BioProject

Sequencing files, and processed data correspond to Figure 3 of Regenerating Human Skeletal Muscle Forms an Emerging Niche In Vivo to Support PAX7 cells. More...

Sequencing files, and processed data correspond to Figure 3 of Regenerating Human Skeletal Muscle Forms an Emerging Niche In Vivo to Support PAX7 cells. Data contains single nucleus RNA seq from Pax7 ablated mdx-NSG mice, control mdx-NSG mice, with or without an injury. These mice offer superior engraftment by human skeletal muscle stem and progenitor cells. Pax7 ablation model enables evaluation of human stem cell niche formation in the absence of mouse Pax7 cell competition. Included in this dataset is everything required to run independent analysis. We have included raw Fastq files and processed files that are ready to be uploaded into Loupe Browser or R-Studio/Seurat V3. To summarize Cloupe Files can be uploaded to Loupe Browers and the BC_Matrix.H5 files can be uploaded directly to R. Furthermore, the RDS files are processed R-program files that can be immediately uploaded into R for analysis. We have included an example R script for users to follow and a few PDFs of excepted UMAPs using all combined files at PCA 35. Overall design: Hicks and Pyle crossed mdx-NSG mice to Rosa-DTX and Pax7-Cre mice to generate homozygous, congenic strains. Mice were then crossed to generate F1 heterozygous mdx-NSG Pax7-DTX mice that resulted in >80% mouse satellite cell ablation after tamoxifen treatment. 12-week-old female litter mate mdx-NSG Pax7-DTX mice were split into the following groups: AP1. Pax7 wildtype, No injury AP2. Pax7 ablation, No injury AP3. Pax7 wildtype, Injury AP4. Pax7 ablation, Injury To generate data, four groups of mice were either given tamoxifen chow or normal chow for 7 days, at which time mice were given an injury with Barium Chloride (BaCl2) or non-injured. To induce Pax7 ablation, 400mg/kg tamoxifen citrate chow (Envigo) was given to mice for 7 days. Pax7 wildtype were given standard chow. To induce injury, mice were then injected intramuscularly in the TA with 1.2% BaCl2 diluted in 50uL 0.9% NaCl Saline. All mice were fed standard chow following injury. Mice were sacrificed at 8 days post injury. Control, non-injured mice were sacrificed at the same time point so that all mice were age-matched. Nuclei were immediately from freshly dissected skeletal muscle isolated following a modified 10X Genomics Frankenstine protocol. All nuclei were collected using the On-Chip Flow Cell gentle sorter to increase nuclei purity from muscle debris. Nuclei were immediately taken for processing using 10X Genomics library construction and sequencing on an Illumina Nova6000. The provided Metrics Summary describes the number of nuclei and sequencing reads for each group. Fastq files were aligned CellRanger and processed using Seurat. Less...