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Sample GSM558054 Query DataSets for GSM558054
Status Public on Jan 03, 2012
Title Cortical neurons-Ctrl-24h-Rep 2
Sample type RNA
 
Source name Murine primary cortical neurons
Organism Mus musculus
Characteristics strain: Swiss Albino mice
age: Gestation day 15-16
tissue: Primary cortical neurons
age of culture: Day 5
time point: 24h
agent: control
Treatment protocol Lactacystin was prepared as 1mM stock solution in DMSO stored at -20°C. Desired concentrations were achieved by dilution with serum-free NB. On day 5 in vitro, the cultured neurons were treated with 1uM lactacystin in NB medium.
Growth protocol Neocortical neurons (gestational days 15 or 16) obtained from foetal cortices of Swiss albino mice were used to prepare the primary cultures employing previous described procedures with modifications [Cheung NS, Beart PM, Pascoe CJ, John CA, Bernard O. Human Bcl-2 protects against AMPA receptor-mediated apoptosis. J Neurochem. 2000; 74: 1613-1620.].
Extracted molecule total RNA
Extraction protocol RNA from samples was extracted using RNeasy Mini Kit (Qiagen Cat. No. 74104) according to the manufacturer’s instructions. 1.5μl of the RNA sample was aliquoted for spectrophotometric quantification using Nanodrop ND-1000 Version 3.2.1 and 1μl for RNA quality analysis using E-gene HDAGT12 genetic analyzer.
Label biotin
Label protocol According to technical manual form Affymetrix, 7μg of extracted total RNA was used for cDNA synthesis. Double-stranded cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) with a T7-dT24 primer. After cleanup, Biotin-labeled cRNA was synthesized by in vitro transcription (Enzo Diagnostic, Inc., NY, USA) and fragmented subsequently.
 
Hybridization protocol 15μg of fragmented cRNA produced above was hybridized to the GeneChip Murine genome U74A and U74Av2 arrays for 16h at 45°C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol The hybridized arrays were washed, stained, and scanned using the Hewlett-Packard GeneArray Scanner G2500A according to the manufacturer’s instructions.
Description Replicate 2
Data processing The data from each array were collected and initially analyzed using Affymetrix Microarray Suite 5.0 software. For comparison of multiple arrays, the signal intensity of each array was scaled to 500. The regulated genes were filtered on fold change 1.5 fold against controls in at least one of three time-points. One-way ANOVA (p<0.05) approach was used to find differentially expressed genes using GeneSpring™ GX 7.3 software (Agilent Technologies, CA, USA).
 
Submission date Jun 21, 2010
Last update date Jan 03, 2012
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 GPL81
Series (1)
GSE22465 Global transcriptomic profiling of lactacystin-mediated neuronal death

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-MurIL2_at 6.9 A 0.973889
AFFX-MurIL10_at 60.7 A 0.382599
AFFX-MurIL4_at 25 A 0.185131
AFFX-MurFAS_at 11.2 A 0.48511
AFFX-BioB-5_at 327.5 P 0.003212
AFFX-BioB-M_at 666.5 P 0.000044
AFFX-BioB-3_at 284.6 P 0.000754
AFFX-BioC-5_at 842 P 0.000297
AFFX-BioC-3_at 768.1 P 0.00006
AFFX-BioDn-5_at 901.7 P 0.000044
AFFX-BioDn-3_at 4645 P 0.00011
AFFX-CreX-5_at 8779.1 P 0.000044
AFFX-CreX-3_at 14329.9 P 0.000044
AFFX-BioB-5_st 14.5 A 0.544587
AFFX-BioB-M_st 26.8 A 0.60308
AFFX-BioB-3_st 16.6 A 0.824672
AFFX-BioC-5_st 19.4 A 0.724854
AFFX-BioC-3_st 8.1 A 0.659339
AFFX-BioDn-5_st 132.3 A 0.083592
AFFX-BioDn-3_st 145.7 M 0.046482

Total number of rows: 12488

Table truncated, full table size 320 Kbytes.




Supplementary file Size Download File type/resource
GSM558054.CEL.gz 2.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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