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GoekeLab / sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
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Are there tissue samples available? #66

Open jackwgoodall opened 1 month ago

jackwgoodall commented 1 month ago

Thank you for this amazing resource. On the AWS landing page it sounds like there are tissue samples processed but I only seem able to find cell lines sequenced?
Apologies if this is just me missunderstanding either the data description or the file descriptions.

cying111 commented 1 month ago

Hi @jackwgoodall ,

thank you for using SG-NEx data resource and for pointing out that the description is unclear. For the core datasets, we have generated 7 core cell lines, and we have also sequenced patient-derived cell lines (which we refer as tissue samples). Then for core cell lines, we have sequenced them in multiple replicates using different sequencing protocols. For patient-derived cell lines, however, we sequenced with direct RNA only and not in replicates. For your information, here are the patient-derived cell lines: NCC24, IM95 and N082, N122, and N104.

Hope this clarifies your questions and let me know if you have other questions! Thank you Warm regards, Ying