title: GSM9038468: Zebrafish head, osr2-/- , scRNA; Danio rerio; RNA-Seq
library_construction_protocol: Library preparation and sequencing was performed at the Molecular Genomics Core Facility (Peter MacCallum Cancer Centre). Single cell suspensions from FACS were spun down and a cell count was performed to determine post-sort viability and cell concentration. Single cell suspension was partitioned and barcoded using the 10X Genomics Chromium iX Controller (10X Genomics) and the Single Cell 3' Library and Gel Bead Kit (V3.1; 10X Genomics;  PN-1000121).  The cells were loaded onto the Chromium Single Cell Chip G (10X Genomics; PN-1000120) to target 10,000 cells. GEM generation and barcoding, cDNA amplification, and library construction was performed according to the 10X Genomics Chromium User Guide. The resulting single cell transcriptome libraries contained unique sample indices for each sample. The libraries were quantified on the Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape and reagents (Agilent, 5067-5585, 5067-5584). Single cell transcriptome libraries were pooled in equimolar ratios before being sequenced on an Illumina NextSeq2000 using P4 100-cycle chemistry. Read1 supplies the cell barcode and UMI, i7 and i5 the sample indexes, and Read2 the 3' sequence of the transcript. Sequencing read lengths were trimmed to 28bp (Read1), 10bp (i7 index), 10bp (i5 index), 91bp (Read2), ensuring compatibility with the 10X Genomics analysis software, Cell Ranger. After sequencing, fastq files were generated using bcl2fastq2 (v.2.20.0.422).
identifiers.namespace: GEO
identifiers.id: GSM9038468_r1