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Sample GSM2788110 Query DataSets for GSM2788110
Status Public on Nov 23, 2017
Title 18Li_LF_rep5
Sample type RNA
 
Source name Liver_LF_rep5
Organism Gallus gallus
Characteristics tissue: Liver
gender: male
diet: LF
Treatment protocol At 63 days of age, the liver, Pectoralis major muscle and abdominal fat were immediately removed and frozen in liquid nitrogen and then stored at -80°C until analyses. Peripheral blood mononucleated cells (PBMC) were isolated, just after sampling by density gradient centrifugation (Ficoll Histopaque).
Growth protocol 2 x 12 chickens per line were placed in individual cages and fed two different diets from 21 to 63 d. These two diets were isocaloric (12.54 MJ ME/kg) and isonitrogenous (190 g CP/kg) but exhibited a high-starch and low-fiber low-lipid contents (LF diet) or a low-starch and high-fiber high-lipid contents (HF diet).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol®. The quantity and quality of extracted RNA was evaluated using the NanoDrop ND-1000 spectrophotometer and the Agilent 2100 BioAnalyzer.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 150ng RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent custom 8 x 60K chicken gene expression microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the the Agilent DNA Mmicroarray scanner using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Sep 20, 2017
Last update date Jan 23, 2018
Contact name Colette DESERT
E-mail(s) colette.desert@agrocampus-ouest.fr
Organization name Agrocampus INRA UMR1348 PEGASE
Street address 65 Rue de St Brieuc
City Rennes
ZIP/Postal code 35042
Country France
 
Platform ID GPL19630
Series (2)
GSE104038 Transcriptome profile of liver, adipose tissue, muscle and PBMC in genetically fat and lean chicken lines submitted to high-fiber and high-fat diet versus standard high-starch diet [Liver]
GSE104042 Transcriptome profile of liver, adipose tissue, muscle and PBMC in genetically fat and lean chicken lines submitted to high-fiber and high-fat diet versus standard high-starch diet

Data table header descriptions
ID_REF
VALUE Normalization was performed by centering on the median, after removal of unexpressed probes.

Data table
ID_REF VALUE
4 4.098296647
8 5.315691957
9 -0.4174561
10 4.586170282
11 -0.753981571
12 -0.483494862
13 -0.230065275
14 1.818017397
16 -0.786958894
17 -2.778643625
18 -2.279072616
19 1.049292174
20 -1.82498234
21 -3.18816412
22 -3.363606126
23 0.122708787
25 -1.166304686
26 0.576074405
27 -3.388697107
28 3.014427071

Total number of rows: 37329

Table truncated, full table size 663 Kbytes.




Supplementary file Size Download File type/resource
GSM2788110_F_18_US10453848_254200410003_S01_GE1_107_Sep09_2_1.txt.gz 11.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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