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Sample GSM462049 Query DataSets for GSM462049
Status Public on Oct 16, 2009
Title Hypertrophic-3
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
ID_REF
VALUE RMA-normalized signal intensity

Data table
ID_REF VALUE
AB112960.CDS1.S1_at 3.2119
AF004856.CDS1.S1_s_at 3.18478
AF004857.CDS1.S1_s_at 3.63603
AF004857.CDS2.S1_s_at 3.06428
AF004857.CDS3.S1_s_at 3.37626
AF059716.CDS1.S1_at 3.36629
AF059717.CDS1.S1_at 3.32434
AF059721.CDS1.S1_at 3.4241
AF059724.CDS1.S1_at 4.54807
AF059725.CDS1.S1_at 3.39534
AF176590.CDS1.S1_s_at 3.52551
AF176591.CDS1.S1_s_at 3.42641
AF176592.CDS1.S1_s_at 3.15386
AF176592.CDS2.S1_s_at 2.79377
AF218359.CDS1.S1_at 3.22327
AF218359.CDS2.S1_at 3.31111
AF218359.CDS3.S1_at 3.16082
AF243438.CDS1.S1_s_at 3.97307
AF243438.CDS10.S1_s_at 3.02685
AF243438.CDS11.S1_s_at 3.85543

Total number of rows: 38535

Table truncated, full table size 1040 Kbytes.




Supplementary file Size Download File type/resource
GSM462049.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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