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Sample GSM537470 Query DataSets for GSM537470
Status Public on May 26, 2011
Title astrocyte_global mRNA (S803681.H52)
Sample type RNA
 
Source name primary human cerebral cortex astrocyte cell line (ScienCell Research Laboratories, cat#1800)
Organism Homo sapiens
Characteristics cell line: primary human cerebral cortex astrocyte cell line (ScienCell Research Laboratories, cat#1800)
passage number: between 4 - 6
cell fraction: global cellular fraction
Growth protocol Primary human cerebral cortex astrocyte cells were cultured in cell specific astrocyte medium containing 2% fetal bovine serum, 1% astrocyte growth supplement and 1% penicillin/streptomycin (ScienCell Research Laboratories). Adherent human U-87 MG astrocytoma/glioblastoma cells were cultured under 5% CO2 in DMEM F12 + 1% L-glutamine (2 mM) (Cambrex, Walkersville, MD) supplemented with 10% fetal calf serum (Gibco, Burlington, ON, Canada), 1% penicillin-streptomycin (Gibco), 1% sodium pyruvate (1 mM) (Gibco) and 1% non-essential amino acids (0.1 mM) (Gibco) at 37°C.
Extracted molecule total RNA
Extraction protocol Total RNA enriched with small RNAs was isolated from the RISC-IP complex and the global cellular fraction using the mirVana kit (Ambion) according to the procedures outlined in the manufacturer’s protocol.
Label biotin
Label protocol Double-stranded cDNA is synthesized from total RNA isolated from cells. Affymetrix’s GeneChip IVT Express kit was used for cDNA synthesis and in vitro transcription to produce biotin-labeled cRNA from the cDNA. The cRNA is fragmented before hybridization. As outlined in detail in http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
 
Hybridization protocol A hybridization cocktail is prepared, including the fragmented target, and probe array controls. It is then hybridized to the probe array during a 16-hour incubation. As outlined in detail in http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
Scan protocol Once the probe array has been hybridized, washed, and stained, it is scanned. Each workstation running Affymetrix Microarray Suite or GCOS can control one scanner. The software defines the probe cells and computes an intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
Description The concentration of RNA samples was determined using Nanodrop ND-1000 Spectrophotometer and the RNA quality of 2 samples was checked on RNA Nano chip using Agilent 2100 Bioanalyzer. All RNA samples displayed no degradation with two sharp ribosomal peaks. Affymetrix’s GeneChip IVT Express kit was used for cDNA synthesis and in vitro transcription.
Data processing The data were processed by Affymetrix Software Command Console and Expression Console using RMA algorithms which consisted of three steps: background correction, quantile normalization (each performed at the individual probe level), and robust linear model fit using log-transformed intensities (at the probe set level). The RMA normalized expression values in the Matrix are the average of 4 replicates for each of the 4 samples.
The overall selection criteria for presence used genes with expression values larger than a threshold 3.5 in more than 50% of samples (2 out of 4).
 
Submission date Apr 26, 2010
Last update date May 26, 2011
Contact name Joanna Moser
Organization name University of Calgary
Department Biochemistry and Molecular Biology
Lab Dr. Marvin Fritzler
Street address 3330 Hospital Drive N.W.
City Calgary
State/province AB
ZIP/Postal code T2N 4N1
Country Canada
 
Platform ID GPL570
Series (1)
GSE21514 The mRNA and microRNA expression profile of the RNA-induced silencing complex in human U-87 astrocytoma cells and primary human astrocytes

Data table header descriptions
ID_REF
VALUE RMA normalized signal

Data table
ID_REF VALUE
1007_s_at 11.4104529
1053_at 8.76003541
117_at 6.012533792
121_at 8.685567454
1255_g_at 6.881998838
1294_at 7.804694025
1316_at 5.900488908
1320_at 6.324064028
1405_i_at 4.207346808
1431_at 4.520504259
1438_at 7.018451481
1487_at 8.607403404
1494_f_at 6.65797771
1552256_a_at 9.829152098
1552257_a_at 9.591770758
1552258_at 5.804046071
1552261_at 5.009456369
1552263_at 7.99458084
1552264_a_at 7.908998416
1552266_at 4.070690503

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM537470_S803681.H52.CEL.gz 5.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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