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Sample GSM523100 Query DataSets for GSM523100
Status Public on Jan 01, 2011
Title Cow 14_Period II
Sample type RNA
 
Source name Cow fed control diet
Organism Bos taurus
Characteristics tissue: Mammary gland
Treatment protocol Twenty-eight Holstein-Friesian dairy cows in mid-lactation were blocked according to parity (2.4 ± 0.63 years), DIM (153 ± 32.8 days), milk yield (25.7 ± 3.08 kg/d) and fat content (4.3 ± 0.12%). Cows were then randomly assigned to treatment groups based to one of the four dietary treatments. The dietary treatments were a basal diet supplemented with either: 2.7% rapeseed oil as a source of cis-9-18:1 (oleic acid), 2.7% soybean oil as a source of cis-9, cis-12-18:2 (linoleic acid), 2.7% linseed oil as a source of ALA or 2.7% of a 1:1:1 mixture of the three oils. The oil supplements were included in the concentrate, which was fed, together with corn silage and grass silage, as a total mixed ration (TMR; Table 1). Corn silage, grass silage and concentrates comprised 52, 12 and 36% of the total TMR, respectively, on a DM basis. The cows were grazing on pasture composed of ryegrass (Lolium perenne L.), with approximately 20% white clover (Trifolium repens L.), during the day (from 8:00h until 16:00h) and were fed the TMR, indoors at night. The paddock was 5 ha in size and the stocking density was 16 cows/ha. Cows grazed the paddocks at an herbage allowance of approximately 5.5 kg of DM/cow per day, and were fed the TMR at a level of about 14.5 kg of DM/cow per day. After the first period of 23 days (Experimental period I, final DIM = 176 ± 32.8 days), all cows were switched to a control diet without oil supplementation for an additional 28 days (Experimental period II; final DIM= 204 ± 32.8 days).
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Santa Clara, CA, Affymetrix).
 
Hybridization protocol Following fragmentation, cRNA were hybridized for 16 hr at 45C with constant rotational mixing at 60 rpm on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using an Affymetrix GeneGhip Scanner 7G and Affymetrix GeneChip Operating Software version 1.4
Description 080312MJA_bovine_100180-42.CEL
Data processing All microarray analysis including preprocessing, normalization and statistical analysis was carried out using R Software (version 2.10 and Bioconductor version 2.5). Data were quality assessed before and after normalization using a number of built-in quality control methods implemented in the Bioconductor affycoretools and associated packages to identify eventual irregularities of array hybridization, RNA degradation, and data normalization. Expression levels of probe sets were summarized using the library GC content-corrected robust multichip average algorithm (GC-RMA; (Wu et al., 2004), employing the empirical Bayes approach for background correction followed by quantile normalization.
 
Submission date Mar 16, 2010
Last update date Jan 01, 2011
Contact name Nuria Mach
E-mail(s) nuria.mach@inra.jouy.fr
Organization name INRA
Department Animal Genetics and Integrative Biology (GABI)
Lab Laboratory of Animal Genetics
Street address Rue de Vilvert
City Jouy-en-Josas
State/province Ile de France
ZIP/Postal code 78350
Country France
 
Platform ID GPL10186
Series (2)
GSE20908 Gene expression of lipid metabolism-related genes correlated with milk fatty acids in dairy cows
GSE20909 Alteration of gene expression in mammary gland tissue of dairy cows in response to dietary unsaturated fatty acids

Data table header descriptions
ID_REF
VALUE Expression levels of probe sets were summarized using the library GC content-corrected robust multichip average algorithm (GC-RMA)

Data table
ID_REF VALUE
NM_001075370_at 82.07891074
NM_001034271_at 78.89655127
NM_001078066_at 22.22031219
NM_001033608_at 36.02330216
NM_001046509_at 20.23505057
NM_001076995_at 13.2975998
XM_870452_at 7.428578131
NM_001038029_at 21.66034099
XM_001249839_at 20.41130731
XM_001249888_at 20.41130731
NM_001034596_at 176.2597577
NM_001046173_at 5.181626735
NM_001080246_at 27.65521871
NM_001046129_at 48.56234227
NM_001034488_at 76.02562513
NM_205786_at 67.8185714
XM_593707_at 40.81520314
XM_863846_at 184.8716781
NM_001035081_at 113.4479998
XR_028430_at 6.8973844

Total number of rows: 11495

Table truncated, full table size 300 Kbytes.




Supplementary file Size Download File type/resource
GSM523100.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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