I've performed an exploratory RNA sequencing on the extracelluar RNA from single organoid cell culture. The goal of this experiment was to see if we could detect biologically relevant gene fragments from the organoid culture media, distinguishing the RNA seq profile from the control samples (culture media without organoids). Positive cellular controls were included.
- Lib prep kit: NEB Single Cell/ low input RNA library prep kit for Illumina
- Seq kit: NextSeq 2x100 bp high output
- Data processing: Cutadapt, STAR aligner, and featurecounts
- DE and data exploration: DESeq2
From the culture media samples, we have an abundance of reads that are uniquely mapping, but do not have genomic annotations:
Gene Counts: ibb.co/d615Zsq
Alignment Counts: ibb.co/thnP2S8
My question is: are there tools available to further classify or investigate the "No feature" reads? Maybe they are all rRNA fragments or unannotated non-coding RNA sequences. Any advice is appreciated!
P.S. the gene fraction indeed contains biologically relevant sequences for the cell type, which is encouraging!