E-GEOD-38863 - Transcriptome analysis of Manila clam (Ruditapes philippinarum) digestive gland after exposure to different concentrations of ibuprofen.

Status
Released on 1 October 2013, last updated on 2 June 2014
Organism
Ruditapes philippinarum
Samples (60)
Array (1)
Protocols (17)
Description
A Ruditapes philippinarum microarray platform was developed to identify digestive gland gene expression profiles in response to 100 µg /l and 1000 µg/l ibuprofen exposure. A comparative analysis of gene expression was conducted in Manila clam R.philippinarum exposed to ibuprofen.Clams were exposed for 1, 3, 5 and 7 days to 0, 100 and 1000 µg IBU/l, and digestive gland gene expression were measured. Gene expression profiling was performed using an Manila clam-specific oligo-DNA microarray of 14,156 probes 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.
Experiment type
transcription profiling by array 
Contacts
Massimo Milan <massimo.milan@unipd.it>, Matozzo Valerio, Milan Massimo, Pauletto marianna
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-38863.idf.txt
Sample and data relationshipE-GEOD-38863.sdrf.txt
Raw data (1)E-GEOD-38863.raw.1.zip
Processed data (1)E-GEOD-38863.processed.1.zip
Array designA-GEOD-15723.adf.txt
Links