|
| Status |
Public on Jul 09, 2019 |
| Title |
Brain2-RRBS-farmed |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Dicentrarchus labrax |
| Characteristics |
tissue: Brain
FISH origin: Farmed (reared in aquarium facilities)
age: 3 years
|
| Treatment protocol |
Wild fish samples stored in RNAlater immediately after dissection and farmed fish samples snap frozen in liquid nitrogen. All samples were then kept at -80ºC until DNA/RNA extraction.
|
| Growth protocol |
Wild fish: Tissues dissected on boat from wild fish caught in the sea by speargun. Farmed fish: Eggs fertilized in a commercial hatchery and raised at the Aquarium facilities of the Institute of Marine Sciences (CSIC) until 3 years old under natural conditions of temperature and photoperiod.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Phenol-Chloroform DNA extraction.
RRBS library preparation using the Premium RRBS Kit from Diagenode (C02030032).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
European sea bass
|
| Data processing |
RRBS raw reads were quality trimmed by the Timmomatic v. 0.32 with the following parameters SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18.
RRBS: Trimmed reads were aligned to the reference genome dicLab v1.0c using BSMAP v. 2.90 in RRBS mode with the following parameters -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -s 12 -S 0 -f 5 -q 0 -u -V 2.
RRBS: Methylation calling was performed by the methratio.py python script that accompanies BSMAP.
RNA-seq reads were decontaminated by BBDuk (v. 37.61) using the following parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=30 minlen=23.
RNA-seq: Reads were aligned to the genome by HISAT2 (v. 2.1.0) using the core hisat2 function with default parameters.
RNA-seq: Reads were counted at the gene level by feature Counts of the Subread package.
Genome_build: dicLab v1.0c (June 2012); http://seabass.mpipz.mpg.de/
Supplementary_files_format_and_content: *.txt: Output of methratio.py was converted using awk to methylkit input. Tab-delimited files contain the coverage and the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per CpG (chromosome, base, strand) covered.
Supplementary_files_format_and_content: *-RNAseq-Feature_Counts.txt: For each tissue, one plain text file is provided with the feature counts per gene per sample.
|
| |
|
| Submission date |
Jan 15, 2019 |
| Last update date |
Jul 11, 2019 |
| Contact name |
Dafni Anastasiadi |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Marine Sciences-CSIC
|
| Department |
Renewable Marine Resources
|
| Lab |
GBR
|
| Street address |
Pg. Marítim de la Barceloneta 37-49
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL23808 |
| Series (1) |
| GSE125124 |
Epimutations in developmental genes underlie the onset of domestication in farmed European sea bass |
|
| Relations |
| BioSample |
SAMN10752254 |
| SRA |
SRX5252083 |
