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Series GSE26985 Query DataSets for GSE26985
Status Public on Feb 15, 2013
Title Toxicogenomic analyses of Ruditapes philippinarum by DNA microarray: new tools for anthropogenic impact assessment on the Venice Lagoon.
Organism Ruditapes philippinarum
Experiment type Expression profiling by array
Summary A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum sampled in four seasons in 4 different areas of Venice Lagoon. For each tissue, total RNA was extracted from four (4) independent biological replicates of digestive gland, each consisting of tissue pools of five (5) animals.
 
Overall design In this study, we analyzed 64 samples (pools of 5 digestive gland). Gene expression profiling was performed using the Agilent-027304 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
 
Contributor(s) Milan M, Bargelloni L
Citation(s) 21569398, 23480613
Submission date Jan 31, 2011
Last update date Sep 09, 2014
Contact name Massimo Milan
E-mail(s) massimo.milan@unipd.it
Phone +39 0498272941
Organization name University of Padova
Department Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene
Street address Viale dell'Università 16
City Legnaro
State/province PD
ZIP/Postal code 35020
Country Italy
 
Platforms (1)
GPL10900 UniversityPadova_Ruditapes philippinarum_4x44K_v1.0
Samples (64)
GSM664687 Alberoni_April_DigestiveGland_POOL1
GSM664688 Alberoni_April_DigestiveGland_POOL2
GSM664689 Alberoni_April_DigestiveGland_POOL3
Relations
BioProject PRJNA135933

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE26985_RAW.tar 32.8 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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