|
| Status |
Public on Nov 30, 2011 |
| Title |
cDNA from parasitic Petromyzon marinus olfactory epithelia |
| Sample type |
SRA |
| |
|
| Source name |
olfactory epithelia, parasitic phase, adult
|
| Organism |
Petromyzon marinus |
| Characteristics |
developmental stage: adult (parasitic)
behavioral phase: feeding
tissue: olfactory epithelium
collection site: Lake Huron and Lake Michigan
collection date: February and March
library: 2
|
| Treatment protocol |
Adult (Library 1) animals captured on spawning habitat in early June. Parasite (Library 2) animals were captured in Northern Lake Huron attached to fish caught by commercial fisherman and recreational anglers. Animals euthanized by overdose of the anesthetic tricaine methanesulfonate (MS-222).
|
| Growth protocol |
tissues collected from free-living animals
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Perfect Pure RNA Tissue Kit (5 Prime, Gaithersburg, MD, USA) according to the manufacturer?s protocol, with an additional round of DNase treatment and wash. The quality of the extracted RNA was verified by gel electrophoresis and RNA concentration was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
1ug of total RNA was used as template for first strand cDNA synthesis using the SMART™ cDNA Synthesis Kit (Clontech Laboratories, Mountain View, CA, USA). 13 cycles of LD-PCR was performed to amplify single-strand cDNA using the Advantage® 2 PCR Kit (Clontech Laboratories) according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS 20 |
| |
|
| Description |
total RNA from sea lamprey olfactory epithelia
|
| Data processing |
The TIGR SeqClean sequence trimming pipeline was used to remove low quality, low complexity, polyA/T and adapter sequences from the cDNA sequences prior to any analyses. Clustering and consensus assembly of the cDNA sequences was performed using the TIGR Gene Indices clustering tools (TGICL) The stringent filtering threshold was set for 95% sequence identity and 90% coverage of the cDNA sequence. Clusters were generated ab initio and by using known full or partial cDNA sequences to seed the clustering. Contigs were used as queries in BLASTX searches against the NCBI protein and nucleotide nr databases to putatively identify their function.
|
| |
|
| Submission date |
Oct 08, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Scot Libants |
| E-mail(s) |
libants@msu.edu
|
| Organization name |
Michigan State University
|
| Department |
Fisheries and Wildlife
|
| Street address |
13 Natural Resources Bldg.
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL11029 |
| Series (1) |
| GSE24467 |
Gene expression in the olfactory epithelia of parasitic and reproductive adult sea lampreys |
|
| Relations |
| SRA |
SRX028149 |
| BioSample |
SAMN00115625 |
