{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alexander Beristain"],"organism":["Mus musculus"],"software":["Cell Ranger"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16176"],"description":["Maternal obesity is associated with increased risk of infertility, implantation failure, miscarriage, and other pregnancy complications. While prior studies have linked obesity to uterine dysfunction and impaired endometrial biology, how obesity alters the cellular and molecular landscape of the early pregnant endometrium remains poorly understood. Here, we perform single-cell RNA sequencing of E5.5 implantation sites from control and obesogenic diet-exposed mice to generate a cellular atlas of the early decidualizing uterus. We identify obesity-associated transcriptional changes across multiple endometrial stromal cell (ESC) states and innate immune populations, including uterine natural killer cells and macrophages. Computational modeling reveals that maternal obesity likely disrupts dis"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Following library generation,  the samples were sequenced using an Illumina NextSeq 2000 instrument using Illumina NextSeq2000 P2 reagent kit indicated in the table following manufacturer’s protocol.","Sample Collection - Implantation sites collected at E5.5 from control Chow (17% fat, 54% carbohydrate, 29% protein (kCal/g), n = 5 ) and high fat/high sucrose (HFHS) diet-exposed (45% fat, 17% sucrose, 18% carbohydrate, 20% protein (kCal/g), n = 5) C57BL/6J mice. Tissues were digested, and single-cell suspensions were generated as described in Koksal et. al. https://doi.org/10.1101/2025.08.13.670199. Cell suspensions were pelleted and cryopreserved at -150°C until library preparation.","Library Construction - Manufacturer's protocol was followed to construct single cell RNA libraries using the Chromium Single Cell 3’ v3.1 dual index kit (10x Genomics).","Nucleic Acid Extraction - Single-cell suspensions were thawed as described in Koksal et. al. https://doi.org/10.1101/2025.08.13.670199 and following FACS, they were used immediately for preparation of single cell RNA libraries using the Chromium Single Cell 3’ v3.1 kit (10x Genomics) according to the manufacturer's protocol to construct cDNA libraries.","Sequencing - Following library generation, the samples were sequenced using an Illumina NextSeq 2000 instrument using Illumina NextSeq2000 P3 reagent kit indicated in the table following manufacturer’s protocol."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Sequencing reads were aligned to mus musculus reference genome mm10-2.1.0 using Cell Ranger v6.0.1.","Data Transformation - Generated data was normalized as described in Koksal et. al. https://doi.org/10.1101/2025.08.13.670199."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"pubmed_abstract":["<h4>SUMMARY</h4>  Maternal obesity is associated with increased risk of infertility, implantation failure, miscarriage, and other pregnancy complications. While prior studies have linked obesity to uterine dysfunction and impaired endometrial biology, how obesity alters the cellular and molecular landscape of the early pregnant endometrium remains poorly understood. Here, we perform single-cell RNA sequencing of embryonic day 5.5 uterus from control and obesogenic mice to generate a cellular atlas of the early decidualizing endometrium. We identify obesity-associated transcriptional changes across multiple Endometrial Stromal Cell (ESC) states and innate immune populations, including uterine natural killer cells and macrophages. Computational modeling reveals that maternal obesity disrupts"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_title":["Obesogenic diet alters decidual differentiation and cell-cell communication in the mouse uterus"],"pubmed_authors":["Patrycja Jazwiec","Alexander Beristain","Koksal, B.; Bellissimo, C.J.; Jazwiec, P.A.; Sloboda, D.M.; Beristain, A.G.","Deborah Sloboda","Christian Bellissimo","Burak Koksal"],"additional_accession":[]},"is_claimable":false,"name":"Obesogenic diet disrupts endometrial stromal cell differentiation in the E5.5 mouse uterus","description":"Maternal obesity is associated with increased risk of infertility, implantation failure, miscarriage, and other pregnancy complications. While prior studies have linked obesity to uterine dysfunction and impaired endometrial biology, how obesity alters the cellular and molecular landscape of the early pregnant endometrium remains poorly understood. Here, we perform single-cell RNA sequencing of E5.5 implantation sites from control and obesogenic diet-exposed mice to generate a cellular atlas of the early decidualizing uterus. We identify obesity-associated transcriptional changes across multiple endometrial stromal cell (ESC) states and innate immune populations, including uterine natural killer cells and macrophages. Computational modeling reveals that maternal obesity likely disrupts dis","dates":{"release":"2026-08-03T00:00:00Z","modification":"2026-08-03T01:00:43.977Z","creation":"2025-11-14T19:27:30.55Z"},"accession":"E-MTAB-16176","cross_references":{"ENA":["ERP185111"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2025.08.13.670199"]}}