Whole Micro-RNA transcriptome profiling of relapsed /refractory and remission Diffuse Large B cell Lymphoma cases to identify differentially expressed micro RNA

ABSTRACT: Purpose: high throughput sequencing technique has revolutionalized research. The aim is to compare the mi-RNA transcriptome expression between Diffuse Large B cell Lymphoma patients who are in complete remission to those who had relpase or were refractory to first line treatment Methods-mi-RNA profiles of primary biopsies of complete remission(n=3) and refractory(n=3)/relapsed(n= 4) diffuse large b cell lymphoma cases were generated, using S5 Ion Torrent. The sequencing reads that passed quality filters were analyzed for differential micro-RNA expression in refractory/relapsed cohort using DESeq2. qRT–PCR validation was performed using SYBR Green assays. Results- we analysed 1.5 million reads mapped to human genome (hg19) per sample, two samples had less than threshold reads reads but micro-RNA having > 10 counts in the same cohort was selected .Reads less than 17 bp were removed using Fastx, then aligned to reference genome hg19 using Bowtie. Differentially expressing micro-RNA in the non responder cohort compared to complete response was found by Dseq . Altered micro-RNA with fold change ≥2.0 and p value 0.001 was selected. Downregulation of three shortlisted mi-RNA was validated with q-RT-PCR. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE179760 | GEO | 2025/02/10

REPOSITORIES: GEO