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Sample GSM801502 Query DataSets for GSM801502
Status Public on Apr 22, 2013
Title mouse miRNA array diabetic_4
Sample type RNA
 
Source name skeletal muscle
Organism Mus musculus
Characteristics group: diabetic
strain: C57BL/KsJ db+
Extracted molecule total RNA
Extraction protocol Total miRNA from tissue sample was isolated from control and diabetic skeletal muscle using Ambion miRNA isolation kit as per manufacture's instruction
Label Cy3
Label protocol Briefly, 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to a ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 h. The labeled samples were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water.
 
Hybridization protocol The hybridization mixture (10X GE blocking agent (4.5µl) and 2X Hi-RPM hybridization buffer (22.5µl)) along with the labelled miRNA sample was heated for 5 min at 100 °C and immediately cooled on ice. Each 45 µL sample was hybridized onto a microarray at 55 °C for 20 h. Slides were then washed for 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C, followed by an acetonitrile wash for 1 min at RT to dry the slides completely.
Scan protocol Slides were scanned on a microarray scanner (G2565BA, Agilent) at 100 and 5% XDR settings. Agilent Feature Extraction software version 9.3.5 was used to extract the raw data.
Description miRNA expression in diabetic skeletal muscle
Data processing From raw data, gBG Sub Signal from four control and treated samples was taken for further analysis. Then median of all signals was taken and this was used as an input file for normalization by using R method. After normalization by R method, we obtained output file in which we applied Z-score statistical test.
Given below is the algorithm used to generate normalized data provided in the VALUE column.
Algorithm used in R for data normalization
Step1: x<- read.table("input_file.txt",header=T,row.names=1,sep="\t")
Step 2: log_x<-log(x,base=2)
Step3: attach(log_x )
Step4:
cnt<-(1/8)*(sort(Signal_1)+sort(Signal_2)+sort(Signal_3)+sort(Signal_4)+
sort(Signal_5)+sort(Signal_6)++sort(Signal_7)+sort(Signal_8))
Step5: value_1<-c(rank(Signal_1))
Step6: value_2<-c(rank(Signal_2))
Step7: value_3<-c(rank(Signal_3))
Step8: value_4<-c(rank(Signal_4))
Step9: value_5<-c(rank(Signal_5))
Step10: value_6<-c(rank(Signal_6))
Step11: value_7<-c(rank(Signal_7))
Step12: value_8<-c(rank(Signal_8))
Step13:
final<-cbind(value_1,value_2,value_3,value_4,value_5,value_6,value_7,val
ue_8)
boxplot(final)
Step14: write.table(final,"f//priyanka/R method/result.txt")
Step15: write.table(final,"result.txt")
 
Submission date Sep 26, 2011
Last update date Apr 22, 2013
Contact name Malabika Datta
E-mail(s) mdatta@igib.res.in
Phone 91 11 27667602
Organization name Institute of Genomics and Integrative Biology
Street address Mall Road
City Delhi
ZIP/Postal code 110 007
Country India
 
Platform ID GPL8824
Series (1)
GSE32376 Control vs Diabetic mice skeletal muscle miRNA microarray

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
DarkCorner 1.122208307
dmr_285 1.4187898
dmr_3 1.4187898
dmr_308 -0.329471548
dmr_316 0.811393173
dmr_31a 1.4187898
dmr_6 0.811393173
hur_1 1.4187898
hur_2 1.4187898
hur_4 1.312524198
hur_5 0.752905931
hur_6 1.4187898
mghv-miR-M1-1 0.752905931
mghv-miR-M1-2 1.205116378
mghv-miR-M1-3 1.4187898
mghv-miR-M1-4 1.4187898
mghv-miR-M1-5 1.4187898
mghv-miR-M1-6 0.752905931
mghv-miR-M1-7-3p 1.030951417
mghv-miR-M1-7-5p 1.4187898

Total number of rows: 598

Table truncated, full table size 14 Kbytes.




Supplementary file Size Download File type/resource
GSM801502_S01_miRNA_diabetic_4.txt.gz 713.3 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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