02177nas a2200277 4500008004100000022001400041245011900055210006900174260000900243300000800252490000700260520133000267653001601597653001701613653001801630653001901648653001601667653003001683653002701713653001301740653003401753100002101787700002501808700001801833856004801851 2015 eng d a1471-216400aNanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.0 aNanoCAGEXL and CapFilter an approach to genome wide identificati c2015 a5970 v163 a
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.
[Link to Protocol, Additional Data, and Supplementary Materials]
10aArabidopsis10aGenes, Plant10aGenome, Plant10aNanotechnology10aPlant Roots10aPromoter Regions, Genetic10aSequence Analysis, DNA10aSoftware10aTranscription Initiation Site1 aCumbie, Jason, S1 aIvanchenko, Maria, G1 aMegraw, Molly uhttp://megraw.cgrb.oregonstate.edu/node/311