biostudies-arrayexpressVeronica BusaMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15743We 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-arrayexpressSequencing - Final libraries were sequenced on Illumina NextSeq2000 and NovaSeq6000 platforms using a 100 bp paired-end protocol.Nucleic Acid Extraction - To isolate total RNA, half of each lysate (519 μl) was mixed with 260 μl absolute ethanol and applied to RNeasy MinElute spin columns (Qiagen). Columns were washed once with Buffer RW1, followed by on-column DNase digestion for 15 min at room temperature. Subsequent washes were performed with Buffer RW1, Buffer RPE, and 80% ethanol. Residual wash solution was removed by centrifugation at maximum speed for 5 min. RNA was eluted in 14 μl RNase-free water and stored at −80°C. RNA quantity and integrity were evaluated using the Agilent TapeStation High Sensitivity RNA ScreenTape assay (Agilent Technologies).Library Construction - To isolate total RNA, half of each lysate (519 μl) was mixed with 260 μl absolute ethanol and applied to RNeasy MinElute spin columns (Qiagen). Columns were washed once with Buffer RW1, followed by on-column DNase digestion for 15 min at room temperature. Subsequent washes were performed with Buffer RW1, Buffer RPE, and 80% ethanol. Residual wash solution was removed by centrifugation at maximum speed for 5 min. RNA was eluted in 14 μl RNase-free water and stored at −80°C. RNA quantity and integrity were evaluated using the Agilent TapeStation High Sensitivity RNA ScreenTape assay (Agilent Technologies).Sample Collection - The dorsal skin from untreated, TPA-treated, and DMBA/TPA-treated mice was dissected, and a spatial grid of 1 mm full-thickness punch biopsies was collected. The grid spanned approximately 2 by 2 cm of dorsal skin. Biopsies for nucleic acid isolation were placed into deep-well 96-well plates on dry ice immediately after collection. DNA and RNA were co-extracted from skin biopsies and liver samples using a modified protocol combining the AllPrep DNA/RNA Micro Kit (Qiagen) and the DNeasy Blood and Tissue Kit (Qiagen). Samples were homogenized in 350 μl Buffer RLT supplemented with 1% β-mercaptoethanol using the TissueLyser II (Qiagen) at 30 Hz for 2 × 3 min. Homogenates were briefly centrifuged, and 700 μl proteinase K mix (12 μl proteinase K in 688 μl nuclease-free water) was added. Lysates were incubated at 56°C for 10 min, resulting in a final volume of 1038 μl. Each sample was then divided equally for RNA and DNA extraction (519 μl per fraction).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Bulk RNA sequencing was demultiplexed, aligned to GRCm38mm10_PhiX, and read count was calculated using the DKFZ/ODCF Roddy pipeline (https://github.com/DKFZ-ODCF/ RNAseqWorkflow). Raw read counts were generated by featureCounts.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusVeronica BusaMikaela BehmfalseBulk RNA 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.2026-06-11T00:00:00Z2026-06-11T13:18:31.048Z2025-11-14T16:13:55.596ZE-MTAB-15743ERP185101EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184