|
| Status |
Public on Jan 10, 2015 |
| Title |
kidney_15WK_male_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
whole kidney,totalRNA,15weeks,male,rep2
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: F344
tissue: whole kidney
Sex: male
age: 15WK
|
| Treatment protocol |
No treatments
|
| Growth protocol |
Female Fischer 344 rats were obtained and housed under AAALAC-approved conditions with a 12-hr light/dark cycle (0600-1800). Rats were housed two per cage in standard polycarbonate cages with hardwood chip bedding maintained at 23 degrees C with a relative humidity of ~50%
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ~30 mg of whole, homogenized, kidney tissue of independent animals using Qiagen miRNeasy Mini Kit according to manufacturer’s protocol. The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260 nm (Nanodrop-1000, Thermo Scientific, Wilmington, DE). The purity and quality of extracted RNA were evaluated using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer. RNA samples with RNA integrity numbers (RINs) greater than 8.0 were used for microarray experiments with an average RIN of 8.5 for all samples.
|
| Label |
Cy3
|
| Label protocol |
Single color (Cy3) Agilent Rat miRNA 8x15k microarrays and reagents were used according to manufacturer’s protocols using 100 nanograms of total RNA.
|
| |
|
| Hybridization protocol |
Hybridizations were conducted accourding to manufacturer's protocol.
|
| Scan protocol |
Arrays were scanned using the Agilent High Resolution C Scanner according to manufacturer's protocols.
|
| Description |
whole ground tissue homogenized
|
| Data processing |
A single file containing the raw intensities (gTotalGeneSignal) of miRNAs from all arrays was generated. An intensity value of 0.1 represented miRNAs that were not expressed. Intensity values of 0.1 were replaced by the minimum intensity value (1.39) across all the arrays. This file containing the raw intensities of all arrays was used as the input file for further data pre-processing in SAS 9.1.3 to remove controls and target redundancy. Out of 15,744 array features, 2,204 features representing controls were removed, resulting in 13,540 features measuring sample miRNAs (677 unique miRNA × 20 replicates per miRNA). Redundant replicates (containing redundant values) were removed, resulting in a dataset containing 677 unique miRNAs. Next, those features which were not expressed (intensity = 1.39) in any of the arrays were discarded, leaving 311 unique features, which were expressed on at least one array. Raw intensity data for all arrays were transposed and transformed to log2 values, and normalization (75th percentile) was performed on the 311 miRNAs.
|
| |
|
| Submission date |
Jan 09, 2015 |
| Last update date |
Jul 07, 2016 |
| Contact name |
Vikrant Vijay |
| E-mail(s) |
[email protected]
|
| Phone |
870-543-7525
|
| Organization name |
US FDA National Center for Toxicological Research
|
| Department |
Division of Systems Biology
|
| Lab |
Personalized Medicine
|
| Street address |
3900 NCTR Road
|
| City |
Jefferson |
| State/province |
AR |
| ZIP/Postal code |
72079 |
| Country |
USA |
| |
|
| Platform ID |
GPL14860 |
| Series (1) |
| GSE64842 |
Rat Life Cycle Kidney miRNA Expression Data |
|
