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Sample GSM386836 Query DataSets for GSM386836
Status Public on Mar 27, 2009
Title Day 7 Chick Liver- Replicate #3
Sample type RNA
 
Source name 7 day-old Chick
Organism Gallus gallus
Characteristics tissue: Liver
genotype: Ross broiler chicken
gender: male
age: 7 day-old
Treatment protocol Samples of liver, duodenum, breast muscle and whole brain were collected on days 0 and 7 post-hatch, snap frozen in liquid nitrogen and stored at -80C prior to isolation of total RNA.
Growth protocol Broiler chicken eggs were hatched and chicks were sampled immediately after emergence from the egg (day 0) and at 7 days post-hatch.
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, Affymetrix).
 
Hybridization protocol Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 42C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 using the EukGE-WS2v5_450 script.
Scan protocol GeneChips were scanned using the Affymetrix GC3000 scanner using factory set PMT settings.
Description Gene expression data for liver from 7 day-old broiler chicken.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to the default value of 500.
 
Submission date Mar 26, 2009
Last update date Mar 26, 2009
Contact name Mark P Richards
E-mail(s) Mark.Richards@ars.usda.gov
Phone 301 504-8892
Fax 301 504-8623
Organization name USDA, ARS
Department ANRI
Lab Animal Biosciences and Biotechnology Laboratory
Street address 10300 Baltimore Avenue
City Beltsville
State/province MD
ZIP/Postal code 20705-2350
Country USA
 
Platform ID GPL3213
Series (1)
GSE15413 Gene expression profiles for different tissues obtained from newly hatched (day 0) and 7 day-old broiler chickens

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 948.351 P 0.000296708
AFFX-BioB-M_at 1508.38 P 4.42873e-05
AFFX-BioB-3_at 1035.49 P 4.42873e-05
AFFX-BioC-5_at 3282.71 P 4.42873e-05
AFFX-BioC-3_at 2786.65 P 4.42873e-05
AFFX-BioDn-5_at 5073.46 P 5.16732e-05
AFFX-BioDn-3_at 10711.9 P 5.16732e-05
AFFX-CreX-5_at 30503.3 P 5.16732e-05
AFFX-CreX-3_at 37992.9 P 4.42873e-05
AFFX-DapX-5_at 3.78151 A 0.876428
AFFX-DapX-M_at 24.4965 A 0.368438
AFFX-DapX-3_at 35.4582 A 0.313723
AFFX-LysX-5_at 2.50411 A 0.927318
AFFX-LysX-M_at 5.39702 A 0.937071
AFFX-LysX-3_at 2.3153 A 0.960339
AFFX-PheX-5_at 4.43849 A 0.814869
AFFX-PheX-M_at 2.34806 A 0.953518
AFFX-PheX-3_at 16.0801 A 0.58862
AFFX-ThrX-5_at 3.29151 A 0.995983
AFFX-ThrX-M_at 6.25751 A 0.686277

Total number of rows: 38535

Table truncated, full table size 1490 Kbytes.




Supplementary file Size Download File type/resource
GSM386836.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM386836.CHP.gz 209.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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