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Sample GSM2210915 Query DataSets for GSM2210915
Status Public on Feb 08, 2017
Title Cortex_22 - treated
Sample type RNA
 
Source name treated (diet containing lithium (40 mmol/kg food for 7 days, followed by 60mmol/kg food for the rest of the experimental period. Total 6 months treatment)
Organism Rattus norvegicus
Characteristics tissue: renal cortex
strain: Wistar
gender: male
Treatment protocol The two kidneys from each animal were cut in half longitudinally; one half was put in 10% neutral buffered formalin for histology, and the other 3 halves were snap frozen in liquid nitrogen and stored at -80°C until further use.
Growth protocol Male Wistar rats were separated in two groups: The control group received a standard rodent diet (Specialty Foods, Perth, Australia) and tap water ad libitum for 6 months. The experimental group was fed 60 mM lithium/kg dry food for 6 months. Water was available ad libitum. All rats given lithium were supplied with a salt block to maintain sodium balance and prevent lithium intoxication. At 6 months, the animals were sacrificed by decapitation and their kidneys removed.
Extracted molecule total RNA
Extraction protocol Total RNA from the kidneys was isolated with TrizolR (Invitrogen, Life Technologies, USA), followed by cleaning in Norgen Total RNA columns (Norgen Biotek Corp., Canada). RNA was quantified using a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and its (purity and) quality determined on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
Label biotin
Label protocol Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
 
Hybridization protocol 50 ng total RNA was processed by using a GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA) and hybridised to Affymetrix Rat Gene 1.0 ST gene chips.
Scan protocol Chips were stained and washed with an Affymetrix GeneChip Fluidics Station 450, and scanned in an Affymetrix GeneChip 7G Plus scanner. All procedures were done according to the manufacturer's instructions.
Data processing Cel files were imported with RMA background correction, quantile normalization, log base 2 transformation, and median polish, using PArtek Genomcis Suite v 6.5 (www.Partek.com). Batch effect removal was applied using ANOVA for the factor Scan date. Gene summary and quantification was performed on the basis of the mean of the expression values of the exons per gene.
probe group file: RaEx-1_0-st-v1.r2.pgf
meta-probeset file: RaEx-1_0-stv1.r2.dt1.rn4.full.mps
 
Submission date Jun 22, 2016
Last update date Feb 08, 2017
Contact name Philipp Strauss
E-mail(s) Philipp.Strauss@uib.no
Organization name University of Bergen
Street address Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst
City Bergen
ZIP/Postal code 5020
Country Norway
 
Platform ID GPL6247
Series (1)
GSE83610 Renal fibrosis mRNA classifier: validation in experimental lithium-induced interstitial fibrosis in the rat kidney

Data table header descriptions
ID_REF
VALUE Normalized gene summary data after batch effect removal.

Data table
ID_REF VALUE
10700068 6.18444
10700069 6.78002
10700070 6.03476
10700071 7.21186
10700072 3.24672
10700073 4.97523
10700074 2.61577
10700075 9.62663
10700076 4.42791
10700077 2.78489
10700078 4.05458
10700079 8.42821
10700080 6.94354
10700081 6.52511
10700082 6.91812
10700083 5.49008
10700084 2.27827
10700085 4.87013
10700086 7.98172
10700087 5.87614

Total number of rows: 28894

Table truncated, full table size 476 Kbytes.




Supplementary file Size Download File type/resource
GSM2210915_22c.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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