single-nucleus transcriptome of six Ceratina calcarata brains: adult females from winter sample
Samples were then loaded into 10X Genomics Gel-beads-in-emulsion wells on Chromium Chips following their protocol for Single Cell 3-prime Reagent Kits (v3). After dissolving the gel beads, nuclei were lysed, and mRNA was reverse transcribed to cDNA. Using PCR, the cDNA was then amplified to create libraries. Libraries were checked for quality using the Agilent Bioanalyzer High Sensitivity chip. Paired-end reads (R1, R2) and sample index reads (I1, I2) were then sequenced from the libraries  on a flow cell lane (L001 or L002) with an Illumina Novaseq 6000 to create base call files. Base call files were input to Cell Ranger (version 6.1.2) to generate fastq files using the function mkfastq. To increase the sequencing depth, the same library was sequenced multiple times, resulting in different fastq files for the same sample (i.e. S3 and S16).