# SpatialData-DB collections, shard 3 Generated from catalog release catalog-2026-11-01. Each collection has an anchor named after its slug, and every page on the site links its own section. The guide for agents is /llms.txt. ## geo-gse334924-camr-kidney - Page: /collections/geo-gse334924-camr-kidney/ - Kind: other - Datasets: 1 - Members: [visium-hd-kidney-cgxlpmq7n6zidcyg0000](/datasets/md/27.md#visium-hd-kidney-cgxlpmq7n6zidcyg0000) ## The extra-islet pancreas supports autoimmunity in human type 1 diabetes. - Page: /collections/bia-s-biad859/ - Kind: publication - Datasets: 2 - Reference: 10.7554/elife.100535 - Members: [phenocycler-pancreas-gywbib2mj2hskhvk0000](/datasets/md/65.md#phenocycler-pancreas-gywbib2mj2hskhvk0000), [phenocycler-pancreas-yriwxhfhzhe30vf60000](/datasets/md/18.md#phenocycler-pancreas-yriwxhfhzhe30vf60000) ## 10x-xenium-ffpe-human-breast-biomarkers - Page: /collections/10x-xenium-ffpe-human-breast-biomarkers/ - Kind: other - Datasets: 12 - Members: [10x-xenium-breast-vplogf8scizfrawp0001](/datasets/md/90.md#10x-xenium-breast-vplogf8scizfrawp0001), [10x-xenium-breast-9lmfx39bvnixqjn10001](/datasets/md/2e.md#10x-xenium-breast-9lmfx39bvnixqjn10001), [10x-xenium-breast-599jjllrprytyghy0001](/datasets/md/8f.md#10x-xenium-breast-599jjllrprytyghy0001), [10x-xenium-breast-ozvryzdtpiejsckv0001](/datasets/md/27.md#10x-xenium-breast-ozvryzdtpiejsckv0001), [10x-xenium-breast-ypn7hojfu3jihgks0001](/datasets/md/53.md#10x-xenium-breast-ypn7hojfu3jihgks0001), [10x-xenium-breast-y6xbzgeqbvggxiz30001](/datasets/md/8f.md#10x-xenium-breast-y6xbzgeqbvggxiz30001), [10x-xenium-breast-xxeynnbtewpilrth0001](/datasets/md/8e.md#10x-xenium-breast-xxeynnbtewpilrth0001), [10x-xenium-breast-2zdd7abgezbfjb500001](/datasets/md/e2.md#10x-xenium-breast-2zdd7abgezbfjb500001), [10x-xenium-breast-nluumpgijbak8b3u0001](/datasets/md/e2.md#10x-xenium-breast-nluumpgijbak8b3u0001), [10x-xenium-breast-dnkj7pgfj8svgwaf0001](/datasets/md/a6.md#10x-xenium-breast-dnkj7pgfj8svgwaf0001), [10x-xenium-breast-kjdketwhcz354k6p0001](/datasets/md/fe.md#10x-xenium-breast-kjdketwhcz354k6p0001), [10x-xenium-breast-r8l8lvxszssmjro40001](/datasets/md/5d.md#10x-xenium-breast-r8l8lvxszssmjro40001) ## Batf3<sup>+</sup> DCs and the 4-1BB/4-1BBL axis are required at the effector phase in the tumor microenvironment for PD-1/PD-L1 blockade efficacy. - Page: /collections/doi-10-1016-j-celrep-2024-114141/ - Kind: replicates - Datasets: 2 - Reference: 10.1016/j.celrep.2024.114141 - Members: [visium-spatial-gene-expression-urinary-bladder-qjcnzcc0wdtdukzf0000](/datasets/md/20.md#visium-spatial-gene-expression-urinary-bladder-qjcnzcc0wdtdukzf0000), [visium-spatial-gene-expression-urinary-bladder-q1tf6pptg5uikwhu0000](/datasets/md/04.md#visium-spatial-gene-expression-urinary-bladder-q1tf6pptg5uikwhu0000) ## Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. - Page: /collections/doi-10-1038-s41593-020-00787-0/ - Kind: publication - Datasets: 12 - Reference: 10.1038/s41593-020-00787-0 - Members: [visium-spatial-gene-expression-brain-gpqpn2hml6lxvukd0000](/datasets/md/3a.md#visium-spatial-gene-expression-brain-gpqpn2hml6lxvukd0000), [visium-spatial-gene-expression-brain-1ueieiyghy9uhfpn0000](/datasets/md/6c.md#visium-spatial-gene-expression-brain-1ueieiyghy9uhfpn0000), [visium-spatial-gene-expression-brain-yow8z6wfrfnxchvy0000](/datasets/md/29.md#visium-spatial-gene-expression-brain-yow8z6wfrfnxchvy0000), [visium-spatial-gene-expression-brain-adwrf9r0zehho0p30000](/datasets/md/9d.md#visium-spatial-gene-expression-brain-adwrf9r0zehho0p30000), [visium-spatial-gene-expression-brain-8n0glw4stres6kek0000](/datasets/md/1a.md#visium-spatial-gene-expression-brain-8n0glw4stres6kek0000), [visium-spatial-gene-expression-brain-snuq58ryiwr14adn0000](/datasets/md/fd.md#visium-spatial-gene-expression-brain-snuq58ryiwr14adn0000), [visium-spatial-gene-expression-brain-casn2tkdgaqzel7o0000](/datasets/md/f0.md#visium-spatial-gene-expression-brain-casn2tkdgaqzel7o0000), [visium-spatial-gene-expression-brain-uexgt45xr1nfcohr0000](/datasets/md/9e.md#visium-spatial-gene-expression-brain-uexgt45xr1nfcohr0000), [visium-spatial-gene-expression-brain-rzbt2zbifdtz8o2e0000](/datasets/md/2b.md#visium-spatial-gene-expression-brain-rzbt2zbifdtz8o2e0000), [visium-spatial-gene-expression-brain-ghc60jgfb6f4x9nu0000](/datasets/md/b9.md#visium-spatial-gene-expression-brain-ghc60jgfb6f4x9nu0000), [visium-spatial-gene-expression-brain-uxjvkqzugu7zjhas0000](/datasets/md/79.md#visium-spatial-gene-expression-brain-uxjvkqzugu7zjhas0000), [visium-spatial-gene-expression-brain-lgk47wcfdp7t3jsh0000](/datasets/md/a0.md#visium-spatial-gene-expression-brain-lgk47wcfdp7t3jsh0000) ## GENE EXPRESSION WITHIN A HUMAN CHOROIDAL NEOVASCULAR MEMBRANE USING SPATIAL TRANSCRIPTOMICS - Page: /collections/doi-10-1101-2023-06-16-544770/ - Kind: comparison - Datasets: 5 - Reference: 10.1101/2023.06.16.544770 - Members: [visium-spatial-gene-expression-eye-g7i8mssryuhfhxnk0000](/datasets/md/d1.md#visium-spatial-gene-expression-eye-g7i8mssryuhfhxnk0000), [visium-spatial-gene-expression-eye-wigngacvzdwmgh7m0000](/datasets/md/2a.md#visium-spatial-gene-expression-eye-wigngacvzdwmgh7m0000), [visium-spatial-gene-expression-eye-knzk6uqr6dubr0gf0000](/datasets/md/ac.md#visium-spatial-gene-expression-eye-knzk6uqr6dubr0gf0000), [visium-spatial-gene-expression-eye-4ninbsd8lnqs6odd0000](/datasets/md/88.md#visium-spatial-gene-expression-eye-4ninbsd8lnqs6odd0000), [visium-spatial-gene-expression-eye-kifzbnzaurywg5ar0000](/datasets/md/e7.md#visium-spatial-gene-expression-eye-kifzbnzaurywg5ar0000) ## Single-nucleus ribonucleic acid-sequencing and spatial transcriptomics reveal the cardioprotection of Shexiang Baoxin Pill (SBP) in mice with myocardial ischemia-reperfusion injury. - Page: /collections/doi-10-3389-fphar-2023-1173649/ - Kind: comparison - Datasets: 2 - Reference: 10.3389/fphar.2023.1173649 - Members: [visium-spatial-gene-expression-heart-codkvx39kwejmhry0000](/datasets/md/0f.md#visium-spatial-gene-expression-heart-codkvx39kwejmhry0000), [visium-spatial-gene-expression-heart-lg5wio3fca7kdt8d0000](/datasets/md/b5.md#visium-spatial-gene-expression-heart-lg5wio3fca7kdt8d0000) ## Single cell- Cluster-RNA seq and Spatial Transcriptomics from the trunk of mouse embryos of different genotypes (wild type, Pax2-GFP, Pax2-GFP; Gata3 knockout) and developmental stages (E8.75, E9.5, E11.5) [Spatial Transcriptomics] - Page: /collections/geo-gse160137/ - Kind: other - Datasets: 4 - Reference: PMID:33976190 - Design: Identify cell heterogenity and state transitions in the developing urinary tract - Members: [visium-spatial-gene-expression-trunk-lyqwdgbz3d0olaiv0000](/datasets/md/aa.md#visium-spatial-gene-expression-trunk-lyqwdgbz3d0olaiv0000), [visium-spatial-gene-expression-trunk-h1okqyqn4gjd0i1l0000](/datasets/md/cb.md#visium-spatial-gene-expression-trunk-h1okqyqn4gjd0i1l0000), [visium-spatial-gene-expression-trunk-ems0unvubrenrru80000](/datasets/md/10.md#visium-spatial-gene-expression-trunk-ems0unvubrenrru80000), [visium-spatial-gene-expression-trunk-x38xfjx03r2bgccf0000](/datasets/md/f1.md#visium-spatial-gene-expression-trunk-x38xfjx03r2bgccf0000) ## Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces - Page: /collections/geo-gse224411/ - Kind: comparison - Datasets: 3 - Reference: PMID:37080163 - Design: The HCC sample was obtained from a Phase I clinical trial that examined cabozantinib plus nivolumab as neoadjuvant therapy for advanced hepatocellular carcinoma. The PDAClymphnode was collected from a patient with pancreatic adenomarcinoma that received noeadjuvant therapy with a pancreatic cancer vaccine (GVAX). The PanIN was collected from a treatment naive pancreatic cancer patient. All three samples were analyzed using spatial transcriptomics. None of the samples had experimental replicates. We performed latent space factorization of the 10x Visium spatial transcriptomics and used SpaceMarkers to identify genes associated with spatially overlapping latent features representing different cell types. For the HCCsinglecell sample, the tumor was enzymatically dissociated into single cells upon surgical resection. Tumor was minced and dissociated in digestion medium containing 0.1% (w/v) collagenase type IV (Invitrogen) in PBS at 37°C for 30 minutes on a shaking incubator set at 60 rpm. Cell collection was enriched with Percoll 40%−80% (GE Life Sciences) at 2000 × g for 25 minutes at RT without break, eliminating debris and erythrocytes. *** Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns *** - Members: [visium-spatial-gene-expression-lymph-node-r4hf2roozxjyehte0000](/datasets/md/aa.md#visium-spatial-gene-expression-lymph-node-r4hf2roozxjyehte0000), [visium-spatial-gene-expression-pancreas-ev4eskgltygysvdz0000](/datasets/md/ce.md#visium-spatial-gene-expression-pancreas-ev4eskgltygysvdz0000), [visium-spatial-gene-expression-liver-0vtapsmidolig4m00000](/datasets/md/59.md#visium-spatial-gene-expression-liver-0vtapsmidolig4m00000) ## Spatiotemporal hepatocyte heterogeneity impacts in vivo gene engineering [Visium Spatial Transcriptomics] - Page: /collections/geo-gse236424/ - Kind: time course - Datasets: 21 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236424 - Design: Spatial transcriptomics of 17 mouse livers, from newborn, juvenile or adult mice, either LV-transduced, 3 days post LV, or age-matched untransduced mice. - Members: [visium-spatial-gene-expression-liver-tcs3jzmacbn3w8jo0000](/datasets/md/9d.md#visium-spatial-gene-expression-liver-tcs3jzmacbn3w8jo0000), [visium-spatial-gene-expression-liver-h1ezj3jjkm0ffs4g0000](/datasets/md/16.md#visium-spatial-gene-expression-liver-h1ezj3jjkm0ffs4g0000), [visium-spatial-gene-expression-liver-bv9qiinbkqkdlefr0000](/datasets/md/41.md#visium-spatial-gene-expression-liver-bv9qiinbkqkdlefr0000), [visium-spatial-gene-expression-liver-dwvoqemwvtdg2piw0000](/datasets/md/d9.md#visium-spatial-gene-expression-liver-dwvoqemwvtdg2piw0000), [visium-spatial-gene-expression-liver-f7xrfjrljdgghmjf0000](/datasets/md/6e.md#visium-spatial-gene-expression-liver-f7xrfjrljdgghmjf0000), [visium-spatial-gene-expression-liver-mfdivwf7feotowti0000](/datasets/md/68.md#visium-spatial-gene-expression-liver-mfdivwf7feotowti0000), [visium-spatial-gene-expression-liver-x8h6rlfcrcau9b3f0000](/datasets/md/d2.md#visium-spatial-gene-expression-liver-x8h6rlfcrcau9b3f0000), [visium-spatial-gene-expression-liver-ex9t5lxwocm1yoks0000](/datasets/md/c2.md#visium-spatial-gene-expression-liver-ex9t5lxwocm1yoks0000), [visium-spatial-gene-expression-liver-gdvptd06wdcwck1j0000](/datasets/md/4e.md#visium-spatial-gene-expression-liver-gdvptd06wdcwck1j0000), [visium-spatial-gene-expression-liver-aozderatufdc5qc80000](/datasets/md/ea.md#visium-spatial-gene-expression-liver-aozderatufdc5qc80000), [visium-spatial-gene-expression-liver-8edq7cuh9asqketz0000](/datasets/md/1c.md#visium-spatial-gene-expression-liver-8edq7cuh9asqketz0000), [visium-spatial-gene-expression-liver-iynuuvve0djflkss0000](/datasets/md/21.md#visium-spatial-gene-expression-liver-iynuuvve0djflkss0000), [visium-spatial-gene-expression-liver-10kuojx7rvbovfwq0000](/datasets/md/92.md#visium-spatial-gene-expression-liver-10kuojx7rvbovfwq0000), [visium-spatial-gene-expression-liver-7duspy9el8rgcvm90000](/datasets/md/6b.md#visium-spatial-gene-expression-liver-7duspy9el8rgcvm90000), [visium-spatial-gene-expression-liver-vcmjrethazqrqiut0000](/datasets/md/59.md#visium-spatial-gene-expression-liver-vcmjrethazqrqiut0000), [visium-spatial-gene-expression-liver-1bo6fib3kbpf05ol0000](/datasets/md/a7.md#visium-spatial-gene-expression-liver-1bo6fib3kbpf05ol0000), [visium-spatial-gene-expression-liver-jxugg9ucr4bvf8xa0000](/datasets/md/7a.md#visium-spatial-gene-expression-liver-jxugg9ucr4bvf8xa0000), [visium-spatial-gene-expression-liver-ke2twoo6wumkeijm0000](/datasets/md/e4.md#visium-spatial-gene-expression-liver-ke2twoo6wumkeijm0000), [visium-spatial-gene-expression-liver-5bjbkdt5warx6alk0000](/datasets/md/38.md#visium-spatial-gene-expression-liver-5bjbkdt5warx6alk0000), [visium-spatial-gene-expression-liver-bnsqnr41hvk8okhr0000](/datasets/md/d4.md#visium-spatial-gene-expression-liver-bnsqnr41hvk8okhr0000), [visium-spatial-gene-expression-liver-1vr8o3q83oqnr06q0000](/datasets/md/d4.md#visium-spatial-gene-expression-liver-1vr8o3q83oqnr06q0000) ## Age-related epithelial defects limit thymic function and regeneration [visium] - Page: /collections/geo-gse240015/ - Kind: time course - Datasets: 2 - Reference: PMID:39112630 - Design: Spatial transcriptomic profiles of thymus from 2-month-old and 18-month-old mice at steady state (day 0; d0). - Members: [visium-spatial-gene-expression-thymus-ny4n35c87ax4xkxw0000](/datasets/md/ad.md#visium-spatial-gene-expression-thymus-ny4n35c87ax4xkxw0000), [visium-spatial-gene-expression-thymus-lvuir4qyvnubpu5z0000](/datasets/md/43.md#visium-spatial-gene-expression-thymus-lvuir4qyvnubpu5z0000) ## Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver - Page: /collections/geo-gse240429/ - Kind: other - Datasets: 4 - Reference: PMID:38199298 - Design: Spatial gene expression profiling by high throughput sequencing The submitter states that the sample C73-D1 has already been uploaded as GSM5616008 that was uploaded as part of GSE185477. The GSM7697871 (C73_D1_VISIUM) records were generated for the convenient retrieval of the complete raw data from SRA. - Members: [visium-spatial-gene-expression-liver-d8eanqnnvayvp7so0000](/datasets/md/7e.md#visium-spatial-gene-expression-liver-d8eanqnnvayvp7so0000), [visium-spatial-gene-expression-liver-t9jmrrlysmqsm0if0000](/datasets/md/87.md#visium-spatial-gene-expression-liver-t9jmrrlysmqsm0if0000), [visium-spatial-gene-expression-liver-uyi1eookadmsgrqi0000](/datasets/md/8c.md#visium-spatial-gene-expression-liver-uyi1eookadmsgrqi0000), [visium-spatial-gene-expression-liver-0er4pnvi60ysgbfw0001](/datasets/md/63.md#visium-spatial-gene-expression-liver-0er4pnvi60ysgbfw0001) ## Spatial deconvolution of tertiary lymphoid structure in human IPF lungs revealed novel CCL19-expressing mural cells - Page: /collections/geo-gse248082/ - Kind: comparison - Datasets: 14 - Reference: PMID:39978854 - Design: Nine human IPF tissues from different patients were used for spatial gene expression transcriptomics, including one fresh frozen sample and eight PPFE samples. - Members: [visium-spatial-gene-expression-lung-6jisvb3ufhgcxvmg0000](/datasets/md/3e.md#visium-spatial-gene-expression-lung-6jisvb3ufhgcxvmg0000), [visium-spatial-gene-expression-lung-9ekdqixele5tlclp0000](/datasets/md/13.md#visium-spatial-gene-expression-lung-9ekdqixele5tlclp0000), [visium-spatial-gene-expression-lung-qrdyadxg4argtvev0000](/datasets/md/6e.md#visium-spatial-gene-expression-lung-qrdyadxg4argtvev0000), [visium-spatial-gene-expression-lung-pglucguycmc4twwg0000](/datasets/md/7c.md#visium-spatial-gene-expression-lung-pglucguycmc4twwg0000), [visium-spatial-gene-expression-lung-pij79y7nshcnnuti0000](/datasets/md/2b.md#visium-spatial-gene-expression-lung-pij79y7nshcnnuti0000), [visium-spatial-gene-expression-lung-3tjlojxehxxonfxp0000](/datasets/md/c9.md#visium-spatial-gene-expression-lung-3tjlojxehxxonfxp0000), [visium-spatial-gene-expression-lung-p7cdvjoc8rrslx9k0000](/datasets/md/01.md#visium-spatial-gene-expression-lung-p7cdvjoc8rrslx9k0000), [visium-spatial-gene-expression-lung-ffypalitqlamavw60000](/datasets/md/bb.md#visium-spatial-gene-expression-lung-ffypalitqlamavw60000), [visium-spatial-gene-expression-lung-d7hdeyfojlo3jzku0000](/datasets/md/56.md#visium-spatial-gene-expression-lung-d7hdeyfojlo3jzku0000), [visium-spatial-gene-expression-lung-bzgnb2336ie6vclj0000](/datasets/md/09.md#visium-spatial-gene-expression-lung-bzgnb2336ie6vclj0000), [visium-spatial-gene-expression-lung-m9y0jpnqlm6oa8il0000](/datasets/md/cc.md#visium-spatial-gene-expression-lung-m9y0jpnqlm6oa8il0000), [visium-spatial-gene-expression-lung-g5oxfhxc00xufzrd0000](/datasets/md/a3.md#visium-spatial-gene-expression-lung-g5oxfhxc00xufzrd0000), [visium-spatial-gene-expression-lung-oz1y9ryjvsuyprgv0000](/datasets/md/10.md#visium-spatial-gene-expression-lung-oz1y9ryjvsuyprgv0000), [visium-spatial-gene-expression-lung-toswpvfjr9zgxbya0000](/datasets/md/e3.md#visium-spatial-gene-expression-lung-toswpvfjr9zgxbya0000) ## Systems-based identification of the Hippo pathway for promoting fibrotic mesenchymal differentiation in systemic sclerosis - Page: /collections/geo-gse249279/ - Kind: other - Datasets: 4 - Reference: PMID:38172207 - Design: Single cell RNA sequencing and spatial sequencing on human scleroderma skin tissues - Members: [visium-spatial-gene-expression-skin-of-body-o4du7wz76vkbi6as0000](/datasets/md/85.md#visium-spatial-gene-expression-skin-of-body-o4du7wz76vkbi6as0000), [visium-spatial-gene-expression-skin-of-body-czymhcw5kzyedwkb0000](/datasets/md/af.md#visium-spatial-gene-expression-skin-of-body-czymhcw5kzyedwkb0000), [visium-spatial-gene-expression-skin-of-body-km7y8x7yvf6rznuv0000](/datasets/md/eb.md#visium-spatial-gene-expression-skin-of-body-km7y8x7yvf6rznuv0000), [visium-spatial-gene-expression-skin-of-body-boczocdycz6pmlcx0000](/datasets/md/73.md#visium-spatial-gene-expression-skin-of-body-boczocdycz6pmlcx0000) ## A spatiotemporal molecular atlas of mouse spinal cord injury identifies a distinct astrocyte subpopulation and therapeutic potential of IGFBP2 - Page: /collections/geo-gse256397/ - Kind: comparison - Datasets: 16 - Reference: PMID:39029468 - Design: 64 spinal cord sections from 9 different C57BL/6J mice were sequenced using 10x Visium, including different position and timepoints. There were 4 distances of rostral (-) and the caudal (+) sections at ±0.5 and ±1.0 mm from the transection injury epicenter and four time points 0 (uninjured), 3, 24 and 72 hpi. Four consecutive cryosections of the same distance at each time points were attached to the same Visium Gene Expression slide. - Members: [visium-spatial-gene-expression-spinal-cord-w5ae7pnqcetocv650000](/datasets/md/92.md#visium-spatial-gene-expression-spinal-cord-w5ae7pnqcetocv650000), [visium-spatial-gene-expression-spinal-cord-hycm2el1c7pe2j7i0000](/datasets/md/3b.md#visium-spatial-gene-expression-spinal-cord-hycm2el1c7pe2j7i0000), [visium-spatial-gene-expression-spinal-cord-vunx01jybzgpmjrt0000](/datasets/md/5b.md#visium-spatial-gene-expression-spinal-cord-vunx01jybzgpmjrt0000), [visium-spatial-gene-expression-spinal-cord-92azjqtnxut49gwu0000](/datasets/md/6c.md#visium-spatial-gene-expression-spinal-cord-92azjqtnxut49gwu0000), [visium-spatial-gene-expression-spinal-cord-iyezb6xyrql0mgjd0000](/datasets/md/53.md#visium-spatial-gene-expression-spinal-cord-iyezb6xyrql0mgjd0000), [visium-spatial-gene-expression-spinal-cord-jiddxdkpkjsyautb0000](/datasets/md/66.md#visium-spatial-gene-expression-spinal-cord-jiddxdkpkjsyautb0000), [visium-spatial-gene-expression-spinal-cord-ki166efxasvpyqnj0000](/datasets/md/33.md#visium-spatial-gene-expression-spinal-cord-ki166efxasvpyqnj0000), [visium-spatial-gene-expression-spinal-cord-attvjrfolr0qejvt0000](/datasets/md/fc.md#visium-spatial-gene-expression-spinal-cord-attvjrfolr0qejvt0000), [visium-spatial-gene-expression-spinal-cord-r2plwmteqhdfn4w70000](/datasets/md/73.md#visium-spatial-gene-expression-spinal-cord-r2plwmteqhdfn4w70000), [visium-spatial-gene-expression-spinal-cord-csgog2gy7prio2jy0000](/datasets/md/9a.md#visium-spatial-gene-expression-spinal-cord-csgog2gy7prio2jy0000), [visium-spatial-gene-expression-spinal-cord-j0pi9ojjnmyvpynz0000](/datasets/md/02.md#visium-spatial-gene-expression-spinal-cord-j0pi9ojjnmyvpynz0000), [visium-spatial-gene-expression-spinal-cord-o0kikbnhvirmnjmn0000](/datasets/md/03.md#visium-spatial-gene-expression-spinal-cord-o0kikbnhvirmnjmn0000), [visium-spatial-gene-expression-spinal-cord-w7qxtwrmro1ysxw10000](/datasets/md/1f.md#visium-spatial-gene-expression-spinal-cord-w7qxtwrmro1ysxw10000), [visium-spatial-gene-expression-spinal-cord-itdmkhxlddlsglvf0000](/datasets/md/4a.md#visium-spatial-gene-expression-spinal-cord-itdmkhxlddlsglvf0000), [visium-spatial-gene-expression-spinal-cord-ahgyb736ejlv3pww0001](/datasets/md/d7.md#visium-spatial-gene-expression-spinal-cord-ahgyb736ejlv3pww0001), [visium-spatial-gene-expression-spinal-cord-yzx2nnttndvyggah0000](/datasets/md/31.md#visium-spatial-gene-expression-spinal-cord-yzx2nnttndvyggah0000) ## Glycolysis in hepatic stellate cells coordinates fibrogenic extracellular vesicle release in a spatial manner to amplify liver fibrosis - Page: /collections/geo-gse259363/ - Kind: comparison - Datasets: 2 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE259363 - Design: Four mouse liver samples from healthy, fibrotic, and fibrotic with intervention group were analyzed for spatial transcriptomics using Visium platform. We crossed HK2fl/fl with PDGFRBcreERT2 (The Jackson Laboratory B6.Cg-Tg(Pdgfrb-cre/ERT2)6096Rha/J) mice to obtain PDGFRBcreERT2/Hk2fl/fl mice and HK2fl/fl littermate controls. The genotype of mice S1, S2, and S4 is HK2fl/fl, the genotype of mouse S3 is PDGFRBcreERT2/Hk2fl/fl. All mice were administered with tamoxifen (75 mg/kg for 5 consecutive days). Mouse S1 was treated with olive oil while mice S2, S3, and S4 were treated with CCl4 twice a week for 6 weeks. - Members: [visium-spatial-gene-expression-liver-5f6yqbwxygy5tjly0000](/datasets/md/fb.md#visium-spatial-gene-expression-liver-5f6yqbwxygy5tjly0000), [visium-spatial-gene-expression-liver-yutnuooibf3sgqpu0000](/datasets/md/48.md#visium-spatial-gene-expression-liver-yutnuooibf3sgqpu0000) ## 10X Visium Spatial transcriptomics of small intestine from mice fed stearic acid-rich high fat diet (HFD) - Page: /collections/geo-gse277106/ - Kind: comparison - Datasets: 2 - Reference: PMID:41616823 - Design: Comparison of expression pfofiles between mice fed CD and stearic acid-rich HFD. - Members: [visium-spatial-gene-expression-small-intestine-s6yc0wuful8bfh5y0000](/datasets/md/45.md#visium-spatial-gene-expression-small-intestine-s6yc0wuful8bfh5y0000), [visium-spatial-gene-expression-small-intestine-7nanaxeehj6whicu0000](/datasets/md/f4.md#visium-spatial-gene-expression-small-intestine-7nanaxeehj6whicu0000) ## Multi-region spatial transcriptome analysis reveals cellular networks and pathways associated with hepatocellular carcinoma recurrence after surgical resection - Page: /collections/geo-gse281759/ - Kind: other - Datasets: 17 - Reference: PMID:41950768 - Design: we conducted a spatial transcriptomic analysis using visium technology from 10x genomics, on multiple sectors per primary tumour from patients with HCC treated with curative intent surgical resection who were without recurrence at 60 months after surgery (A009) and who had early tumour recurrences between 3.6 to 14.0 months (C008, B013, C004) .These patients were part of the PLANet 1.0 longitudinal cohort study and included both chronic viral hepatitis B-positive and-negative individuals. Where possible, as reference, we profiled adjacent non-tumour tissue (‘normal’). Each Primary tumour was sampled from 2-5 distinct regions, and at least one section per region was obtained for spatial transcriptomic analysis. In patient C004, we examined both primary and recurrent tumour sectors. - Members: [visium-spatial-gene-expression-liver-lbiq72ajkp7fhz800001](/datasets/md/8e.md#visium-spatial-gene-expression-liver-lbiq72ajkp7fhz800001), [visium-spatial-gene-expression-liver-jl4g9joy6onxhhso0000](/datasets/md/90.md#visium-spatial-gene-expression-liver-jl4g9joy6onxhhso0000), [visium-spatial-gene-expression-liver-xcov3mprsbk4etb50000](/datasets/md/bd.md#visium-spatial-gene-expression-liver-xcov3mprsbk4etb50000), [visium-spatial-gene-expression-liver-dh0hm1vcd1calqje0000](/datasets/md/ac.md#visium-spatial-gene-expression-liver-dh0hm1vcd1calqje0000), [visium-spatial-gene-expression-liver-wqn77zz1zaetf8ah0000](/datasets/md/f6.md#visium-spatial-gene-expression-liver-wqn77zz1zaetf8ah0000), [visium-spatial-gene-expression-liver-ceosqaylopcenxn20000](/datasets/md/5c.md#visium-spatial-gene-expression-liver-ceosqaylopcenxn20000), [visium-spatial-gene-expression-liver-rrsqniwtik3pny5s0000](/datasets/md/7d.md#visium-spatial-gene-expression-liver-rrsqniwtik3pny5s0000), [visium-spatial-gene-expression-liver-uthanvtjkkqqrgy60000](/datasets/md/5d.md#visium-spatial-gene-expression-liver-uthanvtjkkqqrgy60000), [visium-spatial-gene-expression-liver-ub9rp1fj5z5dappv0000](/datasets/md/d3.md#visium-spatial-gene-expression-liver-ub9rp1fj5z5dappv0000), [visium-spatial-gene-expression-liver-pr8orkajdmu2dlgf0000](/datasets/md/bf.md#visium-spatial-gene-expression-liver-pr8orkajdmu2dlgf0000), [visium-spatial-gene-expression-liver-bnzy1kdo1bfboozg0000](/datasets/md/6b.md#visium-spatial-gene-expression-liver-bnzy1kdo1bfboozg0000), [visium-spatial-gene-expression-liver-une5ozo9i1xou5f80000](/datasets/md/00.md#visium-spatial-gene-expression-liver-une5ozo9i1xou5f80000), [visium-spatial-gene-expression-liver-lupkss7rewkcfu0m0000](/datasets/md/46.md#visium-spatial-gene-expression-liver-lupkss7rewkcfu0m0000), [visium-spatial-gene-expression-liver-mwvdrynlbchccph60000](/datasets/md/74.md#visium-spatial-gene-expression-liver-mwvdrynlbchccph60000), [visium-spatial-gene-expression-liver-mjuivxisyj3nhzip0000](/datasets/md/23.md#visium-spatial-gene-expression-liver-mjuivxisyj3nhzip0000), [visium-spatial-gene-expression-liver-tn7xxkupbupqnc2p0000](/datasets/md/c1.md#visium-spatial-gene-expression-liver-tn7xxkupbupqnc2p0000), [visium-spatial-gene-expression-liver-pktyvj2emzkl3gg50000](/datasets/md/8d.md#visium-spatial-gene-expression-liver-pktyvj2emzkl3gg50000) ## Spatial transcriptomics identifies regional disruptions in brain rhythmic gene expression in a mouse model of Alzheimer’s disease - Page: /collections/geo-gse282203/ - Kind: time course - Datasets: 34 - Reference: PMID:41659563 - Design: Spatial transcriptomics on sagittal brain sections from APP23 transgenic and non-transgenic control mice, collected at four Zeitgeber time points (ZT0, ZT6, ZT12, ZT18) at either 7 or 14 months of age. - Members: [visium-spatial-gene-expression-brain-0ky35oeze07zvop60000](/datasets/md/8f.md#visium-spatial-gene-expression-brain-0ky35oeze07zvop60000), [visium-spatial-gene-expression-brain-nvgggnqlsoyipnmk0000](/datasets/md/9d.md#visium-spatial-gene-expression-brain-nvgggnqlsoyipnmk0000), [visium-spatial-gene-expression-brain-ehditphsboegbvho0000](/datasets/md/48.md#visium-spatial-gene-expression-brain-ehditphsboegbvho0000), [visium-spatial-gene-expression-brain-0n5gerg5mdr41lns0000](/datasets/md/e0.md#visium-spatial-gene-expression-brain-0n5gerg5mdr41lns0000), [visium-spatial-gene-expression-brain-7l6e7qw7exws5r680000](/datasets/md/1c.md#visium-spatial-gene-expression-brain-7l6e7qw7exws5r680000), [visium-spatial-gene-expression-brain-1yb4fcv9ksozpzbq0001](/datasets/md/67.md#visium-spatial-gene-expression-brain-1yb4fcv9ksozpzbq0001), [visium-spatial-gene-expression-brain-knheosxvz6jxqsmv0000](/datasets/md/83.md#visium-spatial-gene-expression-brain-knheosxvz6jxqsmv0000), [visium-spatial-gene-expression-brain-ijeqrlfeoxgexv1l0000](/datasets/md/4d.md#visium-spatial-gene-expression-brain-ijeqrlfeoxgexv1l0000), [visium-spatial-gene-expression-brain-ww36wklgu8cuqeni0000](/datasets/md/a1.md#visium-spatial-gene-expression-brain-ww36wklgu8cuqeni0000), [visium-spatial-gene-expression-brain-x3ucm9yg2rejnwnh0000](/datasets/md/86.md#visium-spatial-gene-expression-brain-x3ucm9yg2rejnwnh0000), [visium-spatial-gene-expression-brain-oldpgxmkwbfi9ro10000](/datasets/md/f8.md#visium-spatial-gene-expression-brain-oldpgxmkwbfi9ro10000), [visium-spatial-gene-expression-brain-r8nc6e9a2dm8kzgi0000](/datasets/md/22.md#visium-spatial-gene-expression-brain-r8nc6e9a2dm8kzgi0000), [visium-spatial-gene-expression-brain-efv0etkgxhizb6xl0000](/datasets/md/c0.md#visium-spatial-gene-expression-brain-efv0etkgxhizb6xl0000), [visium-spatial-gene-expression-brain-9qgyizkyfu6cavzw0000](/datasets/md/18.md#visium-spatial-gene-expression-brain-9qgyizkyfu6cavzw0000), [visium-spatial-gene-expression-brain-bamqgdcqnomyyz8y0000](/datasets/md/c6.md#visium-spatial-gene-expression-brain-bamqgdcqnomyyz8y0000), [visium-spatial-gene-expression-brain-deoz0duzzmbq5bjs0000](/datasets/md/65.md#visium-spatial-gene-expression-brain-deoz0duzzmbq5bjs0000), [visium-spatial-gene-expression-brain-fhtdiasilcp9dozo0000](/datasets/md/51.md#visium-spatial-gene-expression-brain-fhtdiasilcp9dozo0000), [visium-spatial-gene-expression-brain-entrwsdbnqcyztn60000](/datasets/md/e3.md#visium-spatial-gene-expression-brain-entrwsdbnqcyztn60000), [visium-spatial-gene-expression-brain-nvoxnpqo1k9scjda0000](/datasets/md/a8.md#visium-spatial-gene-expression-brain-nvoxnpqo1k9scjda0000), [visium-spatial-gene-expression-brain-juanavnk3vuzdmxe0000](/datasets/md/5f.md#visium-spatial-gene-expression-brain-juanavnk3vuzdmxe0000), [visium-spatial-gene-expression-brain-dknt1nmuafpqyb7u0000](/datasets/md/01.md#visium-spatial-gene-expression-brain-dknt1nmuafpqyb7u0000), [visium-spatial-gene-expression-brain-qbdbiku3qnywqmws0000](/datasets/md/e8.md#visium-spatial-gene-expression-brain-qbdbiku3qnywqmws0000), [visium-spatial-gene-expression-brain-xcs7tolmajnilvmn0000](/datasets/md/f3.md#visium-spatial-gene-expression-brain-xcs7tolmajnilvmn0000), [visium-spatial-gene-expression-brain-gyi5ditpkguuqoji0000](/datasets/md/d5.md#visium-spatial-gene-expression-brain-gyi5ditpkguuqoji0000), [visium-spatial-gene-expression-brain-gribwrtbwtpigu9d0000](/datasets/md/0d.md#visium-spatial-gene-expression-brain-gribwrtbwtpigu9d0000), [visium-spatial-gene-expression-brain-trc0fayqh3prfvpf0000](/datasets/md/16.md#visium-spatial-gene-expression-brain-trc0fayqh3prfvpf0000), [visium-spatial-gene-expression-brain-vhf31cfu1wkrow2v0000](/datasets/md/82.md#visium-spatial-gene-expression-brain-vhf31cfu1wkrow2v0000), [visium-spatial-gene-expression-brain-tpv25rnd5v4t9pnx0000](/datasets/md/a4.md#visium-spatial-gene-expression-brain-tpv25rnd5v4t9pnx0000), [visium-spatial-gene-expression-brain-bazqwkfiechennos0000](/datasets/md/0b.md#visium-spatial-gene-expression-brain-bazqwkfiechennos0000), [visium-spatial-gene-expression-brain-fknzvjc8qqhrda7t0000](/datasets/md/38.md#visium-spatial-gene-expression-brain-fknzvjc8qqhrda7t0000), [visium-spatial-gene-expression-brain-g5jm5iehkruk0fn60000](/datasets/md/80.md#visium-spatial-gene-expression-brain-g5jm5iehkruk0fn60000), [visium-spatial-gene-expression-brain-et7tcqdarpgnfuvk0000](/datasets/md/b5.md#visium-spatial-gene-expression-brain-et7tcqdarpgnfuvk0000), [visium-spatial-gene-expression-brain-mnhluagq1v9pkhur0000](/datasets/md/8f.md#visium-spatial-gene-expression-brain-mnhluagq1v9pkhur0000), [visium-spatial-gene-expression-brain-kazqx1l3g0u2u2cj0000](/datasets/md/cb.md#visium-spatial-gene-expression-brain-kazqx1l3g0u2u2cj0000) ## CDK12/13 inactivation triggers STING-mediated antitumor immunity in preclinical models. - Page: /collections/geo-gse283227/ - Kind: comparison - Datasets: 4 - Reference: 10.1172/JCI193745 - Design: Two CDK12-mutant and two CDK12 wildtype metastatic prostate cancer samples were subjected to spatial transcriptomics analysis to evaluate genes that were differently expressed in CDK12 mutant samples compared to the wildtype. - Members: [visium-hd-urinary-bladder-8lkpkvijvrikzxud0000](/datasets/md/7d.md#visium-hd-urinary-bladder-8lkpkvijvrikzxud0000), [visium-hd-lymph-node-xocpl93ypx5zn2dd0002](/datasets/md/ae.md#visium-hd-lymph-node-xocpl93ypx5zn2dd0002), [visium-hd-lymph-node-hiyzmru5lldcansz0002](/datasets/md/4c.md#visium-hd-lymph-node-hiyzmru5lldcansz0002), [visium-hd-lymph-node-hvb0tlwt4ecs2tri0002](/datasets/md/c5.md#visium-hd-lymph-node-hvb0tlwt4ecs2tri0002) ## Spatial transcriptomics of the human first trimester decidua - Page: /collections/geo-gse301306/ - Kind: comparison - Datasets: 4 - Reference: PMID:42248577 - Design: To investigate the spatial organization of the human decidua, we applied spatial transcriptomics using the Visium platform (10x Genomics) to four tissue sections. Experimental design: matched samples from both the first trimester decidua basalis and decidua parietalis of two independent donors. - Members: [visium-spatial-gene-expression-decidua-basalis-3na1zndwzwzdo23m0000](/datasets/md/db.md#visium-spatial-gene-expression-decidua-basalis-3na1zndwzwzdo23m0000), [visium-spatial-gene-expression-decidua-parietalis-v83jafcdi70tdwiu0000](/datasets/md/76.md#visium-spatial-gene-expression-decidua-parietalis-v83jafcdi70tdwiu0000), [visium-spatial-gene-expression-decidua-parietalis-ld9pyx8as2g1pozq0000](/datasets/md/82.md#visium-spatial-gene-expression-decidua-parietalis-ld9pyx8as2g1pozq0000), [visium-spatial-gene-expression-decidua-basalis-lxm32yqwrn8b5szp0000](/datasets/md/75.md#visium-spatial-gene-expression-decidua-basalis-lxm32yqwrn8b5szp0000) ## Spatial Gene Expression of Human Coronary Arteries Revealed the Molecular Features of Diffuse Intimal Thickening in Explanted Hearts - Page: /collections/geo-gse283269/ - Kind: other - Datasets: 6 - Reference: PMID:40076574 - Design: With six coronary artery samples (three from autopsies, three from freshly explanted hearts) from formalin-fixed paraffin-embedded (FFPE) tissue sections, Visium was used to obtain whole transcriptome profiles of the intimal and medial layers of these blood vessels. Post Visium-sequencing, one sample (Sample2d1) was removed from downstream analysis as it failed to pass our quality control. - Members: [visium-spatial-gene-expression-coronary-artery-h5hx1tnclrweogyi0000](/datasets/md/ec.md#visium-spatial-gene-expression-coronary-artery-h5hx1tnclrweogyi0000), [visium-spatial-gene-expression-coronary-artery-sh2kuent3ecukqpp0000](/datasets/md/11.md#visium-spatial-gene-expression-coronary-artery-sh2kuent3ecukqpp0000), [visium-spatial-gene-expression-coronary-artery-04cpye1550qpuili0000](/datasets/md/e9.md#visium-spatial-gene-expression-coronary-artery-04cpye1550qpuili0000), [visium-spatial-gene-expression-coronary-artery-dosk20km0b4vzft60000](/datasets/md/60.md#visium-spatial-gene-expression-coronary-artery-dosk20km0b4vzft60000), [visium-spatial-gene-expression-coronary-artery-hkanchbuuge2cz7g0000](/datasets/md/52.md#visium-spatial-gene-expression-coronary-artery-hkanchbuuge2cz7g0000), [visium-spatial-gene-expression-coronary-artery-4ahdjbrw4tobinmf0000](/datasets/md/62.md#visium-spatial-gene-expression-coronary-artery-4ahdjbrw4tobinmf0000) ## Spatially resolved chimeric analysis reveals extracellular CKB-mediated ATP uptake at the glioma-astrocyte invasive front - Page: /collections/geo-gse283959/ - Kind: other - Datasets: 4 - Reference: PMID:40991701 - Design: We generated and analyzed spatially resolved RNA profiles in two GBM models: a GSC xenograft model and a TP53, NF1, and PTEN (TNP)-inactivated human neural stem cell-derived model. This approach enabled us to dissect tumor and tumor microenvironment (TME) interactions across spatial contexts. - Members: [visium-spatial-gene-expression-brain-3v5qy19gfj1xa0wc0000](/datasets/md/1e.md#visium-spatial-gene-expression-brain-3v5qy19gfj1xa0wc0000), [visium-spatial-gene-expression-brain-tbq7dhafwpe2etsz0000](/datasets/md/f6.md#visium-spatial-gene-expression-brain-tbq7dhafwpe2etsz0000), [visium-spatial-gene-expression-brain-vzm4l5hebk41g0850000](/datasets/md/8f.md#visium-spatial-gene-expression-brain-vzm4l5hebk41g0850000), [visium-spatial-gene-expression-brain-6cxrwlghsl1tzemd0000](/datasets/md/60.md#visium-spatial-gene-expression-brain-6cxrwlghsl1tzemd0000) ## Multi-omics analysis identifies erythroid cells as the major population in mouse placentas expressing the MHC class II antigen presentation, chemokine, and antibacterial immune response genes [Spatial Transcriptomics] - Page: /collections/geo-gse289170/ - Kind: other - Datasets: 3 - Reference: PMID:41058694 - Design: We collected murine placentas at E12.5 from both syngeneic and semi-allogenic pregnancies, froze them in OCT, cut 10mm sections, placed them on a cryoslide, and performed 10X Genomics Visium CytAssist spacial transcriptomic analysis. - Members: [visium-spatial-gene-expression-placenta-yrk23zyvyhpfsn290000](/datasets/md/c3.md#visium-spatial-gene-expression-placenta-yrk23zyvyhpfsn290000), [visium-spatial-gene-expression-placenta-654wrvv7ldj4f31g0000](/datasets/md/42.md#visium-spatial-gene-expression-placenta-654wrvv7ldj4f31g0000), [visium-spatial-gene-expression-placenta-uasgon9myi6axdjr0000](/datasets/md/89.md#visium-spatial-gene-expression-placenta-uasgon9myi6axdjr0000) ## CITEgeist: Cellular Indexing of Transcriptomes and Epitopes for Guided Exploration of Intrinsic Spatial Trends - Page: /collections/geo-gse289326/ - Kind: comparison - Datasets: 14 - Reference: PMID:41854411 - Design: 12 breast cancer samples from 6 patients (pre-endocrine therapy biopsy samples and matched post-primary-endocrine therapy surgical samples) were used for analysis - Members: [visium-spatial-gene-expression-breast-ylgvrbrjqdcqxlc10000](/datasets/md/b0.md#visium-spatial-gene-expression-breast-ylgvrbrjqdcqxlc10000), [visium-spatial-gene-expression-breast-dldcqjyzwjmfwblm0000](/datasets/md/98.md#visium-spatial-gene-expression-breast-dldcqjyzwjmfwblm0000), [visium-spatial-gene-expression-breast-untmum53qk9bbbqj0000](/datasets/md/4a.md#visium-spatial-gene-expression-breast-untmum53qk9bbbqj0000), [visium-spatial-gene-expression-breast-zijhf2uoqyuhfrw50000](/datasets/md/64.md#visium-spatial-gene-expression-breast-zijhf2uoqyuhfrw50000), [visium-spatial-gene-expression-breast-j9frdfa3wguh2ufp0000](/datasets/md/fb.md#visium-spatial-gene-expression-breast-j9frdfa3wguh2ufp0000), [visium-spatial-gene-expression-breast-wu9plyjmqv7jrb2s0000](/datasets/md/62.md#visium-spatial-gene-expression-breast-wu9plyjmqv7jrb2s0000), [visium-spatial-gene-expression-breast-bszs13nwt4mqaqfk0000](/datasets/md/68.md#visium-spatial-gene-expression-breast-bszs13nwt4mqaqfk0000), [visium-spatial-gene-expression-breast-w8pvgesyhnmluw6e0000](/datasets/md/d0.md#visium-spatial-gene-expression-breast-w8pvgesyhnmluw6e0000), [visium-spatial-gene-expression-breast-y7l6g2vrksw8zkgx0000](/datasets/md/95.md#visium-spatial-gene-expression-breast-y7l6g2vrksw8zkgx0000), [visium-spatial-gene-expression-breast-zmso18frfdgzsibv0000](/datasets/md/0b.md#visium-spatial-gene-expression-breast-zmso18frfdgzsibv0000), [visium-spatial-gene-expression-breast-lekacjiqo6g46vsd0000](/datasets/md/83.md#visium-spatial-gene-expression-breast-lekacjiqo6g46vsd0000), [visium-spatial-gene-expression-breast-refcdwmsxagorl5m0000](/datasets/md/41.md#visium-spatial-gene-expression-breast-refcdwmsxagorl5m0000), [visium-spatial-gene-expression-breast-mczkdlcaffa5shdp0000](/datasets/md/65.md#visium-spatial-gene-expression-breast-mczkdlcaffa5shdp0000), [visium-spatial-gene-expression-breast-uzemuuh0g8ogpt8y0000](/datasets/md/08.md#visium-spatial-gene-expression-breast-uzemuuh0g8ogpt8y0000) ## Glioma-neuronal circuit remodeling induces regional immunosuppression [visium] - Page: /collections/geo-gse289934/ - Kind: other - Datasets: 2 - Reference: PMID:40404658 - Design: Visium Spatial Transcriptomics: Mice (n = 2) intracranially inoculated with the SB28 glioma cell line were euthanized at day 20–22. Brain tissue was harvested, FFPE-embedded, and analyzed using Visium spatial transcriptomic analysis. - Members: [visium-spatial-gene-expression-brain-0ykbv6ktgm7bwsaf0000](/datasets/md/16.md#visium-spatial-gene-expression-brain-0ykbv6ktgm7bwsaf0000), [visium-spatial-gene-expression-brain-28vfdfapmwxnhosv0000](/datasets/md/09.md#visium-spatial-gene-expression-brain-28vfdfapmwxnhosv0000) ## Mouse uterine gene expressions during decidual processes [Visium] - Page: /collections/geo-gse296581/ - Kind: comparison - Datasets: 4 - Reference: PMID:42154563 - Design: The day when the vaginal plug was detected was considered day 1 of pregnancy. Pregnant mice were euthanized by cervical dislocation on designated days of pregnancy for the evaluation of pregnancy phenotypes and sample collection. On day 4, one uterine horn was flushed with saline to confirm the presence of blastocysts. Embryo attachment sites were observed as blue bands soon after intravenous injection of 1% solution of Chicago blue dye (Sigma-Aldrich) in saline on day6. Collected tissues were snap-frozen. For scRNA-seq, frozen tessues were processed by gentleMACS for sample preparation at Takara Bio. The barcoded RNAs were subjected to RNA-sequencing using NovaSeq 6000. For 10x Visium analyses, frozen sections (10 μm) from control or TAZ-uKO were mounted on gene expression slides and sent to KOTAI Biotechnologies for subsequent procedures. After reaction with Proteinase K for 40 min, the sections were hybridized with spatial tags on the slides and reverse-transcribed in situ. The synthesized cDNAs were subjected to RNA-sequencing using DNBseq (MGI), producing 300 million reads/sample. - Members: [visium-spatial-gene-expression-uterus-n8d1dhpflzncde230000](/datasets/md/3e.md#visium-spatial-gene-expression-uterus-n8d1dhpflzncde230000), [visium-spatial-gene-expression-uterus-yap3yzx8pxvzldzz0000](/datasets/md/85.md#visium-spatial-gene-expression-uterus-yap3yzx8pxvzldzz0000), [visium-spatial-gene-expression-uterus-xvqfmb4ouwladbhh0000](/datasets/md/74.md#visium-spatial-gene-expression-uterus-xvqfmb4ouwladbhh0000), [visium-spatial-gene-expression-uterus-4jgsdw843cva5xdc0000](/datasets/md/b2.md#visium-spatial-gene-expression-uterus-4jgsdw843cva5xdc0000) ## Spatial analyses of early, untreated SSc skin identify a proinflammatory vascular niche of macrophage-fibroblast signaling - Page: /collections/geo-gse312932/ - Kind: other - Datasets: 10 - Reference: PMID:41411065 - Design: 10 samples - Members: [10x-xenium-zone-of-skin-7skwmohcm6kgalax0000](/datasets/md/3a.md#10x-xenium-zone-of-skin-7skwmohcm6kgalax0000), [10x-xenium-zone-of-skin-dm9gdcr3p4auihrb0000](/datasets/md/03.md#10x-xenium-zone-of-skin-dm9gdcr3p4auihrb0000), [10x-xenium-zone-of-skin-rvomcstjyipzwaeu0000](/datasets/md/10.md#10x-xenium-zone-of-skin-rvomcstjyipzwaeu0000), [10x-xenium-zone-of-skin-5jdwblfogimfvn540000](/datasets/md/4f.md#10x-xenium-zone-of-skin-5jdwblfogimfvn540000), [10x-xenium-zone-of-skin-kjmvupe8qcmsxstz0000](/datasets/md/cb.md#10x-xenium-zone-of-skin-kjmvupe8qcmsxstz0000), [10x-xenium-zone-of-skin-exllorhiifvxyuy70000](/datasets/md/fa.md#10x-xenium-zone-of-skin-exllorhiifvxyuy70000), [10x-xenium-zone-of-skin-jncpuq99qowym2yf0000](/datasets/md/62.md#10x-xenium-zone-of-skin-jncpuq99qowym2yf0000), [10x-xenium-zone-of-skin-axrbl1y4qcsj8rv70000](/datasets/md/99.md#10x-xenium-zone-of-skin-axrbl1y4qcsj8rv70000), [10x-xenium-zone-of-skin-2bdutsdvxhcxakil0000](/datasets/md/1f.md#10x-xenium-zone-of-skin-2bdutsdvxhcxakil0000), [10x-xenium-zone-of-skin-aiqzqitspgyiqpjj0000](/datasets/md/bc.md#10x-xenium-zone-of-skin-aiqzqitspgyiqpjj0000) ## Adult Mouse Controlled Cortical Impact Visium Spatial Transcriptomics - Page: /collections/geo-gse313407/ - Kind: time course - Datasets: 34 - Reference: PMID:41250842 - Design: Visium (10X Genomics) spatial transcriptiomics prolfiling of the contused left hemisphere of the forebrains of mice given a single controlled cortical impact (CCI). Coronal sections at the focal point of contusion (at the level of the anterior commissure) were profiled from 15-20 weeks-old C57BL/6J mice given a CCI or Sham surgery (no craniectomy or impact). Experiment 1: CCI versus Sham mice at 2 days post-injury (DPI) and 7 DPI. Experiment 2: CCI mice treated with anti-GR-1 antibodies (to deplete circulating neutrophils and monocytes) versus CCI mice treated with control antibodies at 2 DPI and 7 DPI. - Members: [visium-spatial-gene-expression-brain-fpitmpgglfpuffa40001](/datasets/md/1f.md#visium-spatial-gene-expression-brain-fpitmpgglfpuffa40001), [visium-spatial-gene-expression-brain-7m7uuybejvgf6cyi0000](/datasets/md/ab.md#visium-spatial-gene-expression-brain-7m7uuybejvgf6cyi0000), [visium-spatial-gene-expression-brain-puwafyld3j3tpciz0000](/datasets/md/c9.md#visium-spatial-gene-expression-brain-puwafyld3j3tpciz0000), [visium-spatial-gene-expression-brain-zvfnzdex0k95glxw0000](/datasets/md/93.md#visium-spatial-gene-expression-brain-zvfnzdex0k95glxw0000), [visium-spatial-gene-expression-brain-irklqu3dkykmmhvo0000](/datasets/md/28.md#visium-spatial-gene-expression-brain-irklqu3dkykmmhvo0000), [visium-spatial-gene-expression-brain-mondsh5zq1lc3aet0000](/datasets/md/77.md#visium-spatial-gene-expression-brain-mondsh5zq1lc3aet0000), [visium-spatial-gene-expression-brain-low4bllewvqk6w9x0000](/datasets/md/a9.md#visium-spatial-gene-expression-brain-low4bllewvqk6w9x0000), [visium-spatial-gene-expression-brain-cqnrlrcox8j5mhzb0000](/datasets/md/3b.md#visium-spatial-gene-expression-brain-cqnrlrcox8j5mhzb0000), [visium-spatial-gene-expression-brain-hercacfmnzhdfrii0000](/datasets/md/5f.md#visium-spatial-gene-expression-brain-hercacfmnzhdfrii0000), [visium-spatial-gene-expression-brain-hth0wtctp8uqaxoy0000](/datasets/md/01.md#visium-spatial-gene-expression-brain-hth0wtctp8uqaxoy0000), [visium-spatial-gene-expression-brain-npge43djnhowdqqb0000](/datasets/md/a9.md#visium-spatial-gene-expression-brain-npge43djnhowdqqb0000), [visium-spatial-gene-expression-brain-oiykmlaztiud0oue0000](/datasets/md/31.md#visium-spatial-gene-expression-brain-oiykmlaztiud0oue0000), [visium-spatial-gene-expression-brain-jqcy69trsx5djoy30000](/datasets/md/53.md#visium-spatial-gene-expression-brain-jqcy69trsx5djoy30000), [visium-spatial-gene-expression-brain-bt1hr0wo3zqkh5sn0000](/datasets/md/d6.md#visium-spatial-gene-expression-brain-bt1hr0wo3zqkh5sn0000), [visium-spatial-gene-expression-brain-erqbinci6h5bnaib0000](/datasets/md/17.md#visium-spatial-gene-expression-brain-erqbinci6h5bnaib0000), [visium-spatial-gene-expression-brain-q2uluqcymblmjkeu0000](/datasets/md/93.md#visium-spatial-gene-expression-brain-q2uluqcymblmjkeu0000), [visium-spatial-gene-expression-brain-wk9rxjv5ke08vg0x0000](/datasets/md/f0.md#visium-spatial-gene-expression-brain-wk9rxjv5ke08vg0x0000), [visium-spatial-gene-expression-brain-bk6abzewatdc9a300000](/datasets/md/1c.md#visium-spatial-gene-expression-brain-bk6abzewatdc9a300000), [visium-spatial-gene-expression-brain-9xzpuvkbmywvunhe0000](/datasets/md/17.md#visium-spatial-gene-expression-brain-9xzpuvkbmywvunhe0000), [visium-spatial-gene-expression-brain-bbme4hqjifsrzvch0000](/datasets/md/e7.md#visium-spatial-gene-expression-brain-bbme4hqjifsrzvch0000), [visium-spatial-gene-expression-brain-q57toqwwdgfoalge0000](/datasets/md/d0.md#visium-spatial-gene-expression-brain-q57toqwwdgfoalge0000), [visium-spatial-gene-expression-brain-lvbdbfb267ycbcvb0000](/datasets/md/45.md#visium-spatial-gene-expression-brain-lvbdbfb267ycbcvb0000), [visium-spatial-gene-expression-brain-qjlvboxshovquo3w0000](/datasets/md/94.md#visium-spatial-gene-expression-brain-qjlvboxshovquo3w0000), [visium-spatial-gene-expression-brain-whtw2boe5nmhlbhj0000](/datasets/md/22.md#visium-spatial-gene-expression-brain-whtw2boe5nmhlbhj0000), [visium-spatial-gene-expression-brain-hohcqtfi2yh71lsy0000](/datasets/md/b7.md#visium-spatial-gene-expression-brain-hohcqtfi2yh71lsy0000), [visium-spatial-gene-expression-brain-5lddwbqwrwufle0p0000](/datasets/md/6a.md#visium-spatial-gene-expression-brain-5lddwbqwrwufle0p0000), [visium-spatial-gene-expression-brain-wvejqthlymtsytqw0000](/datasets/md/c4.md#visium-spatial-gene-expression-brain-wvejqthlymtsytqw0000), [visium-spatial-gene-expression-brain-f5jvhr3ccakdbiju0000](/datasets/md/88.md#visium-spatial-gene-expression-brain-f5jvhr3ccakdbiju0000), [visium-spatial-gene-expression-brain-qssk7vs7kzzcdb9v0000](/datasets/md/0c.md#visium-spatial-gene-expression-brain-qssk7vs7kzzcdb9v0000), [visium-spatial-gene-expression-brain-ss25ggpdal1nkx5w0000](/datasets/md/31.md#visium-spatial-gene-expression-brain-ss25ggpdal1nkx5w0000), [visium-spatial-gene-expression-brain-sxvb6r9ipsbvm7pw0000](/datasets/md/f0.md#visium-spatial-gene-expression-brain-sxvb6r9ipsbvm7pw0000), [visium-spatial-gene-expression-brain-g5qzmfbbfzsumi2k0000](/datasets/md/c1.md#visium-spatial-gene-expression-brain-g5qzmfbbfzsumi2k0000), [visium-spatial-gene-expression-brain-wfg2ypvsyabuk2mo0000](/datasets/md/4e.md#visium-spatial-gene-expression-brain-wfg2ypvsyabuk2mo0000), [visium-spatial-gene-expression-brain-pspj21elgvyenhiv0000](/datasets/md/e6.md#visium-spatial-gene-expression-brain-pspj21elgvyenhiv0000) ## Single-cell multiomic approaches define a gradual, spatially-regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells [Xenium] - Page: /collections/geo-gse318202/ - Kind: comparison - Datasets: 10 - Reference: PMID:42314674 - Design: Xenium multiplexed in situ hybridization was performed on coronal sections across perinatal timepoints (E15, E18, P2) in order to study the dorsal ventricular-subventricular zone. - Members: [10x-xenium-brain-t9q8m47lh79elptl0000](/datasets/md/ba.md#10x-xenium-brain-t9q8m47lh79elptl0000), [10x-xenium-brain-a2sdchwafb0dcaed0000](/datasets/md/79.md#10x-xenium-brain-a2sdchwafb0dcaed0000), [10x-xenium-brain-lkkacora6z0tyj9e0000](/datasets/md/36.md#10x-xenium-brain-lkkacora6z0tyj9e0000), [10x-xenium-brain-fgamquwesjgi0t3g0000](/datasets/md/87.md#10x-xenium-brain-fgamquwesjgi0t3g0000), [10x-xenium-brain-pquo8vanoik7ybyp0000](/datasets/md/a0.md#10x-xenium-brain-pquo8vanoik7ybyp0000), [10x-xenium-brain-fhnqulqutgvmfhax0000](/datasets/md/8d.md#10x-xenium-brain-fhnqulqutgvmfhax0000), [10x-xenium-brain-5tzhc2y8jokryu9p0000](/datasets/md/41.md#10x-xenium-brain-5tzhc2y8jokryu9p0000), [10x-xenium-brain-aoegu8c28cvs8if10000](/datasets/md/39.md#10x-xenium-brain-aoegu8c28cvs8if10000), [10x-xenium-brain-wjofdi4qqqslm6mj0000](/datasets/md/84.md#10x-xenium-brain-wjofdi4qqqslm6mj0000), [10x-xenium-brain-gro0sdq1nppnday50000](/datasets/md/e1.md#10x-xenium-brain-gro0sdq1nppnday50000) ## Mapping the spatial architecture of glioblastoma from core to edge delineates niche-specific tumor cell states and intercellular interactions [Spatial Transcriptomics] - Page: /collections/geo-gse318562/ - Kind: other - Datasets: 22 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE318562 - Design: We used the Visium V1 platform to survey the spatial landscape of 22 samples along the edge-core axis of nine patients with primary isocitrate dehydrogenase (IDH) wildtype (WT) GBM, and the Xenium platform to analyze nine samples from six patients with primary IDHWT GBM. Each sample was preserved in OCT or FFPE, stained with H&E, and analyzed using the Visium V1 spatial transcriptomic platform. We then used two independent approaches to complement the core and edge designations established intraoperatively. First, we incorporated histopathologic tumor core and edge designations made by a board-certified neuropathologist (S.D.). These were consistent with those based on 5-ALA fluorescence, MRI, and surgical evaluation, but indicated that most samples - even those from the tumor edge - contained some regions of high tumor cell density. Within each sample, manual histologic annotation indicated regions of high tumor cell density (consistent with tumor “core”), low tumor cell density (infiltrative tumor “edge”), microvascular proliferation (MVP), palisading necrosis, predominantly non-malignant white matter, and predominantly non-malignant gray matter. - Members: [visium-spatial-gene-expression-brain-utlkgw42swaiznsi0000](/datasets/md/0d.md#visium-spatial-gene-expression-brain-utlkgw42swaiznsi0000), [visium-spatial-gene-expression-brain-jkeyxj1u2kajy5yg0000](/datasets/md/99.md#visium-spatial-gene-expression-brain-jkeyxj1u2kajy5yg0000), [visium-spatial-gene-expression-brain-hhkczlwtamlbjcyw0000](/datasets/md/5c.md#visium-spatial-gene-expression-brain-hhkczlwtamlbjcyw0000), [visium-spatial-gene-expression-brain-zobmvktkzpsrbi5y0000](/datasets/md/ab.md#visium-spatial-gene-expression-brain-zobmvktkzpsrbi5y0000), [visium-spatial-gene-expression-brain-sxgz4fd202r6afdq0000](/datasets/md/b3.md#visium-spatial-gene-expression-brain-sxgz4fd202r6afdq0000), [visium-spatial-gene-expression-brain-vmopkdr32m5tvxlx0000](/datasets/md/85.md#visium-spatial-gene-expression-brain-vmopkdr32m5tvxlx0000), [visium-spatial-gene-expression-brain-cdb2axjxnf0vea7d0000](/datasets/md/6f.md#visium-spatial-gene-expression-brain-cdb2axjxnf0vea7d0000), [visium-spatial-gene-expression-brain-zfbkf4ahlpxscjdz0000](/datasets/md/44.md#visium-spatial-gene-expression-brain-zfbkf4ahlpxscjdz0000), [visium-spatial-gene-expression-brain-kz6texnhccnk5a5w0000](/datasets/md/05.md#visium-spatial-gene-expression-brain-kz6texnhccnk5a5w0000), [visium-spatial-gene-expression-brain-8mgpnxoqqdq5xzow0000](/datasets/md/21.md#visium-spatial-gene-expression-brain-8mgpnxoqqdq5xzow0000), [visium-spatial-gene-expression-brain-v72zow9rqeuqa8zv0000](/datasets/md/d7.md#visium-spatial-gene-expression-brain-v72zow9rqeuqa8zv0000), [visium-spatial-gene-expression-brain-y9uhyntlefnslbmm0000](/datasets/md/96.md#visium-spatial-gene-expression-brain-y9uhyntlefnslbmm0000), [visium-spatial-gene-expression-brain-rkye9wx00papgmnf0000](/datasets/md/06.md#visium-spatial-gene-expression-brain-rkye9wx00papgmnf0000), [visium-spatial-gene-expression-brain-jzxd9a9a23o6ri5k0000](/datasets/md/25.md#visium-spatial-gene-expression-brain-jzxd9a9a23o6ri5k0000), [visium-spatial-gene-expression-brain-mu7zq5pl1xcmc3v80000](/datasets/md/38.md#visium-spatial-gene-expression-brain-mu7zq5pl1xcmc3v80000), [visium-spatial-gene-expression-brain-s0r98yj00w8ynow10000](/datasets/md/e4.md#visium-spatial-gene-expression-brain-s0r98yj00w8ynow10000), [visium-spatial-gene-expression-brain-q0gbdjyqk80diryq0000](/datasets/md/29.md#visium-spatial-gene-expression-brain-q0gbdjyqk80diryq0000), [visium-spatial-gene-expression-brain-l1ejxrsmcfuxhamc0000](/datasets/md/64.md#visium-spatial-gene-expression-brain-l1ejxrsmcfuxhamc0000), [visium-spatial-gene-expression-brain-wsh6pn2typzvpxg40000](/datasets/md/a3.md#visium-spatial-gene-expression-brain-wsh6pn2typzvpxg40000), [visium-spatial-gene-expression-brain-ornjann0xay3awpp0000](/datasets/md/c3.md#visium-spatial-gene-expression-brain-ornjann0xay3awpp0000), [visium-spatial-gene-expression-brain-xiezromo9xylfu420000](/datasets/md/42.md#visium-spatial-gene-expression-brain-xiezromo9xylfu420000), [visium-spatial-gene-expression-brain-ezydn1onajqrnzpw0000](/datasets/md/b5.md#visium-spatial-gene-expression-brain-ezydn1onajqrnzpw0000) ## Vascular STING activation facilitates NK cell anti-tumor immunity in small cell lung cancer [Spatial_Transcriptome] - Page: /collections/geo-gse318867/ - Kind: other - Datasets: 3 - Reference: PMID:41791380 - Design: Spatial transcriptomics of SCLC patient samples from FFPE tissues (Visium platform) - Members: [visium-spatial-gene-expression-lung-ssgqrlrwfobfude80000](/datasets/md/61.md#visium-spatial-gene-expression-lung-ssgqrlrwfobfude80000), [visium-spatial-gene-expression-lung-iu4da3ynxydahhw40000](/datasets/md/34.md#visium-spatial-gene-expression-lung-iu4da3ynxydahhw40000), [visium-spatial-gene-expression-lung-xqvyvmg3vc5dre460000](/datasets/md/24.md#visium-spatial-gene-expression-lung-xqvyvmg3vc5dre460000) ## Spatial Transcriptomic Activity Atlas of Spinal Sympathetic Neurons Delineates Neural Control of Lipolysis - Page: /collections/geo-gse336196/ - Kind: comparison - Datasets: 10 - Design: 6 slides containing 18 samples (three from RT/saline, Cold, and 2-DG group, for both sexes) were analyzed with Xenium to capture RNA. - Members: [10x-xenium-spinal-cord-1ucxwmlsmmvtvknw0000](/datasets/md/59.md#10x-xenium-spinal-cord-1ucxwmlsmmvtvknw0000), [10x-xenium-spinal-cord-skzshcdz3fip213j0000](/datasets/md/82.md#10x-xenium-spinal-cord-skzshcdz3fip213j0000), [10x-xenium-spinal-cord-9gqvnwniqvfvxju90000](/datasets/md/cd.md#10x-xenium-spinal-cord-9gqvnwniqvfvxju90000), [10x-xenium-spinal-cord-no30qexkfnur0snl0000](/datasets/md/bd.md#10x-xenium-spinal-cord-no30qexkfnur0snl0000), [10x-xenium-spinal-cord-dfpezyouyi7v91o20000](/datasets/md/a7.md#10x-xenium-spinal-cord-dfpezyouyi7v91o20000), [10x-xenium-spinal-cord-osuz9mxsbgoawaz90000](/datasets/md/01.md#10x-xenium-spinal-cord-osuz9mxsbgoawaz90000), [10x-xenium-spinal-cord-rya3wqffxyrls0xk0000](/datasets/md/b1.md#10x-xenium-spinal-cord-rya3wqffxyrls0xk0000), [10x-xenium-spinal-cord-0xshc7mkip9wopke0000](/datasets/md/cf.md#10x-xenium-spinal-cord-0xshc7mkip9wopke0000), [10x-xenium-spinal-cord-bbxhn9vx3pedrsly0000](/datasets/md/de.md#10x-xenium-spinal-cord-bbxhn9vx3pedrsly0000), [10x-xenium-spinal-cord-nizlsdxegmnebcci0000](/datasets/md/1b.md#10x-xenium-spinal-cord-nizlsdxegmnebcci0000) ## Targeting JAK1/3-STAT1 signaling attenuates cytotoxic T lymphocytes activation for the treatment in Stevens-Johnson syndrome and toxic epidermal necrolysis - Page: /collections/geo-gse333617/ - Kind: comparison - Datasets: 4 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE333617 - Design: This study performed single-cell RNA sequencing (scRNA-seq) on blister-derived cells and peripheral blood mononuclear cells (PBMCs) from acute-phase SJS/TEN patients, together with PBMCs from healthy donors (HD). We also performed 10x Visium spatial transcriptomics on lesional skin from patients and on skin from healthy donors. - Members: [visium-spatial-gene-expression-zone-of-skin-wyb8he1ewkohld1e0000](/datasets/md/b3.md#visium-spatial-gene-expression-zone-of-skin-wyb8he1ewkohld1e0000), [visium-spatial-gene-expression-skin-of-body-zeqyuc7ugxmbrn7s0000](/datasets/md/67.md#visium-spatial-gene-expression-skin-of-body-zeqyuc7ugxmbrn7s0000), [visium-spatial-gene-expression-zone-of-skin-wc4cjjsyxcekv9z60000](/datasets/md/db.md#visium-spatial-gene-expression-zone-of-skin-wc4cjjsyxcekv9z60000), [visium-spatial-gene-expression-zone-of-skin-s3thnvrsthtmzvfr0000](/datasets/md/6b.md#visium-spatial-gene-expression-zone-of-skin-s3thnvrsthtmzvfr0000) ## Ultrasound-Mediated BBB Opening Promotes Microglial Reprogramming and Enhanced Endothelial Interactions in the Human Peritumoral Brain [Visium] - Page: /collections/geo-gse338999/ - Kind: other - Datasets: 2 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE338999 - Design: Paired sonicated and non-sonicated peritumoral brain sections from 2 recurrent glioblastoma patients were profiled by 10x Visium to assess spatial transcriptomic changes after LIPU/MB-mediated BBB opening. *************************************************************** Raw sequencing files are not included because these data were generated from human clinical trial specimens, and raw data are being withheld due to patient privacy considerations. *************************************************************** - Members: [visium-spatial-gene-expression-brain-16dblkdpwnl61anm0000](/datasets/md/ea.md#visium-spatial-gene-expression-brain-16dblkdpwnl61anm0000), [visium-spatial-gene-expression-brain-ep55xk5okgp1prgq0000](/datasets/md/ff.md#visium-spatial-gene-expression-brain-ep55xk5okgp1prgq0000) ## A Tissue Virus Microenvironment with Activated Stress Responses Underlies Durable SIV Persistence [Visium] - Page: /collections/geo-gse341607/ - Kind: comparison - Datasets: 18 - Reference: PMID:42614350 - Design: Seven SIV-infected rhesus macaques (Macaca mulatta) were assigned to two ART-timing groups: Early ART / Early ATI (EAEA, n=4: A9T002, RPQ9, A2X015, 05D369), modeling a transient viral reservoir, in which ART was initiated 4 days after intravaginal/intrarectal challenge with SIVmac239 or SIV-ffLuc and maintained for ~4-6 months; and Late ART / Early ATI (LAEA, n=3: A7E005, A7R011, 08M236), modeling a persistent viral reservoir, in which ART was initiated at week 10 after intravenous challenge with barcoded SIVmac239M2 and maintained for 12 months. Following analytical treatment interruption (ATI), animals were necropsied 4-6 days post-ATI (pre-viremic eclipse phase), and gut tissue sites of viral production ('hot' sites) were identified by immunoPET/CT-guided necropsy. Spatial transcriptomics (10x Genomics Visium) was performed on 17 colon and 1 jejunum tissue sections to characterize the host tissue virus microenvironment (VME) surrounding SIV-positive foci, comparing persistent (LAEA) versus transient (EAEA) reservoirs. - Members: [visium-spatial-gene-expression-colon-oyfhjdz8h3dhc8ef0000](/datasets/md/83.md#visium-spatial-gene-expression-colon-oyfhjdz8h3dhc8ef0000), [visium-spatial-gene-expression-colon-163dw1xb4l0egrdr0000](/datasets/md/d3.md#visium-spatial-gene-expression-colon-163dw1xb4l0egrdr0000), [visium-spatial-gene-expression-colon-3adpgz6vegqrpxq30000](/datasets/md/78.md#visium-spatial-gene-expression-colon-3adpgz6vegqrpxq30000), [visium-spatial-gene-expression-colon-36lkgspsdsxom7bx0000](/datasets/md/a4.md#visium-spatial-gene-expression-colon-36lkgspsdsxom7bx0000), [visium-spatial-gene-expression-colon-poq6yn827yh2kmoz0000](/datasets/md/52.md#visium-spatial-gene-expression-colon-poq6yn827yh2kmoz0000), [visium-spatial-gene-expression-colon-pvq2kzpklmygngj40000](/datasets/md/85.md#visium-spatial-gene-expression-colon-pvq2kzpklmygngj40000), [visium-spatial-gene-expression-colon-53kwikiy9ajo6o640000](/datasets/md/a6.md#visium-spatial-gene-expression-colon-53kwikiy9ajo6o640000), [visium-spatial-gene-expression-colon-ytcbrgugobuu2e5s0000](/datasets/md/8c.md#visium-spatial-gene-expression-colon-ytcbrgugobuu2e5s0000), [visium-spatial-gene-expression-colon-jifb8mwmahf1ozrm0000](/datasets/md/8f.md#visium-spatial-gene-expression-colon-jifb8mwmahf1ozrm0000), [visium-spatial-gene-expression-colon-9sphjmypdvwvxvu00000](/datasets/md/79.md#visium-spatial-gene-expression-colon-9sphjmypdvwvxvu00000), [visium-spatial-gene-expression-colon-ad0fnaw5y0sjbxhb0000](/datasets/md/9a.md#visium-spatial-gene-expression-colon-ad0fnaw5y0sjbxhb0000), [visium-spatial-gene-expression-colon-tmkviifvovmftp3l0000](/datasets/md/09.md#visium-spatial-gene-expression-colon-tmkviifvovmftp3l0000), [visium-spatial-gene-expression-jejunum-zy5v5yrq5qlddh500000](/datasets/md/7b.md#visium-spatial-gene-expression-jejunum-zy5v5yrq5qlddh500000), [visium-spatial-gene-expression-colon-g5mrqfvptdfz3qij0000](/datasets/md/21.md#visium-spatial-gene-expression-colon-g5mrqfvptdfz3qij0000), [visium-spatial-gene-expression-colon-iqnhkjatmeyc1wq90000](/datasets/md/88.md#visium-spatial-gene-expression-colon-iqnhkjatmeyc1wq90000), [visium-spatial-gene-expression-colon-ijhwz7upqwmzwyzn0000](/datasets/md/2f.md#visium-spatial-gene-expression-colon-ijhwz7upqwmzwyzn0000), [visium-spatial-gene-expression-colon-fwpvt53zzn6qwblu0000](/datasets/md/27.md#visium-spatial-gene-expression-colon-fwpvt53zzn6qwblu0000), [visium-spatial-gene-expression-colon-wsvqywm08dlx2inh0000](/datasets/md/36.md#visium-spatial-gene-expression-colon-wsvqywm08dlx2inh0000) ## Spatial transcriptomics reveals microenvironmental heterogeneity in osteoarthritic subchondral bone - Page: /collections/geo-gse342703/ - Kind: other - Datasets: 4 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE342703 - Design: Human femoral head specimens were collected from patients undergoing hip arthroplasty, processed into formalin-fixed, EDTA-decalcified, paraffin-embedded tissue blocks, and profiled using both 10x Genomics Visium HD platforms. FFPE sections were processed on the CytAssist instrument, followed by H&E staining, probe extension and library construction according to the manufacturer’s protocols with minor adaptations. Libraries were sequenced on an Illumina NextSeq 2000 platform. - Members: [visium-spatial-gene-expression-pancreas-medsrs3mxyksqn3r0000](/datasets/md/3e.md#visium-spatial-gene-expression-pancreas-medsrs3mxyksqn3r0000), [visium-spatial-gene-expression-head-of-femur-6qsv3u7rqnbjyiar0000](/datasets/md/e5.md#visium-spatial-gene-expression-head-of-femur-6qsv3u7rqnbjyiar0000), [visium-spatial-gene-expression-head-of-femur-qzswmof7s7qlkqbr0000](/datasets/md/1e.md#visium-spatial-gene-expression-head-of-femur-qzswmof7s7qlkqbr0000), [visium-spatial-gene-expression-head-of-femur-cg5e9tnrkkdg7jdq0000](/datasets/md/ca.md#visium-spatial-gene-expression-head-of-femur-cg5e9tnrkkdg7jdq0000) ## geo-gse308952 - Page: /collections/geo-gse308952/ - Kind: other - Datasets: 1 - Members: [stereo-seq-skin-of-body-xlp0803meqbirqm30000](/datasets/md/8b.md#stereo-seq-skin-of-body-xlp0803meqbirqm30000) ## geo-gse294442 - Page: /collections/geo-gse294442/ - Kind: other - Datasets: 1 - Members: [stereo-seq-cardiac-valve-j5e0e9edylotyj3a0000](/datasets/md/18.md#stereo-seq-cardiac-valve-j5e0e9edylotyj3a0000)