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Table 4 NGS in transcriptomics analysis

From: Next-generation sequencing: recent applications to the analysis of colorectal cancer

Samples NGS Application Interesting genes Ref.
15 CRCs Illumina
HiSeq (3′-seq library)
APA changes PPIE, DMKN, PDXK Morris et al. [96]
3 CRC cell lines Roche
GS Junior (primers framing CD44 variable region)
CD44 ASP CD44 CRC specific isoforms Bànky et al. [97]
1 stage III CRC patient (distant, adjacent mucosa and cancer) Illumina
GAIIx (TruSeq RNA)
RNA-seq (novel and fusion transcripts, alternative splicings) List of 14 genes with cancer-associated differential-splicing, PTGFRN-NOTCH2 fusion product Wu et al. [98]
70 CRCs/normal pairs Illumina
HiSeq (TruSeq RNA)
RNA-seq RSPO2/3 fusion transcript Seshagiri et al. [99]
20 CRC cell lines Illumina (ChIP-seq) RNA-seq (genes involved in irinotecan resistance) 20 top-genes
CDC20, CTNNAL1, FZD7, CITED2, ABR, ARHGEF7 and RNMT validated by qPCR
Li et al. [100]
21 CRC cell lines Illumina (ChIP-seq) RNA-seq (genes involved in oxaliplatin resistance) 58 top-genes
15 further validated by qPCR
(e.g. HNF1A, NOTCH1, FZD5, KCND1, FDZ2)
Li et al. [101]
175 CRCs/normal tissue pairs Illumina
HiSeq (TruSeq)
RNA_seq (CRC vs. normal differentially expressed genes) 1138 up-regulated
695 down-regulated
Slattery et al. [102]
HCT116 CRC cell line Illumina
HiSeq
RNA-seq (SNP profiles from single cell and bulk CRC) Genes in WNT, PI3KCA, p53, TGF-β, MMR pathways, fusion transcripts Chen et al. [103]
5 paired primary, mCRC, normal colon and liver tissues Illumina
HiSeq
RNA-seq (comparative transcriptome analysis) Similar expression profiling in CRC and metastasis, RNF43-SUPT4H1 fusion transcript frequent in primary CRCs Lee et al. [104]
217 CRCs/normal mucosa pairs Illumina
HiSeq (TruSeq)
RNA-seq (oncogenes, tumor suppressors’ differential expression) 22 tumor suppressor genes and 27 oncogenes significantly differentially expressed in CRC vs. normal mucosa Slattery et al. [105]