{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Shad Hassan"],"organism":["Rattus norvegicus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16929"],"description":["We investigated neural populations mediating the effects of cagrilintide on energy balance in the dorsal vagal complex (DVC). Single-nucleus RNA sequencing and spatial transcriptomics were performed across mouse, rat, and macaque brainstem tissue. Treatment groups include diet-induced obese animals treated acutely or subchronically with cagrilintide or vehicle. The overarching aim was to identify and characterize the neuronal population showing the strongest and most sustained transcriptional response to treatment. Included in this ArrayExpress ID is the single-cell data for mouse, rat and macaque"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - DIO mice were allocated into groups based on BW. For the acute study, mice were dosed with a single subcutaneous injection of cagrilintide (10 nmol kg-1) or vehicle 0-1 hour after the onset of the light cycle. The mice were euthanized by decapitation under isoflurane anaesthesia 3-4 h after dosing. For the subchronic study, mice were dosed subcutaneously once a day with cagrilintide (10 nmol kg-1) or vehicle 3-4 h after onset of light for 7 days. One group of mice was weight-matched to mice dosed with cagrilintide by daily food restriction","Sequencing - Sequenced on an NovaSeq 6000 with an S2 flow cell (Illumina) using paired-end sequencing","Nucleic Acid Extraction - Frozen tissue was thawed on ice and homogenized in Nuclei EZ Lysis Buffer using a glass tissue douncer. The homogenate was incubated on ice, filtered through a 40 µm cell strainer, and centrifuged. The pellet was resuspended in Nuclei EZ Lysis Buffer and OptiPrep, layered onto 49% OptiPrep, and centrifuged for density purification. Isolated nuclei were collected, washed in nuclei buffer containing PBS, 1% BSA, 2 mM MgCl2, and RNase inhibitor, centrifuged again, and finally resuspended in nuclei buffer. This procedure generated single-nucleus suspensions for downstream hashing and snRNA-seq library preparation.","Library Construction - Single-nucleus suspensions were hashed by incubation with TotalSeq-A anti-nuclear hashtag oligonucleotide-conjugated antibodies on ice, followed by washing and resuspension in nuclei buffer containing DAPI. DAPI-positive nuclei were sorted by flow cytometry and collected into RT Buffer B. The sorted nuclei suspension was adjusted to the required input volume and processed using the Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics) according to the manufacturer’s instructions. A multiplexing hashtag library was generated following the BioLegend TotalSeq-A Cell Hashing protocol for compatibility with the 10x Genomics Single Cell 3′ Reagent Kit v3.1.","Sample Collection - For all experiments that involve RNA sequencing, brains were extracted after sacrifice and the hindbrain portion containing the DVC was dissected out before being fresh frozen on powdered dry ice for intermediate storage in 1.5ml Eppendorf tubes at -80°C. These dissections were later homogenized and incubated in EZ lysis buffer, and subsequently strained through a 40µm filter and spun down"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw counts were normalized with the SCTransform function from Seurat v4.0.0.","Sequence Alignment - Raw sequencing reads were processed using Cell Ranger v7.1.0. Reads were aligned to the Mus musculus (mm10), Rattus norvegicus (Rnor_6.0), or Macaca mulatta (Mmul_10) genome with default parameters."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Rattus norvegicus"],"pubmed_authors":["Tune Pers","Shad Hassan"],"additional_accession":[]},"is_claimable":false,"name":"A Cross-Species Atlas of the Dorsal Vagal Complex Reveals Neural Mediators of Cagrilintide’s Effects on Energy Balance","description":"We investigated neural populations mediating the effects of cagrilintide on energy balance in the dorsal vagal complex (DVC). Single-nucleus RNA sequencing and spatial transcriptomics were performed across mouse, rat, and macaque brainstem tissue. Treatment groups include diet-induced obese animals treated acutely or subchronically with cagrilintide or vehicle. The overarching aim was to identify and characterize the neuronal population showing the strongest and most sustained transcriptional response to treatment. Included in this ArrayExpress ID is the single-cell data for mouse, rat and macaque","dates":{"release":"2026-06-08T00:00:00Z","modification":"2026-06-08T12:32:34.242Z","creation":"2026-04-14T14:03:07.06Z"},"accession":"E-MTAB-16929","cross_references":{"ENA":["ERP192134"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}