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Sample GSM2788099 Query DataSets for GSM2788099
Status Public on Nov 23, 2017
Title 06Li_HF_rep2
Sample type RNA
 
Source name Liver_HF_rep2
Organism Gallus gallus
Characteristics tissue: Liver
gender: male
diet: HF
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 4.735182093
8 5.189633045
9 -1.016873819
10 4.258118617
11 -2.086414752
12 -1.861480136
13 -0.293550832
14 2.211567647
16 -1.356591227
17 -3.310787537
18 -2.051225323
19 -0.251339072
20 -1.507401517
21 -2.966833136
22 -3.56828376
23 -0.331747156
25 -0.918470115
26 0.839740896
27 -3.841302254
28 1.492598483

Total number of rows: 37329

Table truncated, full table size 662 Kbytes.




Supplementary file Size Download File type/resource
GSM2788099_F_06_US10453848_254200410001_S01_GE1_107_Sep09_1_4.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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