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Sample GSM1036086 Query DataSets for GSM1036086
Status Public on Nov 01, 2015
Title SHSY5Y cells_Control 4c_rep2
Sample type RNA
 
Source name SHSY5Y cells_Control 4c
Organism Homo sapiens
Characteristics cell line: SHSY5Y (ATCC N. CRL-2266)
cell type: neuroblastoma
Growth protocol Neuroblastoma cells adherent onto Petri dishes at standard density were collected after mild treatment with Trypsin-PBS solution (5 mg/L).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 3.5 x 106 cells with Qiagen RNAeasy Mini Kit (Qiagen S.p.A., Milan, Italy) following the manufacturer’s instructions (Animal cells Spin protocol), including genomic DNA elimination step in column. The qualitative parameters A260/A280>1.8, A260/A230>1.7; RNA integrity number>7 were evaluated.
Label Cy3
Label protocol cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 5.1).
 
Hybridization protocol Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 5.1).
Scan protocol Each microarray was scanned using an Axon GenePix 4400 A at 532 nm and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA).
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction.
 
Submission date Nov 13, 2012
Last update date Nov 01, 2015
Contact name Alberto Ferrarini
E-mail(s) alberto.ferrarini@univr.it
Phone +39-045-802-7058
Organization name University of Verona
Department Scientific and Technological Department
Lab Plant Functional Genomics Centre
Street address Strada le Grazie, 15
City Verona
State/province Veneto
ZIP/Postal code 37134
Country Italy
 
Platform ID GPL16025
Series (1)
GSE42236 Extreme sensitivity of gene expression in human neurocytes SH-SY5Y to ultra-low doses of a medicinal plant with anxiolytic-like properties

Data table header descriptions
ID_REF
VALUE RMA-normalized signal intensities.

Data table
ID_REF VALUE
AB000409 2512.0978
AB000463 3376.2076
AB000781 156.8134
AB001328 32.5895
AB002294 4285.4776
AB002308 9700.8917
AB002311 1529.9135
AB002313 13354.3952
AB002360 3999.7718
AB002377 3136.2643
AB002381 9039.7651
AB002382 10309.7781
AB002384 26.8719
AB003177 3957.5583
AB003333 8224.1616
AB006589 74.5352
AB006590 180.775
AB006621 64.1391
AB006625 643.9968
AB007457 8320.9726

Total number of rows: 45033

Table truncated, full table size 837 Kbytes.




Supplementary file Size Download File type/resource
GSM1036086_534739A07_590_532.pair.gz 2.9 Mb (ftp)(http) PAIR
Processed data included within Sample table

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