|
| Status |
Public on Jul 01, 2021 |
| Title |
3H_L3_CT |
| Sample type |
SRA |
| |
|
| Source name |
Control
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
FISH origin: laboratory (reared in aquarium facilities)
age: 90 days old
|
| Treatment protocol |
zebrafish larva were treated with LPS for P. aeruginosa. Methylation Bisulfite sequencing was performed as described in Anastasiadi el al., 2018
|
| Growth protocol |
Zebrafish were raised following: Westerfield, M. (2000). The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio). 4th ed., Univ. of Oregon Press, Eugene.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
library preparation following protocol as in Anastasiadi et al 2018
Gonads were extracted, flash frozen in nitrogen liquid. DNA was extracted following the Phenol-Chlorofrom DNA extraction. Bisulfite conversion was carried out using D5020, Zymo Research from 1000 ng of genomic DNA in each sample. Illumina Miseq 2500 wasused for sequencing the library.
Library was constructed following the Illumina’s protocol: “16S metagenomic library preparation” using Nextera XT Index Kit V2 set A, FC-131–2001 kit.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Phenol-Chlorofrom DNA extraction
|
| Data processing |
raw reads were quality trimmed by the Trim Galore! software (v. 0.4.5) with the following parameters --nextera, --quality 20, and --phred64
adapters, the number and quality of the reads were checked using the FastQC software (v. 0.11.6)
the alignments of the pair-end reads were performed using the function “bismark”: --bowtie2, --non-directional, and --score_min 0 + (−0.6 x read length). Bismark software (v. 16.0)
methylation calling bismark_methylation_extractor”: --bedGraph
Supplementary_files_format_and_content: tab-delimited files (sample_name.txt) contain the coverage and the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per CpG (chromosome, base, strand) covered
Genome_build: GRCz11 Danio rerio https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.5/
|
| |
|
| Submission date |
Jul 17, 2019 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Laia Ribas |
| E-mail(s) |
lribas@icm.csic.es, laiaribas79@gmail.com
|
| Organization name |
Institut de Ciencies del Mar
|
| Street address |
Passeig Maritim 37-49
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE134400 |
Zebrafish sex differentiation under LPS-mediated inflamatory process. |
|
| Relations |
| SRA |
SRX6455752 |
| BioSample |
SAMN12306468 |
