GSM6731199: P31 male Bace1-fl/fl; Mus musculus; RNA-Seq
Eight hippocampi from P31 and P192 male and female Bace1fl/fl and Bace1fl/fl;Thy1-cre mice were extracted and snap frozen on dry ice. Hippocampi were then homogenized and lysed in buffer containing 0.01% tween/0.01% NP-40 on ice. Debris removal (Miltenyi) step was included to remove myelin debris, and nuclei were counted and loaded onto a droplet-based 10x Chromium controller to perform single cell partitioning and barcoding. Raw sequencing from the NovaSeq6000 was aligned and annotated using the CellRanger v3.1.0 pipeline. During FASTQ generation, reads with more than 1 mismatch in the 8bp i7 index were excluded. During alignment using STAR (62), only reads with MAPQ scores greater than 255 aligned to annotated transcripts were retained. Reads containing bases with Q30 scores below 3 were also excluded. After alignment, cell barcodes were filtered up to 1 mismatch against a whitelist of 737,500 barcodes provided by 10X Genomics. Barcodes associated with cells were distinguished from ambient mRNA using an adaptively computed UMI threshold. The raw counts matrix was filtered using cutoff values of mitochondrial transcripts below 5% and between 250 and 6,000 unique features.