MBB 342 Lecture Notes - Lecture 9: Rna-Seq, Oligonucleotide, Long Non-Coding Rna
18 Nov 2020
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Why do we study rna: copy slide. Possible bias in rna-seq: degration, rna degrades more often from 5" than 3", you can lose a lot of information about 5" end, doesn"t degrade equally either, can skew gene expression bc of this. Rpkm: has problems and skewed with highly expressed genes, a little bit of change can cause a global shift. Intergenic transcription: transcriptional peaks, read up on it. Non-coding rna: theorized to have large secondary structure, v hard to categorize, functionally important, different tissues express in diff smth. Long non-coding rna: exist, inteons and exons, poly a tails, thought to be used in splicing amongst other things, ~14880, more abundant than microrna even. Identify novel nvrna: obtain orthologous sequences using blastn, multiple sequence alignment using mafft, ncrna prediction using rnaz and qrna, analyze overlapping predicitons and filter false positives lab validation, rt-pcr, rna-seq, etc. Intiation of transcription: must be immediately upstrearm and in the correct orientation.
