biostudies-arrayexpressTallulah AndrewsMus musculuscellranger(v7.0.1)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15294Mice were bred such that they are homozygous for human MAPT (tau), and one of two versions of the APP gene (NL and NLF) referring to the Swedish familial Alazheimer's Disease (AD) variants, and one of human APOE allele E3 or APOE allele E4. APP-NLF+APOE(E3) mice develop amyloid plaques and attention and memory deficits at 16-24 months, whereas APP-NLF+APOE(E4) mice develop this phenotype earlier at 9 months. Three mice of each of the four possible genotypes were sacrificed at 9 months of age, and the prefrontal cortex was dissected and subject to single nucleus RNA sequencing (snRNAseq) with the 10X Chromium platform.biostudies-arrayexpressSample Collection - Mice were sacrificed at 9 months, brains were extracted on ice and dissected to obtain the prefrontal cortex from both hemispheres, tissue was snap frozen on dry ice then stored at -80 for up to 1 month. Nuclei were extracted from frozen tissues using the 10X Chromium Nuclei Isolation with RNase Inhibitor Kit according to directions. Isolated nuclei were suspended in buffer and run on a 10X Chromium to isolate individual nuclei and generate 3' tagged cDNA.Growth Protocol - Mice were group housed, and fed standard chow and water ad libitum for 9 months then sacrificed and dissected. Mice were sacrificed during the light cycle.Sequencing - paired-end reads (1 barcode read + 1 transcript read) with Illumina NovaSeq 6000, targeting 350 million reads per sample.Library Construction - cDNA was collected from the 10X Chromium and converted to sequencing libraries using the 10X 3' scRNAseq Library Construction Kit.Nucleic Acid Extraction - Nuclei were captured and lysed on the 10X Chromium, mRNA transcripts were polyA-selected, 3' tagged and reverse transcribed within nanodroplets.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Processed data contains both raw (unfiltered) UMI counts for all possible droplets, as well as filtered UMI counts for droplets inferred to contain a nucleus by cellranger. UMI counts are corrected for 1 sequencing error automatically by cellranger, and both intronic and exonic reads were counted when quantifying UMIs.Sequence Alignment - Reads were aligned and unique molecular identifiers were counted using cellranger(v7.0.1) including both exonic and intronic reads. Reads were aligned to the 10X filtered mouse genome (gex-mm10-2020-A).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000single nucleus RNA sequencingMus musculusMarco PradoAya ArrarTallulah AndrewsfalsesnRNAseq of humanized mouse model of late-onset Alzheimer's DiseaseMice were bred such that they are homozygous for human MAPT (tau), and one of two versions of the APP gene (NL and NLF) referring to the Swedish familial Alazheimer's Disease (AD) variants, and one of human APOE allele E3 or APOE allele E4. APP-NLF+APOE(E3) mice develop amyloid plaques and attention and memory deficits at 16-24 months, whereas APP-NLF+APOE(E4) mice develop this phenotype earlier at 9 months. Three mice of each of the four possible genotypes were sacrificed at 9 months of age, and the prefrontal cortex was dissected and subject to single nucleus RNA sequencing (snRNAseq) with the 10X Chromium platform.2025-10-07T00:00:00Z2025-10-07T16:42:17.411Z2025-07-01T11:23:44.341ZE-MTAB-15294ERP174383EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0009809EFO_0005518EFO_0003816EFO_0004184