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Sample GSM2229606 Query DataSets for GSM2229606
Status Public on Feb 09, 2017
Title Sclera myopia 3
Sample type RNA
 
Source name Mouse 3, right eye, myopic sclera, 10 days visual form deprivation
Organism Mus musculus
Characteristics strain/background: C57BL/6J
tissue: whole sclera
treatment: visual form deprivation
age: P34
mouse identifier: 3
Treatment protocol Visual form deprivation (VFD) was induced in 12 mice by applying a unilateral frosted hemispherical plastic diffusers over the right eyes. Briefly, frosted hemispherical plastic diffusers were hand-made using caps from 0.2 ml PCR tubes (Molecular BioProducts, San Diego, CA) and rings made from medical tape (inner diameter 6 mm; outer diameter 8 mm). A cap was frosted with fine sandpaper and attached to a ring with Loctite™ Super Glue (Henkel Consumer Adhesives, Avon, OH). On the first day of the experiment (P24), animals were anesthetized via intraperitoneal injection of ketamine (90 mg/kg) and xylazine (10 mg/kg), and diffusers were attached to the skin surrounding the right eye with several stitches using size 5-0 ETHILON™ microsurgical sutures (Ethicon, Somerville, NJ) and reinforced with Vetbond™ glue (3M Animal Care Products, St. Paul, MN). The contralateral untreated left eyes were used as control. Toenails were covered with adhesive tape to prevent mice from removing the diffusers. Animals recovered on a warming pad and were then housed in transparent plastic cages for the duration of the experiment (10 days). A control group comprised of 8 age-matched C57BL/6J mice was maintained under the same experimental conditions as experimental group, but without VFD.
Extracted molecule total RNA
Extraction protocol Both myopic and control eyes were enucleated, cleaned by removing surrounding tissues and the crystalline lens, retina and sclera were dissected, snap-frozen in liquid nitrogen and stored in RNAlater®-ICE (Life Technologies, Grand Island, NY). In order to obtain sufficient amount of tissue for RNA isolation, the retinas or scleras from three myopic or control eyes were pooled for RNA extraction. Three replicates (3 eyes per replicate) were processed in parallel. Total RNA was isolated from the retina and sclera samples using mirVanaTM miRNA isolation kit (Life Technologies, Grand Island, NY) according to the manufacturer’s instructions. RNA concentration was measured using NanoDrop 8000 spectrophotometer (Thermo Scientific, Wilmington, DE). The quality of the total RNA was assessed using Agilent RNA 6000 Nano kit and 2100 Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) following the manufacturer’s instructions.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.
 
Hybridization protocol Microarray hybridization was carried out using miRNA Complete Labeling and Hybridization Kit (Agilent) followed by washing using Gene Expression Wash Buffer Kit following manufacturer's instructions.
Scan protocol Microarrays were scanned on a DNA microarray scanner (Agilent G2565BA) and features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.9.5.3) with default protocols and settings.
Description M3_Sclera
miRNA expression, myopic sclera.
Data processing Gene expression data were analyzed using Partek Genomics Suite 6.6. Data were adjusted to bring the minimal signal to 0.5, normalized using quantile normalization procedure, and log2-transformed. This was followed by the removal of absent features and outliers. The normalized data were then analyzed using ANOVA to identify the differences in miRNA expression levels between myopic and control eyes. Differentially expressed miRNAs were identified using an FDR-adjusted P-value threshold of 0.05 and a cutoff of 2-fold change in expression. Differential expression was calculated as fold change (FC, myopic samples vs control).
 
Submission date Jul 10, 2016
Last update date Feb 09, 2017
Contact name Andrei V Tkatchenko
E-mail(s) avt2130@cumc.columbia.edu
Phone 212-342-5135
Organization name Columbia University
Department Ophthalmology
Street address 160 Ft Washington Ave
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL22134
Series (1)
GSE84220 Large-scale microRNA expression profiling identifies retinal miRNA-mRNA signaling pathways underlying form-deprivation myopia in mice

Data table header descriptions
ID_REF
VALUE Log2 normalized signal intensity

Data table
ID_REF VALUE
miRNABrightCorner30 7.42165
mmu-miR-409-3p 5.89478
mmu-miR-26b-5p 10.8681
mmu-miR-376a-3p 7.19131
mmu-miR-142-5p -1
mmu-miR-224-5p 4.06106
mmu-miR-340-3p 4.99623
mmu-miR-31-5p 7.43951
mmu-miR-2138_v15.0 10.7973
mmu-miR-320-3p 7.36046
mmu-miR-433-5p 4.0273
mmu-miR-669i -1
mmu-miR-877-3p 6.22994
mmu-miR-155-5p 4.90701
mmu-miR-1896 -1
mmu-miR-183-3p 5.01812
mmu-miR-532-5p 6.94291
mmu-miR-467f 6.49819
mmu-miR-329-3p 8.11859
mmu-miR-582-5p_v17.0 -1

Total number of rows: 448

Table truncated, full table size 9 Kbytes.




Supplementary file Size Download File type/resource
GSM2229606_M3_Sclera.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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