title: scRNA-seq of iPSC-CM differentiation: CA1 Day 30
design: We differentiated one LMNA mutant iPSC line derived from an affected female (Patient A1) and two non-mutant iPSC lines (two clones: A and B) derived from her unaffected sister (Control A1) and collected cells for scRNA-seq (12 total samples: 4 Patient and 8 Control samples) across seven time points: Day 0, 2, 4, 9, 16, 19, and 30. Sample processing used the Chromium system and Chromium Single Cell 3 Gene Expression reagent kits v3 (10X Genomics, Pleasanton, CA). We quantied single-cell cDNA libraries and multiplexed libraries by Illumina paired-end sequencing  8 cycles for sample index, 28 cycles for Read 1 (cell barcode + UMI tag), and 100 cycles for Read 2 (cDNA insert). Library sequencing included deep sequencing using Illumina NovaSeq 6000 with the goal of obtaining at least 50,000 raw reads per cell. Using Illumina bcl2fastq2 software, we processed raw data files for index reads and demultiplexed data into sample specific FASTQ files for Read 1 (R1), Read 2 (R2), and sample index (I1). For each sample, SRA raw data files for deep sequencing consists of 24 files = 8 sets of I1_fastq.gz, R1_fastq.gz, and R2_fastq.gz files.