|
| Status |
Public on Dec 05, 2017 |
| Title |
2d_Sm_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Larvae, 2 dph, small
|
| Organism |
Seriola lalandi dorsalis |
| Characteristics |
tissue: Larvae
developmental stage: 2 days post hatching
phenotype: Small
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Larvae from the common rearing tanks were transferred in small batches to the wet lab where they could be measured under a microscope camera setup. Depending on developmental stage, one to several larvae were placed on a microscope slide and euthanized with a lethal dose of MS-222. The larvae were quickly photographed, measured, and sorted by size into vials containing RNAlater® (Ambion). The length of time from the point when the larvae were removed from the water to the point of being placed in RNAlater® was under two minutes. The vials of RNAlater® were kept on ice until being placed in -20°C storage at the NMFS laboratory.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
2dphSm6-21
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix
|
| Data processing |
de novo transcript assembly using Trinity (version r20140717).
Abundance estimation was done using RSEM and bowtie2 (2.2.0).
Counts table was generated using the estimated abundances.
DESeq2 (1.2.10) was used for differential gene expression analysis.
Trinotate (r20140708) was used to annotate the transcripts.
Genome_build: de novo assembly
Supplementary_files_format_and_content: genes.counts.matrix: Tab-delimited text file includes gene counts for each sample.
Supplementary_files_format_and_content: isoforms.counts.matrix: Tab-delimited text file includes isoform counts for each sample.
Supplementary_files_format_and_content: Trinity.fasta: FASTA of assembled transcripts.
Supplementary_files_format_and_content: Trinotate_report.xls: Excel file includes annotation information for transcripts.
|
| |
|
| Submission date |
Aug 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew J Severin |
| E-mail(s) |
[email protected]
|
| Phone |
5152941320
|
| Organization name |
Iowa State University
|
| Department |
Office of Biotechnology
|
| Lab |
448 Bessey Hall (Genome Informatics Facility)
|
| Street address |
2200 Osborn Drive
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50014 |
| Country |
USA |
| |
|
| Platform ID |
GPL22352 |
| Series (1) |
| GSE85882 |
Differential gene expression analysis for California yellowtail (Seriola dorsalis) to investigate slow- and fast-growing larvae over different growth stages |
|
| Relations |
| BioSample |
SAMN05601458 |
| SRA |
SRX2036938 |
