Strategy of probe selection for studying mRNAs that participate in receptor-mediated apoptosis signaling

Abstract

Death receptors (DRs) and the participants of DR mediated signaling are characterized by a large number of mRNA isoforms generated by alternative splicing. Due to their high labor intensity and high cost, conventional methods (RT PCR and RT PCR in real time) are ineffective when the simultaneous detection of a plurality of mRNA isoforms is needed. In this regard, the use of DNA biochips is has prospective appli cations in analyzing the expression of many genes simultaneously. In this paper, we suggest an optimal strat egy of probes selection aimed at detecting the maximum number of mRNA splice variants generated by major participants of DR signaling. The objects of the study were 185 genes that form 1134 mRNA isoforms. As a result, a biochip design was developed that enables the detection of 499 mRNA isoforms (44% of total mRNA splice variants). The proposed strategy combines a high degree of modularity, the use of modern high perfor mance computers, and broad opportunities for setting up the selection criteria in accordance with the objec tives of the study.

Changes in mRNA expression of members of TGFB1-associated pathways in human leukocytes during EBV infection

“…A microarray design was developed using "Splice variants microarray design pipeline" algorithm [14]. A total of 59 target probes were selected including 23 gene "total mRNA" probes (designed to detect all mRNA transcript variants of one gene) and 36 "mRNA transcript variant" probes (designed to detect one specific mRNA transcript variant of one gene; Supplementary Table I).…”

Recent advances of <italic>in vitro</italic> detection methods of RNA biomarkers

“…RNA 生物标志物体外检测是指对人体样本 (血液、体液、组织等)中 RNA 进行的分析检测，与体 内检测方法相比具有简便、 效率高、 检测范围广、 成本 低及信息丰富等特点 [14][15][16][17] . 通常 RNA 生物标志物体 外 检 测 方 法 主 要 是 逆 转 录 聚 合 酶 链 反 应 (Reverse Transcription-Polymerase Chain Reaction, RT-PCR) [18,1 9] 、微阵列 [20,21] 和 RNA 测序 [22][23][24] . RT 2 编码 RNA 生物标志物体外检测 mRNA 由 DNA 转录而来，编码特定的氨基酸， 其表达水平与疾病的类型及预后情况相关联 [24][25][26] .…”