title: single-nuclei RNA-Seq of Chrysemys picta: embryonic liver organoids
design: Single nuclei RNA libraries were generated using the Chromium Single Cell 3 kit (10X Genomics, CA, USA). Loading onto the Chromium Controller was performed to target capture of ~10,000 GEMs per sample for downstream analysis and processed through the Chromium Controller. The sequencing libraries were evaluated for quality on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), then quantified using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Prior to loading onto an Illumina sequencing platform, pooled libraries were quantified using qPCR (Applied Biosystems, Carlsbad, CA, USA). The samples were sequenced at a configuration compatible with the recommended guidelines outlined by 10X Genomics. Raw sequence data (.bcl files) were converted into fastq files and de-multiplexed using the 10X Genomics cellranger mkfastq command. Subsequent UMI and cell barcode de-convolution along with mapping to C. picta genome (Chrysemys_picta_bellii-3.0.3 (GCA_000241765.2)) were performed using 10X Genomics cellranger software package to generate the final digital gene expression matrices and cloupe files.
library_name: Turtle_22_Liver_Organoids