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Differential Transcription Start Site Usage in Brain-Related Samples

ABSTRACT:

RNA-Seq is an effective method to study the transcriptome, but specialized methods are required to identify 5' ends of transcripts. Several published strategies exist for this specific purpose, but their relative merits have not been systematically analyzed. Here, we directly compare the performance of six such methods - testing five with cellular RNA as well as a novel spike-in RNA assay that helps address interpretation challenges that arise from uncertainties in annotation or RNA processing. Using a single human RNA sample, we constructed and sequenced 18 libraries with these methods and one standard, control RNA-Seq library. We find that the CAGE method performed best for mRNA and that most of its unannotated peaks are supported by evidence from other genomic methods. We then applied CAGE to eight brain-related samples and revealed sample-specific transcription start site (TSS) usage as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.

PROVIDER: phs001463 | dbGaP |

SECONDARY ACCESSION(S): PRJNA408204PRJNA408205

REPOSITORIES: dbGaP

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			Action	DRS
	GapExchange_phs001463.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs001463.DifferentialTranscriptionBrain.v1.p1.MULTI.pdf	Pdf
	manifest_phs001463.DifferentialTranscriptionBrain.v1.p1.c1.GRU.pdf	Pdf
	datadict_v2.xsl	Other

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