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Sample GSM462047 Query DataSets for GSM462047
Status Public on Oct 16, 2009
Title Hypertrophic-1
Sample type RNA
Source name Tibiotarsus growth plate, hypertrophic chondrocytes
Organism Gallus gallus
Characteristics tissue: Tibiotarsus growth plate
cell type: Chondrocytes
chondrocyte type: Hypertrophic
age: 1 day
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 hypertrophic 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 3.05269
AF004856.CDS1.S1_s_at 3.51092
AF004857.CDS1.S1_s_at 3.83568
AF004857.CDS2.S1_s_at 3.50067
AF004857.CDS3.S1_s_at 3.47297
AF059716.CDS1.S1_at 3.34383
AF059717.CDS1.S1_at 3.60833
AF059721.CDS1.S1_at 3.37531
AF059724.CDS1.S1_at 4.76161
AF059725.CDS1.S1_at 3.17057
AF176590.CDS1.S1_s_at 3.64913
AF176591.CDS1.S1_s_at 3.43539
AF176592.CDS1.S1_s_at 3.39123
AF176592.CDS2.S1_s_at 3.01675
AF218359.CDS1.S1_at 3.19111
AF218359.CDS2.S1_at 3.39213
AF218359.CDS3.S1_at 3.39238
AF243438.CDS1.S1_s_at 4.21325
AF243438.CDS10.S1_s_at 2.98263
AF243438.CDS11.S1_s_at 4.02727

Total number of rows: 38535

Table truncated, full table size 1040 Kbytes.

Supplementary file Size Download File type/resource
GSM462047.CEL.gz 3.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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