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Sample GSM607693 Query DataSets for GSM607693
Status Public on Aug 11, 2011
Title chicken eye, control, 3 days, biological replicate 6_Chicken_411c
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 2.94393
AF004856.CDS1.S1_s_at 3.05608
AF004857.CDS1.S1_s_at 3.28659
AF004857.CDS2.S1_s_at 3.0926
AF004857.CDS3.S1_s_at 2.58688
AF059716.CDS1.S1_at 3.94235
AF059717.CDS1.S1_at 2.90944
AF059721.CDS1.S1_at 3.52749
AF059724.CDS1.S1_at 4.65218
AF059725.CDS1.S1_at 2.76679
AF176590.CDS1.S1_s_at 3.7081
AF176591.CDS1.S1_s_at 4.04926
AF176592.CDS1.S1_s_at 2.94684
AF176592.CDS2.S1_s_at 2.40776
AF218359.CDS1.S1_at 3.95276
AF218359.CDS2.S1_at 2.96784
AF218359.CDS3.S1_at 2.56699
AF243438.CDS1.S1_s_at 5.21106
AF243438.CDS10.S1_s_at 2.67275
AF243438.CDS11.S1_s_at 2.88977

Total number of rows: 38535

Table truncated, full table size 1040 Kbytes.




Supplementary file Size Download File type/resource
GSM607693_3152_12708_411c_Chicken.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM607693_3152_12708_411c_Chicken.mas5.CHP.gz 406.8 Kb (ftp)(http) CHP
Processed data included within Sample table

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