|
| Status |
Public on Aug 28, 2020 |
| Title |
Bisulfite-Seq LV_T1F4 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Salmo salar |
| Characteristics |
timepoint: T1
|
| Treatment protocol |
Fish from a single management group were sacrificed at a timepoint immediately before initiation of the long-light regime (throughout referred to as T1) and at three timepoints afterwards (T2, T3 and T4).
|
| Growth protocol |
Fish were managed in a tank based experimental system to facilitate a long-light photoperiod regime known to stimulate the onset of sexual maturation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue samples were snap frozen in liquid N2 and stored at -80 °C. gDNA was isolated using DNeasy blood and tissue kit (QIAGEN) as previously described (Mohamed et al., 2018). Tissues were lysed in 360 μL of lysis solution on a Precellys 24 homogenizer for 30s at 4.0 ms−1. Samples were incubated with 40 μL of Proteinase K enzyme at 56 °C for 1 h. Following lysis, samples were treated with RNase (8 μL of RNase A incubated for 2 min at room temperature). DNA was bound to the provided columns, washed twice and eluted in 100 μL at room temperature. gDNA was fragmented (200-400bp) by sonication using Covaris S220, followed by end repair/adenylation and adapter ligation. Bisulfite modification was performed to the DNA fragments using the EZ DNA Methylation-GoldTM Kit (Zymo Research, Inc.)
12 RNA-Seq libraries (2 time points x 3 tissues x 2 biological replicates) were prepared using the TruSeq RNA Sample Preparation Kit (Illumina). Libraries were sequenced on 634 Illumina Nova-Seq 6000 sequencing platform
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Liver T1 library biol. rep. 2
|
| Data processing |
Raw data quality control was implemented using Trim Galore v0.5 to filter bases based on their quality (bases with Q scores > 30 were retained) and remove both universal and indexed adapter sequences. Processed high-quality data were mapped to into the bisulfite-converted version of the Atlantic salmon reference genome ICSASG_v2 (Lien et al., 2016) using BSseeker2 v2.1.8 (Guo et al., 2013) with default parameters for aligning paired-end libraries using Bowtie2 (Langmead & Salzberg 2012).
PCR duplicates were detected and removed using Picard MarkDuplicates (http://broadinstitute.github.io/picard/). Filtered (duplicates-free) reads (110 M PE reads) were retained for downstream methylation analysis with an average genome coverage of 11x in pituitary, ovary and liver.
Methylation calling was conducted using the Python script call-methylation.py within BSseeker2
CG position with 10x coverage were used to infer differential methylation in the R package DSS
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000233375.1
Supplementary_files_format_and_content: 10x_filtered_CG_position files
|
| |
|
| Submission date |
Aug 27, 2020 |
| Last update date |
Aug 28, 2020 |
| Contact name |
Amin Roushdy Mohamed |
| E-mail(s) |
am_rd85@yahoo.com
|
| Organization name |
CSIRO
|
| Department |
Agriculture and Food
|
| Lab |
Aquaculture Genomics
|
| Street address |
306 Carmody Rd, University of Queensland
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23792 |
| Series (2) |
| GSE156997 |
Multitissue DNA methylome profiling during onset of salmon maturation |
| GSE157003 |
Multiomics profiling during onset of Salmon maturation |
|
| Relations |
| BioSample |
SAMN15924861 |
| SRA |
SRX9024645 |
