|
| Status |
Public on Jun 18, 2020 |
| Title |
F274 |
| Sample type |
SRA |
| |
|
| Source name |
Whole larvae
|
| Organism |
Gadus morhua |
| Characteristics |
treatment: High pCO2
age (dph): 6
tank: 149
tissue: Whole larvae
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Larvae preserved in RNALater, were extracted using Rneasy kit( Qiagen), applying a modified protocol( please consult publication for details)
Libraries were consctructed according to manufacturers instructions: IlluminaTruSeq Stranded mRNAseq Sample Prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
[Adaptor trim and quality filter] java -Xmx16G -jar trimmomatic-0.36.jar PE -threads 8 -phred33 R1.fastq.gz R2.fastq.gz -baseout sample.fq ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:4:true
[QC] FastQC using MultiQC
[Bedtools getfasta] create fasta transcriptome from genome annotation file
[Kallisto index] kallisto index -i kallisto_index_gadMor2 gadMor2_predicted_transcripts_filtered.fasta
[Kallisto abundance] kallisto quant -i -o out R1.fastq.gz R2.fastq.gz
Genome_build: Genome and transcriptome information available at https://figshare.com/articles/Transcript_and_genome_assemblies_of_Atlantic_cod/3408247
Genome_build: Genome build: gadMor2.fasta; Annotations gadMor2_annotation_filtered.gff; Transcriptome gadMor2_transcripts_filtered.fasta
Supplementary_files_format_and_content: .tsv transcript abundance data for each sample
|
| |
|
| Submission date |
Jan 29, 2018 |
| Last update date |
Jun 18, 2020 |
| Contact name |
Felix Hans Mittermayer |
| E-mail(s) |
fmittermayer@geomar.de
|
| Organization name |
GEOMAR Helmholtz Centre for Ocean Research
|
| Department |
Evolutionary Ecology of Marine Fishes
|
| Street address |
Düsternbrooker Weg 20
|
| City |
Kiel |
| ZIP/Postal code |
24105 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24273 |
| Series (1) |
| GSE108715 |
Global transcriptom of 3 Atlantic cod larval stages in response to increased pCO2 compared to ambient pCO2 |
|
| Relations |
| BioSample |
SAMN08434900 |
| SRA |
SRX3630012 |
