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Sample GSM685939 Query DataSets for GSM685939
Status Public on Apr 15, 2011
Title Preglaucoma control rep8 (OHN)
Sample type RNA
 
Source name ONH preglaucoma
Organism Mus musculus
Characteristics phenotype: preglaucoma
gender: female
strain: DBA/2J
tissue: optic nerve head
age: 4.5 months
Growth protocol All mice were housed in a 14 h light to 10 h dark cycle
Extracted molecule total RNA
Extraction protocol For tissue harvesting, mice were anesthetized and the left eye was dissected free, and the cornea and lens removed. The optic nerve was cut close to the back of the eye. The optic nerve head was excised using a sharpened 1mm glass capillary centered over the optic nerve and immediately placed in RNAlater® (Qiagen). A small portion of central retina as well as a small portion of choroid and sclera are included in this tissue. This tissue is substantially enriched for the glial lamina. The retina (containing no optic nerve head) was then dissected free from the back of the eye and placed in a separate vial containing RNAlater (Ambion, Austin TX) and stored at 4oC until required. The process was repeated for the right eye. Dissection of each eye was completed in ≤5 minutes (10 minutes per mouse)
Label biotin
Label protocol Biotin-labeled cDNA was synthesized separately from 20ng of each total RNA sample per the manufacturer’s protocols (Ovation™ Biotin System (NuGEN, San Carlos, CA). 2.5 μg of each biotin-labeled and fragmented cDNA sample was then hybridized onto Mouse Genome 430 v2.0 GeneChip™ arrays (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Hybridization and post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
Scan protocol The arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner
Description ONH L126910
Data processing The images were quantified using GeneChipTM Operating Software (GCOS) v1.2. Probe level data were imported into the R statistical software environment (http://www.r-project.org) and expression values for each probe set on the array were summarized using the Robust MultiChip Average (RMA) method with quantile normalization in the R/affy package
 
Submission date Mar 04, 2011
Last update date Dec 15, 2011
Contact name Gareth Rhys Howell
E-mail(s) [email protected]
Phone 207 288 6572
Fax 207 288 6078
Organization name The Jackson Laboratory
Street address 600 Main Street
City Mount Desert
ZIP/Postal code 04609
Country USA
 
Platform ID GPL1261
Series (1)
GSE26299 Gene expression profiling in DBA/2J glaucoma

Data table header descriptions
ID_REF
VALUE RMA quantile-normalized value

Data table
ID_REF VALUE
1415670_at 6.96294951
1415671_at 8.76283223
1415672_at 10.0009322
1415673_at 5.90296088
1415674_a_at 7.28942565
1415675_at 8.37094147
1415676_a_at 9.22540893
1415677_at 8.0585606
1415678_at 11.6457926
1415679_at 9.62306844
1415680_at 6.09827937
1415681_at 6.50463929
1415682_at 7.66976696
1415683_at 7.64359153
1415684_at 7.31269451
1415685_at 7.36421104
1415686_at 11.0966936
1415687_a_at 11.6055459
1415688_at 10.2599003
1415689_s_at 6.09128789

Total number of rows: 45101

Table truncated, full table size 982 Kbytes.




Supplementary file Size Download File type/resource
GSM685939_GC_430_2_L126910_011706_1.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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