GSM5263927: PPMV; Homo sapiens; Mus musculus; Rattus norvegicus; RNA-Seq
Cells were embedded in hydrogels and transplanted in the mice. Hydrogels were reteieved adter 100 days and snap frozen. Nuceli was isolated as per 10X genomic published protocols. Details can be found : https://support.10xgenomics.com/isolation-of-nuclei The Unique Molecular ID (UMI) were generated using Cellranger (v3.1). A custom reference for multiple species was made using the mkref command with FASTA and GTF files for mm10, Ratus6.0.98 and GRCh38. Single nuclei reads were mapped to this custom reference genome using Cellranger.  The sNuc-Seq assay captured unspliced pre-mRNA as well as mature mRNA. However, after alignment, Cellranger only counted reads aligned to exons. A three custom “pre-mRNA” GTF file was created listing each gene transcript locus as an exon, in order to count intronic reads.
GEO Accession
GSM5263927