GSM8563705: brain, ST multiple sclerosis, 3; Homo sapiens; OTHER
After being imaged to do a general morphological analysis and for future spatial alignment of the data, the samples were enzymatically permeabilized for 18 min. This time was assessed using the 10x Visium Tissue Optimization kit (PN-1000191) and following the protocol CG000238 Rev D. The generation of the libraries was performed according to the protocol CG000239 Rev D, using the Gene Expression Reagent kit (PN-1000186), the Library Construction Kit (PN-1000190) and the Dual Index Plate TT Set A (PN-1000215). To assess the correct amplification of the cDNA, QuantStudio 3 from ThermoFisher was used. For full length of cDNA and indexed libraries analysis 4200 TapeStation System from Agilent was used. The seven libraries were loaded at 300pM and sequenced on a NovaSeq 6000 System from Illumina with a sequencing depth of 250 million reads per sample. Sequencing was performed at Institute of Clinical Biology (IKMB, Kiel). The demultiplexing of the data was done using SpaceRanger software (10x – version 1.2.2), creating Fastq files. These files are then used by SpaceRanger count to perform alignment with the human reference genome, tissue detection, fiducial detection and barcode/UMI counting.