Transcriptomics

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Single cell RNA sequencing of KPC1199 cell line [mouse scRNA-seq]


ABSTRACT: In this study we describe a new method for GTO (Genomics Transcriptomics One-Tube) that allows for simeltaneous sequencing of RNA and DNA from a single cell in the same tube. This method relies on dual amplification. The first amplification is done immediately after the mRNA is transcribed to cDNA using SMART-Seq2 protocol (Picelli et al., 2014) to increase the level of cDNA to that comparable to gDNA. The second amplification with universal primers from SeqXE kit for whole genome amplification (from Sigma Aldrich) amplifies the cDNA and gDNA fragments to amounts required for library preparation. The reads generated from this mixed library are separated bioinformatically to exonic and nonexonic reads depending on where they align in the reference genome to generate the RNAseq and DNAseq data respectively. We present data generated from single in-vitro cells of multiple cell lines (A375, BT549, SKBR3, 315A) and also from single in-vivo cells isolated from tumors of an orthotopic tranplantation mouse model of pancreatic cancer (using KPC1199-EGFP cell line).

ORGANISM(S): Mus musculus

PROVIDER: GSE128794 | GEO | 2020/03/30

REPOSITORIES: GEO

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