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Sample GSM5855583 Query DataSets for GSM5855583
Status Public on Feb 02, 2022
Title GDA_gill_18PSU_1
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: 18PSU
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

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1
2
3
4
5
6
7
8
9
10
11
12 0.129727316
13 0.116940456
14 -0.295584213
15 -0.158749057
16 -0.017951299
17 -0.204029163
18 -0.135860183
19 0.375696654
20 0.275994612

Total number of rows: 43833

Table truncated, full table size 759 Kbytes.




Supplementary file Size Download File type/resource
GSM5855583_GDA_18PSU_1.txt.gz 12.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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