The procedure using previously described methods [85 (link),86 (link)] started with a poly(A) tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA. The next step was sample hybridization onto an Affymetrix miRNA 4.1 Array Strip (Affymetrix). The last step was streptavidin-PE addition and array scanning with Affymetrix GeneAtlas system (Affymetrix).
Affymetrix mirna 4.1 array strip
Manufactured by Thermo Fisher Scientific
The Affymetrix miRNA 4.1 Array Strip is a microarray-based platform designed for the detection and quantification of microRNA (miRNA) expression. It provides a comprehensive coverage of miRNAs from multiple species.
Automatically generated - may contain errors
Lab products found in correlation
Geneatlas microarray system, by Thermo Fisher Scientific (1 mentions)
Flash tag biotin hsr, by Thermo Fisher Scientific (1 mentions)
Geneatlas system, by Thermo Fisher Scientific (1 mentions)
Affymetrix human gene 2.1 st array strip, by Thermo Fisher Scientific (1 mentions)
Human gene 2.1 st array strip, by Thermo Fisher Scientific (1 mentions)
Genechip wt plus reagent kit, by Thermo Fisher Scientific (1 mentions)
3 protocols using affymetrix mirna 4.1 array strip
1
Microarray-Based miRNA Expression Profiling
2
Microarray Analysis of miRNA Expression
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The microarray analysis was performed on the GeneAtlas™ Microarray System (Affymetrix). Total RNA from each samplewas labeled with biotin in accordance to Affymetrix Flash Tag™ Biotin HSR (Ref. 901,913, Affymetrix) kit instructions. The labeled molecules were hybridized onto Affymetrix miRNA 4.1 Array Strip (Affymetrix) using the GeneChip GeneAtlas™ Hybridization and Stain Module (Ref. 902,135) reagents (Affymetrix). After hybridization and washing, the arrays were scored on the Imaging Station of the GeneAtlas™ Microarray System. Array data of the samples have been deposited in the Array Express database at EMBL-EBI (www.ebi.ac.uk/arraexpress ) under the accession no. E-MTAB-7060.
3
Microarray Analysis of BM Mononuclear Cells
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RNA and miRNAs isolated from BM mononuclear cells of patients at different time points were pooled to generate one sample per group for microarray experiments. Affymetrix miRNA 4.1 Array Strip (Affymetrix, Santa Clara, CA) and Affymetrix Human Gene 2.1 ST Array Strip (Affymetrix) was used for the study. Generation of sense strand cDNA from the total RNA and subsequent fragmentation and labelling steps were performed using the GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific, Waltham, MA, USA). Finally, the sample was hybridized onto an Affymetrix Human Gene 2.1 ST Array Strip. The Affymetrix GeneAtlas System was used for hybridization, fluidics and scanning steps. Subsequent analyses were performed using BioConductor software. We used the Robust Multiarray Average (RMA) normalization algorithm (from the “Affy” library) for normalization, background correction, and calculation of the expression levels of the examined genes. Microarrays were made and analysed according to the methods described in previous studies.37 (link),38 (link)
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