Nice article. Kindly suggest what is the most convenient method to study lncRNAs? Is there any lncRNA-specific microarray chip designed by any company? If we perform DNA/RNA sequencing, what software be used to find lncRNAs?
Article LncRNA Expression Discriminates Karyotype and Predicts Survi...
Dear sir,
plz contact Agilent technology for microarray chip useful for lncRNA Expression analysis.
GENCODE Custom lncRNA Expression Microarray Design
long non-coding RNA expression array design with probes targeting the Gencode v15 human lncRNA annotation.
Gencode Version 15
Array: gencode.v15.lncrna.2probe.version1
Agilent Design ID (AMADID): 047718
Format: 8x60k
Transcript level
Probes designed against Gencode v15 lncRNAs
2 probes per lncRNA transcript
22001 targeted lncRNA transcripts
17535 randomly selected protein coding targets
Affymetrix also expresses lncRNAs on many of their newer platforms, e.g. the mouse genechip ST 2.0 and Mouse Transcriptome 1.0 chips have these.
This is a challenging question. Not all lncRNAs will be found in a microarray, and so it may not be my first choice. If you have specific lncRNA you wish to test, such as one of those identified in the referenced paper, you may as well just perform qRT-PCR. If you are interested in global lncRNA expression and want to perform RNA-seq to identify global lncRNAs expression in your samples, you would need to start by first considering your library prep. Not all lncRNA are polyadenylated, so you may want to take a random oligimer based approach. Similarly, this would need to be considered for your qRT-PCR, and microarray analyses as well.
Standard alignment (MAPSPLICE/TOPHAT), quantification (RSEM), and DE gene expression analysis programs (DEseq/edgeR) could be used to identify differential expression of lncRNA.
Hi
Better use whole genome and RNA sequencing. You can purchase softwares or try galaxy work station.