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)
Protocol detail
Microarray Analysis of BM Mononuclear Cells
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization : Pomeranian Medical University
Other organizations : Poznan University of Medical Sciences, Jagiellonian University, Medical University of Silesia
Top 5 similar protocols
Variable analysis
independent variables
- Time points at which BM mononuclear cells were collected from patients
- RNA and miRNAs expression levels measured using Affymetrix miRNA 4.1 Array Strip and Affymetrix Human Gene 2.1 ST Array Strip
- Pooling of RNA and miRNAs isolated from BM mononuclear cells of patients at different time points to generate one sample per group for microarray experiments
- Use of Affymetrix miRNA 4.1 Array Strip and Affymetrix Human Gene 2.1 ST Array Strip for the study
- Generation of sense strand cDNA from the total RNA and subsequent fragmentation and labelling steps using the GeneChip™ WT PLUS Reagent Kit
- Hybridization of the sample onto an Affymetrix Human Gene 2.1 ST Array Strip using the Affymetrix GeneAtlas System
- Use of Robust Multiarray Average (RMA) normalization algorithm for normalization, background correction, and calculation of the expression levels of the examined genes
- No positive or negative controls were explicitly mentioned in the provided information.
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!