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| Status |
Public on Jul 07, 2009 |
| Title |
Gene Expression Analysis of Carbonyl Sulfide Neurotoxicity |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by array
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| Summary |
To gain insight into the pathogenesis of carbonyl sulfide induced neurotoxicity, we examined the gene expression profile of exposed rats before the onset of morphological changes (days 1 and 2) using the most consistently affected brain region, the posterior colliculus.
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| Overall design |
Immediately after the cessation of COS exposure on the appropriate day of sacrifice (day 1 or day 2) the rats were deeply anesthetized with intraperitoneal sodium pentobarbital. The posterior colliculi were surgically exposed and removed using a pair of corneal scissors and fine forceps. The samples were immediately placed in RNase-free plastic vials and snap frozen in liquid nitrogen. Three control animals (non-exposed) were processed identically. Total RNAs from frozen brain tissue (posterior colliculus) were isolated with an RNeasy tissue kit (Qiagen, Valencia, CA) according to the manufacturer's protocols. The quality and integrity of the RNA was verified by 260/280 nm absorbance ratio, formaldehyde agarose gel electrophoresis and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA). Gene expression analysis was conducted using Agilent Rat Oligo Microarrays (Agilent Technologies, Palo Alto, CA). Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol. For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner. Two arrays were utilized for each comparison allowing for dye reversals. Data was obtained using the Agilent Feature Extraction software (v8.1), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).
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| Contributor(s) |
Morrison JP, Ton K, Collins JB, Switzer R, Little PB, Morgan D, Sills RC |
| Citation(s) |
19395590 |
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| Submission date |
Jul 07, 2008 |
| Last update date |
Dec 06, 2012 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
[email protected], [email protected]
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| Organization name |
NIEHS
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| Department |
DIR
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| Lab |
Microarray Core
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| Street address |
111 T.W. Alexander Drive
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| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platforms (1) |
| GPL890 |
Agilent-011868 Rat Oligo Microarray G4130A (Feature Number version) |
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| Samples (12)
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| GSM303609 |
Day 0 #2-500ppm vs. Day 0 control pool |
| GSM303610 |
Day 0 control pool vs. Day 0 #2-500ppm |
| GSM303611 |
Day 0 control pool vs. Day 0 #3-500ppm |
| GSM303612 |
Day 0 #3-500ppm vs. Day 0 control pool |
| GSM303613 |
Day 0 control pool vs. Day 0 #9-500ppm |
| GSM303614 |
Day 0 #9-500ppm vs. Day 0 control pool |
| GSM303615 |
Day 1 #6-500ppm vs. Day 1 control pool |
| GSM303616 |
Day 1 control pool vs. Day 1 #6-500ppm |
| GSM303617 |
Day 1 #16-500ppm vs. Day 1 control pool |
| GSM303618 |
Day 1 control pool vs. Day 1 #16-500ppm |
| GSM303619 |
Day 1 control pool vs. Day 1 #19-500ppm |
| GSM303620 |
Day 1 #19-500ppm vs. Day 1 control pool |
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| Relations |
| BioProject |
PRJNA113293 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12018_RAW.tar |
363.6 Mb |
(http)(custom) |
TAR (of TIFF, TXT) |
| Processed data included within Sample table |
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