|
| Status |
Public on Apr 23, 2019 |
| Title |
Post-Hatch Hypoxic Oil 1 |
| Sample type |
SRA |
| |
|
| Source name |
whole body, n=10
|
| Organism |
Cyprinodon variegatus |
| Characteristics |
tissue: whole body
age: 2.5 days post hatch
oil concentration: 115.39 ± 4.40 tPAH29
oxygen concentration: ≤ 2 mg/L
|
| Treatment protocol |
C. variegatus from three life stages (embryonic, post-hatch, or post larval) were subjected to oil exposure (12.5% HEWAF) under normoxic (≥ 5 mg/L oxygen) or hypoxic ( ≤ 2 mg/L oxygen) conditions for 48 hours.
|
| Growth protocol |
Animals were maintained in 30 ppt artificial sea water at 30 °C for duration of experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNEasy, according to manufacturer's protocol
Illumina TruSeq Stranded mRNA kit to construct polyA libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Bases called using Illumina CASAVA software
Read quality assessed using Illumina FastQC software; adpater trimming performed using Trimomatic software
Reads were aligned to C. variegatus genome using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany).
Gene expression (Transcripts per million --TPM) calculated using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany)
Genome_build: C. variegatus genome (NCBI genome ID 13078)
Supplementary_files_format_and_content: CSV text files including TPM expression values
|
| |
|
| Submission date |
Dec 06, 2018 |
| Last update date |
Apr 25, 2019 |
| Contact name |
Elizabeth R. Jones |
| E-mail(s) |
elizabeth.jones@fmarion.edu
|
| Phone |
843-661-1899
|
| Organization name |
Francis Marion University
|
| Department |
Biology
|
| Street address |
4822 E. Palmetto St.
|
| City |
Florence |
| State/province |
SC |
| ZIP/Postal code |
29506 |
| Country |
USA |
| |
|
| Platform ID |
GPL25909 |
| Series (1) |
| GSE123469 |
RNA-seq of developing Cyprinodon variegatus exposed to oil, hypoxia, or both |
|
| Relations |
| BioSample |
SAMN10531238 |
| SRA |
SRX5103164 |
