@article {311, title = {NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.}, journal = {BMC Genomics}, volume = {16}, year = {2015}, month = {2015}, pages = {597}, 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\&$\#$39; 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.

[Link to Protocol, Additional Data, and Supplementary Materials]

[Link to CapFilter Software]

}, keywords = {Arabidopsis, Genes, Plant, Genome, Plant, Nanotechnology, Plant Roots, Promoter Regions, Genetic, Sequence Analysis, DNA, Software, Transcription Initiation Site}, issn = {1471-2164}, doi = {10.1186/s12864-015-1670-6}, author = {Cumbie, Jason S and Ivanchenko, Maria G and Megraw, Molly} }