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Sample GSM1006823 Query DataSets for GSM1006823
Status Public on Dec 04, 2013
Title LSS_liver_Skamania_rep3
Sample type RNA
 
Source name liver, wild fish, Skamania, replicate 3
Organism Catostomus macrocheilus
Characteristics tissue: liver
Stage: reproductive adults
collection site: Skamania
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using STAT-60 (Tel-Test) following the manufacturer's instructions and RNA was resuspended in RNA secure (Ambion) to remove RNAse contamination. RNA was treated with TURBO DNA-free (Ambion) to remove DNA contamination and purified using RNeasy wcolumns (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 1000 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit from Agilent according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Cy3 dye incorporation and cRNA yield were measured using the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (average specific activity =9.27 pmol Cy3/ug cRNA) was fragmented using the Agilent Gene Expression Hybridization kit and hybridized onto custom-designed fathead minnow (15K oligonulceotide) arrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 min with GE Wash Buffer 1 (Agilent), GE Wash buffer 2 (Agilent) kept at 37°C , then 30 sec in Stabilization and Drying solution (Agilent).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k 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 profiling of wild largescale sucker from three sites in the Columbia River
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 035137_D_F_20110628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw intensity data were log2 transformed.
 
Submission date Sep 19, 2012
Last update date Dec 06, 2013
Contact name Alvine C Mehinto
Organization name Southern California Coastal Water Research Project
Lab Center for Envirom & Human Toxicol
Street address 3535 Harbor Blvd, Suite 110
City Costa Mesa
ZIP/Postal code 92626
Country USA
 
Platform ID GPL16082
Series (1)
GSE41016 Microarray analysis of gene response to contaminant accumulation in wild largescale suckers

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity

Data table
ID_REF VALUE
LSS_UF_10001 5.27851415
LSS_UF_10002 11.26026981
LSS_UF_10003 2.354694843
LSS_UF_10004 1.893014659
LSS_UF_10005 1.84874897
LSS_UF_10006 8.510902519
LSS_UF_10007 2.113385061
LSS_UF_10008 7.713468571
LSS_UF_10009 4.14151265
LSS_UF_10010 2.394900783
LSS_UF_10011 2.101208628
LSS_UF_10012 1.979253116
LSS_UF_10013 1.976403465
LSS_UF_10014 8.070347816
LSS_UF_10015 3.527459802
LSS_UF_10016 7.267420633
LSS_UF_10017 6.860432225
LSS_UF_10018 13.66387413
LSS_UF_10019 13.39701405
LSS_UF_10020 11.53617883

Total number of rows: 14758

Table truncated, full table size 358 Kbytes.




Supplementary file Size Download File type/resource
GSM1006823_US83800208_253513710002_S01_GE1-v5_S3_2_3.txt.gz 712.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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