biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsJames ClelandIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17281To test whether sex and diet influence cell-type specific gene expression in the mouse liver, we performed single-nucleus RNA-sequencing on liver tissue from male and female mice fed standard or Western diet.biostudies-arrayexpressNucleic Acid Extraction - Nuclei were released from cryopulverised liver tissue by homogenisation with a Qiagen TissueLyser III in hypotonic lysis buffer, resuspended in Sucrose PBS Triton X-100 MgCl2 (SBPSTM) buffer, fixed with MeOH/BS3, resuspended in SPBSTM and then stored at -80°C until use.Sequencing - Libraries were sequenced on a NovaSeq6000 system with the following read lengths: read 1 34bp, read 2 184bp, index 1 10bp, index 2 10bp.Sample Treatment - Mice were fed standard chow diet (Kliba # 3437) or WD (Research Diets # D16022301i; 40 kcal% non-transfat, 20 kcal% fructose and 2% cholesterol) for 32 weeks.Library Construction - Sci-RNA-seq3 library preparation was performed in 96 well plates by reverse transcription (first index), ligation (second index), second strand synthesis, protease digestion, tagmentation and PCR (third index), bead-cleanup and quality control.Sample Collection - Animals were sacrificed by carbon dioxide inhalation at 38 weeks of age. To partially control for time-of-day effects, mice were sacrificed between 7:00 and 16:00 on two consecutive days, alternating between the four groups. Estrous cycle stage was not assessed in females. Mice were not fasted before organ collection. Half of each liver left lateral lobe was snap-frozen on liquid nitrogen, pulverised with a Covaris CP02 automated tissue pulverizer and stored at -80˚C as described previously (Panten et al. 2024).OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesJames ClelandfalseSingle-nucleus RNA-seq of livers from mice fed standard or Western dietTo test whether sex and diet influence cell-type specific gene expression in the mouse liver, we performed single-nucleus RNA-sequencing on liver tissue from male and female mice fed standard or Western diet.2026-07-12T00:00:00Z2026-07-12T01:00:56.056Z2026-07-02T15:35:19.522ZE-MTAB-17281ERP196100EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0004184EFO_0003969