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Updated: May 5, 2026
09:03
Profiling Individual Human Embryonic Stem Cells by Quantitative RT-PCR
Published on: May 29, 2014
11.1K
Characterization of the human ESC transcriptome by hybrid sequencing
Kin Fai Au1, Vittorio Sebastiano, Pegah Tootoonchi Afshar
1Department of Statistics and Department of Health Research and Policy, Stanford University, Stanford, CA 94305.
Summary
This study combines second- and third-generation sequencing to identify full-length messenger RNA (mRNA) isoforms in human embryonic stem cells (hESCs). Researchers discovered thousands of novel isoforms and previously unidentified gene loci, expanding our understanding of gene expression.
Area of Science:
- Genomics
- Molecular Biology
- Transcriptomics
Background:
- Second-generation sequencing (RNA-Seq) captures transcriptional events but not full-length mRNA isoforms.
- Third-generation sequencing offers longer reads but has limitations in accuracy and throughput.
Purpose of the Study:
- To develop a high-confidence dataset of full-length mRNA isoforms in human embryonic stem cells (hESCs).
- To integrate second- and third-generation sequencing data for comprehensive isoform analysis.
Main Methods:
- Utilized a custom-designed method combining second-generation and third-generation sequencing.
- Applied statistical inference for isoform prediction and quantification.
Main Results:
- Identified 8,084 full-length RefSeq-annotated isoforms and 5,459 predicted isoforms.
- Discovered over one-third novel isoforms, including 273 RNAs from previously unidentified gene loci.
- Found that novel loci expressed in pluripotent cells but not adult tissues can perturb pluripotency gene networks.
Conclusions:
- Gene identification in human cells is likely incomplete.
- The novel identified loci and isoforms contribute to the complexity of gene expression in pluripotent cells.
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