|
| Status |
Public on Mar 24, 2017 |
| Title |
0 hpi |
| Sample type |
SRA |
| |
|
| Source name |
Larvae (~15,000 from single mating)
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
tissue: whole larva
age: 9 dpf
bacterial strain: none
|
| Growth protocol |
Larvae were grown in artificial sea water (ASW; Instant Ocean) at 15 C. Beginning at the onset of feeding (4 dpf), larvae were fed Rhodomonas lens (5,000 cells/ml) ever other day.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Larvae were collected using 100 uM Nitex mesh, washed three times in ASW, pelleted by centrifugation and stored in Trizol. Whole RNA was extracted from Trizol preparations using manufacturers instructions. Polyadenylated RNA was purified using the Poly(A)Purist Kit (Ambion).
Libraries were prepared for SOLiD sequencing using standard ABI protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
Uninfected larvae
|
| Data processing |
Low-quality reads were filtered using the Fastx-toolkit and mapped to the S. purpuratus genome, v43.1 using Bowtie (v0.12.7) with the following parameters: -k 50 -m 50 -n 3 -e 900 --snpfrac 0.4.
RPKM values were determined for each gene using the methods outlined in Mortazavi et al., 2008.
Genome_build: Spur3.1
|
| |
|
| Submission date |
Mar 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Katherine Michele Buckley |
| E-mail(s) |
kbuckley@gmail.com
|
| Organization name |
The George Washington University
|
| Department |
Department of Biological Sciences
|
| Street address |
800 22nd St NW
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20052 |
| Country |
USA |
| |
|
| Platform ID |
GPL23220 |
| Series (1) |
| GSE96940 |
The sea urchin larval response to immune challenge with Vibrio diazotrophicus |
|
| Relations |
| BioSample |
SAMN06629158 |
| SRA |
SRX2662866 |
