|
| Status |
Public on Nov 14, 2017 |
| Title |
72C2_Mass_2 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Sciaenops ocellatus |
| Characteristics |
tissue: whole embryo
developmental stage: 72hpf
concentration: 0g/l
|
| Treatment protocol |
Testing was performed using two different oil types. The first was a naturally weathered oil collected from a slick in the Gulf of Mexico on June 29th, 2010 from the hold of barge number CT02404 (referred to as OFS). The second was a non-weathered source oil MASS recognized as a suitable surrogate for the DWH source oil. Both oils were delivered to the University of Texas Marine Science Institute through proper chain of custody and stored at 4 °C until used. The test was performed in an environmental control chamber set at 25 °C with a 14:10 h light: dark photoperiod. Survival was assessed daily. A minimum of 70% hatching success and 80% subsequent survival was required for the test to be valid.
|
| Growth protocol |
All experiments were approved by the institutional animal care and use committee (IACUC) at the University of Texas at Austin (AUP-2014-00375). Embryonic red drum (Sciaenops ocellatus) were collected from brood stock tanks at the Texas Parks and Wildlife – CCA Marine Development Center in Corpus Christi, Texas, USA and transported under constant aeration to the University of Texas Marine Science Institute. Embryos were subsequently treated with formalin (1 ppt) for one hour with aeration to remove any bacteria. Spawns with low fertilization rates or poor egg quality were not used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Thirty pooled embryos or larvae per replicate were homogenized with a Kontes Pellet Pestle Cordless Motor (Sigma-Aldrich, St. Louis, Missouri) in RNAzol (Molecular Research Center, Cincinnati, Ohio). 200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep kit following the protocol described by the manufacturer (Illumina, San Diego, CA).
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 |
72hrControl
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...
|
| |
|
| Submission date |
Nov 21, 2016 |
| Last update date |
Mar 26, 2021 |
| Contact name |
Gary Hardiman |
| E-mail(s) |
hardiman@musc.edu, g.hardiman@qub.ac.uk, glen@musc.edu
|
| Organization name |
Medical University of South Carolina
|
| Department |
Medicine
|
| Street address |
135 Cannon Street
|
| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
SC |
| Country |
USA |
| |
|
| Platform ID |
GPL22700 |
| Series (1) |
| GSE90113 |
Genome-wide transcriptional responses to Deepwater Horizon oil in red drum (Sciaenops ocellatus) embryos and larvae |
|
| Relations |
| BioSample |
SAMN06045406 |
| SRA |
SRX2365684 |
