characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-09-30T00:24:51Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-09-30T00:24:51Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA113901666
characteristics.characteristic: External Id
characteristics.text: Centre for Gene Therapy and Regenerative Medicine, King’s College London, London, UK -Wellcome Sanger Institute, Cambridge, UK
characteristics.characteristic: INSDC center name
characteristics.text: 2023-09-30T00:24:51Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-09-30T00:24:51Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS15895835
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13084:WSSKNKCLsp12140271
characteristics.characteristic: Submitter Id
characteristics.text: 73
characteristics.unit: year
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: Fresh frozen OCT-embedded skin biopsies were cryosectioned as 10 μm sections, placed onto SuperFrost Plus glass slides (Thermo Fisher Scientific, Waltham, MA, USA) and stored for less than a week at -80˚C prior to high sensitivity library preparation. Optimal RNA integrity on the skin sections was assessed by RNAscope using three housekeeping genes with high (UBC) and medium (PPIB) expressors (Supplementary figure 3B). We also validated the integrity of the Visium library after sequencing: all samples presented good RNA quality (Supplementary figure 3C). However, we excluded 2 of the 32 10X Visium samples from further analysis due to poor tissue attachment to the slide. Visium spatial gene expression slides and reagents were used according to manufacturer instructions (10X Genomics). Each capture area (6.5 x 6.5 mm2) contains 5,000 barcoded spots that were 55 μm in diameter (100 μm center to center between spots) providing an average resolution of 1 to 10 cells up to a maximum of 100 cells depending on tissue area. Fresh frozen skin samples were embedded in OCT, cryo-sectioned and processed according to the recommended protocols (Tissue optimization: CG000238; Gene expression: CG000239). Optimal permeabilization time for 10um skin sections was 20minutes. cDNA libraries were quality controlled using the Agilent Bioanalyser. The cDNA libraries were sequenced on the Illumina HiSeq 4000 system, targeting 300 million reads per section with parameters 28cy R1, 8cy i7 index, 0cy i5 index, 91cy read 2.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: basal cell carcinoma
characteristics.characteristic: disease
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: skin
characteristics.characteristic: organism part
characteristics.text: bcc_­face_forehead1
characteristics.characteristic: sample id
characteristics.text: forehead
characteristics.characteristic: sampling site
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: WSSKNKCLsp12140271
characteristics.characteristic: title