서비스
DNA로부터 전사되는 모든 RNA 전사체(Transcriptome)의 염기서열을 분석하는 기법으로 유전적 병변이나 외부 자극 및 변화하는 환경 조건 등 다양한 상태에서 활성화된 유전자 발현 정보를 파악할 수 있습니다. 테라젠바이오는 해당 오믹스 기술을 이용하여 대장암 전이 기작 규명 연구[1] 및 항암제 효능 검증 연구[2]에 참여한 바 있습니다. 또한 생명활동에 필요한 단백질 변형에 영향을 끼치는 Alternative splicing[3]을 통해 유전자 발현 조절에 대한 종합적인 시각을 제공합니다.
Sample Requirement | 0.1 ~ 1µg Total RNA 0.1 ~ 4µg Total RNA, RIN ≥ 8 |
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Library Kit | Illumina, TaKaRa, Qiagen |
Sequencing Platform | Illumina NovaSeq6000 |
Recommended Sequencing Depth | 20M (million reads) |
Functional annotation
Alternative splicing analysis
RNAseq de novo assembly
Differential expression genes (DEGs)
GO analysis
Heatmap
Gene set enrichment analysis (GSEA)
Gene fusion analysis
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[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
Sample Requirement | Total RNA > 1µg (minimum 100 µg), 20 ng/µl, RIN > 6 |
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Library Kit | PerkinElmer |
Sequencing Platform | Illumina NovaSeq6000 |
Recommended Sequencing Depth | ≥ 20 million read counts per sample |
Alignment against reference genome
Quantification of small RNA
Discovery of novel/known miRNAs
Estimation of differential expressed miRNAs
Prediction of target mRNA
miRNA-mRNA Integrated analysis
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[1] Lee, J. Y., Ryu, D. S., Kim, W. J., & Kim, S. J. (2016). Aberrantly expressed microRNAs in the context of bladder tumorigenesis. Investigative and clinical urology, 57 Suppl 1(Suppl 1), S52–S59.
[2] Kim, M. C. et al., (2014). Identification and characterization of microRNAs in normal equine tissues by Next Generation Sequencing. PloS one, 9(4), e93662.
Pacbio SMRT (Single Molecule, Real-time) 기술을 이용하여 Full length (5’UTR에서 3’poly-A tail을 포함하는)의 Transcript isoform sequencing이 가능합니다[1][2]. 참조 유전체가 없는 종에서 Full transcripts를 확보할 수 있어
Short reads RNA sequencing의 한계점을 보완하며 Fusion genes, Alternative splicing, Genome annotation, Novel transcripts 등의 분석이 가능합니다.
Sample Requirement | RNA > 3µg (minimum 1µg),100ng/µl, RIN > 8 |
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Library Kit | SMRT |
Sequencing Platform | Pacbio Sequel Ⅱ |
Recommended Sequencing Depth | ≥ 15Gb per sample ≥ 100 million read pairs per sample *Depth may vary depending on species |
Clustering & Annotation
Read mapping
Expression
Differential expression genes (DEGs)
[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.
Sample Requirement | Cells >20K (minimum 1K cells), 1000cells/µl |
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Library Kit | 10x Genomics |
Sequencing Platform | Illumina NovaSeq6000 |
Recommended Sequencing Depth | - |
T-SNE
Feature Plot
Heatmap
Phlyogenetic Tree
10X Genomics Report
공간 전사체학(Spatial transcriptomics)은 특정 위치에서 발현되는 유전자를 분석하는 기법으로 조직 시료의 형태학적 정보(Morphological information)와 유전자 발현 정보(Gene expression information)을 동시에 얻을 수 있습니다.
공간 전사체학은 종양 미세환경이나 세포 유형과 구조가 복잡한 신경, 뇌와 같은 이질적 조직 연구에 이상적이며, 유전자 발현 정보와 위치 정보를 기반으로 서로 다른 세포 유형들이 어떻게 상호 작용하는지에 대한 명확한 이해를 제공합니다.
Sample Requirement | Cells >20K (minimum 1K cells), 1000cells/µl |
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Library Kit | Nanostring GeoMx |
Sequencing Platform | Illumina NovaSeq6000 |
Recommended Sequencing Depth | - |
Expression data set
Differential expression genes (DEGs)
Statistical test
Survival curve
GO analysis
Pathway
Heatmap
Gene set enrichment analysis (GSEA)