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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

Genomics

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. 

DNA microarray:  This technique utilizes wells or spots containing DNA probes for the genes of interest.  RNA is isolated from cells or tissue and converted to cDNA.  The cDNA is labeled (different colors for control and treatment) and loaded onto the microarray wells. cDNA will bind to complementary DNA probes if the RNA is expressed.  Through fluorometric procedures, the differential expression of RNA among two samples can be determined.

Quantitative polymerase chain reaction (qPCR):  This technique is used to quantify gene expression on the mRNA level in cells or tissue.  mRNA is converted to cDNA and gene expression is determined by the number of PCR amplification cycles needed to reach a threshold copy number of cDNA.

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. 

Subject Guide

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Joe Wu
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