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Sample GSM428136 Query DataSets for GSM428136
Status Public on Jul 16, 2009
Title Retina C57BL/6J 5 days rep3
Sample type RNA
 
Source name retina, C57BL/6J, 5 days post crush
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 60-90 days
gender: Male
tissue: retina from both eyes
Treatment protocol Optic nerve crush: Mice were deeply anesthetized with a mixture of 13 mg/kg of Rompum and 87 mg/kg of Ketalar. A small incision was made in the lateral aspect of the conjunctiva. With a pair of small forceps the edge of the conjunctiva next to the globe was retracted slightly and rotated laterally, allowing visualization of the posterior aspect of the globe where the optic nerve could be observed. Viewed under a binocular operating microscope, the surrounding connective tissue and muscle was gently separated from the nerve. The exposed optic nerve was grasped for 10 sec with a pair of Dumont cross-clamp #7 forceps (Roboz, cat. #RS=5027, Gaithersburg, MD). This instrument was chosen because its spring action applied a moderate yet constant and consistent force to the optic nerve. The forceps were then removed and the eye was allowed to rotate back into place.
Extracted molecule total RNA
Extraction protocol The tissue was homogenized and extracted according to the RNA-Stat-60 protocol as described by the manufacturer (Tel-Test, Friendswood, TX). The quality and purity of RNA was assessed using an Agilent Bioanalyzer 2100 system.
Label Cy3
Label protocol The RNA from each sample was processed with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX) to produce labeled cRNA.
 
Hybridization protocol Standard Protocol for Illumina Sentrix 6 Mouse BeadChip microarrays
Scan protocol Illumina BeadArray Reader and BeadScan scan protocol
Description C57BL/6J retina, total RNA isolation 5 days after optic nerve crush: The exposed optic nerve was grasped for 10 sec with a pair of Dumont cross-clamp #7 forceps
Data processing Using Microsoft Excel, we normalized the data using the formula 2 (z-score of log2 [intensity]) + 8
 
Submission date Jul 15, 2009
Last update date Jul 15, 2009
Contact name William Edwin Orr
E-mail(s) weorr@utmem.edu
Phone 901 448-3635
Fax 901 448-5028
Organization name University of Tennessee Health Science Center
Department Ophthalmology
Lab Vision Core
Street address 930 Madison Avenue, Suite 757
City Memphis
State/province TN
ZIP/Postal code 38163
Country USA
 
Platform ID GPL4234
Series (1)
GSE17117 Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush

Data table header descriptions
ID_REF
VALUE normalized signal: 2 (z-score of log2 [intensity]) + 8

Data table
ID_REF VALUE
102450270 6.84
104200035 6.76
100730138 6.72
102320427 6.65
102630735 6.80
100450435 6.91
101230594 6.40
100780541 6.76
104200184 6.66
105360286 6.37
103060411 6.94
100630193 6.54
105270286 6.45
101690685 6.48
100060180 6.50
107100563 6.84
100450451 6.50
100610092 6.25
104810452 15.23
6840019 13.27

Total number of rows: 46116

Table truncated, full table size 631 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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