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Sample GSM1092212 Query DataSets for GSM1092212
Status Public on Oct 24, 2014
Title Day6neurons_OGD_2hr OGD
Sample type RNA
 
Source name Day6neurons_OGD_2hr OGD
Organism Mus musculus
Characteristics age: Gestation day 15
strain: Swiss Albino Mouse
cell type: Murine primary cortical neurons
age of culture: Day 6
ogd treatment: 2hr
24hr reperfusion: +
Treatment protocol Primary neuronal cultures from day 6 were subjected to oxygen-glucose deprivation (OGD) conditions as previously described (Ziu et al. 2011). Glucose-free Earle’s balanced salt solution (EBSS) was saturated with a mixture gas of 5% CO2, 95% N2, in a ProOx in vitro chamber (BioSpherix, USA) at 37ºC overnight, with O2 maintained at 0.1%. Day 6 neuronal cultures were washed twice with this medium and incubated for 2, 4, 6, 8hr in the chamber. OGD was terminated by replacing the glucose-free EBSS with reperfusion medium (Neurobasal medium with L-glutamine and Penicillin-streptomycin, without B27 supplement). Control cultures were treated identically, but without exposure to OGD conditions. During reperfusion, the cells were maintained in a regular 5% CO2 incubator for 24hrs.
Growth protocol Primary cultures of cortical neurons were established from E15 Swiss albino mouse brains. The cortices were dissected from E15 mouse embryos and washed with Hanks’ balanced salt solution (HBSS, 14025-092, Gibco, Invitrogen, USA). The cortical slices was dissociated with 0.05% (w/v) trypsin in HBSS without Ca2+/Mg2+ (14175-095, Gibco, Invitrogen, USA) for 30 min at 37 °C and neutralized with 1mg/ml trypsin inhibitor (T6522, Sigma, USA). Single cells were obtained by gentle trituration in Neurobasal medium (21103-049, Gibco, Invitrogen, USA) supplemented with B27 (17504-044, Invitrogen, USA), L-glutamine and Penicillin-streptomycin (Gibco, Invitrogen, USA). The cells were counted by trypan blue exclusion and seeded on to poly-d-lysine coated 24 well plates at a density of 120, 000 cells/cm2. Cultures were maintained at 37 °C with 5% CO2 in a tissue culture incubator. Cells were harvested on Days 2, 4, 6, 8.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells by a single-step method using Trizol (Invitrogen, Life Technologies, USA) according to the manufacturers’ protocol. The concentration and integrity of the RNA were determined using Nanodrop ND-2000c spectrophotometry (Nanodrop Tech, Rockland, Del) and denaturing polyacrylamide gel electrophoresis, respectively. Thereafter, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre, USA).
Label Cy3
Label protocol Agilent Quick Amp Labeling Kit was used for sample labeling.
 
Hybridization protocol Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.
Scan protocol Slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software.
Data processing Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity mRNAs and lncRNAs were filtered.
 
Submission date Mar 04, 2013
Last update date Oct 24, 2014
Contact name Kandiah Jeyaseelan
E-mail(s) erijeya@nus.edu.sg
Organization name National University of Singapore
Department Biochemistry
Street address 8 Medical Drive
City Singapore
ZIP/Postal code 117597
Country Singapore
 
Platform ID GPL15691
Series (2)
GSE44833 Long non-coding RNAs and microRNAs involved in integrated co-regulation of neuronal maturation [mRNA and lncRNA expression]
GSE44834 Long non-coding RNAs and microRNAs involved in integrated co-regulation of neuronal maturation

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity

Data table
ID_REF VALUE
ASMM9PARTA049521 49.08401299
ASMM9PARTA014347 5.376294248
ASMM9PARTA017757 15.61661858
ASMM9PARTA048762 5.376294248
ASMM9PARTA051693 33.82302994
ASMM9PARTA049169 13.65222319
ASMM9PARTA016808 75.80422736
ASMM9PARTA046515 27.29370609
ASMM9PARTA010571 163.70658
ASMM9PARTA006644 2477.738125
mouselincRNA1210-_P1 45.03266648
MM9LINCRNAEXON10371+_P1 12.23265112
ASMM9PARTA005038 24.30714759
ASMM9PARTA009196 22.01002227
ASMM9PARTA008398 1341.6401
ASMM9PARTA051672 22.61034342
ASMM9PARTA014246 137.844319
humanlincRNA2392+_P1 8.698452736
MM9LINCRNAEXON10405-_P1 6.936852459
MM9LINCRNAEXON10315+_P1 44.68260214

Total number of rows: 29929

Table truncated, full table size 857 Kbytes.




Supplementary file Size Download File type/resource
GSM1092212_mmu-eNeud6-OGD_2hr_raw_data.txt.gz 2.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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