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Sample GSM462045 Query DataSets for GSM462045
Status Public on Oct 16, 2009
Title Proliferative-3
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
VALUE RMA-normalized signal intensity

Data table
AB112960.CDS1.S1_at 3.06373
AF004856.CDS1.S1_s_at 3.12783
AF004857.CDS1.S1_s_at 3.85573
AF004857.CDS2.S1_s_at 3.15732
AF004857.CDS3.S1_s_at 3.53463
AF059716.CDS1.S1_at 3.48849
AF059717.CDS1.S1_at 3.50069
AF059721.CDS1.S1_at 3.45134
AF059724.CDS1.S1_at 4.66803
AF059725.CDS1.S1_at 3.47961
AF176590.CDS1.S1_s_at 3.6965
AF176591.CDS1.S1_s_at 3.46168
AF176592.CDS1.S1_s_at 3.39869
AF176592.CDS2.S1_s_at 2.78443
AF218359.CDS1.S1_at 3.26155
AF218359.CDS2.S1_at 2.98786
AF218359.CDS3.S1_at 3.10633
AF243438.CDS1.S1_s_at 3.57947
AF243438.CDS10.S1_s_at 2.96154
AF243438.CDS11.S1_s_at 3.61752

Total number of rows: 38535

Table truncated, full table size 1040 Kbytes.

Supplementary file Size Download File type/resource
GSM462045.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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