scRNA for 6-dpf zebrafish brain pericytes-1 (CRX2013866)
A total of 3000 cells were used for single-cell library preparation with the 10X Genomics platform. The cells and cell barcode-labeled beads were encapsulated in droplets using microfluidic technology. The droplets containing cells and beads were collected, and the cells were lysed within the droplets, linking the cell's mRNA with the cell barcode on the bead to form single-cell Gel bead in EMulsion (GEM). Reverse transcription was performed in the droplets, generating cDNA libraries. Sample indexes on the library sequences were used to differentiate the origin of the target sequences. The library was then subjected to reverse transcription and pre-amplification, and the amplified products were quality-checked using Invitrogen Qubit 3.0 Fluorometer (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent).   CellRanger, the official software provided by 10X Genomics, was used for sample quality control, which integrated the STA software to evaluate the number of high-quality cells, gene counts, and genome alignment rates from the sequenced reads (https://www.10xgenomics.com/). The optimized sequencing results were aligned to the GRCz11 database to obtain transcriptomic data for each captured cell. Further quality control was performed to remove multi-cells, doublets, or unbound cells. Using R language and Seurat package functionality (Stuart et al., 2019), clustering analysis of individual cells and comparisons between cell clusters were conducted.