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Sample GSM270509 Query DataSets for GSM270509
Status Public on Nov 03, 2008
Title Bovine liver at 9h, bio rep 6
Sample type RNA
 
Source name Bovine liver sample of 9 hours after LPS intra-mammary infusion
Organism Bos taurus
Characteristics cow id: 4600
Treatment protocol Sterile polyvinyl catheters (Micro-Renathane) were inserted into the jugular vein of the cows. The catheters were flushed with a sterile 0.9% NaCl solution containing 50 IU Na-heparin (Loevens Kemiske Fabrik, Ballerup, Denmark). At time 0 the right front quarter was infused with 200 microgram E. coli LPS (0111:B4) (Sigma-Aldrich, Brøndby, Denmark) dissolved in 10 mililiter 0.9% NaCl solution, the left front quarter serving as control was infused with 10 mililiter 0.9% NaCl solution.
Growth protocol 8 healthy, high yielding Holstein-Friesian dairy cows in their first lactation (9 to 12 weeks after calving) were chosen for this study. The udder health of the cows was evaluated based on somatic cell count (SCC) and bacteriological examinations. All cows had SCC < 100000 on both front quarters and SCC < 138000 on both behind quarters, and were free from mastitis pathogens.
Extracted molecule total RNA
Extraction protocol RNA from liver biopsies was isolated using Trizol Reagent (Invitrogen, Taastrup, Denmark)
Label biotin
Label protocol 5 microgram RNA was labeled using the SuperScript Choice System (Life Technologies) according to the manufacturer’s instructions, except for using an oligo-dT primer containing a T7 RNA polymerase promoter site. Biotin labeled cRNA was prepared using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale NY, USA).
 
Hybridization protocol 15 microgram of cRNA was loaded onto the probe array cartridge of Bovine Genome Array
Scan protocol Probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (Hewlett Packard GeneArray Scanner G2500A).
Description A102-22
Data processing The data were analyzed using GeneChip Robust Multi-array Analysis (GCRMA) algorithm. In this algorithm, raw intensity values are background corrected based on a model using sequence information followed by quantile normalization. The expression measure is given as log base 2 scale.
 
Submission date Mar 03, 2008
Last update date Feb 05, 2016
Contact name Peter Sørensen
E-mail(s) pso@mbg.au.dk
Organization name Aarhus University
Department Molecular Biology and Genetics
Street address Blichers Alle 1
City Tjele
ZIP/Postal code 8830
Country Denmark
 
Platform ID GPL2112
Series (1)
GSE10695 Gene expression profiling of liver from dairy cows subjected to intra-mammary LPS treatment: time course

Data table header descriptions
ID_REF
VALUE Signal intensity, log base 2 scale normalized by GCRMA

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.980465526
AFFX-BioB-5_at 7.645964556
AFFX-BioB-M_at 8.683624774
AFFX-BioC-3_at 9.802867262
AFFX-BioC-5_at 9.217626884
AFFX-BioDn-3_at 11.78710151
AFFX-BioDn-5_at 11.43810784
AFFX-Bt-A00196-1_s_at 2.100515958
AFFX-Bt-AB076373-1_at 2.224448014
AFFX-Bt-AF292559-1_at 2.126451314
AFFX-Bt-AF292559-2_s_at 3.395097425
AFFX-Bt-AF292559-3_s_at 3.014177884
AFFX-Bt-AF292559-4_s_at 2.113092516
AFFX-Bt-AF292560-1_s_at 2.920905448
AFFX-Bt-AF298789-1_at 2.155044241
AFFX-Bt-AF323980-1_at 2.412537966
AFFX-Bt-AJ002682-1_s_at 2.244961443
AFFX-Bt-AJ002682-2_s_at 2.079914562
AFFX-Bt-AJ132968-1_at 2.278158697
AFFX-Bt-AY056050-1_at 2.597471443

Total number of rows: 24128

Table truncated, full table size 676 Kbytes.




Supplementary file Size Download File type/resource
GSM270509.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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