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Sample GSM607701 Query DataSets for GSM607701
Status Public on Aug 11, 2011
Title chicken eye, control, 3 days, biological replicate 4_Chicken_436c
Sample type RNA
 
Source name retina/RPE, control, 3 days
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 2.93691
AF004856.CDS1.S1_s_at 3.20484
AF004857.CDS1.S1_s_at 3.70461
AF004857.CDS2.S1_s_at 3.11415
AF004857.CDS3.S1_s_at 2.67075
AF059716.CDS1.S1_at 4.20638
AF059717.CDS1.S1_at 2.7863
AF059721.CDS1.S1_at 3.42106
AF059724.CDS1.S1_at 4.99813
AF059725.CDS1.S1_at 3.03465
AF176590.CDS1.S1_s_at 3.61691
AF176591.CDS1.S1_s_at 3.71599
AF176592.CDS1.S1_s_at 2.81518
AF176592.CDS2.S1_s_at 2.41871
AF218359.CDS1.S1_at 4.43391
AF218359.CDS2.S1_at 2.68136
AF218359.CDS3.S1_at 2.60788
AF243438.CDS1.S1_s_at 4.9501
AF243438.CDS10.S1_s_at 2.41704
AF243438.CDS11.S1_s_at 3.04238

Total number of rows: 38535

Table truncated, full table size 1040 Kbytes.




Supplementary file Size Download File type/resource
GSM607701_3156_12757_436c_Chicken.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM607701_3156_12757_436c_Chicken.mas5.CHP.gz 407.0 Kb (ftp)(http) CHP
Processed data included within Sample table

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