Gene expression profile of clinical LUAD tumors and their paired non-cancerous adjacent tissues by RNA-seq analysis
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PROVIDER: PRJNA589320 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Transcriptomic analysis of clinical tissue samples is important in the precision medicine research. To explore the relationship between transcriptome and full proteome, 51 LUAD tumor tissues and 49 paired non-cancerous adjacent tissues were systematically analyzed by RNA sequencing. Methods: RNASeq reads were adapter trimmed and data quality was assessed with the FastQC (version 0.11.7) software before any data filtering criteria may apply. Reads were mapped onto the human reference genome (GRCh38.p12 assembly) by using hisat2 software (v2.0.4). The mapped reads were assembled into transcripts or genes by using StringTie software (v1.3.4d) and the genome annotation file (hg38_ucsc.annotated.gtf). For quantification purpose, the relative abundance of transcript/gene was measured by a normalized metrics, FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Results: In our study, RNA-seq analysis identified 16,188 genes with FPKM > 1, providing an opportunity to explore the relationship between the transcriptome and full proteome. Conclusions: Our study provided an opportunity to explore the relationship between the transcriptome and full proteome of clinical LUAD tumors and their paired non-cancerous adjacent tissues.
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