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BMC Genomics. 2015 Aug 13;16:597. doi: 10.1186/s12864-015-1670-6.

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.

Author information

1
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA. cumbiej@onid.orst.edu.
2
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA. ivanchem@science.oregonstate.edu.
3
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA. megrawm@science.oregonstate.edu.
4
Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA. megrawm@science.oregonstate.edu.
5
Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA. megrawm@science.oregonstate.edu.

Abstract

BACKGROUND:

Identifying the transcription start sites (TSS) of genes is essential for characterizing promoter regions. Several protocols have been developed to capture the 5' end of transcripts via Cap Analysis of Gene Expression (CAGE) or linker-ligation strategies such as Paired-End Analysis of Transcription Start Sites (PEAT), but often require large amounts of tissue. More recently, nanoCAGE was developed for sequencing on the Illumina GAIIx to overcome these difficulties.

RESULTS:

Here we present the first publicly available adaptation of nanoCAGE for sequencing on recent ultra-high throughput platforms such as Illumina HiSeq-2000, and CapFilter, a computational pipeline that greatly increases confidence in TSS identification. We report excellent gene coverage, reproducibility, and precision in transcription start site discovery for samples from Arabidopsis thaliana roots.

CONCLUSION:

nanoCAGE-XL together with CapFilter allows for genome wide identification of high confidence transcription start sites in large eukaryotic genomes.

PMID:
26268438
PMCID:
PMC4534009
DOI:
10.1186/s12864-015-1670-6
[Indexed for MEDLINE]
Free PMC Article

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