Gene expression analysis of the impact of TDP-43 knockout in human cells.

Purpose: The goal of this stuydy was to apply transcriptome profiling (RNA-seq) to human cells that either express or which lack the TDP-43 protein. Methods: mRNA profiles of TDP-43 KO HeLa cells and "rescued" TDP-43 KO cells wherein a wildtype TDP-43 transgene was re-expressed at endogenous levels were generated by deep sequencing, in triplicate, on Illumina’s HiSeq 2500 using 2x70bp paired-end reads, generating 104.4-128.2 million reads (52.2-64.1 million pairs) per sample. . The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat2 followed by Cufflinks Cuffmerge and Cuffdiff to define transcripts and establish their abundance and finally to perform differential gene expression analysis, using the assembled known plus novel transcripts . Results: Using an optimized data analysis workflow, we mapped approximately 50-60 million reads per sample to the human genome (build hg19) and identified transcripts whose abundance differed between the TDP-43 KO versus "rescued" conditions. Conclusions: Our study presents a detailed analysis of the impact of the knockout of TDP-43 on the transcriptome of a human cell line. The results reported here should provide a framework for defining transcripts whose abundnace and splicing are regulated by TDP-43. Examination of the transcriptome of human cells that lack and which express TDP-43.