|
| Status |
Public on Feb 02, 2022 |
| Title |
GDA_gill_3PSU_4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Gills of cod from Gdansk Bay
|
| Organism |
Gadus morhua |
| Characteristics |
location: Gdansk Bay
tissue: gill
gender: male
salinity: 3PSU
|
| Treatment protocol |
Fish were transported in containers with sea water to the Marine Station of the University of Gdansk in Hel for the experiment. Briefly, fish were divided into two tanks, termed here as salinity reference: GDA 8PSU and KIEL 18PSU and acclimated for 14 days in 10°C, in recirculated water with natural salinities of the geographic origin. Next, fish from each localization were divided and transferred to separate nine tanks and again acclimated. Two of the nine tanks represented controls (salinity reference) for fish from Gdansk Bay and Kiel Bight. In other tanks salinity was reduced or elevated. In all tanks, salinity was changed gradually (1PSU per hour) in order to minimize acute stress response.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the ISOLATE II RNA Mini Kit (Bioline). Concentration of extracted RNA was determined at 260 nm on microplate using the Epoch Microplate Spectrophotometer (BioTek Instruments). The RNA integrity was verified using an Agilent Bioanalyser (Agilent Technologies)
|
| Label |
Cy5
|
| Label protocol |
Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol
|
| |
|
| Channel 2 |
| Source name |
mix of all samples
|
| Organism |
Gadus morhua |
| Characteristics |
tissue: gill
|
| Treatment protocol |
Fish were transported in containers with sea water to the Marine Station of the University of Gdansk in Hel for the experiment. Briefly, fish were divided into two tanks, termed here as salinity reference: GDA 8PSU and KIEL 18PSU and acclimated for 14 days in 10°C, in recirculated water with natural salinities of the geographic origin. Next, fish from each localization were divided and transferred to separate nine tanks and again acclimated. Two of the nine tanks represented controls (salinity reference) for fish from Gdansk Bay and Kiel Bight. In other tanks salinity was reduced or elevated. In all tanks, salinity was changed gradually (1PSU per hour) in order to minimize acute stress response.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the ISOLATE II RNA Mini Kit (Bioline). Concentration of extracted RNA was determined at 260 nm on microplate using the Epoch Microplate Spectrophotometer (BioTek Instruments). The RNA integrity was verified using an Agilent Bioanalyser (Agilent Technologies)
|
| Label |
Cy3
|
| Label protocol |
Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol
|
| |
|
| |
| Hybridization protocol |
Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol
|
| Scan protocol |
Arrays were scanned in an Agilent Technologies Scanner G2505C US10353831, according to the manufacturer’s protocol GE2_1010_Sep10
|
| Data processing |
Data were extracted using the Agilent Feature Extraction software (version 10.10.1.1) following the Agilent protocol GE2_1010_Sep10. Arrays normalization was performed using the Limma package in R. The raw mean signal (gMeanSignal) was background corrected (normexp method). Next lowess and quantile normalization were performed.
|
| |
|
| Submission date |
Feb 01, 2022 |
| Last update date |
Feb 02, 2022 |
| Contact name |
Magdalena Malachowicz |
| E-mail(s) |
mwarzecha@iopan.gda.pl
|
| Organization name |
Institute of Oceanology Polish Academy of Sciences
|
| Street address |
Powstańców Warszawy
|
| City |
Sopot |
| ZIP/Postal code |
81-712 |
| Country |
Poland |
| |
|
| Platform ID |
GPL18775 |
| Series (1) |
| GSE195878 |
Diverse transcriptome response to salinity change in cod subpopulations from the Baltic Sea |
|
