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Sample GSM1092207 Query DataSets for GSM1092207
Status Public on Oct 24, 2014
Title Maturing neurons Day 2
Sample type RNA
 
Source name Maturing neurons Day 2
Organism Mus musculus
Characteristics age: Gestation day 15
strain: Swiss Albino Mouse
cell type: Murine primary cortical neurons
age of culture: Day 2
ogd treatment: -
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 72.07996472
ASMM9PARTA014347 67.26853809
ASMM9PARTA017757 22.3601754
ASMM9PARTA048762 38.04217956
ASMM9PARTA051693 20.66549477
ASMM9PARTA049169 10.9808239
ASMM9PARTA016808 40.13937645
ASMM9PARTA046515 39.06460984
ASMM9PARTA010571 97.61475971
ASMM9PARTA006644 1034.482841
mouselincRNA1210-_P1 74.38874225
MM9LINCRNAEXON10371+_P1 18.33460144
ASMM9PARTA005038 36.62619688
ASMM9PARTA009196 36.77140509
ASMM9PARTA008398 836.8133167
ASMM9PARTA051672 72.05351968
ASMM9PARTA014246 273.9593439
humanlincRNA2392+_P1 19.30180284
MM9LINCRNAEXON10405-_P1 35.42989783
MM9LINCRNAEXON10315+_P1 51.89292672

Total number of rows: 29929

Table truncated, full table size 857 Kbytes.




Supplementary file Size Download File type/resource
GSM1092207_mmu-eNeu_d2_lncRNAmRNA_raw_data.txt.gz 2.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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