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T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing
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Published on: January 12, 2021

RNA-sequence analysis of human B-cells.

Jonathan M Toung1, Michael Morley, Mingyao Li

  • 1Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

Genome Research
|May 4, 2011
PubMed
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RNA-sequencing (RNA-seq) reveals the gene expression profile of human B-cells, identifying thousands of genes and transcripts. Deep sequencing is crucial for accurate expression level measurement and isoform analysis.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • RNA-sequencing (RNA-seq) is a powerful tool for quantifying gene and transcript expression.
  • Understanding B-cell gene expression is vital for immunology and disease research.

Purpose of the Study:

  • To characterize the gene expression profile of human B-cells using RNA-seq.
  • To determine optimal sequencing parameters for gene expression studies.
  • To investigate alternative splicing and gene density across chromosomes.

Main Methods:

  • Sequencing of complementary DNA fragments from cultured human B-cells.
  • Analysis of 879 million 50-bp reads (44 Gb) to identify genes and transcripts.
  • Investigation of sequencing depth's impact on expression measurement accuracy.

Main Results:

  • Identified 20,766 genes and 67,453 alternatively spliced transcripts.
  • Over 90% of multi-exon genes exhibit alternative splicing, with one predominant isoform.
  • Accurate expression measurement requires approximately 500 million reads, while 100 million detects most genes.

Conclusions:

  • Deep sequencing is essential for precise quantification of gene and isoform expression levels.
  • Gene expression levels correlate with biological processes.
  • The study provides a valuable resource for B-cell gene expression analysis.