Transcriptional profiling using RNA-seq to study hypoxia-mediated gene regulation

Surendra K. Shukla, Ryan J. King, Pankaj K. Singh

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations


Exposing cells to a hypoxic environment leads to significant physiological and molecular alterations. Most of the hypoxic responses are regulated by the transcription factors known as hypoxia-inducible factors (HIFs). HIF1, a heterodimer of hypoxia-stabilized subunit HIF-1alpha and a constitutively expressed subunit HIF-1beta, serves as a key transcription factor that regulates gene expressions which are involved in cell growth, metabolism, and proliferation. The global expression patterns can be analyzed by utilizing RNA-Seq to understand the cellular alterations in hypoxia. This technique enables us to understand the comprehensive regulation of gene expression by specific factors or environmental stimuli. Here, we describe the complete process of studying hypoxia-mediated gene expression by using RNA-Seq, including the hypoxic treatment of cells, RNA isolation, RNA quality check, cDNA library preparation, and library quality check.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages12
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Gene expression
  • HIF
  • High-throughput sequencing
  • Hypoxia
  • RNA-Seq

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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