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Sample GSM523953 Query DataSets for GSM523953
Status Public on Mar 19, 2010
Title Chicken 5A vs 2B Cy35
Sample type RNA
 
Channel 1
Source name Liver from control bird 5A
Organism Gallus gallus
Characteristics protocol: Control
tissue: liver
Treatment protocol Twenty-four female birds were selected from one room and spilt into 2 groups, control (C) or crated, transported, slaughtered (CTS). C birds were killed outside the home pen by cervical dislocation immediately prior to feeding, while CTS birds experienced the normal transport to slaughter procedure (i.e. catching, crating, transport, lairage, shackling, slaughter; total 3.25h) with the entire flock after 8h food withdrawal. Liver samples were collected from all selected birds within an hour of death.
Extracted molecule total RNA
Extraction protocol A two step extraction method was used, using first Trizol then QIAGEN Rneasy kit, following the protocol at http://www.ark-genomics.org/protocols IGF100.00: Isolation of total RNA.
Label Cy3
Label protocol Based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols).
 
Channel 2
Source name Liver from CTS bird 2B
Organism Gallus gallus
Characteristics protocol: CTS
tissue: liver
Treatment protocol Twenty-four female birds were selected from one room and spilt into 2 groups, control (C) or crated, transported, slaughtered (CTS). C birds were killed outside the home pen by cervical dislocation immediately prior to feeding, while CTS birds experienced the normal transport to slaughter procedure (i.e. catching, crating, transport, lairage, shackling, slaughter; total 3.25h) with the entire flock after 8h food withdrawal. Liver samples were collected from all selected birds within an hour of death.
Extracted molecule total RNA
Extraction protocol A two step extraction method was used, using first Trizol then QIAGEN Rneasy kit, following the protocol at http://www.ark-genomics.org/protocols IGF100.00: Isolation of total RNA.
Label Cy5
Label protocol Based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols).
 
 
Hybridization protocol Based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols), with full dye swap.
Scan protocol Scanned on GenePix 4200A 01 Autoloader based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols). The array layout is built in each slide file.
Description Ross 308 broiler chickens were housed in eight rooms each containing 266 birds and were raised to slaughter weight, reaching a density of 34kg/m2 at 49 days of age. The birds were fed in four meals per day and provided with ad libitum access to water.
Data processing LOESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. S+ArrayAnalyzer 2.1 built in S-Plus 7.0 Enterprise Developer (Insightful Corporation, Seattle, Washington) was used.
 
Submission date Mar 18, 2010
Last update date Mar 18, 2010
Contact name Zhangrui Cheng
E-mail(s) zcheng@rvc.ac.uk
Phone 01707666663
Organization name Royal Veterinary College
Department Production and Population Health
Lab Reproduction
Street address Hawkshead Lane
City Hatfield
State/province Hertfordshire
ZIP/Postal code AL9 7TA
Country United Kingdom
 
Platform ID GPL10227
Series (1)
GSE20953 Expression data from broiler chickens in response to the combined stressors of catching, transport and slaughter

Data table header descriptions
ID_REF
VALUE normalized log2 ratio representing CTS/Control

Data table
ID_REF VALUE
1 -0.483140835
2 -0.476843326
3 0.119752529
4 -0.057918671
5 -0.031782565
6 0.182975499
7 0.082138079
8 0.137446786
9 0.421404821
10 -0.082866679
11 0.043355358
12 0.173031291
13 0.293147982
14 0.066493229
15 0.257057736
16 0.338733953
17
18 0.429946061
19 0.604045258
20 0.296309736

Total number of rows: 21888

Table truncated, full table size 374 Kbytes.




Supplementary file Size Download File type/resource
GSM523953_CSO1_31_5A2B_CY35.txt.gz 1.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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