Total/mRNA Sequencing

Theragen Bio provides differentially Expressed Gene (DEG) analysis between normal and control groups from various samples such as human, organoids, plants, and xenocrafts andbased on this analysis, we provide the necessary basis for gene function research. Gene set enrichment analysis (GSEA) is possible to identify genes related to biological characteristics that have statistical significance under certain conditions (e.g., normal cells vs cancer cells). In addition, we also provide information on previously unidentified transcripts, alternative splicing, and gene fusion

Sample/Laboratory Information

Bioinformatics

Features & Benefits

• Obtain extensive data at the gene level that can capture all biological changes
• Possible to obtain known or unknown information at the gene level
• Quantitative measurement at the gene level is possible even without reference genome information.

Reference

[1] Nakayama, M. et al., (2020). Loss of wild-type p53 promotes mutant p53-driven metastasis through acquisition of survival and tumor-initiating properties. Nature communications, 11(1), 2333.

[2] Hong, E. et al., (2020). Inhibition of TGF-β signalling in combination with nal-IRI plus 5-Fluorouracil/Leucovorin suppresses invasion and prolongs survival in pancreatic tumour mouse models. Scientific reports, 10(1), 2935.

[3] Cha, S. et al., (2021). Differential activation mechanisms of two isoforms of Gcr1 transcription factor generated from spliced and un-spliced transcripts in Saccharomyces cerevisiae. Nucleic acids research, 49(2), 745–759.

[4] Yun, S. M. et al., (2013). PPP1R1B-STARD3 chimeric fusion transcript in human gastric cancer promotes tumorigenesis through activation of PI3K/AKT signaling. Oncogene, 33(46), 5341–5347. https://doi.org/10.1038/onc.2013.472

[5] Yoon, K. et al., (2013). Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers. Genome Research, 23(7), 1109–1117. https://doi.org/10.1101/gr.145706.112

[6] Kim, K. et al., (2018). Pathway profiles based on gene-set enrichment analysis in the honey bee Apis mellifera under brood rearing-suppressed conditions. Genomics, 110(1), 43–49. https://doi.org/10.1016/j.ygeno.2017.08.004

[7] Sakai, E. et al., (2017). Combined Mutation of Apc, Kras, and Tgfbr2 Effectively Drives Metastasis of Intestinal Cancer. Cancer Research, 78(5), 1334–1346. https://doi.org/10.1158/0008-5472.can-17-3303

[8] Park, Y. et al., (2020). Destablilization of TRAF6 by DRAK1 Suppresses Tumor Growth and Metastasis in Cervical Cancer Cells. Cancer Research, 80(12), 2537–2549. https://doi.org/10.1158/0008-5472.can-19-3428

[9] Lee, J. et al., (2021). Brassinosteroid‐BZR1/2‐WAT1 module determines the high level of auxin signalling in vascular cambium during wood formation. New Phytologist, 230(4), 1503–1516. https://doi.org/10.1111/nph.17265

Isoform Sequencing (De novo)

Isoform sequencing allows for sequencing and analysis of full-length isoforms while preventing errors that may arise from short-read sequencing. By using PacBio-based long-read sequencing, clustering, and annotation, unigenes can be created. Additionally, Illumina-based short-read sequencing can be used to calculate RNA-seq expression for unigenes.

Application

• Alternative splicing
• Alternative polyadenylation (APA)
• Fusion transcripts
• Long non-coding RNAs (lncRNAs)
• Isoform phasing
• Genome annotation

Sample/Laboratory Information

Bioinformatics

Reference

[1] Jo, I. H. et al., (2017). Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. Genes, 8(9), 228.

[2] Hong, C. P.et al., (2022). Long-read transcriptome sequencing provides insight into lignan biosynthesis during fruit development in Schisandra chinensis. BMC genomics, 23(1), 17.