NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1411067 Query DataSets for GSM1411067
Status Public on Jul 06, 2015
Title kidney_G03_injSaline-024h_rep1
Sample type RNA
 
Source name kidney
Organism Rattus norvegicus
Characteristics strain: Wister
Sex: male
weight: 200-300g
group: Group 3
injury: Yes
treatment: Saline
time (h): 24
tissue: kidney
Treatment protocol Briefly, rats were anesthetized by isofluorane inhalation induction followed by ketamine (40-80 mg/kg) and xylazine (5-10 mg/kg) intraperitoneally. Rats were premedicated with Valproic acid (150mg/kg), dexamethasone (3mg/kg) or saline (control) intraperitoneally thirty minutes prior to surgery. A sterile surgical site was prepared and midline incision was performed to access the abdominal cavity. Left kidney was located and its renal artery was clamped using an atraumatic microaneurysm clamp. The abdomen was reapproximated to prevent dehydration and maintain body temperature. Following 45 minutes of warm ischemia the abdomen was reopened and the renal clamp was removed to allow reperfusion. Reperfusion was confirmed by observing the color change in the kidney (pale to bright red). This was immediately followed by a right nephrectomy. The abdomen was then closed by suturing muscles with 6-O prolene and skin with 4-O nylon and clips.
Growth protocol Male Wister rats (200-300g) were purchased from Harlan Laboratories and housed in accordance with the Guidelines for the Care and Use of Laboratory Animals. All experiments were conducted according to NIH and institutional guidelines with the approval of Madigan Army Medical Center Institutional Animal Care and Use Committee.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the kidney tissue using Trizol (Invitrogen, Carlsbad, CA) followed by column purification with miRNeasy-96 kits (Qiagen, GmbH, Germany) to remove residual salt and organic solvents. Total RNA quality and quantity were evaluated using an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA) and verified using the NanoDrop ND-1000 Spectrophotometer (NanoDrop, Wilmington, DE).
Label biotin
Label protocol An initial input of 100 ng total RNA per sample was synthesized to cRNA using the Ambion Whole Transcript (WT) Expression Kit (Ambion, #4411974) according to manufacturer’s recommendations. Then 10 µg cRNA was used as a template to synthesize cDNA which were fragmented and labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix, #901524).
 
Hybridization protocol Fragmented, labeled cDNA were hybridized to Affymetrix RatGene 1.1 ST array plates on an Affymetrix GeneTitan following manufacturer’s instructions using the GeneTitan Hybridization, Wash and Stain Kit for WT array plates (Affymetrix, #901622).
Scan protocol Array plates were scanned immediately after hybridization, wash and staining by the Affymetrix GeneTitan using default settings.
Data processing Microarray data was processed for background adjustment, normalization, and summarization using the interPLIER gene level method (background = PM-GCBG, normalization method = Sketch-Quantile) in Affymetrix Expression Console software (Version 1.1).
 
Submission date Jun 12, 2014
Last update date Jul 07, 2015
Contact name Christine Baer
E-mail(s) christine.e.baer2.ctr@mail.mil
Organization name Excet, Inc. / USACEHR
Department Environmental Health Program
Street address 568 Doughten Drive
City Ft. Detrick
State/province MD
ZIP/Postal code 21702-5010
Country USA
 
Platform ID GPL11534
Series (1)
GSE58438 Renoprotective Effects of Valproic Acid and Dexamethasone in Acute Kidney Ischemia-Reperfusion Injury

Data table header descriptions
ID_REF
VALUE PLIER normalized signal intensity

Data table
ID_REF VALUE
10700001 1599.91
10700002 100.986
10700003 963
10700004 83.0347
10700005 673.669
10700006 32.9467
10700007 27.1865
10700008 4.10517
10700009 220.667
10700010 18.7799
10700011 26.661
10700012 52.6464
10700013 1295.42
10700014 912.545
10700015 142.41
10700016 19.7831
10700017 104.218
10700018 6.17934
10700019 38.9348
10700020 2080.3

Total number of rows: 29214

Table truncated, full table size 481 Kbytes.




Supplementary file Size Download File type/resource
GSM1411067_MD-13-071.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.