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Sample GSM562353 Query DataSets for GSM562353
Status Public on Jul 14, 2010
Title pCDNA/P19_undifferentiated
Sample type RNA
Source name pCDNA/P19, undifferentiated state
Organism Mus musculus
Characteristics cell type: embryonic carcinoma cell line
cell line: P19
genotype/variation: carrying an empty vector
Treatment protocol To induce neural differentiation of these P19 cell lines, cells were allowed to aggregate in culture medium with 5×10-7 M all-trans-retinoic acid (RA) for 4 days. After aggregation, cells were replated onto cell culture grade dishes or poly-L-Lysine coated cell-disks for two days.
Growth protocol P19 cells were cultured in alpha-modified Eagle’s essential medium (Sigma) containing 10% FCS and 2 mM L-glutamine.
Extracted molecule total RNA
Extraction protocol Total RNAs were prepared using ISOGENE (Nippon Gene, Toyama Japan) at each state of these cells according to the manufacture’s instruction. The qualities and integrities of these RNAs were verified by gel electrophoresis and by Agilent Bioanalyzer (Böblingen, Germany).
Label Cy3
Label protocol Cy3-labeled cRNA probes were synthesized according to the manufacture’s instruction (Agilent, Quick Amp Labeling Kit). Briefly mentioned, 0.2μg of each total RNA was reverse transcribed to double-stranded cDNA using T7 promoter sequence adding to oligo dT nucleotide as a primer. cRNAs were transcribed from these double-stranded cDNAs by T7 RNA polymerase.
Hybridization protocol Cy3-labeled cRNAs were hybridized to Whole Mouse Genome oligo-DNA microarray (Agilent) at 65°C for 17 hours using Gene Expression Hybridization Kit (Agilent) and washed using Gene Expression Wash Pack (Agilent).
Scan protocol Intensities of Cy3-fluorescent signals were scanned by Agilent DNA microarray scanner.
Description Gene expression of pCDNA/P19 cells in the undifferentiated state
Data processing The raw data was converted into the quantitative data using Agilent Feature Extraction software version Data were further normalized using GeneSpringGX10 using Median shift normalization to the 75th percentile and baseline transformed to the median of all samples.
Submission date Jul 02, 2010
Last update date Jul 13, 2010
Contact name Kohzo Nakayama
E-mail(s) kohzona@
Phone +81-263-37-2594
Fax +81-263-37-2594
Organization name Shinshu University
Department Anatomy
Street address Asahi
City Matsumoto
ZIP/Postal code 390-8621
Country Japan
Platform ID GPL7202
Series (1)
GSE22690 The intracellular domain of amyloid precursor protein induces the dynamic change of the gene expression profile in P19 cells.

Data table header descriptions
VALUE median normalized signal intensity

Data table
A_51_P331831 1.67609
A_51_P280918 0.850274
A_52_P258194 0.369411
A_52_P214630 0.151302
A_52_P579519 3.01969

Total number of rows: 41252

Table truncated, full table size 633 Kbytes.

Supplementary file Size Download File type/resource
GSM562353.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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