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Sample GSM664631 Query DataSets for GSM664631
Status Public on Feb 03, 2011
Title Skin, day 5, fish 1
Sample type RNA
 
Channel 1
Source name Skin of infected salmon
Organism Salmo salar
Characteristics disease state: challenged with L. salmonis
Treatment protocol Salmon louse of LsGulen strain were reared in the hatchery and egg strings were collected and placed into an incubator until they reached the copepodid stage. Atlantic salmon were challenged with L. salmonis (approximately 100 copepodids per fish).
Growth protocol Salmon (100-200 g) was kep in tanks with sea water
Extracted molecule total RNA
Extraction protocol RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with RNeasy mini kit (QIAGEN)
Label Cy5
Label protocol Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol
 
Channel 2
Source name Skin of control salmon
Organism Salmo salar
Characteristics disease state: none
Treatment protocol Salmon louse of LsGulen strain were reared in the hatchery and egg strings were collected and placed into an incubator until they reached the copepodid stage. Atlantic salmon were challenged with L. salmonis (approximately 100 copepodids per fish).
Growth protocol Salmon (100-200 g) was kep in tanks with sea water
Extracted molecule total RNA
Extraction protocol RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with RNeasy mini kit (QIAGEN)
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 GenePix 4100A at a resolution of 5 microns
Description Time-point 3 of 5, biological replicate 1 of 4
Data processing GenePix Pro 6.0 was used for spot to grid alignment, feature extraction and quantification. After removal of flagged spots lowess normalization was performed
 
Submission date Jan 31, 2011
Last update date Feb 03, 2011
Contact name Aleksei Krasnov
E-mail(s) aleksei.krasnov@nofima.no
Phone +47 97602165
Organization name Nofima AS
Department Fish Health
Street address Osloveien 1
City Aas
ZIP/Postal code 1430
Country Norway
 
Platform ID GPL10705
Series (2)
GSE26981 Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in skin of Atlantic salmon
GSE27013 Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in Atlantic salmon

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

Data table
ID_REF VALUE
12 NULL
14 NULL
15 NULL
16 0.064022
17 NULL
18 NULL
19 0.435895
20 -2.70063
21 NULL
22 -0.149459
24 -0.332475
25 0.117652
26 0.336811
27 -0.658121
28 NULL
30 NULL
32 1.32406
33 -0.028552
34 0.457707
35 -0.0407954

Total number of rows: 42144

Table truncated, full table size 538 Kbytes.




Supplementary file Size Download File type/resource
GSM664631.gpr.gz 3.3 Mb (ftp)(http) GPR
Processed data included within Sample table

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