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Sample GSM1376693 Query DataSets for GSM1376693
Status Public on Apr 24, 2016
Title larvae grown in 10 ppt of salinity rep 4
Sample type RNA
 
Source name larvae, 10 ppt of salinity, replicate 4
Organism Solea senegalensis
Characteristics treatment: 10 ppt of salinity
tissue: larvae
Treatment protocol Homogenization of tissues, including juvenile organs and the pools of larvae and embryos was carried out in the Fast-prep FG120 instrument (Bio101) using Lysing Matrix D (Q-Bio- Gene) for 40 s at speed setting 6.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from 50 mg of tissues or pools of embryos and larvae using the RNeasy Mini Kit (Qiagen).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression larvae grew in 10 ppt of salinity
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.
 
Submission date Apr 29, 2014
Last update date Apr 24, 2016
Contact name Rocio Bautista
E-mail(s) rociobm@uma.es
Phone 0034951952789
Organization name Universidad de Malaga
Department Edificio de Bioinnovacion
Lab Plataforma Andaluza de Bioinformatica
Street address C/ Severo Ochoa, 34. Parque Tecnologico
City Campanillas
State/province Malaga
ZIP/Postal code 29590
Country Spain
 
Platform ID GPL18543
Series (1)
GSE57173 Transcriptomic responses of early developmental larval stages exposed to a hypoosmotic environment in the flatfish Senegalese solea

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
12 0.4865451
13 0.47818518
14 0.4228773
15 0.48814154
16 0.5955372
17 0.49072027
18 0.3249979
19 0.35702467
20 0.49607277
21 0.034284115
22 0.5006778
23 0.42900395
24 0.50552416
25 0.017394543
26 0.2969241
27 0.21586847
28 0.5165918
29 1.238687
30 0.5226009
31 0.46846056

Total number of rows: 45209

Table truncated, full table size 720 Kbytes.




Supplementary file Size Download File type/resource
GSM1376693_SALINITY_10_4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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