Swine

A Globin Blocker to Increase Sequencing Efficiency for QuantSeq 3' mRNA-Seq in Porcine Blood

Authors
  • Kyu-Sang Lim (Iowa State University)
  • Qian Dong (Iowa State University)
  • Pamela Moll (Lexogen GmbH)
  • Jana Vitkovska (Lexogen GmbH)
  • Gregor Wiktorin (Lexogen GmbH)
  • Stephanie Bannister (Lexogen GmbH)
  • Dalia Daujotyte (Lexogen GmbH)
  • Christopher K. Tuggle (Iowa State University)
  • Jack C. M. Dekkers (Iowa State University)

Abstract

Blood is an extremely valuable source to investigate animal biology, including whole genome gene expression. The efficiency of gene expression profiling is hampered by the high proportions of hemoglobin (HB) mRNA of erythrocytes, which decreases the resolution of QuantSeq 3' mRNA-sequencing in blood. Here, we used different concentrations of a globin blocker (GB), which includes a HB-specific oligonucleotide mix, as a novel method to decrease sequencing of HB RNA. While reads for HBA and HBB accounted for 19.4 and 36.9% of total reads in non-GB samples, GB under optimal concentrations reduced HBA and HBB reads on average to 8.7 and 2.3% of total reads, respectively. The number of genes that could be reliably detected was of approximately 2,200 genes greater in GB samples than in non-GB samples. In conclusion, the use of this GB procedure increases the resolution of gene expression data from QuantSeq in porcine blood samples.

How to Cite:

Lim, K., Dong, Q., Moll, P., Vitkovska, J., Wiktorin, G., Bannister, S., Daujotyte, D., Tuggle, C. K. & Dekkers, J. C., (2018) “A Globin Blocker to Increase Sequencing Efficiency for QuantSeq 3' mRNA-Seq in Porcine Blood”, Iowa State University Animal Industry Report 15(1). doi: https://doi.org/10.31274/ans_air-180814-318

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Published on
01 Jan 2018
Peer Reviewed