title: Visium Spatial Gene Expression of Female Canary Brain Slice, 17B Control Group,10XGenomics slide number: V12N14-299
design: According to the manufacturer's instructions, 20-m sections were loaded onto 10X Genomics Visium Spatial Gene Expression Slides. The slices were taken between 200 to 250 m medial from the lateral border of the HVC. The permeabilization conditions were optimized for bird brains using the Visium Spatial Tissue Optimization & Reagent Kit (10X Genomics GmbH, Hamburg). The capture area has 4992 Spots, 55 m in diameter each, and a 100 m center-to-center distance. The libraries of the barcoded cDNA generated from each section were produced following the 10X Genomics Visium library preparation protocol. Indexed libraries were pooled equimolarly and sequenced in a 28/90 paired-end run using the 100 cycles Novaseq sequencing kit v1.5 (#20028316) with NovaSeq XP 2-Lane Kit v1.5 (#20043130) on a Novaseq6000 platform with a S2 flow cell at a minimum of 140 million fragments per sample (140-189M fragments/sample). Demultiplexing was done using the Illumina BCL convert software (v4.2.7.).