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Sample GSM607679 Query DataSets for GSM607679
Status Public on Aug 11, 2011
Title chicken eye, control, 6 hours, biological replicate 5_Chicken_425c
Sample type RNA
 
Source name retina/RPE, control, 6 hours
Organism Gallus gallus
Characteristics tissue: retina/RPE
breed: White Leghorn
age: less than 2 weeks
Treatment protocol At one week of age, either a (+) or a (-) 15 diopter lens was adhered to one eye of each chick for a period of either 6 hours or 3 days.
Growth protocol One day old chicks were maintained under a 12 hour light:dark cycle.
Extracted molecule total RNA
Extraction protocol Trizol/Rneasy extraction of total RNA was performed according to manufacturer's instructions.
Label biotin
Label protocol Fragmented, biotinylated cDNA was prepared from 100ng of total RNA according to the Nugen Ovation Kit protocol.
 
Hybridization protocol 3.75ug of labeled cDNA were hybridized to an Affymetrix Chicken Genome Array for 16 hours at 45°C. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol Gene Chips were scanned using the Affymetrix 7G Scanner.
Description Gene expression data from control eye, no lens
Data processing Affymetrix Command Console was used to quantify expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. CEL files were imported into Partek Genomic Suite(v.6.4) where RMA was applied yielding normalized, log2 transformed signal intensities. All resultiing p-values were corrected for multiple comparisons using the Benjamini-Hochberg step-up method to yield False Discovery Rates (FDR) as implemented in Partek. An FDR of <10% was considered significant
 
Submission date Oct 12, 2010
Last update date Aug 13, 2011
Contact name Alice M McGlinn
E-mail(s) mcglinn@mail.med.upenn.edu
Phone 215-898-6508
Fax 215-898-0528
Organization name University of Pennsylvania School of Medicine
Department Ophthalmology
Lab Dr Richard Stone
Street address 602D Richards Building 3700 Hamilton Walk
City Philadelphia
State/province PA
ZIP/Postal code 19104-6075
Country USA
 
Platform ID GPL3213
Series (1)
GSE24641 Image defocus and altered retinal gene expression in chicks

Data table header descriptions
ID_REF
VALUE log2 transformed RMA data

Data table
ID_REF VALUE
AB112960.CDS1.S1_at 3.21786
AF004856.CDS1.S1_s_at 2.98718
AF004857.CDS1.S1_s_at 3.62378
AF004857.CDS2.S1_s_at 2.99841
AF004857.CDS3.S1_s_at 2.62841
AF059716.CDS1.S1_at 4.42942
AF059717.CDS1.S1_at 2.92731
AF059721.CDS1.S1_at 3.43877
AF059724.CDS1.S1_at 4.53623
AF059725.CDS1.S1_at 2.67427
AF176590.CDS1.S1_s_at 3.64324
AF176591.CDS1.S1_s_at 3.58383
AF176592.CDS1.S1_s_at 2.80223
AF176592.CDS2.S1_s_at 2.76588
AF218359.CDS1.S1_at 3.98348
AF218359.CDS2.S1_at 2.83193
AF218359.CDS3.S1_at 2.34762
AF243438.CDS1.S1_s_at 4.9119
AF243438.CDS10.S1_s_at 2.26816
AF243438.CDS11.S1_s_at 3.04402

Total number of rows: 38535

Table truncated, full table size 1040 Kbytes.




Supplementary file Size Download File type/resource
GSM607679_3156_12747_425c_Chicken.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM607679_3156_12747_425c_Chicken.mas5.CHP.gz 406.8 Kb (ftp)(http) CHP
Processed data included within Sample table

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