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| Status |
Public on Aug 25, 2012 |
| Title |
Comparison of gene expression profile of Ruditapes philippinarum sampled in Marghera and Alberoni |
| Organism |
Ruditapes philippinarum |
| Experiment type |
Expression profiling by array
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| Summary |
Digestive Gland Samples: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum. Total RNA was extracted from three (3) independent biological replicates of digestive gland for each sampling site, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified1,127 probes differentially expressed.
Gills Samples: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in gills of R. philippinarum. Total RNA was extracted from three (3) independent biological replicates of gills for each sampling site, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified1,127 probes differentially expressed.
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| Overall design |
Digestive Gland Samples: In this study, we analyzed six (6) samples, three (3) pools of digestive gland of Manila clam sampled in Marghera and three(3) pools of digestive gland of Manila clam sampled in Alberoni. Gene expression profiling was performed using the Agilent-019810 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.
Gills Samples: In this study, we analyzed six (6) samples, three (3) pools of gills of Manila clam sampled in Marghera and three(3) pools of gills of Manila clam sampled in Alberoni. Gene expression profiling was performed using the Agilent-019810 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.
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| Contributor(s) |
Milan M, Bargelloni L |
| Citation(s) |
21569398 |
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| Submission date |
Feb 09, 2011 |
| Last update date |
Sep 04, 2012 |
| Contact name |
Massimo Milan |
| E-mail(s) |
massimo.milan@unipd.it
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| Phone |
+39 0498272941
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| Organization name |
University of Padova
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| Department |
Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene
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| Street address |
Viale dell'Università 16
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| City |
Legnaro |
| State/province |
PD |
| ZIP/Postal code |
35020 |
| Country |
Italy |
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| Platforms (1) |
| GPL10900 |
UniversityPadova_Ruditapes philippinarum_4x44K_v1.0 |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA137531 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE27194_RAW.tar |
71.9 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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