Question about downloading RNA-seq long reads and short reads for the same sample

Question

[tunl]

We need to use RNA-seq long reads and short reads from the same sample to do some comparisons. I was wondering which websites may have both RNA-seq long reads (e.g. PacBio reads) and short reads for the same sample so we could download from there?

Any advice would be greatly appreciated.

Thank you very much in advance!

[Sej Modha]

You might want to look at Illumina hiseq and pacbio isoseq data on same set of samples- combined analysis help?

[tunl]

Thank you so much for your suggestion! I looked at this posting, but the paper they mentioned there does not provide their long reads and short reads datasets for downloading. This seems to be the situation in many papers: they do not provide their datasets of long reads and short reads. So I was wondering if there is any public website that collects some long reads and short reads datasets for the same samples so we could download from there? Thanks a lot!

[GenoMax]

The datasets for that paper are available: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1254204 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1254205

[Sej Modha]

I am not exactly sure what you are after but I found this paper https://www.nature.com/articles/s41467-017-00050-4 that mentions that some PacBio data is available online: http://datasets.pacb.com.s3.amazonaws.com/2015/IsoSeqHumanMCF7Transcriptome/list.html

[tunl]

Thank you so much! This PacBio site looks great. I'll take a look.

[tunl]

Thank you so much for providing me the GSM datasets links! I really appreciate it. I looked into these datasets, but this paper only gave us the processed data (aligned reads for Illumina; error-corrected reads for PacBio).

Answer 1

[magdoll]

The MCF-7 dataset as mentioned above does have a long read data and public short read data.

I've compiled a (very selective) list of PacBio long read RNA publications, some of them do have accompanying short read data: https://github.com/PacificBiosciences/IsoSeq_SA3nUP/wiki/Iso-Seq-Publications

[tunl]

This is great. Thanks a lot! I’ll take a look at them.

[tunl]

[DELETED, sorry I initially replied at a wrong place]

[tunl]

For the "previously published MCF-7 Illumina dataset" (http://www.genomebiology.com/2014/15/1/R15), I can't seem to find the Illumina dataset from this paper (it mentioned "Additional file 1", but "Additional file 1" is actually a .xls file (a Table).) Any ideas? Thanks so much!