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Sample GSM825138 Query DataSets for GSM825138
Status Public on Nov 02, 2011
Title S02 Control 14-Af3
Sample type RNA
 
Source name untreated control
Organism Rattus norvegicus
Characteristics strain: Fisher 344
genotype/variation: Big Blue Transgenic
gender: male
age: 6 weeks
tissue: kidney
Treatment protocol Male, 6-week-old Big Blue rats were treated with Aristolochic Acid as its sodium salt at 10.0 mg/kg body weight by gavage (4 ml/kg body weight) 5 times a week for 12 weeks. The animals were sacrificed 1 day after the last treatment. The kidneys were isolated, flash frozen in liquid nitrogen, and stored at - 80°C.
Growth protocol All animal procedures followed the recommendations of the NCTR Institutional Animal Care and Use Committee for the handling, maintenance, treatment, and sacrifice of the rats.
Extracted molecule total RNA
Extraction protocol RNAs were isolated from about 40-50 mg rat kidney tissue suspended in RNA-Later ICE (Ambion Inc., Austin, TX) using mirVanaTM miRNA isolation kit (Ambion). This kit combines the advantages of acid-phenol:chloroform extraction and glass solid-phase extraction and can yield high quality of microRNA-retaining total RNAs. RNA concentrations were determined on NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, Delaware) and the qualities were checked on on an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) using an RNA6000 Nano LabChip (Agilent).
Label Cy3
Label protocol To perform the miRNA array experiment, total RNA (2 to 5 µg) was first size fractionated using a YM-100 Microcon centrifugal filter (Millipore). The small RNAs (< 300 nt) were then 3’-extended with a poly(A) tail using poly(A) polymerase. Thereafter, an oligonucleotide tags was ligated to the poly(A) tail for later staining with fluorescent dye Cy3.
 
Hybridization protocol Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).
Scan protocol Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).
Description CTL_14
Data processing Raw intensities experienced the adjustments of data-filtering, log 2 transformation, gene centering and normalization with a cyclic LOWESS (locally weighted regression). MiRNAs with all 6 samples intensities larger than the intensity threshold of 32 were considered detectable.
 
Submission date Nov 01, 2011
Last update date Nov 02, 2011
Contact name Fanxue Meng
E-mail(s) fanxue.meng@fda.hhs.gov
Phone 870-543-7082
Organization name National Center for Toxicological Research
Street address 3900 NCTR Road, HFT-130
City Jefferson
State/province AR
ZIP/Postal code 72079
Country USA
 
Platform ID GPL14819
Series (1)
GSE33360 Discovery of novel microRNAs in rat kidney using microarray analyses

Data table header descriptions
ID_REF
VALUE The normalized intensity using cyclic lowess normalization method

Data table
ID_REF VALUE
age-miR-198 20.4139914
age-miR-222 158.3943372
age-miR-506 2.154634509
age-miR-507 1.711641587
age-miR-508 1.401780084
age-miR-509a 2.107300546
age-miR-509b 2.577277592
age-miR-510 1.533526532
age-miR-513a 1.935107871
age-miR-513b 0.036923775
age-miR-513c 0.036241131
age-miR-513d 1.239433456
age-miR-513e 0.033505738
age-miR-514 0.318802794
bta-let-7e 20977.9591
bta-miR-105b 1.572523304
bta-miR-106 95.44794224
bta-miR-1224 17.62896606
bta-miR-1225-3p 8.814623103
bta-miR-124a 0.707143151

Total number of rows: 5619

Table truncated, full table size 138 Kbytes.




Supplementary file Size Download File type/resource
GSM825138_CTL_14.txt.gz 465.6 Kb (ftp)(http) TXT
Processed data included within Sample table

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