Transcriptome Analysis of Type 1 Diabetes Mesenchymal Stem Cells

Total RNA was isolated from random T1D-MSCs (n = 11) and C-MSCs (n = 10) by the Trizol method (Invitrogen, USA) and purified by RNeasy commercial kit (QIAGEN, USA) according to the manufacturers’ recommendations. RNA integrity was evaluated by microfluidic electrophoresis using Agilent 6000 RNA Nano chips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only RNA samples that were free of proteins and phenol and that featured an RNA Integrity Number (RIN) ≥ 9.0 were used. Random RNA samples of T1D-MSCs and C-MSCs were selected (n = 4 for each group) and the global gene expression was analyzed by the One-color Microarray-Based Gene Expression Analysis Protocol system (Agilent Technologies) on glass slides with four microarrays of 44,000 probes each (4 × 44 k). The preprocess and statistical microarray analyses were performed using algorithms available in the R platform (R Foundation, Vienna, Austria) through the Linear Models for Microarray Data (LIMMA) package [56 (link)]. Heatmaps were generated by the HeatMapViewer module of GenePattern 2.0 software [57 (link)]. Genes with p < 0.05 and fold change (FC) > 2.0 were considered differentially expressed. Microarray data were deposited in the public database ArrayExpress (http://www.ebi.ac.uk/arrayexpress [ArrayExpress:E-MTAB-2976]).

Free full text: Click here

de Lima K.A., de Oliveira G.L., Yaochite J.N., Pinheiro D.G., de Azevedo J.T., Silva Jr W.A., Covas D.T., Couri C.E., Simões B.P., Voltarelli J.C., Oliveira M.C, & Malmegrim K.C. (2016). Transcriptional profiling reveals intrinsic mRNA alterations in multipotent mesenchymal stromal cells isolated from bone marrow of newly-diagnosed type 1 diabetes patients. Stem Cell Research & Therapy, 7, 92.

Publication 2016

Trizol method Agilent 6000 RNA Nano chips Agilent 2100 Bioanalyzer One-color Microarray-Based Gene Expression Analysis Protocol system R platform

Chips Electrophoresis Gene expression Gene expression microarray analysis Genes Microarray Phenol Proteins Trizol

Corresponding Organization : Universidade de São Paulo

Top 5 similar protocols

Variable analysis

independent variables

T1D-MSCs
C-MSCs

dependent variables

Global gene expression

control variables

RNA integrity (RIN ≥ 9.0)
Absence of proteins and phenol in RNA samples

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.

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?

Revolutionizing how scientists
search and build protocols!