title: snRNA-Seq of mouse: 5d-Injured TA muscle of Xbp1fl/fl mice
design: Freshly isolated 5d-injured TA muscle tissues were processed for the isolation of nuclei. The nuclei were pooled from 3-4 mice in each group. snRNA-seq libraries were generated using Chromium Next GEM Single Cell 3 Gene Expression v3.1 kit (10X Genomics) according to the manufacturers protocol. Sequencing was performed on an Illumina NextSeq 2000 system with the pair-end sequencing settings Read1  28 bp, i7 index  10bp, i5 index  10bp and Read2  90 bp. The Cell Ranger Software Suite (10X Genomics, v7.0.0) was used for data demultiplexing, transcriptome alignment, and UMI counting. Raw base call files were demultiplexed using cellranger mkfastq. The mouse genome, refdata-cellranger-mm10-1.2.0 from the 10x Genomics support website , was used as reference for read alignments and gene counting with cellranger count. Elimination of RNA background was performed using SoupX R package.