I have samples from xenograft tumors with both human and mouse cells. Samples are from Singleron technology and I used celescope for preprocessing with human & mouse combined genome. From the QC I see there are 6k cells.
From the estimated number of cells, I would like to know how to get the number of mouse and human cells.
Any help is appreciated. Thank you.
1 answer
From the marker genes of each cluster, we can determine whether the cluster belongs to human or mouse. Human genes are all capitalized, while mouse genes only have the first letter capitalized. Just sum up the number of cluster cells belonging to human or mouse respectively.
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell species at the cluster level is simple, it cannot distinguish mutiplets. If you want to filter mutiplets, you can do it at the cell-level. For example:https://divingintogeneticsandgenomics.com/post/mixing-mouse-and-human-10x-single-cell-rnaseq-data/
Log in to answer this question.
-
Well-established methods to distinguish malignant vs normal epithelial cells in mouse scRNA-seq dat…
written by andromeda.milky42 •
-
cell ranger count
written by archanaverma433 •
-
Visium spatial transcriptomics - mouse + human xenograft
written by Sy80 •
-
Human Rat xenograft
written by chiara.sdn •
-
What is the best practice for the analysis of single-cell RNA-seq of mouse and human mixed cells?
written by Dan •
-
Filtering out mouse cells based on mouse/human genes ratio
written by fifty_fifty •
-
RNA-seq data from human tumors in mice (PDTX)
written by Tom_L
-
RSEM for xenograft samples: augmented genomes and multi-mapped reads
written by NaskoMak •
-
Cancer Patient Derived Xenograft (PDX) Genomic Analysis
written by bioinformatics.cancer
-
RNASeq with mixed tissues
written by ddzhangzz
You have used the tag
snRNA-seq. I am not familiar with singleron tech but if you have sequence data you may be able to usexenomeorbbsplit.shto assign the reads to human/mouse bins. Unless there are cell specific barcodes it may not be possible to get the number of cells (which is what you are looking for).https://singleron.bio/products/focuscope/ seems to indicate xenograft use case.