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Sample GSM400141 Query DataSets for GSM400141
Status Public on Nov 01, 2009
Title Olfactory_Epithelium_Rat-33
Sample type RNA
 
Source name Olfactory epithelium of rat 33 (litter4)
Organism Rattus norvegicus
Characteristics strain: Brown Norway
tissue: Olfactory epithelium
gender: Not known
litter: Litter4
age: 3-5 days
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Nucleospin RNA kit according to the manufacturer’s (Macherey-Nagel) instructions, which included an in-column DNase treatment before RNA elution to ensure the absence of genomic DNA. Recovered RNA was quantified using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA integrity was assessed with RNA 6000 Nano LabChip kit using the Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with an RNA Integrity Number (RIN) greater than 8.5 were used for further analysis (RNA profiling analysis and semi quantitative reverse transcription PCR analysis). Because of the application of this strict quality threshold, the left sample from one adult olfactory epithelium was not studied.
Label Cy3
Label protocol RNA samples were labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit (p/n 5184-3523) according to the manufacturer’s instructions. Briefly, 350 ng of total RNA was used as template and copied into cDNA by reverse transcription and concomitant amplification with T7-polymerase; cyanine-3 (Cy3)-labeled CTP was used for labeling. Cy3 labeling was monitored with a Nanodrop ND-1000 spectrophotometer and was found to be between 1.2 and 1.9 pmol/μl.
 
Hybridization protocol Hybridization was performed using the Agilent Gene Expression Hybridization kit (p/n 5188-5242), following the manufacturer’s instructions. Briefly, 1650 ng of labeled cRNA was mixed with Hybridization Buffer and Blocking Agent and subjected to fragmentation (by incubation for 30 min at 60°C in the dark). Hybridizations onto 4x44K Whole Rat Genome 60-mer oligonucleotide microarrays (G4131F) (Agilent Technologies) were performed in a rotary oven (65°C, 17 h and 10 rpm) in the dark. Slides were disassembled and washed in Gene Expression wash Buffers I and II according to the manufacturer’s instructions, and dried using a nitrogen-filled air gun before scanning.
Scan protocol Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent DNA Microarray Scanner), using Agilent parameters. Feature Extraction software version 9.5 was used to extract and analyze the signals.
Description OE_rat33_litter4.txt
Data processing Array results were analyzed using GeneSpring GX software version 7.3 (Agilent Technologies), via the Enhanced Agilent Feature Extraction Import Preprocessor. Data were normalized in two steps using the algorithms supplied with the Feature Extraction software. Data were first transformed to convert any negative value to 0.01, then normalization was performed by using a per-chip 50th percentile method that normalizes each chip to its median, allowing comparison between chips. A second normalization step was applied to the results for each gene across all the arrays in the study (normalize to median): the median of all the values obtained for a given gene was calculated and used as the normalization standard for that gene, such that, regardless of absolute differences in the expression of the various genes, they are placed on the same scale for comparison.
 
Submission date May 05, 2009
Last update date May 05, 2009
Contact name Francis Galibert
E-mail(s) francis.galibert@univ-rennes1.fr
Organization name CNRS UMR6061/Université Rennes1
Department Génétique et Developpement
Street address 2 av du Pr Léon Bernard
City RENNES
ZIP/Postal code 35043
Country France
 
Platform ID GPL4135
Series (2)
GSE15953 RNA profiles of rat olfactory epithelia : individual and age related variations (age experiment)
GSE15954 RNA profiles of rat olfactory epithelia : individual and age related variations

Data table header descriptions
ID_REF
VALUE GeneSpring GX 7.3 normalized signal intensity
FLAG Detection call

Data table
ID_REF VALUE FLAG
12 0.7578392 A
13 0.77401733 A
14 1.0965279 P
15 0.77218175 A
16 1.1502036 P
17 1.0436579 P
18 0.9283534 P
19 0.9118271 P
20 0.86958617 P
21 0.01 A
22 1.433649 P
23 0.7082425 P
24 1.399677 P
25 0.9939412 P
26 2.0679228 P
27 0.95087385 P
28 1.2139456 P
30 0.87148017 P
32 0.98816603 P
33 1.079745 P

Total number of rows: 41012

Table truncated, full table size 692 Kbytes.




Supplementary file Size Download File type/resource
GSM400141.txt.gz 8.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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