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Transcriptomics: Home

Introduction

This guide is designed to assist you in your transcriptomics research endeavors.

Please do not hesitate to contact me for questions or comments

Transcriptomics

TRANSCRIPTOMICS:  This is another discipline in the OMIC field and aims to understand the complete set of RNA of an organism, in particular factors that lead to alterations in RNA expression.

Methods for transcriptomic studies

Northern blot:  This procedure is similar to the familiar procedure known as the Western blot for protein detection except we are detecting RNA.  RNA are separated by size using electrophoresis and detected using a probe complementary to the RNA of interest. 

RNA sequencing:  Similar to DNA sequencing, this method focuses on a broad view of cellular or tissue level RNA expression by using next generation sequencing.

Nanostring nCounter:  This technology uses color coded barcode probes to detect nucleic acid expression (PCR without amplification?)

Chromatin immunoprecipitation (ChIP) with or without sequencing:  ChIP is a way to determine whether a transcription factor binds to a certain gene of interest.  ChIP can be followed by qPCR to determine transcription factor binding to one or a small set of genes. ChIP can also be followed by sequencing to determine the full gamut of binding activity for a particular transcription factor. 

Your transcriptome can be sequenced using the technologies for high throughput genome sequencing.  This is called RNA seq.  The principle are similar but have differences.  For instance, mapping of short reads obtained from RNA seq experiments to reference requires an aligner that is splice aware so reads that span exons can be detected and this helps in the case of novel transcript discovery.  See my guide for RNA sequencing analysis on this page.

Subject Guide

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Joe Wu
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