Submitting to GEO: 10x Fixed RNA profiling (Single Cell Gene Expression Flex)

Question

[psm]

Hi all,

I have FASTQ files generated for a multiplexed 10X single cell gene expression flex run (16 samples). The cells were processed into unfiltered and filtered count matrices separated by sample.

I want to upload these into GEO. But GEO requires that the FASTQ be separated by sample... Seems like an awful lot of work considering the RNA flex is probe based anyway, not sure why anyone would go through the effort of realigning the sequencing reads to the probe set reference...

Anybody have any experiencing uploading multiplexed RNA-flex experiments to GEO? (Or do you recommend any other public repository?)

Thanks in advance!

Answer 1

[matthewsmith]

I did this recently as well, the accession isn't public yet. 10X has a knowledge base article about how to submit the data generated with CellPlex data here, which I assumed also applies to the flex/FRP output given it also generated with cellranger multi.

They specify you should state how many cells were detected by cellranger multi so someone can reproduce your results. Also, it's important to include the unassigned reads. I initially submitted the BAM for unassigned as a supplemental file but GEO rejected that. So I added an additional sample that was just the unassigned reads to the GEO record.

Answer 2

[psm]

In case anyone ever runs into this problem, what I did was submit the sample-specific BAM files generated by our sequencing facility as the raw input, and submitted the unfiltered and filtered raw counts for each sample as the processed file. Not sure whether the raw sequencing reads/ BAM files will ever be useful for anyone, since the the assay is probe-based.

[ATpoint]

Probe annotations might change over time. Different software might handle off-targets differently. Reproducibility demands that raw data are shared. People might use data for things beyond what CellRanger does by default.