title: GSM6364826: late gastrula replicate 1; Lytechinus variegatus; RNA-Seq
library_construction_protocol: Single cell encapsulation was performed using the Chromium Single Cell Chip B kit on the 10x Genomics Chromium Controller. Single cell cDNA and libraries were prepared using the Chromium Single Cell 3' Reagent kit v3 Chemistry. Libraries were sequenced by Genewiz on the Illumina Hiseq (2x150 bp paired-end runs). Single cell unique molecular identifier (UMI) counting was performed using Cell Ranger Single Cell Software Suite 3.0.2 from 10X Genomics. Duplicate blastula and gastrula stage libraries were aggregated using the cellranger aggr function. Cellranger gene expression matrices were further analyzed using the R package Seurat v 3.1.4. A seurat object was created by simply combining the individual datasets and then normalized by scaling gene expression in each cell by total gene expression. The top 2000 highly variable genes were then used for downstream analysis. The batch effects between samples were corrected by Harmony with default setting. UMAP analysis was performed with the following parameters: dims = 1:20, resolution = 1.