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Sample GSM607687 Query DataSets for GSM607687
Status Public on Aug 11, 2011
Title chicken eye, control, 3 days, biological replicate 3_Chicken_408c
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 2.93547
AF004856.CDS1.S1_s_at 3.14691
AF004857.CDS1.S1_s_at 3.74248
AF004857.CDS2.S1_s_at 2.91825
AF004857.CDS3.S1_s_at 2.53813
AF059716.CDS1.S1_at 4.18796
AF059717.CDS1.S1_at 2.73568
AF059721.CDS1.S1_at 3.54486
AF059724.CDS1.S1_at 4.60058
AF059725.CDS1.S1_at 2.97358
AF176590.CDS1.S1_s_at 3.57987
AF176591.CDS1.S1_s_at 3.66749
AF176592.CDS1.S1_s_at 2.81208
AF176592.CDS2.S1_s_at 2.56583
AF218359.CDS1.S1_at 4.14417
AF218359.CDS2.S1_at 2.47388
AF218359.CDS3.S1_at 2.36507
AF243438.CDS1.S1_s_at 4.87413
AF243438.CDS10.S1_s_at 2.40579
AF243438.CDS11.S1_s_at 3.07096

Total number of rows: 38535

Table truncated, full table size 1040 Kbytes.




Supplementary file Size Download File type/resource
GSM607687_3152_12702_408c_Chicken.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM607687_3152_12702_408c_Chicken.mas5.CHP.gz 407.5 Kb (ftp)(http) CHP
Processed data included within Sample table

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