RNA-Seq (Nagalakshmi, et al., 2008; Mortazavi, et al., 2008), also known as Whole transcriptome sequencing investigates the RNA content from a sample through high throughput sequencing of cDNA. This exciting technology has important applications such as the improvement of existing genome annotations, discovery of novel genes and transcripts (Roberts, et al., 2011), revealing alternative splicing events and measuring the differential expression of genes across samples. This study examines the transcriptional responses of B-cells to the influenza vaccine using RNA-Seq. Five subjects received the flu vaccine. RNA was extracted at 11 different time points and sequenced using RNA-Seq. The RNA-Seq data was aligned to the reference genome using Tophat. The aligned reads were assembled into transcripts and the differential expression of the transcripts was measured across the samples using Cufflinks. The resultant data was analyzed by a downstream analysis algorithm to only select for "novel" genes that correlate with well-annotated genes known to be important in immunity. This analysis led to the selection of two "novel" genes that that are most likely to be of interest for further functional characterization.

Library of Congress Subject Headings

Genetic transcription; Nucleotide sequence; Influenza vaccines--Research; Influenza--Genetic aspects; Immunity

Publication Date


Document Type



Skuse, Gary

Advisor/Committee Member

Welle, Stephen


Note: imported from RIT’s Digital Media Library running on DSpace to RIT Scholar Works in December 2013. Physical copy available from RIT's Wallace Library at QH450.2 .M36 2013


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