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The SG-NEx project is an international collaboration that was initiated at the Genome Institute of Singapore. The aim of the SG-NEx Project is to generate reference transcriptomes for 5 of the most commonly used cancer cell lines using Nanopore long read RNA-Seq data:

Transcriptome profiling is done using PCR-cDNA sequencing ("PCR-cDNA"), amplification-free cDNA sequencing ("direct cDNA"), direct sequencing of native RNA (“direct RNA”), and short read RNA-Seq. All samples are sequenced with at least 3 high quality replicates. For a subset of samples, we used sequin spike-in RNAs.

Content

• Email list
• Data Download and Release History
• Data Processing
• Use Cases and Applications
• Data Access Tutorials
• Contributors
• Citing the SG-NEx project
• Contact

Sign up for data release notifications and updates

You can sign up for the sg-nex-updates email list to receive notifications about upcoming data releases:

https://groups.google.com/forum/#!forum/sg-nex-updates/join

Data Download

Pre-Release (v0.2)

Data can be downloaded here

Notes on data usage: This site provides early access to the SG-NEx data. These data can be used in research and publications, but we ask data users to refrain from publishing a systematic comparison that is described in the pre-print until the final manuscript is published. If you are uncertain, please feel free to reach out (Contact).

Release History

You can find previous releases here in the release history

Data Processing

We collaborated with nf-core to develop nanoseq, a standardardized pipeline for Nanopore RNA-Seq data processing.

Reference files

Details on reference files can be found here.

Use Cases and Applications

You can browse a list of articles that review or use the SG-NEx data here.

Data Access Tutorials

Coming soon! Please refer to Data Download in the meantime.

Contributors

GIS Sequencing Platform and Data Generation
Hwee Meng Low, Yao Fei, Sarah Ng, Wendy Soon, CC Khor

Cancer Genomics and RNA Modifications
Viktoriia Iakovleva, Puay Leng Lee, Lixia Xin, Hui En Vanessa Ng, Jia Min Loo, Xuewen Ong, Hui Qi Amanda Ng, Suk Yeah Polly Poon, Hoang-Dai Tran, Kok Hao Edwin Lim, Huck Hui Ng, Boon Ooi Patrick Tan, Huck-Hui Ng, N.Gopalakrishna Iyer, Wai Leong Tam, Wee Joo Chng, Leilei Chen, Ramanuj DasGupta, Yun Shen Winston Chan, Qiang Yu, Torsten Wüstefeld, Wee Siong Sho Goh

Statistical Modeling and Data Analytics
Ying Chen, Nadia M. Davidson, Harshil Patel, Yuk Kei Wan, Naruemon Pratanwanich, Christopher Hendra, Laura Watten, Chelsea Sawyer, Dominik Stanojevic, Philip Andrew Ewels, Andreas Wilm, Mile Sikic, Alexandre Thiery, Michael I. Love, Alicia Oshlak, Jonathan Göke

Citing the SG-NEx project

If you use the SG-NEx data in your research, please specify the release version and cite the pre-print that describes this data resource:

Chen, Ying, et al. "A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines." bioRxiv (2021). doi: https://doi.org/10.1101/2021.04.21.440736

Please see the note on data usage (under Data Download).

Contact

Questions about SG-NEx? Please add an entry in the Discussions Forum. You can also contact Jonathan Göke