The SG-NEx project was initiated by the Genome Institute of Singapore with the aim to generate reference transcriptomes for 5 of the most commonly used cancer cell lines using Nanopore RNA-Seq data. The following cell lines are used for sequencing:
- A549 (Lung Cancer)
- MCF7 (Breast Cancer)
- Hct116 (Colon Cancer)
- K562 (Leukemia)
- HepG2 (Liver Cancer)
Transcriptome profiling is done using PCR-cDNA sequencing ("PCR-cDNA"), amplification-free cDNA sequencing ("direct cDNA"), and direct sequencing of native RNA (“direct RNA”).
Data can be downloaded here
Notes on data usage: This site provides early access to the SG-NEx data for research. Please note that the data is under publication embargo until the SG-NEx project is published.
Basecalling was done using albacore-2.3.1. Alignment was done with minimap2 using the following parameters:
- Alignment to genome: -ax splice -I 32G -t 3
- Alignment to transcriptome: -ax map-ont -t 3
Details on reference files can be found here.
GIS Sequencing Platform
Hwee Meng Low, Wendy Soon, CC Khor
GIS Genome Innovation Lab
Yao Fei, Sarah Ng
Cancer Genomics
Torsten Wüstefeld, Viktoriia Iakovleva, Ramanuj DasGupta, Shumei Chia, Lixia Xin, Shyam Prabhakar, Puay Leng Lee, Yu Qiang, Wai Leong Tam, Patrick Tan, Sho Goh
Statistical Modeling and Data Analytics
Chen Ying, Naruemon Pratanwanich, Andreas Wilm, Alexandre Thiery, Jonathan Göke