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Sample GSM1429675 Query DataSets for GSM1429675
Status Public on Dec 10, 2014
Title Dahl Salt Resistant rats (Dahl R) 3
Sample type RNA
 
Source name Dahl R Rat fed with Low-salt (0.3%) diet
Organism Rattus norvegicus
Characteristics strain: Dahl Salt Resistant rats (Dahl R)
tissue: Kidney
gender: Male
age: 53 days
Treatment protocol After weaning all rats were fed with Low-salt (0.3%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley).
Growth protocol All rats born on the same day were selected and weaned at 30 days of age.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Cy3
Label protocol Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, for each sample 1 μg of total RNA were linearly amplified and labeled with Cy3-dCTP. Labelled cRNAs purified with Qiagen RNAeasy Mini Kit, and sample concentration and specific activity (pmol cy3/μg cRNA) were measured in a NanoDrop® ND-1000 spectrophotometer.
 
Hybridization protocol A total of 1μg of labeled cRNA was prepared for fragmentation adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, heated at 60 °C for 30 min, and finally diluted by addition with 55μl 2×GE Hybridization buffer. A volume of 100μl of hybridization solution was then dispensed in the gasket slide and assembled to the custom Rat Long Non-coding RNA Array microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.
Scan protocol The hybridized arrays were washed, fixed and scanned using the Agilent DNA microarray scanner (part number G2505B) following Agilent Technologies’ guidelines.
Description mRNA and LncRNA expression
Data processing Raw data .txt files were extracted using Agilent Feature Extraction Software (version 10.5.1.1) and imported into the Agilent GeneSpring GX software (version11.0) for further analysis. The 9 microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (Quantile normalization). Differentially expressed lncRNAs and genes with statistically significance were identified through Volcano Plot filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.0). GO analysis and Pathway analysis was performed in the standard enrichment computation method.
 
Submission date Jul 07, 2014
Last update date Dec 10, 2014
Contact name Bina Joe
E-mail(s) bina.joe@utoledo.edu
Phone 419-383-4415
Organization name University of Toledo, College of Medicine and Life Sciences
Department Department of Physiology and Pharmacology
Lab Center for Hypertension and Personalized Medicine
Street address Block Health Science Bldg, 3000 Arlington Ave
City Toledo
State/province Ohio
ZIP/Postal code 43614
Country USA
 
Platform ID GPL15690
Series (1)
GSE59165 Genome-wide identification of rat long non-coding RNAs (microarray)

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
AB006881_P1 4.7342005
AB007601_P1 5.203745
AB008752_P1 5.735652
AB011529_P1 14.073116
AB011534_P1 8.548199
AB012139_P1 8.004327
AB012662_P1 16.5236
AB013453_P1 17.424175
AB013454_P1 8.902454
AB020504_P1 7.5894485
AB020614_P1 9.197568
AB020616_P1 8.600058
AB026288_P1 12.877786
AB027292_P1 4.958
AB032083_P1 5.4199586
AB032425_P1 14.455299
AB042272_P1 3.8633642
AB042273_P1 3.710284
AB066220_P1 5.34652
AB072240_P1 4.8891716

Total number of rows: 19407

Table truncated, full table size 545 Kbytes.




Supplementary file Size Download File type/resource
GSM1429675_Dahl_R-98392.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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