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Sample GSM604719 Query DataSets for GSM604719
Status Public on Nov 22, 2010
Title CORNEA, replicate 2
Sample type RNA
 
Channel 1
Source name Total RNA from corneas of adult mice (CORNEA 2)
Organism Mus musculus
Characteristics tissue: Cornea
strain: C57BL/6J
Treatment protocol not applicable
Growth protocol not applicable
Extracted molecule total RNA
Extraction protocol Total RNA extracted with the miRNeasy kit (Qiagen)
Label Hy3
Label protocol One µg total RNA from sample and reference (Eye sample) was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
 
Channel 2
Source name Total RNA from entire eyeballs from adult mice
Organism Mus musculus
Characteristics tissue: Entire Eyeball
strain: C57BL/6J
Treatment protocol not applicable
Growth protocol not applicable
Extracted molecule total RNA
Extraction protocol Total RNA extracted with the miRNeasy kit (Qiagen)
Label Hy5
Label protocol One µg total RNA from sample and reference (Eye sample) was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
 
 
Hybridization protocol The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 12.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
Scan protocol After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).
Description (6) (CORNEA 2)
Slide 6
present call rate per slide: 0.574539363484087
Hy3 raw: 1_Exiqon_13973495_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973495_S01_Cropped.txt
Data processing The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Project_Summary Report version 3.5 results presented in Sample data tables.
When calling of a particular miRNA failed on an array this is indicated by the acronym null. The criteria for deciding that the calling of a miRNA had failed on a particular array, was that 3 or more of the 4 replicated measures of this miRNA were flagged (i.e. the signal is below background) by the image analysis software. Further, all capture probes with Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide is indicated by the acronym null.
 
Submission date Oct 05, 2010
Last update date Nov 17, 2010
Contact name Marianthi Karali
E-mail(s) karali@tigem.it
Organization name Telethon Institute for Genetics & Medicine (TIGEM)
Street address Via Pietro Castellino, 111
City Naples
ZIP/Postal code 80131
Country Italy
 
Platform ID GPL7723
Series (1)
GSE22882 microRNA profiling in Mouse Eye: Retina, Lens, Cornea, Retinal Pigment Epithelium

Data table header descriptions
ID_REF
VALUE normalized, log2 (Hy3/Hy5) ratios

Data table
ID_REF VALUE
27263 -0.36
17888 -0.12
17749 0.31
42769 -0.15
19004 0.07
42668 -0.07
46437 -0.54
42505 0.00
46436 0.01
46435 -0.47
42768 -0.22
46438 -1.29
42778 null
9938 -0.44
42534 null
10916 -2.69
19581 -1.76
31026 -1.59
17935 null
42953 -1.43

Total number of rows: 1382

Table truncated, full table size 15 Kbytes.




Supplementary file Size Download File type/resource
GSM604719_0_Exiqon_13973495_S01_Cropped.txt.gz 777.8 Kb (ftp)(http) TXT
GSM604719_1_Exiqon_13973495_S01_Cropped.txt.gz 876.1 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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