Protocol Dependence of Sequencing-based Gene Expression Measurements

ABSTRACT: RNA samples from human tissues (brain and liver) and cell lines (K562 and HL60) were used to assess RNA fragmentation, RNA fractionation, cDNA synthesis, and single versus multiple tag counting. Technical replicates and different cDNA synthesis protocols were compared. Though protocols employing polyA RNA selection generate the highest number of non-ribosomal reads and the most precise measurements for coding transcripts, such protocols were found to detect only a fraction of the non-ribosomal RNA in human cells. PolyA RNA excludes thousands of annotated and even more unannotated transcripts, resulting in an incomplete view of the transcriptome. Ribosomal-depleted RNA provides a more cost-effective method for generating complete transcriptome coverage. Expression measurements using si

ORGANISM(S): Homo sapiens

SUBMITTER: John Thompson 

PROVIDER: E-GEOD-28123 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress