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Sample GSM584546 Query DataSets for GSM584546
Status Public on Dec 31, 2013
Title Ctrl-Rep 2
Sample type RNA
 
Source name Rat primary cortical neurons
Organism Rattus norvegicus
Characteristics strain: Wistar
age: Gestation day 15-16
tissue: Primary cortical neurons
age of culture: Day 21
treatment: Ctrl
Treatment protocol After 21 days in culture, the neurons formed large clusters separated by fasciculated bundles of axons. The axonal bundles were injured by either direct transection with a fine goniotomy knife (Chung et al, 2003, Journal of Neuroscience) or underwent stretch injury via puffing of sterile oxygen (Chung et al, 2005, Journal of Neurotrauma). After the appropriate time, the cells were lysed and mRNA collected using a Qiagen RNeasy isolation kit. At least twelve wells were pooled for each timepoint, and three different cultures from different pregnant rats was used.
Growth protocol Cortical neurons were isolated from E17 Hooded Wistar rat embryos as described previously (Chung et al, 2005, Experimental Neurology). Briefly, cortices from embryos were removed and cortical tissue from 8-10 pups was pooled and placed into HEPES buffer with 0.1% trypsin (Sigma) and incubated at 37C for 15 minutes. After three washes with warm HEPES, the tissue was gently triturated and passed through a 20mm gauze filter and plated at a density of 5x105 cells per well onto 19mm2 glass coverslips. Cells were maintained in Neurobasal medium (Gibco) supplemented with 10% B-27 supplement.
Extracted molecule total RNA
Extraction protocol RNA was extracted and cleaned up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol with a hybridization duration of 17h.
Scan protocol Standard Illumina scanning protocol with a scan factor = 0.65
Description Replicate 2
1901185003_F
Data processing The data were normalised using median normalisation with GeneSpring Ver 7.3
 
Submission date Aug 18, 2010
Last update date Dec 31, 2013
Contact name Minghui Jessica Chen
Organization name Menzies Research Institute
Department Neuroscience group
Lab A/P Steve Cheung
Street address Menzies Research Institute, University of Tasmania, Private Bag 24
City Hobart
State/province Tasmania
ZIP/Postal code 7001
Country Australia
 
Platform ID GPL8031
Series (1)
GSE23653 Comparative global transcriptomic profiling of mild and severe neurotrauma in an in vitro neuronal model

Data table header descriptions
ID_REF
VALUE Median normalisation, p<0.05

Data table
ID_REF VALUE
ILMN_160502 1.0801833
ILMN_160506 1.000476
ILMN_160514 0.95631343
ILMN_160517 0.95933974
ILMN_160518 1.0667691
ILMN_160521 1.0133048
ILMN_160524 1.052471
ILMN_160537 1.0349768
ILMN_160538 0.9504573
ILMN_160546 1.06311
ILMN_160550 0.994492
ILMN_160553 1.0373195
ILMN_160554 0.9479217
ILMN_160556 0.9543154
ILMN_160558 1.0291444
ILMN_160560 1.071868
ILMN_160566 0.99431664
ILMN_160572 1.006909
ILMN_160574 0.96448106
ILMN_160576 0.81108975

Total number of rows: 22226

Table truncated, full table size 459 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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