relations |
| BioSample |
SAMN33749428 |
| SRA |
SRX19666812 |
