GSM7234201: ChickTrunk_2_Visium; Gallus gallus; OTHER
The Visium Spatial Gene Expression Slide PN-2000233 and associated protocol  (CG000239) from 10X Genomics were used. Fresh frozen HH24 trunk tissues were transversely cryo-sectioned to approximate single cell thickness (10um) and carefully  placed within the fiducial frame on the equilibrated slide within a cryostat set to -20C.  The slide was fixed in methanol at -20C for 30 min and air dried. The slide was then  stained with H&E and imaged using a Zeiss LSM 800 confocal microscope. Tissue was  permeabilized to release mRNA that bound to spatially barcoded capture probes. Library preparation was done following the Visium Spatial Gene Expression User Guide  using supplied reagents in Visium kit (10X Genomics). Whole transcriptome libraries  were sequenced and analyzed using Space Ranger (1.0.0) and Loupe browser. 10X  Genomics' automated image alignment software had trouble detecting one capture area  and we manually selected it in its Loupe browser based on 10X's suggestion. Data was  generated for four individual Visium capture areas.