|
| Status |
Public on Jul 02, 2018 |
| Title |
Testis5-RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
D. labrax testis
|
| Organism |
Dicentrarchus labrax |
| Characteristics |
tissue: testis
|
| Treatment protocol |
Samples stored in RNAlater immediately after dissection and kept at -80 until DNA/RNA extraction
|
| Growth protocol |
Tissues dissected on boat from wild fish caught in the sea by speargun
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA extraction
mRNA-Seq sample preparation kit (Illumina Inc., Cat. # RS-122-2001x2)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
FoldChange.csv
Testis-GeneExpression.csv
|
| 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
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
Methylation calling was performed by the methratio.py python script that accompanies BSMAP.
Supplementary_files_format_and_content: 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
RNA-seq reads were aligned with the GEMtools RNAseq pipeline v1.7 which is based on the GEM mapper. The pipeline aligns the reads in a sample in three phases, mapping against the reference genome (dicLab v1.0c), against a reference transcriptome (COMBINED ANNOTATION track) and against a de novo transcriptome, generated from the input data to detect new junction sites. After mapping, all alignments were filtered to increase the number of uniquely mapped reads. The filtering criteria included a minimum intron length of 20 bp, a maximum exon overlap of 5 bp and a filter step against a reference annotation.
The TMM method was used for gene expression normalization and the EdgeR method was used for differential expression analysis.
The link of the published genome to verify: http://seabass.mpipz.mpg.de/ and the information of the publication: Tine M et al. Nat. Commun. 2014;5:5770.
The annotation used for the RNA-seq data is based on the "NEW_COMBINED_ANNOTATION" of the sea bass genome browser that can be found in the server: http://seabass.mpipz.mpg.de/DOWNLOADS/
Supplementary_files_format_and_content: For each tissue, one comma-separated file is provided with the copy million number per transcript ID as annotated in the COMBINED ANNOTATION track of the genome
Supplementary_files_format_and_content: Comma-separated file with differential gene expression data containing log2FoldChange values and statistics including p-adjusted values
Supplementary_files_format_and_content: dicLab v1.0c (June 2012)
Supplementary_files_format_and_content: Muscle-GeneExpression.csv: counts per milion
Supplementary_files_format_and_content: Testis-GeneExpression.csv: counts per milion
Supplementary_files_format_and_content: FoldChange.csv: differential expression
|
| |
|
| Submission date |
Sep 28, 2017 |
| Last update date |
May 15, 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) |
| GSE104366 |
Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species |
|
| Relations |
| BioSample |
SAMN07714535 |
| SRA |
SRX3226020 |
