biostudies-arrayexpressVeronica BusaMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15745We generated meso-scale grids from mouse back skin by collecting paired whole-exome sequencing (WES) and bulk RNA sequencing (bulk RNA), retaining coordinate information to preserve spatial context across the grids. Grids were derived from untreated mice (UN, n = 4), mice treated with the cell-cycle activator TPA for twelve weeks (TO, n = 3), and mice treated with the carcinogen DMBA followed by repeated TPA until the first visible papilloma (DT, n = 3). Cumulatively, we collected 690 bulk RNA and 476 WES samples, the majority of which are paired. All DT animals developed papillomas, whereas no macroscopic skin alterations were observed in UN or TO mice.biostudies-arrayexpressNucleic Acid Extraction - 350 μl RLT buffer (from the AllPrep DNA/RNA Micro Kit) containing 1% β-Mercaptoethanol (Sigma-Aldrich) was added to each sample (containing one biopsy) and the tissue was homogenised in a Qiagen TissueLyzer II using 2 cycles of 3 minutes at 30 Hz. After lysis 688 μl of nuclease-free water and 12 μl proteinase K (from DNeasy Blood and Tissue Kit) was added to the lysate and incubated at 56°C for 10 minutes. Half of the sample (519 ul) was used for DNA extraction. 519 μl Buffer AL (Qiagen Blood & Tissue) was added, mix by vortexing, and incubated at 56°C for 30 minutes at 500 rpm. An equal volume (519 μl) of absolute ethanol was added to samples and mixed thoroughly.Library Construction - The precipitated mixture was transferred to a DNeasy Mini spin 96-well spin plate (Qiagen), washed twice with 700 μl buffer AW1 and twice with buffer AW2. After drying the membrane for 3 minutes at 20,000 x g DNA was eluted using two consecutive elutions of 30 µl pre-warmed AE buffer (70°C). The quality of the DNA was assessed using a Genomic DNA ScreenTape (Agilent Technologies).Sample Collection - DNA was isolated from 1 mm3 mouse back skin biopsies and livers using a modified and combined version of the AllPrep DNA/RNA Micro Kit (Qiagen) and DNeasy Blood and Tissue Kit (Qiagen).Sequencing - Dual indexed whole exome capture libraries were prepared from mouse biopsies and matched livers using SureSelect XT HS and XT Low Input Enzymatic Fragmentation protocol (Agilent). SureSelectXT Low Input Target Enrichment System was used with Mouse All Exon capture kit (49.6 Mb). Exome libraries were sequenced on Illumina NovaSeq6000 sequencers using a 100 bp paired-end read protocol.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Whole exome sequencing was demultiplexed and aligned to GRCm38mm10_PhiX using the DKFZ/ODCF Roddy pipeline (https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows). Somatic variants were called using GATK v4.0.9.0 Mutect2 with liver samples from the same animal as a matched normal, and filtered using FilterMutectCalls. Somatic variants were annotated using VEP v110.1UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000exome sequencingMus musculusVeronica BusaMikaela BehmfalseWhole exome sequencing grid of untreated, TPA-treated, and DMBA+TPA-treated mouse back skinWe generated meso-scale grids from mouse back skin by collecting paired whole-exome sequencing (WES) and bulk RNA sequencing (bulk RNA), retaining coordinate information to preserve spatial context across the grids. Grids were derived from untreated mice (UN, n = 4), mice treated with the cell-cycle activator TPA for twelve weeks (TO, n = 3), and mice treated with the carcinogen DMBA followed by repeated TPA until the first visible papilloma (DT, n = 3). Cumulatively, we collected 690 bulk RNA and 476 WES samples, the majority of which are paired. All DT animals developed papillomas, whereas no macroscopic skin alterations were observed in UN or TO mice.2026-06-11T00:00:00Z2026-06-11T13:19:00.291Z2025-11-13T16:30:27.567ZE-MTAB-15745ERP184384EFO_0002944EFO_0005396EFO_0004170EFO_0005518EFO_0003816EFO_0004184