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Title: Comparison of Chamelea gallina gene expression profiles among different season and collection sites      
dateReleased:
01-08-2016
description:
A C. gallina microarray platform was developed to assess variations on transcritpomic profiles between different seasons and sampling sites A comparative analysis of gene expression was conducted in Chamelea gallina collected in two different areas along Abruzzi coasts subjected to different mortality events. In particular sampling activities have been performed in collaboration with fishing cooperatives along Abruzzi coasts, Chamelea gallina clams have been collected from two sites (T4 and T7) at 0.25 mi (ca. 0.4 km) at commercial size (25 mm) and harvested by hydraulic dredge. The harvesting has been conducted in three periods of 2014 (July, August and September). The time of sampling has been obliged by a dramatic reduction of harvesting in T4 that has been reported by fishing cooperatives during spring. After sampling, clams have been kept with ice till their arrival in laboratory, within 6 hours. From each sampling site and each period, the digestive gland of 30 clams has been dissected and frozen at -21°C, for a total of 150 clams divided in 5 pools for each period and each site of sampling. During the clam sampling, from the same sites, the upper layer of bed sediments (0–10 cm) was collected by a small grab sampler in July and September. Composite sediment samples have been refrigerated during transport and stored at − 20 °C within a few hours from sampling, until analysis. Briefly, about 400 g of sediment have been suitably homogenized and dried in an oven at 40 ° C for 24 hours, then crushed, ground and sieved to 2 mm. A portion of about 100 g for each sample has been further ground and screened to 0.2 mm for heavy metal analysis. The content of cadmium (Cd), lead (Pb) and arsenic (As) have been performed, after extraction by aqua regia, by Inductively Coupled Plasma-Optical Emission Spectrometer ( ICP-OES…..) the analysis have been recorded as means triplicate measurements. The determination of Hg have been done in Atomic Adsorption with Hydride System. Ten grams (accuracy ± 0.0001 g) of dry and homogenized sediment of 0.2 mm has been put into a clean centrifuge tube, and a 1:1 (v/v) acetone/n-hexane (5 mL), and surrogate standard mixture (2-fluorobiphenyl and 4-terphenyl-d14) solutions were then added, after extraction and clean-up processes, the samples were analyzed with a gas chromatographer–electron capture detector (GM-ECD) to evaluate concentrations of Polycyclic aromatic hydrocarbons (PAHs) and organophosphate pesticides (OPPs). Organochloride pesticides (OCPs) have been analysed, after purification, with static headspace GC Gene expression profiling was performed using an Chamelea gallina-specific oligo-DNA microarray of15,019 probes representing 12,064 transcripts 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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-76635
refinement:
raw
alternateIdentifiers:
76635
keywords:
functional genomics
dateModified:
01-17-2016
availability:
available
types:
gene expression
name:
Chamelea gallina
ID:
A-GEOD-21308
name:
University Padova Chamelea gallina 8x15K
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-76635/E-GEOD-76635.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-76635/E-GEOD-76635.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76635
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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