PM scRNA-seq
Single-cell RNA sequencing libraries were generated using the Seq-Well platform. Following tissue dissociation, single-cell suspensions were diluted to approximately 10,000–20,000 cells per array. For selected samples, technical replicates were created by splitting cell suspensions across multiple arrays processed in parallel. Cells were loaded onto arrays containing RNA capture beads, sealed with a membrane, and incubated to allow cell lysis and RNA hybridization. Beads were recovered, and reverse transcription, second-strand synthesis, and whole transcriptome amplification were performed. Amplified cDNA was purified and quantified prior to library preparation.  Sequencing libraries were prepared using Nextera XT tagmentation with dual indexing and sequenced on Illumina NextSeq 500/550 or NovaSeq 6000 instruments using paired-end configurations optimized for cell barcode and UMI capture with transcript readout. NextSeq base call files were converted to FASTQ format using bcl2fastq, while NovaSeq runs produced FASTQs directly. Libraries were initially shallow sequenced for quality control and subsequently sequenced more deeply across multiple lanes, resulting in variable numbers of FASTQ pairs per sample.  Reads were processed using the Drop-seq tools pipeline and aligned to the hg38 transcriptome using standard parameters.