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Sample GSM462044 Query DataSets for GSM462044
Status Public on Oct 16, 2009
Title Proliferative-2
Sample type RNA
 
Source name Tibiotarsus growth plate, proliferative chondrocytes
Organism Gallus gallus
Characteristics tissue: Tibiotarsus growth plate
cell type: Chondrocytes
chondrocyte type: Proliferative
age: 3 weeks
Treatment protocol Not Applicable.
Growth protocol Hypertrophic chondrocytes from 1-day-old chicks; proliferative chondrocytes from 3-week-old chicks.
Extracted molecule total RNA
Extraction protocol RLT Lysis buffer followed by RNeasy Mini-Kit.
Label biotin
Label protocol Affymetrix One Cycle Target Labeling Kit according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA).
 
Hybridization protocol Hybridized to Affymetrix GeneChip Chicken Genome Arrays for 16 h at 45°C; washing with Affymetrix GeneChip Fluidics Station 400.
Scan protocol Affymetrix GCS3000 Scanner.
Description Pooled isolated proliferative chondrocytes.
Data processing Expression analysis was performed using GeneSifter software (VizXLab). CEL data were subjected to a Robust Multichip Average (RMA) to adjust for background and quantile normalization. Pairwise t-test analysis was performed to identify genes that are differentially expressed in proliferative versus hypertrophic chondrocytes. All genes were subjected to a filter of 3-fold change in gene expression, with a P value of 0.05 deemed significant. P values were adjusted for multiple testing comparisons using Benjamini and Hochberg method in order to control the false discovery rate.
 
Submission date Oct 14, 2009
Last update date Oct 14, 2009
Contact name Paul A Bartell
Organization name Penn State University
Department Poultry Science
Street address 205 Henning Bldg.
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL3213
Series (1)
GSE18568 Chondrocyte Gene Expression in Proliferative and Hypertrophic Chondrocytes of Chick

Data table header descriptions
ID_REF
VALUE RMA-normalized signal intensity

Data table
ID_REF VALUE
AB112960.CDS1.S1_at 3.09276
AF004856.CDS1.S1_s_at 3.4995
AF004857.CDS1.S1_s_at 3.82198
AF004857.CDS2.S1_s_at 3.25077
AF004857.CDS3.S1_s_at 3.83133
AF059716.CDS1.S1_at 3.5485
AF059717.CDS1.S1_at 3.61467
AF059721.CDS1.S1_at 3.25363
AF059724.CDS1.S1_at 4.88596
AF059725.CDS1.S1_at 3.48316
AF176590.CDS1.S1_s_at 3.61347
AF176591.CDS1.S1_s_at 3.67394
AF176592.CDS1.S1_s_at 3.3694
AF176592.CDS2.S1_s_at 2.72495
AF218359.CDS1.S1_at 3.42107
AF218359.CDS2.S1_at 3.21433
AF218359.CDS3.S1_at 3.30619
AF243438.CDS1.S1_s_at 4.03408
AF243438.CDS10.S1_s_at 3.12347
AF243438.CDS11.S1_s_at 3.75559

Total number of rows: 38535

Table truncated, full table size 1039 Kbytes.




Supplementary file Size Download File type/resource
GSM462044.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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