# SpatialData-DB collections, shard 0 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. ## Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. - Page: /collections/doi-10-1016-j-cell-2020-05-039/ - Kind: replicates - Datasets: 16 - Reference: 10.1016/j.cell.2020.05.039 - Members: [spatial-transcriptomics-skin-of-body-wn4nrjekj3fmu2fa0000](/datasets/md/26.md#spatial-transcriptomics-skin-of-body-wn4nrjekj3fmu2fa0000), [spatial-transcriptomics-skin-of-body-nivuzi5rsnesadt30000](/datasets/md/02.md#spatial-transcriptomics-skin-of-body-nivuzi5rsnesadt30000), [spatial-transcriptomics-skin-of-body-4ipnbthwmnavca8t0000](/datasets/md/77.md#spatial-transcriptomics-skin-of-body-4ipnbthwmnavca8t0000), [spatial-transcriptomics-skin-of-body-ytrs2j6bybsnzouy0001](/datasets/md/c2.md#spatial-transcriptomics-skin-of-body-ytrs2j6bybsnzouy0001), [spatial-transcriptomics-skin-of-body-7ueelo33xfiktlqw0000](/datasets/md/72.md#spatial-transcriptomics-skin-of-body-7ueelo33xfiktlqw0000), [spatial-transcriptomics-skin-of-body-oi8oxldwpqujj4yj0000](/datasets/md/39.md#spatial-transcriptomics-skin-of-body-oi8oxldwpqujj4yj0000), [spatial-transcriptomics-skin-of-body-agdwjomfz5n7ublk0000](/datasets/md/72.md#spatial-transcriptomics-skin-of-body-agdwjomfz5n7ublk0000), [spatial-transcriptomics-skin-of-body-edfikawpv9v4ygjf0000](/datasets/md/55.md#spatial-transcriptomics-skin-of-body-edfikawpv9v4ygjf0000), [spatial-transcriptomics-skin-of-body-rjtjbjkluytqd4px0000](/datasets/md/bb.md#spatial-transcriptomics-skin-of-body-rjtjbjkluytqd4px0000), [spatial-transcriptomics-skin-of-body-ch0nzdwih6gm7go80000](/datasets/md/11.md#spatial-transcriptomics-skin-of-body-ch0nzdwih6gm7go80000), [spatial-transcriptomics-skin-of-body-lkkjhy77ikfwntnc0000](/datasets/md/a4.md#spatial-transcriptomics-skin-of-body-lkkjhy77ikfwntnc0000), [spatial-transcriptomics-skin-of-body-zmo1zwqv834b8bo60000](/datasets/md/1b.md#spatial-transcriptomics-skin-of-body-zmo1zwqv834b8bo60000), [visium-spatial-gene-expression-skin-of-body-gw0frghhyc29jhhq0000](/datasets/md/ce.md#visium-spatial-gene-expression-skin-of-body-gw0frghhyc29jhhq0000), [visium-spatial-gene-expression-skin-of-body-sphyjjnmwgoey1h20000](/datasets/md/8b.md#visium-spatial-gene-expression-skin-of-body-sphyjjnmwgoey1h20000), [visium-spatial-gene-expression-skin-of-body-lymztfpcjbilqiqs0000](/datasets/md/43.md#visium-spatial-gene-expression-skin-of-body-lymztfpcjbilqiqs0000), [visium-spatial-gene-expression-skin-of-body-gahuikaiqrp7cad20000](/datasets/md/0f.md#visium-spatial-gene-expression-skin-of-body-gahuikaiqrp7cad20000) ## Assessment of spatial transcriptomics for oncology discovery. - Page: /collections/doi-10-1016-j-crmeth-2022-100340/ - Kind: comparison - Datasets: 2 - Reference: 10.1016/j.crmeth.2022.100340 - Members: [visium-spatial-gene-expression-intestine-vqgjxw1oze8yksgt0000](/datasets/md/90.md#visium-spatial-gene-expression-intestine-vqgjxw1oze8yksgt0000), [visium-spatial-gene-expression-intestine-8nqxdxegn0erhplu0000](/datasets/md/f5.md#visium-spatial-gene-expression-intestine-8nqxdxegn0erhplu0000) ## Genome-wide spatial expression profiling in formalin-fixed tissues. - Page: /collections/doi-10-1016-j-xgen-2021-100065/ - Kind: comparison - Datasets: 15 - Reference: 10.1016/j.xgen.2021.100065 - Members: [visium-spatial-gene-expression-brain-2baptkej0f14p9v00000](/datasets/md/ab.md#visium-spatial-gene-expression-brain-2baptkej0f14p9v00000), [visium-spatial-gene-expression-brain-urvcdeixvihnmrkv0000](/datasets/md/62.md#visium-spatial-gene-expression-brain-urvcdeixvihnmrkv0000), [visium-spatial-gene-expression-brain-1g91cdizplsejeqw0000](/datasets/md/63.md#visium-spatial-gene-expression-brain-1g91cdizplsejeqw0000), [visium-spatial-gene-expression-lung-0vd8xbza2w1eivbg0000](/datasets/md/60.md#visium-spatial-gene-expression-lung-0vd8xbza2w1eivbg0000), [visium-spatial-gene-expression-lung-kkloasvidfrpl92i0000](/datasets/md/ae.md#visium-spatial-gene-expression-lung-kkloasvidfrpl92i0000), [visium-spatial-gene-expression-brain-fkecmyqss7qcrkp60000](/datasets/md/ef.md#visium-spatial-gene-expression-brain-fkecmyqss7qcrkp60000), [visium-spatial-gene-expression-kidney-ighjm1dnf6mhdthe0000](/datasets/md/4f.md#visium-spatial-gene-expression-kidney-ighjm1dnf6mhdthe0000), [visium-spatial-gene-expression-lung-bagaoau0anqdczb50000](/datasets/md/65.md#visium-spatial-gene-expression-lung-bagaoau0anqdczb50000), [visium-spatial-gene-expression-lung-l0jamrhpl5ooablk0000](/datasets/md/cf.md#visium-spatial-gene-expression-lung-l0jamrhpl5ooablk0000), [visium-spatial-gene-expression-kidney-iww4qfcrssd1az5w0000](/datasets/md/38.md#visium-spatial-gene-expression-kidney-iww4qfcrssd1az5w0000), [visium-spatial-gene-expression-kidney-9idicri1ttjnxys50000](/datasets/md/19.md#visium-spatial-gene-expression-kidney-9idicri1ttjnxys50000), [visium-spatial-gene-expression-lung-ewfmj1cbhckpkbhn0000](/datasets/md/d2.md#visium-spatial-gene-expression-lung-ewfmj1cbhckpkbhn0000), [visium-spatial-gene-expression-brain-w3yre0qwse4zz05q0000](/datasets/md/16.md#visium-spatial-gene-expression-brain-w3yre0qwse4zz05q0000), [visium-spatial-gene-expression-brain-u0fy1huwto1gos0a0000](/datasets/md/18.md#visium-spatial-gene-expression-brain-u0fy1huwto1gos0a0000), [visium-spatial-gene-expression-brain-xrzib5m4gkkp7o4a0000](/datasets/md/ec.md#visium-spatial-gene-expression-brain-xrzib5m4gkkp7o4a0000) ## Spatial transcriptomics of the lacrimal gland features macrophage activity and epithelium metabolism as key alterations during chronic inflammation. - Page: /collections/doi-10-3389-fimmu-2022-1011125/ - Kind: comparison - Datasets: 4 - Reference: 10.3389/fimmu.2022.1011125 - Members: [visium-spatial-gene-expression-eye-enl8dni7gjosapyy0000](/datasets/md/3e.md#visium-spatial-gene-expression-eye-enl8dni7gjosapyy0000), [visium-spatial-gene-expression-eye-usj9j9hnz6rnx8yu0000](/datasets/md/47.md#visium-spatial-gene-expression-eye-usj9j9hnz6rnx8yu0000), [visium-spatial-gene-expression-eye-bclrrn9mozqpstfi0000](/datasets/md/29.md#visium-spatial-gene-expression-eye-bclrrn9mozqpstfi0000), [visium-spatial-gene-expression-eye-trp86aypnzngq3jv0000](/datasets/md/2d.md#visium-spatial-gene-expression-eye-trp86aypnzngq3jv0000) ## Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST] - Page: /collections/geo-gse144239/ - Kind: replicates - Datasets: 4 - Reference: PMID:32579974 - Design: Patient tumors were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing - Members: [visium-spatial-gene-expression-skin-of-body-cng4vwtznpggkwr50000](/datasets/md/06.md#visium-spatial-gene-expression-skin-of-body-cng4vwtznpggkwr50000), [visium-spatial-gene-expression-skin-of-body-przlsoxsaaay3bcp0000](/datasets/md/d8.md#visium-spatial-gene-expression-skin-of-body-przlsoxsaaay3bcp0000), [visium-spatial-gene-expression-skin-of-body-e0vtoymthl8ak2lm0000](/datasets/md/f1.md#visium-spatial-gene-expression-skin-of-body-e0vtoymthl8ak2lm0000), [visium-spatial-gene-expression-skin-of-body-pueccjpikmrc6vok0000](/datasets/md/b0.md#visium-spatial-gene-expression-skin-of-body-pueccjpikmrc6vok0000) ## Neuroinflammatory astrocyte subtypes in the mouse brain [Visium] - Page: /collections/geo-gse165098/ - Kind: comparison - Datasets: 6 - Reference: PMID:34413515 - Design: Brains from 3 saline- and 3 LPS-injected female mice were sectioned to 10 um and used for Visium Spatial Transcriptomics - Members: [visium-spatial-gene-expression-brain-1akqzn54oskfrgyw0000](/datasets/md/6a.md#visium-spatial-gene-expression-brain-1akqzn54oskfrgyw0000), [visium-spatial-gene-expression-brain-ntch0n4tu5drbdbb0000](/datasets/md/6b.md#visium-spatial-gene-expression-brain-ntch0n4tu5drbdbb0000), [visium-spatial-gene-expression-brain-eqehqgf3jyujgf0b0000](/datasets/md/2b.md#visium-spatial-gene-expression-brain-eqehqgf3jyujgf0b0000), [visium-spatial-gene-expression-brain-axny8olbaob042tk0000](/datasets/md/7e.md#visium-spatial-gene-expression-brain-axny8olbaob042tk0000), [visium-spatial-gene-expression-brain-xsj7bxpib3k9kucv0000](/datasets/md/09.md#visium-spatial-gene-expression-brain-xsj7bxpib3k9kucv0000), [visium-spatial-gene-expression-brain-kine2r1fbx0juecd0000](/datasets/md/10.md#visium-spatial-gene-expression-brain-kine2r1fbx0juecd0000) ## Spatiotemporal transcriptome analysis reveals critical roles for mechano-sensing genes at the border zone in remodeling after myocardial infarction - Page: /collections/geo-gse176092/ - Kind: other - Datasets: 14 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176092 - Design: Integrative analysis of single-cardimyocyte analysis and spatial transcriptomics after myocardial infarction in mouse - Members: [visium-spatial-gene-expression-heart-gz1j9udwv94kc0jk0000](/datasets/md/c8.md#visium-spatial-gene-expression-heart-gz1j9udwv94kc0jk0000), [visium-spatial-gene-expression-heart-ypenwt8xbrtbwq390000](/datasets/md/b1.md#visium-spatial-gene-expression-heart-ypenwt8xbrtbwq390000), [visium-spatial-gene-expression-heart-xwfgchkkcspepnxa0000](/datasets/md/27.md#visium-spatial-gene-expression-heart-xwfgchkkcspepnxa0000), [visium-spatial-gene-expression-heart-nywcseckyj0k7uuv0000](/datasets/md/19.md#visium-spatial-gene-expression-heart-nywcseckyj0k7uuv0000), [visium-spatial-gene-expression-heart-fummkcvivtnityta0000](/datasets/md/7d.md#visium-spatial-gene-expression-heart-fummkcvivtnityta0000), [visium-spatial-gene-expression-heart-gko4cbpm6ftpte420000](/datasets/md/de.md#visium-spatial-gene-expression-heart-gko4cbpm6ftpte420000), [visium-spatial-gene-expression-heart-6nyboepi3sauweyv0000](/datasets/md/8f.md#visium-spatial-gene-expression-heart-6nyboepi3sauweyv0000), [visium-spatial-gene-expression-heart-67uuu6ovgeooruv90000](/datasets/md/53.md#visium-spatial-gene-expression-heart-67uuu6ovgeooruv90000), [visium-spatial-gene-expression-heart-flfiwgv5hn1skulx0000](/datasets/md/d4.md#visium-spatial-gene-expression-heart-flfiwgv5hn1skulx0000), [visium-spatial-gene-expression-heart-u6rzqxhyk4odoi7p0000](/datasets/md/24.md#visium-spatial-gene-expression-heart-u6rzqxhyk4odoi7p0000), [visium-spatial-gene-expression-heart-blcjz7vwby5rtvkz0000](/datasets/md/e0.md#visium-spatial-gene-expression-heart-blcjz7vwby5rtvkz0000), [visium-spatial-gene-expression-heart-nqzpciduee0b6anr0000](/datasets/md/01.md#visium-spatial-gene-expression-heart-nqzpciduee0b6anr0000), [visium-spatial-gene-expression-heart-d2kvu209zoul7hfv0000](/datasets/md/00.md#visium-spatial-gene-expression-heart-d2kvu209zoul7hfv0000), [visium-spatial-gene-expression-heart-fzimwos3e7auelmr0000](/datasets/md/37.md#visium-spatial-gene-expression-heart-fzimwos3e7auelmr0000) ## Perturb-map coupled with spatial transcriptomics identifies mutation associated gene signatures in a mouse model of lung adenocarcinoma - Page: /collections/geo-gse193460/ - Kind: other - Datasets: 4 - Reference: PMID:35290801 - Design: Male C57BL/6J mice were injected intravenously with KP (Kras G12D, p53 deleted) cells transduced with a Pro-Code/CRISPR library targeting 35 different genes associated with tumor-immune interaction. 10X Visium spatial transcriptomics profiling was performed on 4 separate sections of mouse lung from 3 different mice. Annotations for specific genes targeted in visium spots capturing tumor cells were generated by parallel hyperion imaging on a serial section to identify the linked protein barcode. - Members: [visium-spatial-gene-expression-lung-jw1qke1em0t5yavw0000](/datasets/md/a5.md#visium-spatial-gene-expression-lung-jw1qke1em0t5yavw0000), [visium-spatial-gene-expression-lung-jh4nrtq37xpu9gy80000](/datasets/md/ff.md#visium-spatial-gene-expression-lung-jh4nrtq37xpu9gy80000), [visium-spatial-gene-expression-lung-mqfjgohe4o2jofme0000](/datasets/md/20.md#visium-spatial-gene-expression-lung-mqfjgohe4o2jofme0000), [visium-spatial-gene-expression-lung-u85eukbi8vetoy8h0000](/datasets/md/18.md#visium-spatial-gene-expression-lung-u85eukbi8vetoy8h0000) ## Spatial transcriptomics (Visium, 10x Genomics) data of Duchenne mouse models - Page: /collections/geo-gse199659/ - Kind: comparison - Datasets: 4 - Reference: PMID:37582915 - Design: healthy controls (C57BL10 and DBA/2J) and DMD affected mouse models (mdx and D2-mdx samples) all n=1 - Members: [visium-spatial-gene-expression-quadriceps-femoris-d7coefbtyq5n1wll0000](/datasets/md/d4.md#visium-spatial-gene-expression-quadriceps-femoris-d7coefbtyq5n1wll0000), [visium-spatial-gene-expression-quadriceps-femoris-f5rebb5o0uawuq2o0000](/datasets/md/20.md#visium-spatial-gene-expression-quadriceps-femoris-f5rebb5o0uawuq2o0000), [visium-spatial-gene-expression-quadriceps-femoris-v3uvupfcfpyzmbji0000](/datasets/md/8f.md#visium-spatial-gene-expression-quadriceps-femoris-v3uvupfcfpyzmbji0000), [visium-spatial-gene-expression-quadriceps-femoris-xnilmmqjqj2sadkc0000](/datasets/md/90.md#visium-spatial-gene-expression-quadriceps-femoris-xnilmmqjqj2sadkc0000) ## Spatial RNA-sequencing of day7 and day 21 post-LCMV Cl13 infection following transient CD4+ T cell depletion (Visium) - Page: /collections/geo-gse200720/ - Kind: time course - Datasets: 8 - Reference: PMID:36450262 - Design: Spleens from Control or CD4+ T cell-depleted mice on Day 7 and Day 21 post-LCMV Cl13 infection (2 mice per condition total, conducted in two separate rounds of experiments) and were frozen fresh, stored, and processed as instructed by the Visium kit (10x Genomics). 10 μm sections were generated from frozen spleens and placed on barcoded slides (10x Genomics). The Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics) was used to generate barcoded cDNA libraries. H&E stained tissues on Visium slides were imaged using a Nikon Eclipse Ti2 inverted microscope. Spleen tissue on Visium slides was permeabilized for 18 minutes to extract mRNA and downstream library preparation and sequencing were conducted according to manufacturer’s protocol. - Members: [visium-spatial-gene-expression-spleen-jn3a6u639lrtxy4u0000](/datasets/md/1f.md#visium-spatial-gene-expression-spleen-jn3a6u639lrtxy4u0000), [visium-spatial-gene-expression-spleen-lci0wmz9zedg7whh0000](/datasets/md/c9.md#visium-spatial-gene-expression-spleen-lci0wmz9zedg7whh0000), [visium-spatial-gene-expression-spleen-f4jfyttsmjgv3rvz0000](/datasets/md/95.md#visium-spatial-gene-expression-spleen-f4jfyttsmjgv3rvz0000), [visium-spatial-gene-expression-spleen-0pt3yfx2kmeq3wgi0000](/datasets/md/ea.md#visium-spatial-gene-expression-spleen-0pt3yfx2kmeq3wgi0000), [visium-spatial-gene-expression-spleen-zgegw2aydt4ialcn0000](/datasets/md/3f.md#visium-spatial-gene-expression-spleen-zgegw2aydt4ialcn0000), [visium-spatial-gene-expression-spleen-7ein6nzuqx7hrblh0000](/datasets/md/46.md#visium-spatial-gene-expression-spleen-7ein6nzuqx7hrblh0000), [visium-spatial-gene-expression-spleen-a9evylomydpunkyq0000](/datasets/md/90.md#visium-spatial-gene-expression-spleen-a9evylomydpunkyq0000), [visium-spatial-gene-expression-spleen-3unaxsoqddhp068w0000](/datasets/md/2c.md#visium-spatial-gene-expression-spleen-3unaxsoqddhp068w0000) ## Spatial transcriptomics reveals ovarian cancer subclones with different microenvironments - Page: /collections/geo-gse211956/ - Kind: comparison - Datasets: 8 - Reference: PMID:38570491 - Design: 8 spatial RNA-seq experiments (10x Genomics Visium) and 5 single-cell RNA-seq experiments (10x Genomics Chromium) using high-grade serous ovarian carcinoma (HGSOC) samples - Members: [visium-spatial-gene-expression-ovary-zcmdcaa58gvtscyu0000](/datasets/md/25.md#visium-spatial-gene-expression-ovary-zcmdcaa58gvtscyu0000), [visium-spatial-gene-expression-ovary-kfbjidgavd8g004o0000](/datasets/md/2e.md#visium-spatial-gene-expression-ovary-kfbjidgavd8g004o0000), [visium-spatial-gene-expression-ovary-knvozo5yfjwdxdwj0000](/datasets/md/f2.md#visium-spatial-gene-expression-ovary-knvozo5yfjwdxdwj0000), [visium-spatial-gene-expression-ovary-1koulpst5eqhjdgz0000](/datasets/md/af.md#visium-spatial-gene-expression-ovary-1koulpst5eqhjdgz0000), [visium-spatial-gene-expression-ovary-1rycabwetsgew5zw0000](/datasets/md/2c.md#visium-spatial-gene-expression-ovary-1rycabwetsgew5zw0000), [visium-spatial-gene-expression-ovary-781jmid39zg5ejy80000](/datasets/md/07.md#visium-spatial-gene-expression-ovary-781jmid39zg5ejy80000), [visium-spatial-gene-expression-ovary-l07pkqe3qrs3lx6d0000](/datasets/md/4c.md#visium-spatial-gene-expression-ovary-l07pkqe3qrs3lx6d0000), [visium-spatial-gene-expression-ovary-ox6jeskj2nqonpkp0000](/datasets/md/f3.md#visium-spatial-gene-expression-ovary-ox6jeskj2nqonpkp0000) ## Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples - Page: /collections/geo-gse221571/ - Kind: time course - Datasets: 14 - Reference: PMID:36720873 - Design: Gene expression profiiles of spatially resolved transcriptomics data generated from degraded or challenging samples - Members: [visium-spatial-gene-expression-brain-ilzavnlxx7rx0ryt0000](/datasets/md/12.md#visium-spatial-gene-expression-brain-ilzavnlxx7rx0ryt0000), [visium-spatial-gene-expression-brain-mu3wudaxrksdydgu0000](/datasets/md/7b.md#visium-spatial-gene-expression-brain-mu3wudaxrksdydgu0000), [visium-spatial-gene-expression-brain-izixdwihyrlholj00000](/datasets/md/97.md#visium-spatial-gene-expression-brain-izixdwihyrlholj00000), [visium-spatial-gene-expression-brain-a8obazxn0ko59hsw0000](/datasets/md/a5.md#visium-spatial-gene-expression-brain-a8obazxn0ko59hsw0000), [visium-spatial-gene-expression-brain-d3bh1be10zhgmzo00000](/datasets/md/7e.md#visium-spatial-gene-expression-brain-d3bh1be10zhgmzo00000), [visium-spatial-gene-expression-bone-tissue-gbtgzu3bir8sltgf0000](/datasets/md/92.md#visium-spatial-gene-expression-bone-tissue-gbtgzu3bir8sltgf0000), [visium-spatial-gene-expression-brain-jzww7nnq0bo4ef8l0000](/datasets/md/5b.md#visium-spatial-gene-expression-brain-jzww7nnq0bo4ef8l0000), [visium-spatial-gene-expression-brain-dad0rb6qqmkp58y30000](/datasets/md/12.md#visium-spatial-gene-expression-brain-dad0rb6qqmkp58y30000), [visium-spatial-gene-expression-bone-tissue-26q9dnmh98is1i190000](/datasets/md/c7.md#visium-spatial-gene-expression-bone-tissue-26q9dnmh98is1i190000), [visium-spatial-gene-expression-bone-tissue-evilphspm6lyomhe0000](/datasets/md/be.md#visium-spatial-gene-expression-bone-tissue-evilphspm6lyomhe0000), [visium-spatial-gene-expression-bone-tissue-soa0r1krsuw7sz4g0000](/datasets/md/90.md#visium-spatial-gene-expression-bone-tissue-soa0r1krsuw7sz4g0000), [visium-spatial-gene-expression-bone-tissue-na8j1b2cliltjri50000](/datasets/md/23.md#visium-spatial-gene-expression-bone-tissue-na8j1b2cliltjri50000), [visium-spatial-gene-expression-brain-bq97t0elgbsrawts0000](/datasets/md/42.md#visium-spatial-gene-expression-brain-bq97t0elgbsrawts0000), [visium-spatial-gene-expression-bone-tissue-kmbzvpljcjrl9wqt0000](/datasets/md/4c.md#visium-spatial-gene-expression-bone-tissue-kmbzvpljcjrl9wqt0000) ## Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section - Page: /collections/geo-gse232910/ - Kind: time course - Datasets: 18 - Reference: PMID:37667091 - Design: Tissue sections processed with MALDI-MSI were eventually analyzed using Visium. Controls for some of the samples are included. *** From Submitter: We are restricted to deposit raw sequencing from humans to SRA. Those will be deposited on the Swedish federated EGA node and we will link when it became available to us. *** - Members: [visium-spatial-gene-expression-caudate-nucleus-yr0idb4v5jdxbe0v0001](/datasets/md/3b.md#visium-spatial-gene-expression-caudate-nucleus-yr0idb4v5jdxbe0v0001), [visium-spatial-gene-expression-brain-9oob4rtizfs3gm0f0000](/datasets/md/fd.md#visium-spatial-gene-expression-brain-9oob4rtizfs3gm0f0000), [visium-spatial-gene-expression-brain-22mgqoczdfcz4mcb0000](/datasets/md/1f.md#visium-spatial-gene-expression-brain-22mgqoczdfcz4mcb0000), [visium-spatial-gene-expression-brain-1lrf6gcliodt0ycf0000](/datasets/md/44.md#visium-spatial-gene-expression-brain-1lrf6gcliodt0ycf0000), [visium-spatial-gene-expression-brain-aiuybdzibujlxz2e0000](/datasets/md/7a.md#visium-spatial-gene-expression-brain-aiuybdzibujlxz2e0000), [visium-spatial-gene-expression-caudate-nucleus-l85st1k7twhkzsxn0000](/datasets/md/16.md#visium-spatial-gene-expression-caudate-nucleus-l85st1k7twhkzsxn0000), [visium-spatial-gene-expression-caudate-nucleus-xcj39salzzaztbht0000](/datasets/md/6e.md#visium-spatial-gene-expression-caudate-nucleus-xcj39salzzaztbht0000), [visium-spatial-gene-expression-brain-3twfiwomyaun6akm0000](/datasets/md/34.md#visium-spatial-gene-expression-brain-3twfiwomyaun6akm0000), [visium-spatial-gene-expression-caudate-nucleus-to4axftowfxqcxi30000](/datasets/md/0b.md#visium-spatial-gene-expression-caudate-nucleus-to4axftowfxqcxi30000), [visium-spatial-gene-expression-caudate-nucleus-falarjfzxa08lugh0000](/datasets/md/86.md#visium-spatial-gene-expression-caudate-nucleus-falarjfzxa08lugh0000), [visium-spatial-gene-expression-brain-ndruwpiolecfrryg0000](/datasets/md/ef.md#visium-spatial-gene-expression-brain-ndruwpiolecfrryg0000), [visium-spatial-gene-expression-brain-0gbanh3wz4pnn3ge0000](/datasets/md/f5.md#visium-spatial-gene-expression-brain-0gbanh3wz4pnn3ge0000), [visium-spatial-gene-expression-brain-afea4tdp1fgir4ns0000](/datasets/md/1f.md#visium-spatial-gene-expression-brain-afea4tdp1fgir4ns0000), [visium-spatial-gene-expression-brain-hpzouv6miwuaws5n0000](/datasets/md/58.md#visium-spatial-gene-expression-brain-hpzouv6miwuaws5n0000), [visium-spatial-gene-expression-brain-wr3lfk5p4qubo8jv0000](/datasets/md/04.md#visium-spatial-gene-expression-brain-wr3lfk5p4qubo8jv0000), [visium-spatial-gene-expression-brain-db9frr4t3habi8010000](/datasets/md/94.md#visium-spatial-gene-expression-brain-db9frr4t3habi8010000), [visium-spatial-gene-expression-brain-cafmpwlyujewi8uf0000](/datasets/md/70.md#visium-spatial-gene-expression-brain-cafmpwlyujewi8uf0000), [visium-spatial-gene-expression-brain-qgzq3dsf979grecy0000](/datasets/md/62.md#visium-spatial-gene-expression-brain-qgzq3dsf979grecy0000) ## Comparing 10x Visium spatial transcriptomic technologies - Page: /collections/geo-gse254652/ - Kind: other - Datasets: 4 - Reference: PMID:40156041 - Design: Samples were captured over 5 10x Genomics Visium fresh-frozen (FF) slides and 3 formalin-fixed paraffin-embedded (FFPE) slides and sequenced over 6 Illumina runs. A matching scRNA-seq sample of the 3 mouse spleens (708, 709, 713): 10x scRNA-seq with the large BioLegend panel of antibody derived tags (ADTs) was captured over 1 GEM wells and GEX, ADT, and HTO were sequenced over 1 Illumina run. - Members: [visium-spatial-gene-expression-spleen-3x0ken5d1qfkfkxi0000](/datasets/md/57.md#visium-spatial-gene-expression-spleen-3x0ken5d1qfkfkxi0000), [visium-spatial-gene-expression-spleen-zkggykt0tkdsvqn30000](/datasets/md/3f.md#visium-spatial-gene-expression-spleen-zkggykt0tkdsvqn30000), [visium-spatial-gene-expression-spleen-9orebv8bzzzpnfm70000](/datasets/md/dc.md#visium-spatial-gene-expression-spleen-9orebv8bzzzpnfm70000), [visium-spatial-gene-expression-spleen-15aeem3e3brzoztl0000](/datasets/md/ce.md#visium-spatial-gene-expression-spleen-15aeem3e3brzoztl0000) ## Specific oncogenic drivers differently shaped the composition and functional diversity of immune cells in the microenvironment of experimental gliomas - Page: /collections/geo-gse269545/ - Kind: comparison - Datasets: 3 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE269545 - Design: Two healthy (sham operated) and two GL261 bearing hemispheres from C57BL/6 male mice were used for the analysis using 10X Visium Spatial Transcriptionics kit. - Members: [visium-spatial-gene-expression-brain-13witqirtdtax1vu0000](/datasets/md/7b.md#visium-spatial-gene-expression-brain-13witqirtdtax1vu0000), [visium-spatial-gene-expression-brain-iemalyvwqzdmuzwe0000](/datasets/md/4a.md#visium-spatial-gene-expression-brain-iemalyvwqzdmuzwe0000), [visium-spatial-gene-expression-brain-841ef87usul2vjmq0000](/datasets/md/cf.md#visium-spatial-gene-expression-brain-841ef87usul2vjmq0000) ## INFLAMMATION-INDUCED SENESCENT-LIKE GLIA REWIRE CELLULAR NETWORKS IN MULTIPLE SCLEROSIS [Spatial transcriptomic] - Page: /collections/geo-gse277435/ - Kind: replicates - Datasets: 12 - Reference: PMID:41006208 - Design: Visium profile of 12 slices of human brain tissue from progressive MS patients. - Members: [visium-spatial-gene-expression-brain-white-matter-onuctwgtydkgg6zz0000](/datasets/md/90.md#visium-spatial-gene-expression-brain-white-matter-onuctwgtydkgg6zz0000), [visium-spatial-gene-expression-brain-white-matter-pihjs7d8b5cygy7l0000](/datasets/md/a1.md#visium-spatial-gene-expression-brain-white-matter-pihjs7d8b5cygy7l0000), [visium-spatial-gene-expression-brain-white-matter-uwpt1s8l8ajk02gb0000](/datasets/md/11.md#visium-spatial-gene-expression-brain-white-matter-uwpt1s8l8ajk02gb0000), [visium-spatial-gene-expression-brain-white-matter-vl3vblizwqssdq6i0000](/datasets/md/e2.md#visium-spatial-gene-expression-brain-white-matter-vl3vblizwqssdq6i0000), [visium-spatial-gene-expression-brain-white-matter-xbnidrc4bqj97dnk0000](/datasets/md/c3.md#visium-spatial-gene-expression-brain-white-matter-xbnidrc4bqj97dnk0000), [visium-spatial-gene-expression-brain-white-matter-jqtqarwbwzmezy1u0000](/datasets/md/b4.md#visium-spatial-gene-expression-brain-white-matter-jqtqarwbwzmezy1u0000), [visium-spatial-gene-expression-brain-white-matter-l01eagvuttawordy0000](/datasets/md/06.md#visium-spatial-gene-expression-brain-white-matter-l01eagvuttawordy0000), [visium-spatial-gene-expression-brain-white-matter-zye6b68eyohpbyeu0000](/datasets/md/85.md#visium-spatial-gene-expression-brain-white-matter-zye6b68eyohpbyeu0000), [visium-spatial-gene-expression-brain-white-matter-bqkhe8shmbvs9xgz0000](/datasets/md/fb.md#visium-spatial-gene-expression-brain-white-matter-bqkhe8shmbvs9xgz0000), [visium-spatial-gene-expression-brain-white-matter-vn9q7uh3nsjxtfng0000](/datasets/md/af.md#visium-spatial-gene-expression-brain-white-matter-vn9q7uh3nsjxtfng0000), [visium-spatial-gene-expression-brain-white-matter-l4ooapynbwojdxtj0000](/datasets/md/75.md#visium-spatial-gene-expression-brain-white-matter-l4ooapynbwojdxtj0000), [visium-spatial-gene-expression-brain-white-matter-4jarer0xsu6fc27o0000](/datasets/md/e6.md#visium-spatial-gene-expression-brain-white-matter-4jarer0xsu6fc27o0000) ## Spatial transcriptomics and in situ immune cell profiling of the host ectocervical landscape of HIV infected Kenyan sex working women - Page: /collections/geo-gse290350/ - Kind: comparison - Datasets: 10 - Reference: PMID:39687623 - Design: In this study we compared gene expression between samples from female sex workers who are living with HIV (HIV group; n=5), and healthy female sex workers (control group; n=5. All of the participants were in the follicular menstrual stage. Ectocervical tissue were obtained as part of our broader cohort. longitudinal investigation within the Sex Worker Outreach Program in Pumwani, Nairobi, Kenya *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. *************************************************************** - Members: [visium-spatial-gene-expression-ectocervix-qroa93zuyxbsgj9x0000](/datasets/md/ab.md#visium-spatial-gene-expression-ectocervix-qroa93zuyxbsgj9x0000), [visium-spatial-gene-expression-ectocervix-wx4v0tyrjd1hz3ik0000](/datasets/md/8d.md#visium-spatial-gene-expression-ectocervix-wx4v0tyrjd1hz3ik0000), [visium-spatial-gene-expression-ectocervix-j1mx3knhgs1pc4ip0000](/datasets/md/e3.md#visium-spatial-gene-expression-ectocervix-j1mx3knhgs1pc4ip0000), [visium-spatial-gene-expression-ectocervix-scvav6qnoupppd6t0000](/datasets/md/e0.md#visium-spatial-gene-expression-ectocervix-scvav6qnoupppd6t0000), [visium-spatial-gene-expression-ectocervix-crl0qega9bgxadnz0000](/datasets/md/69.md#visium-spatial-gene-expression-ectocervix-crl0qega9bgxadnz0000), [visium-spatial-gene-expression-ectocervix-82ptwdlzbulpv7vn0000](/datasets/md/da.md#visium-spatial-gene-expression-ectocervix-82ptwdlzbulpv7vn0000), [visium-spatial-gene-expression-ectocervix-gtfyvsghv5gn4cb30000](/datasets/md/f9.md#visium-spatial-gene-expression-ectocervix-gtfyvsghv5gn4cb30000), [visium-spatial-gene-expression-ectocervix-soux6t1okx7qdhv30000](/datasets/md/17.md#visium-spatial-gene-expression-ectocervix-soux6t1okx7qdhv30000), [visium-spatial-gene-expression-ectocervix-yqmyycjqkok9wjwu0000](/datasets/md/ac.md#visium-spatial-gene-expression-ectocervix-yqmyycjqkok9wjwu0000), [visium-spatial-gene-expression-ectocervix-7ybgodirq6m7ogkm0000](/datasets/md/e1.md#visium-spatial-gene-expression-ectocervix-7ybgodirq6m7ogkm0000) ## Single cell approaches define the murine leptomeninges:cortical brain interface as a distinct cellular neighborhood comprised of neural and nonneural cell types - Page: /collections/geo-gse296134/ - Kind: other - Datasets: 7 - Reference: PMID:40780964 - Design: Multiplexed in situ hybridization-based spatial transcriptomics using the 10X genomics Xenium platform was used to analyze coronal sections adult mouse (C57BL6). - Members: [10x-xenium-forebrain-biycfikbybnaxwex0000](/datasets/md/85.md#10x-xenium-forebrain-biycfikbybnaxwex0000), [10x-xenium-forebrain-ahkr5qrolcrl8co20000](/datasets/md/66.md#10x-xenium-forebrain-ahkr5qrolcrl8co20000), [10x-xenium-forebrain-ikkcr5azcocosldc0000](/datasets/md/91.md#10x-xenium-forebrain-ikkcr5azcocosldc0000), [10x-xenium-forebrain-ajjkf4t19lrvtqe00000](/datasets/md/4a.md#10x-xenium-forebrain-ajjkf4t19lrvtqe00000), [10x-xenium-forebrain-s58rknc54s6m26qx0000](/datasets/md/08.md#10x-xenium-forebrain-s58rknc54s6m26qx0000), [10x-xenium-forebrain-aja4rkp9phqpjzl40000](/datasets/md/31.md#10x-xenium-forebrain-aja4rkp9phqpjzl40000), [10x-xenium-forebrain-ygmcr8ampltlzlpd0000](/datasets/md/5e.md#10x-xenium-forebrain-ygmcr8ampltlzlpd0000) ## Spatial transcriptomics from paired pancreas and associated draining lymph nodes reveals a lymphotoxin-beta signature in human type 1 diabetes - Page: /collections/geo-gse296626/ - Kind: comparison - Datasets: 35 - Reference: PMID:40475580 - Design: Spatial transcriptomics using the 10x Genomics Visium spatial gene expression assay performed on human donor pancreas and associated pancreatic lymph node sections from non-diabeitc controls, non-diabetic islet autoantibody positive donors at high risk, and T1D donors. - Members: [visium-spatial-gene-expression-pancreatic-lymph-node-ozmxztjp6gkni8l50000](/datasets/md/37.md#visium-spatial-gene-expression-pancreatic-lymph-node-ozmxztjp6gkni8l50000), [visium-spatial-gene-expression-pancreatic-lymph-node-ru4tixgodlpfcnbx0000](/datasets/md/ec.md#visium-spatial-gene-expression-pancreatic-lymph-node-ru4tixgodlpfcnbx0000), [visium-spatial-gene-expression-pancreatic-lymph-node-zfq74iadrtvcmyz50000](/datasets/md/be.md#visium-spatial-gene-expression-pancreatic-lymph-node-zfq74iadrtvcmyz50000), [visium-spatial-gene-expression-pancreas-ksg2clnarqhg6hu90000](/datasets/md/e4.md#visium-spatial-gene-expression-pancreas-ksg2clnarqhg6hu90000), [visium-spatial-gene-expression-pancreatic-lymph-node-7htpxy0eypnhgeza0000](/datasets/md/2c.md#visium-spatial-gene-expression-pancreatic-lymph-node-7htpxy0eypnhgeza0000), [visium-spatial-gene-expression-pancreas-elmpsym5wjbcbizz0000](/datasets/md/c2.md#visium-spatial-gene-expression-pancreas-elmpsym5wjbcbizz0000), [visium-spatial-gene-expression-pancreas-hr84cmrxz1gw0ied0000](/datasets/md/c3.md#visium-spatial-gene-expression-pancreas-hr84cmrxz1gw0ied0000), [visium-spatial-gene-expression-pancreatic-lymph-node-hcwvwclfizhctlzs0000](/datasets/md/39.md#visium-spatial-gene-expression-pancreatic-lymph-node-hcwvwclfizhctlzs0000), [visium-spatial-gene-expression-pancreatic-lymph-node-5yvu7wgouka5hc9e0000](/datasets/md/55.md#visium-spatial-gene-expression-pancreatic-lymph-node-5yvu7wgouka5hc9e0000), [visium-spatial-gene-expression-pancreatic-lymph-node-bzhhid7hebk3lqc80000](/datasets/md/a8.md#visium-spatial-gene-expression-pancreatic-lymph-node-bzhhid7hebk3lqc80000), [visium-spatial-gene-expression-pancreas-lql0yezktpic0ggc0000](/datasets/md/ab.md#visium-spatial-gene-expression-pancreas-lql0yezktpic0ggc0000), [visium-spatial-gene-expression-pancreas-xkmyewsqyj4x2zn30000](/datasets/md/07.md#visium-spatial-gene-expression-pancreas-xkmyewsqyj4x2zn30000), [visium-spatial-gene-expression-pancreas-m7wgmnmpstedf51q0000](/datasets/md/d5.md#visium-spatial-gene-expression-pancreas-m7wgmnmpstedf51q0000), [visium-spatial-gene-expression-pancreatic-lymph-node-se3b3wx7bn4paeot0000](/datasets/md/38.md#visium-spatial-gene-expression-pancreatic-lymph-node-se3b3wx7bn4paeot0000), [visium-spatial-gene-expression-pancreas-lunpk2f1ef1ysuvn0000](/datasets/md/5c.md#visium-spatial-gene-expression-pancreas-lunpk2f1ef1ysuvn0000), [visium-spatial-gene-expression-pancreas-lolqf7actka79aqa0000](/datasets/md/ea.md#visium-spatial-gene-expression-pancreas-lolqf7actka79aqa0000), [visium-spatial-gene-expression-pancreas-cvpshj7wi15zvmuf0000](/datasets/md/41.md#visium-spatial-gene-expression-pancreas-cvpshj7wi15zvmuf0000), [visium-spatial-gene-expression-pancreatic-lymph-node-m0xm1liia8tvha9k0000](/datasets/md/f5.md#visium-spatial-gene-expression-pancreatic-lymph-node-m0xm1liia8tvha9k0000), [visium-spatial-gene-expression-pancreas-phhmz9ildolxqb0m0000](/datasets/md/e3.md#visium-spatial-gene-expression-pancreas-phhmz9ildolxqb0m0000), [visium-spatial-gene-expression-pancreatic-lymph-node-j4pltum8vor3d8pv0000](/datasets/md/07.md#visium-spatial-gene-expression-pancreatic-lymph-node-j4pltum8vor3d8pv0000), [visium-spatial-gene-expression-pancreas-knqwdtvdohdyad0r0000](/datasets/md/78.md#visium-spatial-gene-expression-pancreas-knqwdtvdohdyad0r0000), [visium-spatial-gene-expression-pancreas-zu5tpbwwrif36xvi0000](/datasets/md/5c.md#visium-spatial-gene-expression-pancreas-zu5tpbwwrif36xvi0000), [visium-spatial-gene-expression-pancreatic-lymph-node-8lpyv6indt3hxloo0000](/datasets/md/23.md#visium-spatial-gene-expression-pancreatic-lymph-node-8lpyv6indt3hxloo0000), [visium-spatial-gene-expression-pancreas-z9rvpgngwwvz5swj0000](/datasets/md/c4.md#visium-spatial-gene-expression-pancreas-z9rvpgngwwvz5swj0000), [visium-spatial-gene-expression-pancreas-pgr0oeeeuv1fmift0000](/datasets/md/f6.md#visium-spatial-gene-expression-pancreas-pgr0oeeeuv1fmift0000), [visium-spatial-gene-expression-pancreas-ymqtbl3ocjehmq5j0000](/datasets/md/b6.md#visium-spatial-gene-expression-pancreas-ymqtbl3ocjehmq5j0000), [visium-spatial-gene-expression-pancreas-cswvu1clqhxbm4vg0000](/datasets/md/55.md#visium-spatial-gene-expression-pancreas-cswvu1clqhxbm4vg0000), [visium-spatial-gene-expression-pancreas-yii40foshfgndmae0000](/datasets/md/85.md#visium-spatial-gene-expression-pancreas-yii40foshfgndmae0000), [visium-spatial-gene-expression-pancreatic-lymph-node-hd9env2mfir6x5rh0000](/datasets/md/fa.md#visium-spatial-gene-expression-pancreatic-lymph-node-hd9env2mfir6x5rh0000), [visium-spatial-gene-expression-pancreas-clg39wpvjd9eizrn0000](/datasets/md/1a.md#visium-spatial-gene-expression-pancreas-clg39wpvjd9eizrn0000), [visium-spatial-gene-expression-pancreatic-lymph-node-frimuaoyfnty1doc0000](/datasets/md/60.md#visium-spatial-gene-expression-pancreatic-lymph-node-frimuaoyfnty1doc0000), [visium-spatial-gene-expression-pancreas-9eqcbje6x5pd8hy60000](/datasets/md/e8.md#visium-spatial-gene-expression-pancreas-9eqcbje6x5pd8hy60000), [visium-spatial-gene-expression-pancreatic-lymph-node-geger1lelshsjjln0000](/datasets/md/df.md#visium-spatial-gene-expression-pancreatic-lymph-node-geger1lelshsjjln0000), [visium-spatial-gene-expression-pancreatic-lymph-node-udiymq2qihd6eqhi0000](/datasets/md/3c.md#visium-spatial-gene-expression-pancreatic-lymph-node-udiymq2qihd6eqhi0000), [visium-spatial-gene-expression-pancreas-s4djzdlxa84ontzg0000](/datasets/md/c6.md#visium-spatial-gene-expression-pancreas-s4djzdlxa84ontzg0000) ## Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain [spatial transcriptomics] - Page: /collections/geo-gse296789/ - Kind: replicates - Datasets: 21 - Reference: PMID:42241279 - Design: We obtained tissue blocks of postmortem human brain containing dACC from 10 neurotypical adult brain donors. We used the 10x Genomics Visium and 3’ Single Cell Gene Expression platforms to generate paired spatial transcriptomics and single-nucleus RNA-seq data of the human dACC. We performed a second spatial transcriptomics experiment using the Visium Spatial Proteogenomics (Visium-SPG) platform for four of the 10 donors. *************************************************************** Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data. *************************************************************** - Members: [visium-spatial-gene-expression-anterior-cingulate-cortex-ghfsihjhgksnjbqq0000](/datasets/md/67.md#visium-spatial-gene-expression-anterior-cingulate-cortex-ghfsihjhgksnjbqq0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-greodwx77pzqphnu0000](/datasets/md/a6.md#visium-spatial-gene-expression-anterior-cingulate-cortex-greodwx77pzqphnu0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-7ve5ovdgydddw9ad0000](/datasets/md/e3.md#visium-spatial-gene-expression-anterior-cingulate-cortex-7ve5ovdgydddw9ad0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-bet78tluamp8ao7l0000](/datasets/md/09.md#visium-spatial-gene-expression-anterior-cingulate-cortex-bet78tluamp8ao7l0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-ntvwa3nyzjusgunc0000](/datasets/md/1c.md#visium-spatial-gene-expression-anterior-cingulate-cortex-ntvwa3nyzjusgunc0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-n8km6ht6vqgpvqsb0000](/datasets/md/06.md#visium-spatial-gene-expression-anterior-cingulate-cortex-n8km6ht6vqgpvqsb0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-az6s2wqbpjhz5oyk0000](/datasets/md/73.md#visium-spatial-gene-expression-anterior-cingulate-cortex-az6s2wqbpjhz5oyk0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-7mphgedsojfw1n3w0000](/datasets/md/4a.md#visium-spatial-gene-expression-anterior-cingulate-cortex-7mphgedsojfw1n3w0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-6m20y9d1w7ae2gly0000](/datasets/md/63.md#visium-spatial-gene-expression-anterior-cingulate-cortex-6m20y9d1w7ae2gly0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-ntfo1qngtgow4ske0000](/datasets/md/fb.md#visium-spatial-gene-expression-anterior-cingulate-cortex-ntfo1qngtgow4ske0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-j7aadyuy2cfppnil0000](/datasets/md/20.md#visium-spatial-gene-expression-anterior-cingulate-cortex-j7aadyuy2cfppnil0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-uv5d9tnzeac0g8ts0000](/datasets/md/b8.md#visium-spatial-gene-expression-anterior-cingulate-cortex-uv5d9tnzeac0g8ts0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-g97wkoosutwhxma60001](/datasets/md/9d.md#visium-spatial-gene-expression-anterior-cingulate-cortex-g97wkoosutwhxma60001), [visium-spatial-gene-expression-anterior-cingulate-cortex-xukjegrpbjea2zeo0000](/datasets/md/7f.md#visium-spatial-gene-expression-anterior-cingulate-cortex-xukjegrpbjea2zeo0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-q7o08gkkonrwufpu0000](/datasets/md/86.md#visium-spatial-gene-expression-anterior-cingulate-cortex-q7o08gkkonrwufpu0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-3wld9ttdkartgxfg0000](/datasets/md/8c.md#visium-spatial-gene-expression-anterior-cingulate-cortex-3wld9ttdkartgxfg0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-8wvy8q8xas3qoj1n0000](/datasets/md/ed.md#visium-spatial-gene-expression-anterior-cingulate-cortex-8wvy8q8xas3qoj1n0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-7sad0vtpdppiw3xs0000](/datasets/md/97.md#visium-spatial-gene-expression-anterior-cingulate-cortex-7sad0vtpdppiw3xs0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-cudpnekwppyotpoq0000](/datasets/md/cf.md#visium-spatial-gene-expression-anterior-cingulate-cortex-cudpnekwppyotpoq0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-n4z4m2qgvgkepsyy0000](/datasets/md/8a.md#visium-spatial-gene-expression-anterior-cingulate-cortex-n4z4m2qgvgkepsyy0000), [visium-spatial-gene-expression-anterior-cingulate-cortex-phf1m9jgzvnqjmth0000](/datasets/md/d0.md#visium-spatial-gene-expression-anterior-cingulate-cortex-phf1m9jgzvnqjmth0000) ## In silico reconstruction of primary and metastatic tumor architecture using GIS-augmented spatial transcriptomics - Page: /collections/geo-gse298286/ - Kind: other - Datasets: 12 - Reference: PMID:41734374 - Design: Twelve primary and metastatic bone tumor samples from estrogen receptor positive metastatic breast cancer patients were analyzed using spatial transcriptomics. Two additional primary and metastatic bone tumor samples were analyzed using spatial transcriptomics and proteomics. - Members: [visium-spatial-gene-expression-bone-tissue-ytnznbz7ptt4b1te0000](/datasets/md/4c.md#visium-spatial-gene-expression-bone-tissue-ytnznbz7ptt4b1te0000), [visium-spatial-gene-expression-bone-tissue-wjel31swozk9dsks0000](/datasets/md/15.md#visium-spatial-gene-expression-bone-tissue-wjel31swozk9dsks0000), [visium-spatial-gene-expression-bone-tissue-c1j4hj9qoftw42d50000](/datasets/md/9b.md#visium-spatial-gene-expression-bone-tissue-c1j4hj9qoftw42d50000), [visium-spatial-gene-expression-breast-42pffp7l0gohi7uz0000](/datasets/md/47.md#visium-spatial-gene-expression-breast-42pffp7l0gohi7uz0000), [visium-spatial-gene-expression-bone-tissue-m2ljcyeq2ohbfhvp0000](/datasets/md/3c.md#visium-spatial-gene-expression-bone-tissue-m2ljcyeq2ohbfhvp0000), [visium-spatial-gene-expression-breast-z8smynoj3amzssfd0000](/datasets/md/87.md#visium-spatial-gene-expression-breast-z8smynoj3amzssfd0000), [visium-spatial-gene-expression-bone-tissue-fgoqjnuef1ictvfa0000](/datasets/md/40.md#visium-spatial-gene-expression-bone-tissue-fgoqjnuef1ictvfa0000), [visium-spatial-gene-expression-breast-havhoynzrunahkdk0000](/datasets/md/95.md#visium-spatial-gene-expression-breast-havhoynzrunahkdk0000), [visium-spatial-gene-expression-breast-9afr9rvvm8ans7km0000](/datasets/md/56.md#visium-spatial-gene-expression-breast-9afr9rvvm8ans7km0000), [visium-spatial-gene-expression-bone-tissue-xewjpitvo3k4npip0000](/datasets/md/5e.md#visium-spatial-gene-expression-bone-tissue-xewjpitvo3k4npip0000), [visium-spatial-gene-expression-bone-tissue-tw7mhlkmgtnhafpo0000](/datasets/md/da.md#visium-spatial-gene-expression-bone-tissue-tw7mhlkmgtnhafpo0000), [visium-spatial-gene-expression-breast-qbmivzta1undi7jo0000](/datasets/md/83.md#visium-spatial-gene-expression-breast-qbmivzta1undi7jo0000) ## Profiling the Microenvironment in Tuberous Sclerosis Complex-Associated Angiomyolipoma: Insights from Spatial Gene Expression Analysis - Page: /collections/geo-gse299165/ - Kind: comparison - Datasets: 3 - Reference: PMID:41309810 - Design: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from one TSC-associated AML, one sporadic AML, and one RCC case were analyzed using the CytAssist Visium spatial transcriptomics platform. Comparative analysis aimed to identify transcriptional differences among the three tumor types while preserving spatial context. - Members: [visium-spatial-gene-expression-kidney-inw7ifkuusoljz2k0001](/datasets/md/ed.md#visium-spatial-gene-expression-kidney-inw7ifkuusoljz2k0001), [visium-spatial-gene-expression-kidney-jtucmwbshywbqhsg0000](/datasets/md/90.md#visium-spatial-gene-expression-kidney-jtucmwbshywbqhsg0000), [visium-spatial-gene-expression-kidney-cifntendyu3dcqi30000](/datasets/md/d6.md#visium-spatial-gene-expression-kidney-cifntendyu3dcqi30000) ## Spatial transcriptomic profiling of seborrhoeic keratoses - Page: /collections/geo-gse299660/ - Kind: other - Datasets: 4 - Reference: PMID:42413572 - Design: The dataset is comprised of different subtypes of seborrhoeic keratoses with and without immune cell infiltration. - Members: [visium-spatial-gene-expression-zone-of-skin-y7ds4kj6swfxi1fw0000](/datasets/md/89.md#visium-spatial-gene-expression-zone-of-skin-y7ds4kj6swfxi1fw0000), [visium-spatial-gene-expression-zone-of-skin-2uarmyqrciqja4wr0000](/datasets/md/28.md#visium-spatial-gene-expression-zone-of-skin-2uarmyqrciqja4wr0000), [visium-spatial-gene-expression-zone-of-skin-ecuwewtwebguzglx0000](/datasets/md/fb.md#visium-spatial-gene-expression-zone-of-skin-ecuwewtwebguzglx0000), [visium-spatial-gene-expression-zone-of-skin-yfzuml4pnjz7k7ym0000](/datasets/md/3c.md#visium-spatial-gene-expression-zone-of-skin-yfzuml4pnjz7k7ym0000) ## Single-cell and spatial transcriptomic analyses of gene therapy-associated retinal inflammation in non-human primates - Page: /collections/geo-gse304504/ - Kind: time course - Datasets: 4 - Reference: PMID:42137601 - Design: NHPs received subretinal injections of AAV vectors as follows: NHP1 AAV2-CAG-hRPE65 in both eyes; NHP2 AAV8-GRK1-mScarlet AND AAV8-GRK1-hRPGR in two separate blebs per eye. Retinal biopsies were taken from injected blebs, as well as an uninjected control area. - Members: [visium-spatial-gene-expression-retina-tto8rncx1jnvfdzf0000](/datasets/md/e0.md#visium-spatial-gene-expression-retina-tto8rncx1jnvfdzf0000), [visium-spatial-gene-expression-retina-vtlvjhwv09cowcj80000](/datasets/md/cf.md#visium-spatial-gene-expression-retina-vtlvjhwv09cowcj80000), [visium-spatial-gene-expression-retina-e27plcmnderkihii0000](/datasets/md/c3.md#visium-spatial-gene-expression-retina-e27plcmnderkihii0000), [visium-spatial-gene-expression-retina-gdx1luyjts3oqfve0000](/datasets/md/0e.md#visium-spatial-gene-expression-retina-gdx1luyjts3oqfve0000) ## Schizophrenia-linked gene expression changes across cortical layers and cellular microenvironments in human prefrontal cortex [Visium] - Page: /collections/geo-gse307403/ - Kind: replicates - Datasets: 62 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE307403 - Design: The study includes fresh-frozen postmortem human brain tissue sections obtained from the dorsolateral prefrontal cortex (DLPFC) of 32 donors with schizophrenia (SCZ) and 31 neurotypical controls (NTC). A single 10-µm-thick cryosection per donor was analyzed using the 10x Genomics Visium spatial transcriptomics platform (v1, 3' Gene Expression), yielding a total of 63 samples. The primary comparison was made between diagnostic groups: 32 SCZ samples and 31 NTC samples. *************************************************************** Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data. *************************************************************** - Members: [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-nw5d4zzndxfmt1t70000](/datasets/md/5c.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-nw5d4zzndxfmt1t70000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-kw4ibodtyrhxl7ev0000](/datasets/md/66.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-kw4ibodtyrhxl7ev0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-m6uspmesdld9wn2c0000](/datasets/md/35.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-m6uspmesdld9wn2c0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-n0yqddzvnxnnz13l0000](/datasets/md/59.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-n0yqddzvnxnnz13l0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-eke2922uejro1jsu0000](/datasets/md/79.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-eke2922uejro1jsu0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-6sndvrmjovmljbaz0000](/datasets/md/2c.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-6sndvrmjovmljbaz0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-dqnigwjpa59gwidw0000](/datasets/md/b2.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-dqnigwjpa59gwidw0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-jw0lflcbrvcz2c6y0000](/datasets/md/e8.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-jw0lflcbrvcz2c6y0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-8zupwpfzcuujlof80000](/datasets/md/43.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-8zupwpfzcuujlof80000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-sjs7x781k7hg4j7w0000](/datasets/md/56.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-sjs7x781k7hg4j7w0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-t13j8xplgz1o0deq0000](/datasets/md/98.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-t13j8xplgz1o0deq0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-yt2pilxrtubuirr70000](/datasets/md/3f.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-yt2pilxrtubuirr70000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-bjx5k3exgboh3gwr0000](/datasets/md/cd.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-bjx5k3exgboh3gwr0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-gsfezppgbtkouqho0000](/datasets/md/c4.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-gsfezppgbtkouqho0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-2svoiz1aprre8g4w0000](/datasets/md/08.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-2svoiz1aprre8g4w0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-x6ewki0sqd6sgjjx0000](/datasets/md/be.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-x6ewki0sqd6sgjjx0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-nsecltibr9tzqual0000](/datasets/md/2c.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-nsecltibr9tzqual0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-z7kdcmrk3w5nlwqb0000](/datasets/md/70.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-z7kdcmrk3w5nlwqb0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-j7b8n0rnhye8jiai0000](/datasets/md/77.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-j7b8n0rnhye8jiai0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ffu7oxhdbet4rndr0000](/datasets/md/c8.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ffu7oxhdbet4rndr0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-gn9z6m3ukqmalhhu0000](/datasets/md/96.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-gn9z6m3ukqmalhhu0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-4zljqbme3ao0r7fp0000](/datasets/md/be.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-4zljqbme3ao0r7fp0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-0mcocd8l5jehbnh10000](/datasets/md/13.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-0mcocd8l5jehbnh10000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-5limlkzqcj8nl4wd0000](/datasets/md/8a.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-5limlkzqcj8nl4wd0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-xwdjzemkm6x1axtq0000](/datasets/md/6e.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-xwdjzemkm6x1axtq0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-n6lsdhogydgvx8h30000](/datasets/md/7c.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-n6lsdhogydgvx8h30000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-uatffxo3y75w2bug0000](/datasets/md/fd.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-uatffxo3y75w2bug0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-cshbvixcj7y5pvja0000](/datasets/md/2c.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-cshbvixcj7y5pvja0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-2qgjqqr6qkkkkwx50000](/datasets/md/58.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-2qgjqqr6qkkkkwx50000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-diy3fo7qhe2pewjj0000](/datasets/md/91.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-diy3fo7qhe2pewjj0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-sotbiodinheijj8k0000](/datasets/md/24.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-sotbiodinheijj8k0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-peq7poofcc1d0efw0000](/datasets/md/53.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-peq7poofcc1d0efw0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-dfkqso7aekohds5m0000](/datasets/md/f3.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-dfkqso7aekohds5m0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-hflxkxv6xhcedhzx0000](/datasets/md/ab.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-hflxkxv6xhcedhzx0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-jtnuizu1v0lziave0000](/datasets/md/50.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-jtnuizu1v0lziave0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-a3ojmdptqifykvu40000](/datasets/md/28.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-a3ojmdptqifykvu40000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ajxo1rjji26ozdyd0000](/datasets/md/ae.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ajxo1rjji26ozdyd0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-uqaukrxlal3wxfat0000](/datasets/md/fd.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-uqaukrxlal3wxfat0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-vlwewqlez1pn1m1g0000](/datasets/md/14.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-vlwewqlez1pn1m1g0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-mhuh1pjqdogm8mjd0000](/datasets/md/ce.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-mhuh1pjqdogm8mjd0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-mcqxkrjo8duwgdvt0000](/datasets/md/9d.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-mcqxkrjo8duwgdvt0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-3wdmig08tauifmzf0000](/datasets/md/c3.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-3wdmig08tauifmzf0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-uwiear0alhzsv5bv0000](/datasets/md/f3.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-uwiear0alhzsv5bv0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-gf72yj1tqt9q0mut0000](/datasets/md/2f.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-gf72yj1tqt9q0mut0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-hoyman9vfpmhstbn0000](/datasets/md/7c.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-hoyman9vfpmhstbn0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-lvcms8buwylvjwfk0000](/datasets/md/40.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-lvcms8buwylvjwfk0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-4rcazv0gciugbwkx0000](/datasets/md/fb.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-4rcazv0gciugbwkx0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-mjdjihbea4v23cvc0000](/datasets/md/8c.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-mjdjihbea4v23cvc0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-wvyfw7ts4agzuzqa0000](/datasets/md/0b.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-wvyfw7ts4agzuzqa0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ifnuvsgd6lux3yxi0000](/datasets/md/2c.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ifnuvsgd6lux3yxi0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-lytrdqixws4ect7t0000](/datasets/md/2e.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-lytrdqixws4ect7t0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-wb176yy5zf7kfe8s0000](/datasets/md/ff.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-wb176yy5zf7kfe8s0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-fcn6lhoilcn1zpwk0000](/datasets/md/9b.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-fcn6lhoilcn1zpwk0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-fj3pfv173h9gaidz0000](/datasets/md/36.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-fj3pfv173h9gaidz0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-im6gaccipqdtq6nv0000](/datasets/md/bb.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-im6gaccipqdtq6nv0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ejgkpittmt19ylkg0000](/datasets/md/55.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ejgkpittmt19ylkg0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-6rajuuelep8tpnkw0000](/datasets/md/24.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-6rajuuelep8tpnkw0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-beak1dbv8roimjvz0000](/datasets/md/df.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-beak1dbv8roimjvz0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-eac18kk4eckffarz0000](/datasets/md/c0.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-eac18kk4eckffarz0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ilykhg8vgbte2tri0000](/datasets/md/e3.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-ilykhg8vgbte2tri0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-axnp86u9uikvtzam0000](/datasets/md/58.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-axnp86u9uikvtzam0000), [visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-iwm5ns5xhaf9fo330000](/datasets/md/51.md#visium-spatial-gene-expression-dorsolateral-prefrontal-cortex-iwm5ns5xhaf9fo330000) ## Hypoxia inducible factor network reflects kidney disease progression in diabetes and sodium-glucose co-transporters inhibition. - Page: /collections/geo-gse317226/ - Kind: publication - Datasets: 4 - Reference: 10.1038/s41392-026-02653-0 - Design: Formalin fixed paraffin embedded (FFPE) biopsy cores from four individuals with type 2 diabetes (T2D) not treated with SGLT2i were sectioned, placed on a slide, and run through the VisiumHD platform (v1; 10x). Each slide is comprised of a grid of 8 um by 8 um squares and each square or spot is covered in a lawn of one unique barcode identifier that anneals to any RNA within that grid space. *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. *************************************************************** - Members: [visium-hd-kidney-evwiddojjpqrifei0000](/datasets/md/dd.md#visium-hd-kidney-evwiddojjpqrifei0000), [visium-hd-kidney-sw5atclwij7ysypj0000](/datasets/md/63.md#visium-hd-kidney-sw5atclwij7ysypj0000), [visium-hd-kidney-onzzwz2qfhhgmn2r0000](/datasets/md/d9.md#visium-hd-kidney-onzzwz2qfhhgmn2r0000), [visium-hd-kidney-bv10bjqz5kli5nmu0000](/datasets/md/15.md#visium-hd-kidney-bv10bjqz5kli5nmu0000) ## Inflammatory immune modulators of AML lung infiltration and respiratory failure - Page: /collections/geo-gse319763/ - Kind: comparison - Datasets: 3 - Design: Spatial Transcriptomics Xenium (5k plex planel) on paraffin sections from Normal and AML-infiltrated anonymized human lung biopsies. - Members: [10x-xenium-lung-rdg9xtwitzkujb9g0000](/datasets/md/c4.md#10x-xenium-lung-rdg9xtwitzkujb9g0000), [10x-xenium-lung-zahza4mmarne4xvy0000](/datasets/md/b9.md#10x-xenium-lung-zahza4mmarne4xvy0000), [10x-xenium-lung-4fiksindul6y1d9z0000](/datasets/md/93.md#10x-xenium-lung-4fiksindul6y1d9z0000) ## Interleukin-34 induced Arg1+ macrophages play a key role in breast cancer brain metastasis - Page: /collections/geo-gse325996/ - Kind: other - Datasets: 2 - Reference: PMID:42166785 - Design: To study the tumorenvironment and the cell types present in those breast cancer brain metastases, we generated spatial transcriptomics data from two biological replicates of the cerebellar BCBM generated from HP organoids. - Members: [visium-spatial-gene-expression-brain-k1rlg2yy5069migq0000](/datasets/md/13.md#visium-spatial-gene-expression-brain-k1rlg2yy5069migq0000), [visium-spatial-gene-expression-brain-hvr2exfs9ivl4x1u0000](/datasets/md/40.md#visium-spatial-gene-expression-brain-hvr2exfs9ivl4x1u0000) ## Pericyte K<sub>ATP</sub> channel hyperactivity redistributes cortical blood flow in a CADASIL mouse model. - Page: /collections/geo-gse335702/ - Kind: comparison - Datasets: 8 - Reference: 10.1038/s44161-026-00844-0 - Design: Spatial gene expression profiling of mouse brain and isolated cerebral vasculature comparing TgNotch3^WT (control) and TgNotch3^R169C (CADASIL model) transgenic mice, using 10x Genomics Visium CytAssist (FFPE, Mouse Transcriptome Probe Set v1.0, mm10-2020-A). 2023 batch: 4 standard Visium samples processed with Space Ranger 2.0.1 (cerebral vessel samples manually aligned). 2024 batch: 4 Visium HD samples processed with Space Ranger 3.1.1 (8 um bin submitted). - Members: [visium-hd-brain-modwllfdgqab1kdg0000](/datasets/md/d1.md#visium-hd-brain-modwllfdgqab1kdg0000), [visium-hd-brain-zmfhjkr2uerajwvb0000](/datasets/md/86.md#visium-hd-brain-zmfhjkr2uerajwvb0000), [visium-hd-brain-msqlvc4lxfz5oufn0000](/datasets/md/5a.md#visium-hd-brain-msqlvc4lxfz5oufn0000), [visium-hd-brain-995ozkuuvgtlqdbo0000](/datasets/md/c5.md#visium-hd-brain-995ozkuuvgtlqdbo0000), [visium-spatial-gene-expression-brain-hjsuy7aompwzsyz20001](/datasets/md/d0.md#visium-spatial-gene-expression-brain-hjsuy7aompwzsyz20001), [visium-spatial-gene-expression-brain-tbjlmdbkxa4aqaew0000](/datasets/md/45.md#visium-spatial-gene-expression-brain-tbjlmdbkxa4aqaew0000), [visium-spatial-gene-expression-cerebral-blood-vessel-ki8ggxo6splhrbdg0000](/datasets/md/d2.md#visium-spatial-gene-expression-cerebral-blood-vessel-ki8ggxo6splhrbdg0000), [visium-spatial-gene-expression-cerebral-blood-vessel-nmhfck98muzofmix0000](/datasets/md/2b.md#visium-spatial-gene-expression-cerebral-blood-vessel-nmhfck98muzofmix0000) ## Mapping the Tissue Architecture and Endothelial-PEC Network in Hepatic Angiomyolipoma Using Single-cell and Spatial Transcriptomics [Spatial Transcriptomics] - Page: /collections/geo-gse344843/ - Kind: other - Datasets: 3 - Reference: PMID:42841778 - Design: This study employed an integrated multi-omics approach to characterize the cellular and spatial landscape of hepatic angiomyolipoma (HAML). Fresh tumor and paired normal tissues from one patient were processed for single-nucleus RNA sequencing (snRNA-seq) using the 10x Genomics platform. For spatial transcriptomics (ST), FFPE sections from three HAML specimens were mounted on Visium slides, processed for H&E staining, and sequenced to generate spatially resolved gene expression profiles. snRNA-seq data were quality-controlled and clustered using Seurat, with cell types annotated via canonical markers and SingleR. ST data were analyzed with SpaceRanger and Seurat, and cell-type deconvolution was performed using Robust Cell Type Decomposition (RCTD) and Multimodal Intersection Analysis (MIA) to map snRNA-seq-defined populations onto tissue sections. PEC characterization included differential expression, pseudotime trajectory (Monocle2), transcription factor regulatory network (SCENIC), and copy number variation (InferCNV) analyses. Cell–cell communication was inferred using CellChat. Validation experiments included immunohistochemistry, immunofluorescence, and western blotting for selected markers and signaling pathways in paired tumor and normal tissues. - Members: [visium-spatial-gene-expression-liver-47ukxghoxfxpnqbu0001](/datasets/md/10.md#visium-spatial-gene-expression-liver-47ukxghoxfxpnqbu0001), [visium-spatial-gene-expression-liver-vxzhppqa4mpytj8e0000](/datasets/md/c6.md#visium-spatial-gene-expression-liver-vxzhppqa4mpytj8e0000), [visium-spatial-gene-expression-liver-n0zetr5adfuzjdb70000](/datasets/md/00.md#visium-spatial-gene-expression-liver-n0zetr5adfuzjdb70000) ## T cell-mediated microglial activation triggers myelin pathology in a mouse model of amyloidosis. - Page: /collections/geo-gse243120/ - Kind: publication - Datasets: 5 - Reference: 10.1038/s41593-024-01682-8 - Members: [vizgen-merscope-brain-aelh8tjyrbavogvj0000](/datasets/md/57.md#vizgen-merscope-brain-aelh8tjyrbavogvj0000), [vizgen-merscope-brain-hhvg9yohbdwhduds0000](/datasets/md/91.md#vizgen-merscope-brain-hhvg9yohbdwhduds0000), [vizgen-merscope-brain-hzrmfjcth8wijaez0000](/datasets/md/85.md#vizgen-merscope-brain-hzrmfjcth8wijaez0000), [vizgen-merscope-brain-vid9g1qvx0jnxfnt0000](/datasets/md/2f.md#vizgen-merscope-brain-vid9g1qvx0jnxfnt0000), [vizgen-merscope-brain-hohst99nzb18lqji0000](/datasets/md/7f.md#vizgen-merscope-brain-hohst99nzb18lqji0000) ## geo-gse267315 - Page: /collections/geo-gse267315/ - Kind: other - Datasets: 4 - Members: [stereo-seq-ovary-fqkpd5las74ns6xl0000](/datasets/md/62.md#stereo-seq-ovary-fqkpd5las74ns6xl0000), [stereo-seq-ovary-xsfqdwf2kmalbsox0000](/datasets/md/fd.md#stereo-seq-ovary-xsfqdwf2kmalbsox0000), [stereo-seq-ovary-c92wndu8iwxbey6d0000](/datasets/md/e2.md#stereo-seq-ovary-c92wndu8iwxbey6d0000), [stereo-seq-ovary-mqgoobslv0xfowxo0000](/datasets/md/ae.md#stereo-seq-ovary-mqgoobslv0xfowxo0000) ## geo-gse222383 - Page: /collections/geo-gse222383/ - Kind: other - Datasets: 1 - Members: [stereo-seq-brain-qmzn8kmzwsyuf0q10000](/datasets/md/88.md#stereo-seq-brain-qmzn8kmzwsyuf0q10000)