|
| Status |
Public on Jan 25, 2017 |
| Title |
Female_SK48_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
adult lice (Pacific Canada)
|
| Organism |
Lepeophtheirus salmonis |
| Characteristics |
Sex: Female
feeding group: Sox
time (h): 48
|
| Treatment protocol |
There was no treatment applied to the lice during the experiment.
|
| Growth protocol |
Adult female lice were obtained from Atlantic salmon in a salmon farm near Broughton Archipegalo, British Columbia (BC) in 2011, and brought back to the Pacific Biological Station, Nanaimo, BC, Canada for exposure experiments. Time from the farms to the start of the experiments was > 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lice were flash frozen individually and kept at -80 degrees Celcius until RNA extraction. Total RNA was extracted from frozen tissue using TRIzol reagent® (Life Technologies), on-column DNase digestion (QIAGEN) followed by RNEasy column purification as per manufacturers’ instructions (QIAGEN). Purified total RNA was tested by agarose gel and automated electrophoresis (Experion; Bio-Rad) and spec.
|
| Label |
Cy5-CTP
|
| Label protocol |
Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created for each of the above experiments, ensuring each experimental condition was included in the pool.
|
| |
|
| Channel 2 |
| Source name |
all condition pool
|
| Organism |
Lepeophtheirus salmonis |
| Characteristics |
sample type: reference
|
| Treatment protocol |
There was no treatment applied to the lice during the experiment.
|
| Growth protocol |
Adult female lice were obtained from Atlantic salmon in a salmon farm near Broughton Archipegalo, British Columbia (BC) in 2011, and brought back to the Pacific Biological Station, Nanaimo, BC, Canada for exposure experiments. Time from the farms to the start of the experiments was > 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lice were flash frozen individually and kept at -80 degrees Celcius until RNA extraction. Total RNA was extracted from frozen tissue using TRIzol reagent® (Life Technologies), on-column DNase digestion (QIAGEN) followed by RNEasy column purification as per manufacturers’ instructions (QIAGEN). Purified total RNA was tested by agarose gel and automated electrophoresis (Experion; Bio-Rad) and spec.
|
| Label |
Cy3-CTP
|
| Label protocol |
Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created for each of the above experiments, ensuring each experimental condition was included in the pool.
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized to oligonucleotide microarrays as per manufacturers' instructions for Low-Input Quick Amp kits (Agilent; v6.5). Arrays were designed using previously annotated ESTs from both Pacific and Atlantic L. salmonis (Yasuike et al. 2012; eArray design ID 024389; Agilent).
|
| Scan protocol |
Scanned at 5 micrometer resolution on a ScanArray Express (Perkin Elmer) and quantified on Imagene (v8.1; BioDiscovery).
|
| Description |
Female_48
|
| Data processing |
For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed in GeneSpring GX11 (Agilent). Each array was normalized using an intensity-dependent Lowess normalization. All entities on the array are presented in the attached matrix file here, however, for the analysis, quality control filters for each of the ttreatments retained probes that pass the following criteria in at least 65% of the samples in any one condition: raw signal ≥ 500 in both channels and no poor quality flags.
|
| |
|
| Submission date |
Apr 12, 2016 |
| Last update date |
Jan 27, 2017 |
| Contact name |
Ben F Koop |
| E-mail(s) |
bkoop@uvic.ca
|
| Phone |
(250) 472-4067
|
| Organization name |
The University of Victoria
|
| Department |
Biology
|
| Lab |
Centre for Biomedical Research
|
| Street address |
PO Box 3020 STN CSC
|
| City |
Victoria |
| State/province |
BC |
| ZIP/Postal code |
V8W 3N5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL15566 |
| Series (1) |
| GSE80220 |
Enhanced transcriptomic responses in the Pacific salmon louse Lepeophtheirus salmonis oncorhynchi to the non-native Atlantic Salmon Salmo salar suggests increased parasite fitness |
|
