|
| Status |
Public on Aug 20, 2014 |
| Title |
PP T1 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Tegula funebralis |
| Characteristics |
population: northern CA
tissue: whole animal
location: Pigeon Point, San Mateo County
|
| Treatment protocol |
At the start of each experiment, treatment animals were placed in a temperature-programmable incubator (Thermo Precision Model 818) and air temperature was increased by 3 °C every half hour (starting at 15 °C) to simulate a natural rate of heating that snails experience in the intertidal. This gradual increase was continued until the target temperature of 34 °C was reached; the incubator stayed at this target temperature for the remaining 2 hours and 20 min of the experiment. Each heat stress trial lasted a total of 5.5 hours (including the ramp time), which is an estimate of a typical low tide period for *C. funebralis *in the intertidal. Control animals were exposed to 15 °C in air in the same incubator for 5.5 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole animals were frozen in liquid nitrogen, ground to a powder, and the RNA of each individual was extracted using standard Trizol reagent methods.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
treated
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequences were removed.
Sequences were used to construct de novo transcriptome assemblies (CLC Genomics Workbench v.6), one for each population. The 4 population assemblies were then reciprocally blasted and the resulting contigs were trimmed, so all 4 assemblies were comparable.
Assemblies were annotated using Blast2Go.
Reads were mapped back to these assemblies (CLC Genomics Workbench v.6).
Differential expression between geographic regions and between control and heat stress conditions was examined with the program DESeq in R.
Genome_build: no available genome; reference sequences used was de novo transcriptome assemblies from this study
Supplementary_files_format_and_content: tab-delimited text file include normalized expression values for each of the 12 samples for each of the contigs in the reference assembly
|
| |
|
| Submission date |
Apr 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lani Gleason |
| E-mail(s) |
[email protected]
|
| Organization name |
Scripps Institution of Oceanography
|
| Department |
Marine Biology Research Division
|
| Lab |
Burton Lab
|
| Street address |
8750 Biological Grade
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL18616 |
| Series (1) |
| GSE57142 |
RNA-seq Reveals Regional Differences in Transcriptome Response to Heat Stress in the Marine Snail Chlorostoma funebralis |
|
| Relations |
| BioSample |
SAMN02740964 |
| SRA |
SRX529255 |
