|
| Status |
Public on Aug 01, 2017 |
| Title |
MS+/EMB-_rep6 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Copepodid larvae_MS+/EMB-
|
| Organism |
Lepeophtheirus salmonis oncorhynchi |
| Characteristics |
species: Copepodid lice (Pacific Canada)
presence of f. margolisi: Positive
emb concentration (ppb): 0
|
| Treatment protocol |
Emamectin benzoate was prepared to 1 ug/L (ppb) using fresh sea water. A total of 28 pools of ~75 copepodid larvae derived from individual egg strings were divided into control (0 ppb EMB) and treated (1 ppb EMB) groups, n = 14 for each group. Half of each group (i.e. control and treated) was derived from egg strings that tested positive for F. margolisi infection (n = 7/group). The remaining pools were derived from F. margolisi negative eggs.
|
| Growth protocol |
One pigmented egg string collected from ovigerous L. salmonis was placed into a sterile flask containing 300 mL of aerated seawater and incubated at 10°C for six to eight days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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_reference
|
| Organism |
Lepeophtheirus salmonis oncorhynchi |
| Characteristics |
sample type: pooled reference
|
| Treatment protocol |
Emamectin benzoate was prepared to 1 ug/L (ppb) using fresh sea water. A total of 28 pools of ~75 copepodid larvae derived from individual egg strings were divided into control (0 ppb EMB) and treated (1 ppb EMB) groups, n = 14 for each group. Half of each group (i.e. control and treated) was derived from egg strings that tested positive for F. margolisi infection (n = 7/group). The remaining pools were derived from F. margolisi negative eggs.
|
| Growth protocol |
One pigmented egg string collected from ovigerous L. salmonis was placed into a sterile flask containing 300 mL of aerated seawater and incubated at 10°C for six to eight days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 |
10025_Block2.txt
|
| Data processing |
For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed in GeneSpring GX14.5 (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 three experiments 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 |
Feb 08, 2017 |
| Last update date |
Aug 02, 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) |
| GSE94692 |
Effects of the vertically transmitted microsporidian Facilispora margolisi and the parasiticide emamectin benzoate on salmon lice (Lepeophtheirus salmonis) |
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