# SpatialData-DB collections, shard 2 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. ## Spatiotemporal single-cell profiling reveals T cell clonal dynamics and phenotypic plasticity in human graft-versus-host disease. - Page: /collections/geo-gse307215-gvhd-gut/ - Kind: publication - Datasets: 8 - Reference: 10.1038/s41590-026-02631-2 - Design: A multimodal, longitudinal study integrating pre-transplant MLR-based alloreactive T cell fingerprinting, time-series bulk TCR sequencing in peripheral blood, and single-cell RNA/TCR-seq and high-resolution spatial transcriptomics of gut biopsies to resolve the clonal, phenotypic, and spatial dynamics of T cells in human GVHD from patients following allogeneic hematopoietic cell transplantation (alloHCT). - Members: [visium-hd-intestine-tjh4dtk27dsixjfl0000](/datasets/md/37.md#visium-hd-intestine-tjh4dtk27dsixjfl0000), [visium-hd-intestine-rthvgk7nalatfzpc0000](/datasets/md/14.md#visium-hd-intestine-rthvgk7nalatfzpc0000), [visium-hd-intestine-w99j3sgoeu0qjecr0000](/datasets/md/7d.md#visium-hd-intestine-w99j3sgoeu0qjecr0000), [visium-hd-intestine-eloxdggapws0gky00000](/datasets/md/2c.md#visium-hd-intestine-eloxdggapws0gky00000), [visium-hd-intestine-bpx9eapm9ikwcmym0000](/datasets/md/47.md#visium-hd-intestine-bpx9eapm9ikwcmym0000), [visium-hd-intestine-jfs0efhnhs5lebu70000](/datasets/md/f8.md#visium-hd-intestine-jfs0efhnhs5lebu70000), [visium-hd-intestine-f5cr2dmhhwncakas0000](/datasets/md/e4.md#visium-hd-intestine-f5cr2dmhhwncakas0000), [visium-hd-intestine-alhphciycr1gxyj80000](/datasets/md/e7.md#visium-hd-intestine-alhphciycr1gxyj80000) ## 10x-ffpe-human-brain-cancer-human-immuno-oncology-profiling-panel-custom-add-on - Page: /collections/10x-ffpe-human-brain-cancer-human-immuno-oncology-profiling-panel-custom-add-on/ - Kind: other - Datasets: 1 - Members: [10x-xenium-brain-ihsxybfbeamn3zxa0001](/datasets/md/db.md#10x-xenium-brain-ihsxybfbeamn3zxa0001) ## 10x-human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard - Page: /collections/10x-human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard/ - Kind: other - Datasets: 2 - Members: [10x-xenium-colon-zculrf9ps0sifyjc0001](/datasets/md/24.md#10x-xenium-colon-zculrf9ps0sifyjc0001), [10x-xenium-colon-ojcc9qmt64w5g87p0001](/datasets/md/d1.md#10x-xenium-colon-ojcc9qmt64w5g87p0001) ## Spatial mapping of the total transcriptome by in situ polyadenylation. - Page: /collections/doi-10-1038-s41587-022-01517-6/ - Kind: comparison - Datasets: 7 - Reference: 10.1038/s41587-022-01517-6 - Members: [visium-spatial-gene-expression-skeletal-muscle-tissue-jdj6hhh4soldeywf0000](/datasets/md/e2.md#visium-spatial-gene-expression-skeletal-muscle-tissue-jdj6hhh4soldeywf0000), [visium-spatial-gene-expression-skeletal-muscle-tissue-iuhwzylkhiwge93e0000](/datasets/md/ac.md#visium-spatial-gene-expression-skeletal-muscle-tissue-iuhwzylkhiwge93e0000), [visium-spatial-gene-expression-skeletal-muscle-tissue-3cjkiuk3yctvwhlw0000](/datasets/md/ac.md#visium-spatial-gene-expression-skeletal-muscle-tissue-3cjkiuk3yctvwhlw0000), [visium-spatial-gene-expression-skeletal-muscle-tissue-r3fosx88vvhntnii0000](/datasets/md/57.md#visium-spatial-gene-expression-skeletal-muscle-tissue-r3fosx88vvhntnii0000), [visium-spatial-gene-expression-skeletal-muscle-tissue-71kbxteocpzp1ul30000](/datasets/md/4a.md#visium-spatial-gene-expression-skeletal-muscle-tissue-71kbxteocpzp1ul30000), [visium-spatial-gene-expression-skeletal-muscle-tissue-ozmtkfnj4r8cuamo0000](/datasets/md/4a.md#visium-spatial-gene-expression-skeletal-muscle-tissue-ozmtkfnj4r8cuamo0000), [visium-spatial-gene-expression-skeletal-muscle-tissue-k7uqsprpmbnr31rb0000](/datasets/md/ee.md#visium-spatial-gene-expression-skeletal-muscle-tissue-k7uqsprpmbnr31rb0000) ## Single-cell transcriptomic analysis of endometriosis. - Page: /collections/doi-10-1038-s41588-022-01254-1/ - Kind: publication - Datasets: 2 - Reference: 10.1038/s41588-022-01254-1 - Members: [visium-spatial-gene-expression-uterus-geix6qkoftjeoukp0000](/datasets/md/fa.md#visium-spatial-gene-expression-uterus-geix6qkoftjeoukp0000), [visium-spatial-gene-expression-uterus-vjokfgowb7foedu20000](/datasets/md/1a.md#visium-spatial-gene-expression-uterus-vjokfgowb7foedu20000) ## TREM1 + regulatory myeloid cells expand in steatohepatitis-HCC and associate with poor prognosis and therapeutic resistance to immune checkpoint blockade - Page: /collections/doi-10-1101-2022-11-09-515839/ - Kind: replicates - Datasets: 2 - Reference: 10.1101/2022.11.09.515839 - Members: [visium-spatial-gene-expression-liver-vpnsjlpbfylwnxhc0000](/datasets/md/53.md#visium-spatial-gene-expression-liver-vpnsjlpbfylwnxhc0000), [visium-spatial-gene-expression-liver-flnv2snjfpvti2p90000](/datasets/md/20.md#visium-spatial-gene-expression-liver-flnv2snjfpvti2p90000) ## Spotiphy: generative modeling in single-cell spatial whole transcriptomics - Page: /collections/doi-10-5281-zenodo-10520022/ - Kind: comparison - Datasets: 2 - Reference: 10.5281/zenodo.10520022 - Members: [visium-spatial-gene-expression-brain-yl0e3r7l9tec5zrr0000](/datasets/md/79.md#visium-spatial-gene-expression-brain-yl0e3r7l9tec5zrr0000), [visium-spatial-gene-expression-brain-ohcc5opsxgyogp8c0000](/datasets/md/37.md#visium-spatial-gene-expression-brain-ohcc5opsxgyogp8c0000) ## The spatial landscape of gene expression isoforms in tissue sections - Page: /collections/geo-gse153859/ - Kind: other - Datasets: 3 - Reference: PMID:36928528 - Design: Visium Spatial Transcriptomics profiles of 2 mouse hippocampal samples (CBS1, CBS2) and 1 mouse olfactory bulk sample (MOB) sequence with short (illumina) and long (Nanopore) reads. - Members: [visium-spatial-gene-expression-hippocampal-formation-0dnopd5zwse5gguy0000](/datasets/md/04.md#visium-spatial-gene-expression-hippocampal-formation-0dnopd5zwse5gguy0000), [visium-spatial-gene-expression-olfactory-bulb-vgrdans9c9uuoetw0000](/datasets/md/d4.md#visium-spatial-gene-expression-olfactory-bulb-vgrdans9c9uuoetw0000), [visium-spatial-gene-expression-hippocampal-formation-hm3cgzhjtup5nltp0000](/datasets/md/e0.md#visium-spatial-gene-expression-hippocampal-formation-hm3cgzhjtup5nltp0000) ## Cell type inference in human lung tissue by domain adaptation of single-cell and spatial transcriptomic data - Page: /collections/geo-gse172416/ - Kind: other - Datasets: 2 - Reference: PMID:35191503 - Design: Two normal lung samples were acquired from lung specimen from one patient who underwent surgical resection for lung cancer. The samples were cryosectioned and processed for Visium Spatial Transcritpomic analysis. - Members: [visium-spatial-gene-expression-lung-vwol9tzgufcl5lgt0000](/datasets/md/b8.md#visium-spatial-gene-expression-lung-vwol9tzgufcl5lgt0000), [visium-spatial-gene-expression-lung-uojkw2adljukkhsa0000](/datasets/md/b1.md#visium-spatial-gene-expression-lung-uojkw2adljukkhsa0000) ## Spatial transcriptomics of human brain metastases - Page: /collections/geo-gse179572/ - Kind: replicates - Datasets: 6 - Reference: PMID:35584630 - Design: After surgical resection, parts of six human brain metastases were embedded in OCT and frozen in a dry ice/2-methylbutane bath. 10 μM sections were placed on Visium gene expression slides which were stored at -80C until use. Slides were methanol fixed and stained with H&E and imaged at 10X on a Biotek Lionheart microscope. Tissues were permeabilized and libraries generated according to the manufacturer's protocols. Images for all samples are available in all_spatial_images.tar.gz. - Members: [visium-spatial-gene-expression-brain-bpht1hc9gkb6atk30000](/datasets/md/56.md#visium-spatial-gene-expression-brain-bpht1hc9gkb6atk30000), [visium-spatial-gene-expression-brain-xwdtx4apeuwo19ko0000](/datasets/md/f5.md#visium-spatial-gene-expression-brain-xwdtx4apeuwo19ko0000), [visium-spatial-gene-expression-brain-o8k14yfdockrld0x0000](/datasets/md/cd.md#visium-spatial-gene-expression-brain-o8k14yfdockrld0x0000), [visium-spatial-gene-expression-brain-5bseuml4hyxpdggb0000](/datasets/md/d3.md#visium-spatial-gene-expression-brain-5bseuml4hyxpdggb0000), [visium-spatial-gene-expression-brain-89zsz2pvjz1mkovl0000](/datasets/md/d8.md#visium-spatial-gene-expression-brain-89zsz2pvjz1mkovl0000), [visium-spatial-gene-expression-brain-deckdgwpftxxaqcr0000](/datasets/md/8b.md#visium-spatial-gene-expression-brain-deckdgwpftxxaqcr0000) ## Spatial Multi-omics Reveals the Heterogeneity of Tumor Microenvironment in the OSF-Associated OSCC - Page: /collections/geo-gse220978/ - Kind: replicates - Datasets: 4 - Reference: PMID:38229179 - Design: Samples from 4 OSF-associated OSCC patients were analysed by Spatial Transcriptomics sequencing (ST) and airflow-assisted desorption electrospray ionization-mass spectrometry imaging (AFADESI-MSI) - Members: [visium-spatial-gene-expression-mouth-yxjovfqsb2jys3w50000](/datasets/md/fe.md#visium-spatial-gene-expression-mouth-yxjovfqsb2jys3w50000), [visium-spatial-gene-expression-mouth-md2tnyhkh1wx6lw90000](/datasets/md/d4.md#visium-spatial-gene-expression-mouth-md2tnyhkh1wx6lw90000), [visium-spatial-gene-expression-mouth-c7cqcqlhh5aupp0x0000](/datasets/md/d5.md#visium-spatial-gene-expression-mouth-c7cqcqlhh5aupp0x0000), [visium-spatial-gene-expression-mouth-vyolxdrijjzvf0hs0000](/datasets/md/85.md#visium-spatial-gene-expression-mouth-vyolxdrijjzvf0hs0000) ## Time-series spatial transcriptomic analysis of murine colon undergoing AOM-DSS tumorigenesis with and without LXR activation - Page: /collections/geo-gse227598/ - Kind: time course - Datasets: 5 - Reference: PMID:39567700 - Design: Wild type C57BL/6J male mice were fed with either a control (standard) diet or a diet with LXR agonist GW3965. Mice were injected with 10mg/kg body weight azoxymethane (AOM). One week after AOM injection, mice were exposed to DSS in drinking water for 7 days followed by 7 days of recovery (DSS-cycle). This DSS cycle was repeated two more times for a total of 3 times with 7 days between each cycle. Colonic Swiss rolls were collected on day22, day43 or day70 (only for STD Diet) after AOM injection, processed and submitted for sequencing. Colonic Swiss rolls from mice fed with standard (for 43 days, defined as d0 as they were untreated) diet but no AOM or DSS were used as control. - Members: [visium-spatial-gene-expression-colon-ogmlndrngj6doyxn0000](/datasets/md/63.md#visium-spatial-gene-expression-colon-ogmlndrngj6doyxn0000), [visium-spatial-gene-expression-colon-ewuc7e7xdhdlr1s70000](/datasets/md/d8.md#visium-spatial-gene-expression-colon-ewuc7e7xdhdlr1s70000), [visium-spatial-gene-expression-colon-txsrh3xgm44vfett0000](/datasets/md/fe.md#visium-spatial-gene-expression-colon-txsrh3xgm44vfett0000), [visium-spatial-gene-expression-colon-9mxwzubwjc12pguc0000](/datasets/md/5d.md#visium-spatial-gene-expression-colon-9mxwzubwjc12pguc0000), [visium-spatial-gene-expression-colon-hexmiiiglceuxlzt0000](/datasets/md/a2.md#visium-spatial-gene-expression-colon-hexmiiiglceuxlzt0000) ## Pharmacological targeting Netrin-1 inhibits EMT in cancer [Visium] - Page: /collections/geo-gse234266/ - Kind: comparison - Datasets: 2 - Reference: PMID:37532929 - Design: To induce tumorigenesis on Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ (LKPR), Tamoxifen was diluted at 25 mg/ml in sunflower seed oil, 10% EtOH (Sigma). Four daily intraperitoneal (IP) injections of 2.5 mg tamoxifen were administered at P28 to LKPR mice. After 7-9 week after Tamoxifen injection tumour appearance and size were detected by daily observation and palpation. Mice were euthanized when tumour size was reached or when mice presented signs of distress. To determine the effect of anti-Netrin-1 molecule (NP137) on primary tumour, LKPR mice were treated intraperitoneally at 10 mg/kg every two days from 4 weeks after Tamoxifen injection and until the death of animal. Control and NP137-treated skin tumours from LKPR mice were dissected, rinsed one part of the tumors has been kept for immunochemistry. Tumour tissues were pre-fixed in 4% PFA for 2 h at room temperature, rinsed in PBS, before to be embedded in FFPE. To analyze the spatial distribution and localization of different EMT tumors states previously described by scRNA-seq in Control and anti-Netrin-1 treated skin SCC tumors, we used VISIUM technology for spatial transcriptomic analysis (10X Genomics). FFPE tissue section were places on Visium slides and prepared according to 10X Genomics protocols. After H&E staining, imaging and decrosslinking steps, tissue sections were incubated with human specific probes targeting 10,551 genes (10X genomics, Visium Mouse Transcriptome probe Set v1.0). - Members: [visium-spatial-gene-expression-skin-of-body-icpu1hlfpv8enojr0000](/datasets/md/41.md#visium-spatial-gene-expression-skin-of-body-icpu1hlfpv8enojr0000), [visium-spatial-gene-expression-skin-of-body-xdub0kesbbj0mwwu0000](/datasets/md/85.md#visium-spatial-gene-expression-skin-of-body-xdub0kesbbj0mwwu0000) ## A Proteomic Atlas of Atherosclerosis: The Contribution of Proteoglycans to Sex Differences, Plaque Phenotypes and Outcomes - Page: /collections/geo-gse241346/ - Kind: other - Datasets: 2 - Reference: PMID:37646165 - Design: Visium for formalin-fixed paraffin-embedded (FFPE) spatial gene expression slide and reagent kit was used according to manufacturer instructions (PN: 1000338; 10X Genomics). Each capture area (6.5 x 6.5 mm2) contains 5,000 barcoded spots that are 55 μm in diameter (100 μm center-to-center distance) providing an average resolution of 1 to 10 cells. A 5μm tissue section from one carotid plaque sample was placed onto one capture area of a Visium Spatial Gene Expression slide. Two carotid plaque samples were selected from Asymptomatic male patients who undergone carotid endrarterectomy for spatial RNA-seq. Deparaffinization, DAPI immunofluorescence staining, image acquisition and decrosslinking were performed as specified in the Visium Spatial Gene Expression for FFPE – Deparaffinization, Decrosslinking, Immunofluorescence Staining & Imaging protocol (CG000410) and performed at the Core Facility Imaging, Medical University of Vienna. Fluorescent images were acquired with an Olympus IX83 microscope equipped with a Hamamathsu Orca FLash camera for fluorescence image capture. and parameters following those specified in the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide sequencing instructions (read 1: 28 cycles; i7 index read: 10 cycles; i5 index read: 10 cycles; and read 2: 50 cycles) yielding 149 million sequenced reads. The FASTQ files and the manually aligned histology images were analyzed with Space Ranger 1.3.1 and the human probeset provided by 10X genomics (Visium Human Transcriptome Probe Set v1.0 GRCh38-2020-A). Visualization of spatial cluster output from Space Ranger as well as differential gene expression analysis to determine cluster- pecific up- or downregulated genes was performed on Loupe Browser 6.0.0 (10X Genomics). - Members: [visium-spatial-gene-expression-carotid-artery-segment-1nz1fjmjlmhsbwxu0000](/datasets/md/57.md#visium-spatial-gene-expression-carotid-artery-segment-1nz1fjmjlmhsbwxu0000), [visium-spatial-gene-expression-carotid-artery-segment-e0yyit0kah9gz3ul0000](/datasets/md/87.md#visium-spatial-gene-expression-carotid-artery-segment-e0yyit0kah9gz3ul0000) ## Germinal Center Dark Zone harbors ATR-dependent determinants of T-cell exclusion that are also identified in aggressive lymphoma – Visium_FFPE_Spatial_Trasciptomics_project - Page: /collections/geo-gse260998/ - Kind: comparison - Datasets: 2 - Reference: PMID:38562878 - Design: Whole-genome transcriptomic profiling was performed on formalin-fixed tissue sections of mouse FFPE mesenteric lymph nodes from two samples: one with a knocked Aicda gene (B6.129P2-Aicdatm1(cre)Mnz/J, Jackson, RRID no 007770) and the other under wild-type conditions for Aicda gene (B6N;129-Ilktm1Star/J, Jackson, RRID no 023310). grant ID : *22145* grant title: *Linking genetic evolution, stromal and immune contextures to unravel tumor heterogeneity in aggressive B-cell lymphomas* name of the funding source:* A.I.R.C. (Associazione Italiana Ricerca Cancro) * - Members: [visium-spatial-gene-expression-mesenteric-lymph-node-xrr2nuhqjqzzgaq40000](/datasets/md/5d.md#visium-spatial-gene-expression-mesenteric-lymph-node-xrr2nuhqjqzzgaq40000), [visium-spatial-gene-expression-mesenteric-lymph-node-a2nxwr8ailmfe5fz0000](/datasets/md/8f.md#visium-spatial-gene-expression-mesenteric-lymph-node-a2nxwr8ailmfe5fz0000) ## Microglial mechanisms drive amyloid-β clearance in immunized patients with Alzheimer’s disease [dataset3] - Page: /collections/geo-gse263079/ - Kind: other - Datasets: 8 - Reference: PMID:40050704 - Design: 4 donors, 4 brain areas: Left Middle Frontal Gyrus, Left Superior Temporal Gyrus, Left Inferior Parietal Lobule, Posterior Hippocampus of 3 nAD donors and 1 lecanemab-immunized AD donor Please note that Seurat object(s) were removed on March 17, 2025, as they were uploaded prior to revisions and contained outdated cell/spot annotations. Any Seurat objects downloaded before this date should not be used. For access to updated Seurat objects, please contact dgate@northwestern.edu. - Members: [visium-spatial-gene-expression-inferior-parietal-cortex-m25y8ikx3fvxe2000000](/datasets/md/9c.md#visium-spatial-gene-expression-inferior-parietal-cortex-m25y8ikx3fvxe2000000), [visium-spatial-gene-expression-hippocampal-formation-cduw1sqemn47oq1r0000](/datasets/md/26.md#visium-spatial-gene-expression-hippocampal-formation-cduw1sqemn47oq1r0000), [visium-spatial-gene-expression-middle-frontal-gyrus-rnwun5o19x3t46br0000](/datasets/md/92.md#visium-spatial-gene-expression-middle-frontal-gyrus-rnwun5o19x3t46br0000), [visium-spatial-gene-expression-middle-frontal-gyrus-x3mgn1nsmwru7syt0000](/datasets/md/c5.md#visium-spatial-gene-expression-middle-frontal-gyrus-x3mgn1nsmwru7syt0000), [visium-spatial-gene-expression-hippocampal-formation-las9taygmxg8lrbd0000](/datasets/md/fc.md#visium-spatial-gene-expression-hippocampal-formation-las9taygmxg8lrbd0000), [visium-spatial-gene-expression-superior-temporal-gyrus-apuzagrwvk4jmz060000](/datasets/md/e9.md#visium-spatial-gene-expression-superior-temporal-gyrus-apuzagrwvk4jmz060000), [visium-spatial-gene-expression-superior-temporal-gyrus-1dexpsbet9g7sqs30000](/datasets/md/60.md#visium-spatial-gene-expression-superior-temporal-gyrus-1dexpsbet9g7sqs30000), [visium-spatial-gene-expression-inferior-parietal-cortex-phqw51cmgiyx1mkm0000](/datasets/md/5f.md#visium-spatial-gene-expression-inferior-parietal-cortex-phqw51cmgiyx1mkm0000) ## An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus [spatial-visium] - Page: /collections/geo-gse264692/ - Kind: replicates - Datasets: 9 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE264692 - Design: We obtained tissue blocks of postmortem human brain containing anterior hippocampus 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 hippocampus. We performed a second spatial transcriptomics experiment using the Visium Spatial Proteogenomics (Visium-SPG) platform for two 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-hippocampal-formation-0beq3mk8qqmnapyy0000](/datasets/md/c4.md#visium-spatial-gene-expression-hippocampal-formation-0beq3mk8qqmnapyy0000), [visium-spatial-gene-expression-hippocampal-formation-iwfmmwylc8zw9vwk0000](/datasets/md/0d.md#visium-spatial-gene-expression-hippocampal-formation-iwfmmwylc8zw9vwk0000), [visium-spatial-gene-expression-hippocampal-formation-jgz8uccbjncneb7m0000](/datasets/md/b1.md#visium-spatial-gene-expression-hippocampal-formation-jgz8uccbjncneb7m0000), [visium-spatial-gene-expression-hippocampal-formation-ktrit8wwdt3d4uum0000](/datasets/md/da.md#visium-spatial-gene-expression-hippocampal-formation-ktrit8wwdt3d4uum0000), [visium-spatial-gene-expression-hippocampal-formation-lcramtczu6uhrloz0000](/datasets/md/bd.md#visium-spatial-gene-expression-hippocampal-formation-lcramtczu6uhrloz0000), [visium-spatial-gene-expression-hippocampal-formation-pwmvg2vw9mu6kgfr0000](/datasets/md/9f.md#visium-spatial-gene-expression-hippocampal-formation-pwmvg2vw9mu6kgfr0000), [visium-spatial-gene-expression-hippocampal-formation-magqtcjouyfr3oc00000](/datasets/md/26.md#visium-spatial-gene-expression-hippocampal-formation-magqtcjouyfr3oc00000), [visium-spatial-gene-expression-hippocampal-formation-o7ywtecozzfuunkr0000](/datasets/md/a4.md#visium-spatial-gene-expression-hippocampal-formation-o7ywtecozzfuunkr0000), [visium-spatial-gene-expression-hippocampal-formation-tkczclecw8j3nede0000](/datasets/md/05.md#visium-spatial-gene-expression-hippocampal-formation-tkczclecw8j3nede0000) ## Vascular invasion-associated gene expression is detectable in pre-surgical biopsies of stage I lung adenocarcinoma [Spatial Transcriptomics] - Page: /collections/geo-gse273378/ - Kind: replicates - Datasets: 16 - Reference: PMID:41876493 - Design: 16 samples from 14 patient tumors within the validation cohort were selected for 10x Genomics Visium for FFPE spatial whole-transcriptome profiling. All samples were selected to be stage IA/IB at the time of collection except for one that was upstaged to stage IIA under the 8th TNM edition (this sample was excluded from the bulk RNA-seq validation cohort when evaluating the performance of VI predictor scores). Samples were chosen based on 1) the presence of pathological features of interest (e.g., VI foci, representative LUAD histologic patterns) and 2) more than 50% of RNA fragments being greater than 200 nucleotides (DV200) after extraction with the AllPrep DNA/RNA Universal Kit (Qiagen) during bulk RNA-seq library preparation. - Members: [visium-spatial-gene-expression-lung-1k46b540ncwx7uwd0000](/datasets/md/a9.md#visium-spatial-gene-expression-lung-1k46b540ncwx7uwd0000), [visium-spatial-gene-expression-lung-0z2ocll5kslpin1h0000](/datasets/md/19.md#visium-spatial-gene-expression-lung-0z2ocll5kslpin1h0000), [visium-spatial-gene-expression-lung-hj3bv1wffevnoidr0000](/datasets/md/56.md#visium-spatial-gene-expression-lung-hj3bv1wffevnoidr0000), [visium-spatial-gene-expression-lung-n5cwmqqscod1oh9t0000](/datasets/md/a9.md#visium-spatial-gene-expression-lung-n5cwmqqscod1oh9t0000), [visium-spatial-gene-expression-lung-6ectad3i87tuhngr0000](/datasets/md/4f.md#visium-spatial-gene-expression-lung-6ectad3i87tuhngr0000), [visium-spatial-gene-expression-lung-oseo0dflcubkhwsd0000](/datasets/md/d6.md#visium-spatial-gene-expression-lung-oseo0dflcubkhwsd0000), [visium-spatial-gene-expression-lung-uokodmwmzoiqjm7f0000](/datasets/md/43.md#visium-spatial-gene-expression-lung-uokodmwmzoiqjm7f0000), [visium-spatial-gene-expression-lung-852kflvrvobyueqa0000](/datasets/md/6b.md#visium-spatial-gene-expression-lung-852kflvrvobyueqa0000), [visium-spatial-gene-expression-lung-cguxn904qga6pplt0000](/datasets/md/56.md#visium-spatial-gene-expression-lung-cguxn904qga6pplt0000), [visium-spatial-gene-expression-lung-yedtfhnib0gfwrmh0000](/datasets/md/66.md#visium-spatial-gene-expression-lung-yedtfhnib0gfwrmh0000), [visium-spatial-gene-expression-lung-fx2wcfj8kjgzpspn0000](/datasets/md/8d.md#visium-spatial-gene-expression-lung-fx2wcfj8kjgzpspn0000), [visium-spatial-gene-expression-lung-u4qk9fijzjzgbags0000](/datasets/md/8e.md#visium-spatial-gene-expression-lung-u4qk9fijzjzgbags0000), [visium-spatial-gene-expression-lung-v5xotk4ueidqtzeu0000](/datasets/md/9e.md#visium-spatial-gene-expression-lung-v5xotk4ueidqtzeu0000), [visium-spatial-gene-expression-lung-zq0jv0niaaqvvk9r0000](/datasets/md/1d.md#visium-spatial-gene-expression-lung-zq0jv0niaaqvvk9r0000), [visium-spatial-gene-expression-lung-4jy41dx0kcjkpg9f0000](/datasets/md/75.md#visium-spatial-gene-expression-lung-4jy41dx0kcjkpg9f0000), [visium-spatial-gene-expression-lung-vzxi2ia2ehukc4zu0000](/datasets/md/60.md#visium-spatial-gene-expression-lung-vzxi2ia2ehukc4zu0000) ## Spatial transcriptomics characterization of ecosystems in the immune tumor microenvironment of diffuse large B-cell lymphoma - Page: /collections/geo-gse276542/ - Kind: other - Datasets: 9 - Reference: PMID:42010788 - Design: DLBCL FFPE (formalin-fixed paraffin-embedded) samples were collected from eight different patients, including two resections and eight biopsies (n=10 in total); n=6 pre-treatment biopsies from six different patients, n=2 longitudinal biopsies (before and after R-CHOP therapy) from an additional patient, and n=2 different pre-treatment biopsies from another patient. Samples were obtained from the Pathology Department at Hospital Saint Louis in Paris, France. Additionally, two adjacent sections from a healthy lymph node (LN) and two from a non-metastatic tonsil were collected from individuals undergoing non-cancer-related surgeries at Hospital Bichat and Robert Debré in Paris, France. All the samples were analyzed using Visium spatial transcriptomics (10X Genomics) - Members: [visium-spatial-gene-expression-palatine-tonsil-mehb6uwnlqr99pfd0000](/datasets/md/f4.md#visium-spatial-gene-expression-palatine-tonsil-mehb6uwnlqr99pfd0000), [visium-spatial-gene-expression-lymph-node-9x2xwqs7j5oyabfw0000](/datasets/md/37.md#visium-spatial-gene-expression-lymph-node-9x2xwqs7j5oyabfw0000), [visium-spatial-gene-expression-palatine-tonsil-yg14qzjwrm1rjkxs0000](/datasets/md/76.md#visium-spatial-gene-expression-palatine-tonsil-yg14qzjwrm1rjkxs0000), [visium-spatial-gene-expression-lymph-node-e3vtozcj8zj8w1lx0000](/datasets/md/df.md#visium-spatial-gene-expression-lymph-node-e3vtozcj8zj8w1lx0000), [visium-spatial-gene-expression-lymph-node-6xyddmjh5njl9u3q0000](/datasets/md/dd.md#visium-spatial-gene-expression-lymph-node-6xyddmjh5njl9u3q0000), [visium-spatial-gene-expression-lymph-node-td78zhhhfmk4e9vt0000](/datasets/md/1d.md#visium-spatial-gene-expression-lymph-node-td78zhhhfmk4e9vt0000), [visium-spatial-gene-expression-lymph-node-wylo2x32aztw8unu0000](/datasets/md/bd.md#visium-spatial-gene-expression-lymph-node-wylo2x32aztw8unu0000), [visium-spatial-gene-expression-lymph-node-kihsfxjuhiiyaeyn0000](/datasets/md/35.md#visium-spatial-gene-expression-lymph-node-kihsfxjuhiiyaeyn0000), [visium-spatial-gene-expression-lymph-node-lysw0o5btvxysfdy0000](/datasets/md/36.md#visium-spatial-gene-expression-lymph-node-lysw0o5btvxysfdy0000) ## Type I interferon drives T cell cytotoxicity by upregulation of interferon regulatory factor 7 in autoimmune kidney diseases in mice. - Page: /collections/geo-gse294965/ - Kind: publication - Datasets: 9 - Reference: 10.1038/s41467-025-59819-7 - Design: 8 slides containing 63 samples (biopsies from 32 ANCA, 19 lupus nephritis, 6 anti-GBM, and healthy tissues from tumor nephrectomies of 6 control patients) were analyzed with Xenium to capture RNA. One additional slide (Sample: 0011186) was used for Xenium + phenocycler run. - Members: [10x-xenium-kidney-9ljczd7y0xhujqdg0000](/datasets/md/fa.md#10x-xenium-kidney-9ljczd7y0xhujqdg0000), [10x-xenium-kidney-xegzupnucmc2pas70000](/datasets/md/3c.md#10x-xenium-kidney-xegzupnucmc2pas70000), [10x-xenium-kidney-cptkrrrj8gm6v9og0000](/datasets/md/96.md#10x-xenium-kidney-cptkrrrj8gm6v9og0000), [10x-xenium-kidney-w1xabjjj3mzwkfse0000](/datasets/md/88.md#10x-xenium-kidney-w1xabjjj3mzwkfse0000), [10x-xenium-kidney-asap8kris9wygxur0000](/datasets/md/80.md#10x-xenium-kidney-asap8kris9wygxur0000), [10x-xenium-kidney-tbgsnnoqj1gjlkz20000](/datasets/md/d3.md#10x-xenium-kidney-tbgsnnoqj1gjlkz20000), [10x-xenium-kidney-7spk0u7nsakjcybb0000](/datasets/md/4d.md#10x-xenium-kidney-7spk0u7nsakjcybb0000), [10x-xenium-kidney-ngpzck7ptmngmazm0000](/datasets/md/59.md#10x-xenium-kidney-ngpzck7ptmngmazm0000), [10x-xenium-kidney-yv8wjzbpeflbdkcx0000](/datasets/md/2d.md#10x-xenium-kidney-yv8wjzbpeflbdkcx0000) ## Spatial gene expression and microenvironmental changes in the transition of nevus to melanoma - Page: /collections/geo-gse298774/ - Kind: replicates - Datasets: 11 - Reference: PMID:42258703 - Design: Slides with both nevus and melanoma were used for 10X Visium spatial transcriptomics - Members: [visium-spatial-gene-expression-skin-of-body-lsogq0mssez8d4n00000](/datasets/md/f3.md#visium-spatial-gene-expression-skin-of-body-lsogq0mssez8d4n00000), [visium-spatial-gene-expression-skin-of-body-kieaqjj38m0t4zdj0000](/datasets/md/92.md#visium-spatial-gene-expression-skin-of-body-kieaqjj38m0t4zdj0000), [visium-spatial-gene-expression-skin-of-body-kfiu82eyghqtz58t0000](/datasets/md/e5.md#visium-spatial-gene-expression-skin-of-body-kfiu82eyghqtz58t0000), [visium-spatial-gene-expression-skin-of-body-ywxihgb4nsc6rc3z0000](/datasets/md/1a.md#visium-spatial-gene-expression-skin-of-body-ywxihgb4nsc6rc3z0000), [visium-spatial-gene-expression-skin-of-body-wuaoxpdfjggaxy8x0000](/datasets/md/bc.md#visium-spatial-gene-expression-skin-of-body-wuaoxpdfjggaxy8x0000), [visium-spatial-gene-expression-skin-of-body-7a9otsjbdsmwhb6t0000](/datasets/md/e8.md#visium-spatial-gene-expression-skin-of-body-7a9otsjbdsmwhb6t0000), [visium-spatial-gene-expression-skin-of-body-siqesijiwokggaaz0000](/datasets/md/cb.md#visium-spatial-gene-expression-skin-of-body-siqesijiwokggaaz0000), [visium-spatial-gene-expression-skin-of-body-fgt7gtfizluosn8w0000](/datasets/md/ff.md#visium-spatial-gene-expression-skin-of-body-fgt7gtfizluosn8w0000), [visium-spatial-gene-expression-skin-of-body-pg7sr8mkg4mzsmmh0000](/datasets/md/c9.md#visium-spatial-gene-expression-skin-of-body-pg7sr8mkg4mzsmmh0000), [visium-spatial-gene-expression-skin-of-body-xgmw508hsll5dngo0000](/datasets/md/ca.md#visium-spatial-gene-expression-skin-of-body-xgmw508hsll5dngo0000), [visium-spatial-gene-expression-skin-of-body-odo4iqvdvxrgkgiy0000](/datasets/md/3b.md#visium-spatial-gene-expression-skin-of-body-odo4iqvdvxrgkgiy0000) ## Infusible Extracellular Matrix Biomaterial Enhances and Expedites Cell-Specific Pro-Repair Following Acute Myocardial Infarction - Page: /collections/geo-gse299772/ - Kind: comparison - Datasets: 12 - Reference: PMID:41292930 - Design: Gene expression profiling of 10x Genomic Chromium single nucleus RNA-Seq or Visium spatial transcriptomics from the left ventricular myocardium short axis sections on injured Sprague Dawley female rats (225-250 g). Injuries include I/R (45 minutes of ischemia followed by reperfusion). - Members: [visium-spatial-gene-expression-heart-cff1y378fh6ifs2i0000](/datasets/md/10.md#visium-spatial-gene-expression-heart-cff1y378fh6ifs2i0000), [visium-spatial-gene-expression-heart-2bx2mnaxtjqf5yom0000](/datasets/md/aa.md#visium-spatial-gene-expression-heart-2bx2mnaxtjqf5yom0000), [visium-spatial-gene-expression-heart-uujd20mnwlz79zlu0000](/datasets/md/aa.md#visium-spatial-gene-expression-heart-uujd20mnwlz79zlu0000), [visium-spatial-gene-expression-heart-ngbmmhtvtww2qtva0000](/datasets/md/db.md#visium-spatial-gene-expression-heart-ngbmmhtvtww2qtva0000), [visium-spatial-gene-expression-heart-8q77i4iirjzg9x1f0000](/datasets/md/e8.md#visium-spatial-gene-expression-heart-8q77i4iirjzg9x1f0000), [visium-spatial-gene-expression-heart-h2vvvnzz1rgm6o6c0000](/datasets/md/41.md#visium-spatial-gene-expression-heart-h2vvvnzz1rgm6o6c0000), [visium-spatial-gene-expression-heart-ozklzvvhlmoevkf70000](/datasets/md/32.md#visium-spatial-gene-expression-heart-ozklzvvhlmoevkf70000), [visium-spatial-gene-expression-heart-rr3g3onztpslmotd0001](/datasets/md/db.md#visium-spatial-gene-expression-heart-rr3g3onztpslmotd0001), [visium-spatial-gene-expression-heart-6k5z9xh7pxlfcoyp0000](/datasets/md/50.md#visium-spatial-gene-expression-heart-6k5z9xh7pxlfcoyp0000), [visium-spatial-gene-expression-heart-p9nyfxwovxbkjt6e0000](/datasets/md/1f.md#visium-spatial-gene-expression-heart-p9nyfxwovxbkjt6e0000), [visium-spatial-gene-expression-heart-axgdcjemcceusk3k0000](/datasets/md/9d.md#visium-spatial-gene-expression-heart-axgdcjemcceusk3k0000), [visium-spatial-gene-expression-heart-vgxhn9yxlxxpnm1y0000](/datasets/md/57.md#visium-spatial-gene-expression-heart-vgxhn9yxlxxpnm1y0000) ## The cervicovaginal microbiome associates with spatially restricted host transcriptional signatures throughout the human ectocervical epithelium and submucosa - Page: /collections/geo-gse300112/ - Kind: comparison - Datasets: 12 - Reference: PMID:41218071 - Design: In this study we compared gene expression between ectocervical tissue samples (n=21) from women with pre-defined groups of microbiome profiles (L. crispatus: 4, L. iners: 6, Gardnerella: 6, highly diverse: 5) using visium spatial transcriptomics. Ectocervical tissue were obtained as part of our broader longitudinal investigation within the Sex Worker Outreach Program in Pumwani, Nairobi, Kenya *************************************************************** Due to patient privacy concerns, the raw data cannot be held in a public database. *************************************************************** - Members: [visium-spatial-gene-expression-ectocervix-gl82ofmlkuqcd1fj0000](/datasets/md/ec.md#visium-spatial-gene-expression-ectocervix-gl82ofmlkuqcd1fj0000), [visium-spatial-gene-expression-ectocervix-db3dapcvwwrpnjab0000](/datasets/md/ec.md#visium-spatial-gene-expression-ectocervix-db3dapcvwwrpnjab0000), [visium-spatial-gene-expression-ectocervix-kowmtbthsuumf1bv0000](/datasets/md/aa.md#visium-spatial-gene-expression-ectocervix-kowmtbthsuumf1bv0000), [visium-spatial-gene-expression-ectocervix-kjcjr03dlvbekajc0000](/datasets/md/9b.md#visium-spatial-gene-expression-ectocervix-kjcjr03dlvbekajc0000), [visium-spatial-gene-expression-ectocervix-pknxyma7pugfv4ga0000](/datasets/md/8b.md#visium-spatial-gene-expression-ectocervix-pknxyma7pugfv4ga0000), [visium-spatial-gene-expression-ectocervix-gcwkhafoji80oaqb0000](/datasets/md/f6.md#visium-spatial-gene-expression-ectocervix-gcwkhafoji80oaqb0000), [visium-spatial-gene-expression-ectocervix-elupqkcgw7xiwiub0000](/datasets/md/eb.md#visium-spatial-gene-expression-ectocervix-elupqkcgw7xiwiub0000), [visium-spatial-gene-expression-ectocervix-szj1xj0uqqoccwq40000](/datasets/md/70.md#visium-spatial-gene-expression-ectocervix-szj1xj0uqqoccwq40000), [visium-spatial-gene-expression-ectocervix-7hpfmd9glljnyrjf0000](/datasets/md/2e.md#visium-spatial-gene-expression-ectocervix-7hpfmd9glljnyrjf0000), [visium-spatial-gene-expression-ectocervix-1iwvc4xhl1ykli6i0000](/datasets/md/f5.md#visium-spatial-gene-expression-ectocervix-1iwvc4xhl1ykli6i0000), [visium-spatial-gene-expression-ectocervix-ykit1oqjomk3nrwj0000](/datasets/md/98.md#visium-spatial-gene-expression-ectocervix-ykit1oqjomk3nrwj0000), [visium-spatial-gene-expression-ectocervix-oskhjv0lwrwys3nj0000](/datasets/md/e3.md#visium-spatial-gene-expression-ectocervix-oskhjv0lwrwys3nj0000) ## Intercellular signaling and synaptic deconstruction uncovered by single-cell and spatial transcriptomics in an AD tauopathy model - Page: /collections/geo-gse305314/ - Kind: time course - Datasets: 4 - Reference: PMID:41249845 - Design: Multiome-seq: Joint snRNA-seq and scATAC-seq performed using 10x Genomics platform. Spatial-seq: performed using 10x Genomics Visium platform. Both consist of AD model rat hippocampal or cortex tissues from 10 month and 20 months old samples and wild-type counterparts. - Members: [visium-spatial-gene-expression-brain-bmoownf15h335jfb0000](/datasets/md/0a.md#visium-spatial-gene-expression-brain-bmoownf15h335jfb0000), [visium-spatial-gene-expression-brain-csrggcwa9jtmoxqb0000](/datasets/md/67.md#visium-spatial-gene-expression-brain-csrggcwa9jtmoxqb0000), [visium-spatial-gene-expression-brain-9e2psd8vpbbkfakv0000](/datasets/md/01.md#visium-spatial-gene-expression-brain-9e2psd8vpbbkfakv0000), [visium-spatial-gene-expression-brain-hlf2as2rjwep2asx0000](/datasets/md/98.md#visium-spatial-gene-expression-brain-hlf2as2rjwep2asx0000) ## Spatial transcriptomic profiling of the human aortic valve reveals cellular sex differences near sites of calcification - Page: /collections/geo-gse306288/ - Kind: other - Datasets: 8 - Reference: PMID:42206364 - Design: Aortic valves were dissected and split in half for single cell and spatial trenacriptomics. Cells were isolated from human healthy and diseased aortic valve leaflets and run through 10X genomics single cell RNA sequencing workflows. For a subset of patients, tissues were cryopreserved and using for 10X Visium workflows. - Members: [visium-spatial-gene-expression-aortic-valve-leaflet-h4zfyd8pampmpqxc0000](/datasets/md/37.md#visium-spatial-gene-expression-aortic-valve-leaflet-h4zfyd8pampmpqxc0000), [visium-spatial-gene-expression-aortic-valve-leaflet-5xgznibqfjvindej0000](/datasets/md/1f.md#visium-spatial-gene-expression-aortic-valve-leaflet-5xgznibqfjvindej0000), [visium-spatial-gene-expression-aortic-valve-leaflet-tvxqmno2xos3pgbo0000](/datasets/md/11.md#visium-spatial-gene-expression-aortic-valve-leaflet-tvxqmno2xos3pgbo0000), [visium-spatial-gene-expression-aortic-valve-leaflet-wgo4au1uydiwhf2t0000](/datasets/md/a8.md#visium-spatial-gene-expression-aortic-valve-leaflet-wgo4au1uydiwhf2t0000), [visium-spatial-gene-expression-aortic-valve-leaflet-mdqbomk6rwenfiyy0000](/datasets/md/f5.md#visium-spatial-gene-expression-aortic-valve-leaflet-mdqbomk6rwenfiyy0000), [visium-spatial-gene-expression-aortic-valve-leaflet-aljdknjr1njebjge0000](/datasets/md/9a.md#visium-spatial-gene-expression-aortic-valve-leaflet-aljdknjr1njebjge0000), [visium-spatial-gene-expression-aortic-valve-leaflet-m6zyyy6oybewa4mm0000](/datasets/md/9e.md#visium-spatial-gene-expression-aortic-valve-leaflet-m6zyyy6oybewa4mm0000), [visium-spatial-gene-expression-aortic-valve-leaflet-yp2vk7bdysrwnimr0000](/datasets/md/7c.md#visium-spatial-gene-expression-aortic-valve-leaflet-yp2vk7bdysrwnimr0000) ## Spatial transcriptomics dataset of non-human primates - Page: /collections/geo-gse313530/ - Kind: other - Datasets: 18 - Reference: PMID:42146464 - Design: Fresh frozen dorsal root ganglia from non-human primates were recovered from organ donors and tissue samples were processed with 10X VISIUM. Raw seq files were run with 10X SpaceRanger to determine gene counts per barcode. Seurat was used for clustering. - Members: [visium-spatial-gene-expression-dorsal-root-ganglion-tjircswivvipjpdd0000](/datasets/md/dc.md#visium-spatial-gene-expression-dorsal-root-ganglion-tjircswivvipjpdd0000), [visium-spatial-gene-expression-dorsal-root-ganglion-vmdji4bplw9nef6y0000](/datasets/md/b4.md#visium-spatial-gene-expression-dorsal-root-ganglion-vmdji4bplw9nef6y0000), [visium-spatial-gene-expression-dorsal-root-ganglion-8cscduzaohow64vk0000](/datasets/md/4b.md#visium-spatial-gene-expression-dorsal-root-ganglion-8cscduzaohow64vk0000), [visium-spatial-gene-expression-dorsal-root-ganglion-gbxvtt1jfltm4yb50000](/datasets/md/94.md#visium-spatial-gene-expression-dorsal-root-ganglion-gbxvtt1jfltm4yb50000), [visium-spatial-gene-expression-dorsal-root-ganglion-lbojd3wmk8lbcsuq0000](/datasets/md/c4.md#visium-spatial-gene-expression-dorsal-root-ganglion-lbojd3wmk8lbcsuq0000), [visium-spatial-gene-expression-dorsal-root-ganglion-gmwzukfoey2kk7ld0000](/datasets/md/7e.md#visium-spatial-gene-expression-dorsal-root-ganglion-gmwzukfoey2kk7ld0000), [visium-spatial-gene-expression-dorsal-root-ganglion-pveli4htiitwwhr60000](/datasets/md/1d.md#visium-spatial-gene-expression-dorsal-root-ganglion-pveli4htiitwwhr60000), [visium-spatial-gene-expression-dorsal-root-ganglion-uvbw8tjaze34eie30000](/datasets/md/13.md#visium-spatial-gene-expression-dorsal-root-ganglion-uvbw8tjaze34eie30000), [visium-spatial-gene-expression-dorsal-root-ganglion-1nclat9njjltwyvn0000](/datasets/md/ce.md#visium-spatial-gene-expression-dorsal-root-ganglion-1nclat9njjltwyvn0000), [visium-spatial-gene-expression-dorsal-root-ganglion-qfejndgbhoaj04dw0000](/datasets/md/93.md#visium-spatial-gene-expression-dorsal-root-ganglion-qfejndgbhoaj04dw0000), [visium-spatial-gene-expression-dorsal-root-ganglion-bczxujx9f2gbcplh0000](/datasets/md/b5.md#visium-spatial-gene-expression-dorsal-root-ganglion-bczxujx9f2gbcplh0000), [visium-spatial-gene-expression-dorsal-root-ganglion-2g580jsybgvdqmow0000](/datasets/md/d5.md#visium-spatial-gene-expression-dorsal-root-ganglion-2g580jsybgvdqmow0000), [visium-spatial-gene-expression-dorsal-root-ganglion-eweblfef15ruzgm40000](/datasets/md/65.md#visium-spatial-gene-expression-dorsal-root-ganglion-eweblfef15ruzgm40000), [visium-spatial-gene-expression-dorsal-root-ganglion-dk7o0sbmnnkwjddk0000](/datasets/md/9b.md#visium-spatial-gene-expression-dorsal-root-ganglion-dk7o0sbmnnkwjddk0000), [visium-spatial-gene-expression-dorsal-root-ganglion-178ooj6qvhdnyrnj0000](/datasets/md/af.md#visium-spatial-gene-expression-dorsal-root-ganglion-178ooj6qvhdnyrnj0000), [visium-spatial-gene-expression-dorsal-root-ganglion-q9bwtsdpo1ck4br90000](/datasets/md/48.md#visium-spatial-gene-expression-dorsal-root-ganglion-q9bwtsdpo1ck4br90000), [visium-spatial-gene-expression-dorsal-root-ganglion-l8c3iymej9c6yft50000](/datasets/md/61.md#visium-spatial-gene-expression-dorsal-root-ganglion-l8c3iymej9c6yft50000), [visium-spatial-gene-expression-dorsal-root-ganglion-vyfjuyafetwlq1z70000](/datasets/md/ea.md#visium-spatial-gene-expression-dorsal-root-ganglion-vyfjuyafetwlq1z70000) ## Neoadjuvant modified FOLFIRINOX plus nivolumab in borderline-resectable pancreatic ductal adenocarcinoma: a pilot phase 1 trial. - Page: /collections/geo-gse313662/ - Kind: publication - Datasets: 6 - Reference: 10.1038/s41467-026-68976-2 - Design: Xenium 5K Prime was applied to six archival resected PDAC patient tumors post treatment with FOLFIRINOX and nivolumab - Members: [10x-xenium-pancreas-ufioalxhktlsi5fo0000](/datasets/md/eb.md#10x-xenium-pancreas-ufioalxhktlsi5fo0000), [10x-xenium-pancreas-tcu9oysndcev2oij0000](/datasets/md/3b.md#10x-xenium-pancreas-tcu9oysndcev2oij0000), [10x-xenium-pancreas-n9zxbmgr8ccbuhgn0000](/datasets/md/07.md#10x-xenium-pancreas-n9zxbmgr8ccbuhgn0000), [10x-xenium-pancreas-mzxq72gzik9tyopx0000](/datasets/md/89.md#10x-xenium-pancreas-mzxq72gzik9tyopx0000), [10x-xenium-pancreas-jm7bhoa22mgdgtlh0000](/datasets/md/7f.md#10x-xenium-pancreas-jm7bhoa22mgdgtlh0000), [10x-xenium-pancreas-higbtiqvmwkydmvw0000](/datasets/md/c7.md#10x-xenium-pancreas-higbtiqvmwkydmvw0000) ## Spatial transcriptomic analysis of human iPSC-derived hemanoids at day 16 and day 28 - Page: /collections/geo-gse324601/ - Kind: time course - Datasets: 2 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE324601 - Design: Human iPSC-derived hemanoids were generated via directed differentiation toward hematopoietic lineages. Organoids were collected at day 16 and day 28, sectioned, and processed for spatial gene expression analysis using the 10x Genomics Visium v1 platform. Libraries were prepared according to the manufacturer’s protocol and sequenced to generate spatially resolved gene expression profiles for each developmental stage. - Members: [visium-spatial-gene-expression-hematopoietic-system-yalpocf0f3htyeoz0000](/datasets/md/37.md#visium-spatial-gene-expression-hematopoietic-system-yalpocf0f3htyeoz0000), [visium-spatial-gene-expression-hematopoietic-system-sflgb23jgpnypgra0000](/datasets/md/18.md#visium-spatial-gene-expression-hematopoietic-system-sflgb23jgpnypgra0000) ## Single Nuclei and Spatial Transcriptomic Datasets in Brain Metastases - Page: /collections/geo-gse325196/ - Kind: comparison - Datasets: 12 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE325196 - Design: Single nuclei, Xenium, and six of the Visium standard specimens were derived from flash frozen brain mestasis blocks while the remaining six Visium standard specimens were derived from 10um cut formalin-fixed and paraffin embedded sections prior to submission for sequencing. - Members: [visium-spatial-gene-expression-brain-mo5bu6tzc45dnb550000](/datasets/md/52.md#visium-spatial-gene-expression-brain-mo5bu6tzc45dnb550000), [visium-spatial-gene-expression-brain-cfjnirmtaqpzo3by0000](/datasets/md/37.md#visium-spatial-gene-expression-brain-cfjnirmtaqpzo3by0000), [visium-spatial-gene-expression-brain-l5ltppuospvcctrn0000](/datasets/md/7b.md#visium-spatial-gene-expression-brain-l5ltppuospvcctrn0000), [visium-spatial-gene-expression-brain-xwe97uxwa8wji0hr0000](/datasets/md/a2.md#visium-spatial-gene-expression-brain-xwe97uxwa8wji0hr0000), [visium-spatial-gene-expression-brain-ooh3hvcsi4f3frzk0000](/datasets/md/de.md#visium-spatial-gene-expression-brain-ooh3hvcsi4f3frzk0000), [visium-spatial-gene-expression-brain-fn26rgc30i0lxtdy0000](/datasets/md/a7.md#visium-spatial-gene-expression-brain-fn26rgc30i0lxtdy0000), [visium-spatial-gene-expression-brain-1y4sb5uzzwr598ym0000](/datasets/md/7b.md#visium-spatial-gene-expression-brain-1y4sb5uzzwr598ym0000), [visium-spatial-gene-expression-brain-2qwrtpis3ve3knap0000](/datasets/md/9d.md#visium-spatial-gene-expression-brain-2qwrtpis3ve3knap0000), [visium-spatial-gene-expression-brain-ryjv3s1tp6caxu0w0000](/datasets/md/6c.md#visium-spatial-gene-expression-brain-ryjv3s1tp6caxu0w0000), [visium-spatial-gene-expression-brain-ednx8wnrhxvbk2uv0000](/datasets/md/f4.md#visium-spatial-gene-expression-brain-ednx8wnrhxvbk2uv0000), [visium-spatial-gene-expression-brain-tfhaeh73dyxcpokd0000](/datasets/md/f4.md#visium-spatial-gene-expression-brain-tfhaeh73dyxcpokd0000), [visium-spatial-gene-expression-brain-0e1pbmeyeiio3rtf0000](/datasets/md/28.md#visium-spatial-gene-expression-brain-0e1pbmeyeiio3rtf0000) ## A skin–kidney neutrophil axis links UV exposure to renal angiogenesis and tissue remodeling in healthy and lupus kidneys. [Spatial Transcriptomics] - Page: /collections/geo-gse333529/ - Kind: other - Datasets: 4 - Reference: PMID:42679049 - Design: Spatial transcriptomics (10X Genomics Visium) *************************************************************** paint privacy concerns *************************************************************** - Members: [visium-spatial-gene-expression-kidney-kjexgscyy9litfqf0000](/datasets/md/4d.md#visium-spatial-gene-expression-kidney-kjexgscyy9litfqf0000), [visium-spatial-gene-expression-kidney-xeedwjlibhidouqo0000](/datasets/md/81.md#visium-spatial-gene-expression-kidney-xeedwjlibhidouqo0000), [visium-spatial-gene-expression-kidney-qsovzb25u6f9hvuw0000](/datasets/md/3f.md#visium-spatial-gene-expression-kidney-qsovzb25u6f9hvuw0000), [visium-spatial-gene-expression-kidney-dy8yh4aov5ieufu00000](/datasets/md/00.md#visium-spatial-gene-expression-kidney-dy8yh4aov5ieufu00000) ## Xenium spatial transcriptomics identifies mesenchymal fibroblast expansion and conserved fibrotic ECM programs in keloid - Page: /collections/geo-gse341250/ - Kind: comparison - Datasets: 2 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE341250 - Design: Normal skin from one Asian donor and keloid biopsies from Asian (AN), White non-Hispanic (WNH), and Hispanic/Latino (H/L) donors were collected under UCLA IRB approval with written informed consent and processed as FFPE sections. Xenium ST was performed using the 10x Genomics 260-gene human skin panel plus a 100-gene custom add-on panel enriched for fibrosis, ECM remodeling, growth factor signaling, and inflammatory pathways. After quality control, the dataset included 8,749 cells from normal skin and 41,264, 54,831, and 22,489 cells from AN, WNH, and H/L keloid, respectively, with average and median transcript counts of 167 and 125 per cell. Cells with nCount_RNA >5 were analyzed in Seurat v5.3.05 and Xenium Explorer. Since normal skin was available only from the Asian donor, direct normal–keloid comparisons were restricted to the Asian samples, whereas comparisons across keloid samples were considered exploratory lesion-level observations. - Members: [10x-xenium-skin-of-body-zji63tcbtlkijsky0000](/datasets/md/be.md#10x-xenium-skin-of-body-zji63tcbtlkijsky0000), [10x-xenium-skin-of-body-pblpikfm2hq3qgde0000](/datasets/md/c7.md#10x-xenium-skin-of-body-pblpikfm2hq3qgde0000) ## Single-cell spatial transcriptomic profiling defines a pathogenic inflammatory niche in chronic active multiple sclerosis lesions. - Page: /collections/geo-gse284005/ - Kind: publication - Datasets: 17 - Reference: 10.1016/j.immuni.2025.10.003 - Members: [vizgen-merscope-white-matter-tvfpgxr7aek10uuj0000](/datasets/md/a7.md#vizgen-merscope-white-matter-tvfpgxr7aek10uuj0000), [vizgen-merscope-white-matter-w4joksv1nlf6y6ta0000](/datasets/md/f2.md#vizgen-merscope-white-matter-w4joksv1nlf6y6ta0000), [vizgen-merscope-white-matter-ibd5qtkhlbek5mbb0000](/datasets/md/aa.md#vizgen-merscope-white-matter-ibd5qtkhlbek5mbb0000), [vizgen-merscope-white-matter-lknbfqgwf3oremeh0000](/datasets/md/38.md#vizgen-merscope-white-matter-lknbfqgwf3oremeh0000), [vizgen-merscope-white-matter-v6hu0vaxgjbx1rel0000](/datasets/md/f8.md#vizgen-merscope-white-matter-v6hu0vaxgjbx1rel0000), [vizgen-merscope-white-matter-f3lnyrpbrwwsdfnu0000](/datasets/md/f8.md#vizgen-merscope-white-matter-f3lnyrpbrwwsdfnu0000), [vizgen-merscope-white-matter-uoav3fnmqqhptdse0000](/datasets/md/e9.md#vizgen-merscope-white-matter-uoav3fnmqqhptdse0000), [vizgen-merscope-white-matter-ictwzpnreanaxkef0000](/datasets/md/a3.md#vizgen-merscope-white-matter-ictwzpnreanaxkef0000), [vizgen-merscope-white-matter-qt1a43xenwcmuqlg0000](/datasets/md/7c.md#vizgen-merscope-white-matter-qt1a43xenwcmuqlg0000), [vizgen-merscope-white-matter-da2uzo9jwzt9a6zh0000](/datasets/md/32.md#vizgen-merscope-white-matter-da2uzo9jwzt9a6zh0000), [vizgen-merscope-white-matter-bsclgfu0lxujwzll0000](/datasets/md/34.md#vizgen-merscope-white-matter-bsclgfu0lxujwzll0000), [vizgen-merscope-white-matter-i8oh04zekn0ztkso0000](/datasets/md/b0.md#vizgen-merscope-white-matter-i8oh04zekn0ztkso0000), [vizgen-merscope-white-matter-cjc81yi0yfqxgqsb0000](/datasets/md/7e.md#vizgen-merscope-white-matter-cjc81yi0yfqxgqsb0000), [vizgen-merscope-white-matter-07fa5j59drhiaa660000](/datasets/md/66.md#vizgen-merscope-white-matter-07fa5j59drhiaa660000), [vizgen-merscope-white-matter-2bk6q0qkfbzk4yl30000](/datasets/md/d2.md#vizgen-merscope-white-matter-2bk6q0qkfbzk4yl30000), [vizgen-merscope-white-matter-42vartr8cbmki1jm0000](/datasets/md/ec.md#vizgen-merscope-white-matter-42vartr8cbmki1jm0000), [vizgen-merscope-white-matter-6macr0wsl2mw0pt90000](/datasets/md/1f.md#vizgen-merscope-white-matter-6macr0wsl2mw0pt90000) ## Multi-omic landscape of human gliomas from diagnosis to treatment and recurrence. - Page: /collections/bia-s-biad1579/ - Kind: publication - Datasets: 32 - Reference: 10.1016/j.ccell.2025.11.006 - Members: [mibi-tof-brain-3r6u75bdwrwyys9o0000](/datasets/md/8c.md#mibi-tof-brain-3r6u75bdwrwyys9o0000), [mibi-tof-brain-kafhjlduxubzsmni0000](/datasets/md/1a.md#mibi-tof-brain-kafhjlduxubzsmni0000), [mibi-tof-brain-pffh6ea9pzvqsncx0000](/datasets/md/20.md#mibi-tof-brain-pffh6ea9pzvqsncx0000), [mibi-tof-brain-yxuciqlgldkfz4xh0000](/datasets/md/2a.md#mibi-tof-brain-yxuciqlgldkfz4xh0000), [mibi-tof-brain-18xdurxyftm9wz4w0000](/datasets/md/8d.md#mibi-tof-brain-18xdurxyftm9wz4w0000), [mibi-tof-brain-nspqugxb3axiogum0000](/datasets/md/fe.md#mibi-tof-brain-nspqugxb3axiogum0000), [mibi-tof-brain-8vsio4gwmvye7li50000](/datasets/md/61.md#mibi-tof-brain-8vsio4gwmvye7li50000), [mibi-tof-brain-skwfwjcgmezy5nll0000](/datasets/md/4a.md#mibi-tof-brain-skwfwjcgmezy5nll0000), [mibi-tof-brain-ttzu7nhy9zqxwjrr0000](/datasets/md/22.md#mibi-tof-brain-ttzu7nhy9zqxwjrr0000), [mibi-tof-brain-jjnzfpi6nocofjwp0000](/datasets/md/6b.md#mibi-tof-brain-jjnzfpi6nocofjwp0000), [mibi-tof-brain-onntguethrplyogh0000](/datasets/md/a3.md#mibi-tof-brain-onntguethrplyogh0000), [mibi-tof-brain-njudwjzzc394vhv50000](/datasets/md/9c.md#mibi-tof-brain-njudwjzzc394vhv50000), [mibi-tof-brain-0hsatnalpaosyt920000](/datasets/md/de.md#mibi-tof-brain-0hsatnalpaosyt920000), [mibi-tof-brain-cfi8p7y6kvvciihh0000](/datasets/md/76.md#mibi-tof-brain-cfi8p7y6kvvciihh0000), [mibi-tof-brain-251aodb4oqi8d1vc0000](/datasets/md/eb.md#mibi-tof-brain-251aodb4oqi8d1vc0000), [mibi-tof-brain-pm92fpddibgpbisd0000](/datasets/md/ce.md#mibi-tof-brain-pm92fpddibgpbisd0000), [mibi-tof-brain-wlltzvqeo82tth1g0000](/datasets/md/4a.md#mibi-tof-brain-wlltzvqeo82tth1g0000), [mibi-tof-brain-xbcs0zkgtqawu6tm0000](/datasets/md/9d.md#mibi-tof-brain-xbcs0zkgtqawu6tm0000), [mibi-tof-brain-woattxathvpaxb7h0000](/datasets/md/1b.md#mibi-tof-brain-woattxathvpaxb7h0000), [mibi-tof-brain-uc7q1zlfgqueba5v0000](/datasets/md/c7.md#mibi-tof-brain-uc7q1zlfgqueba5v0000), [mibi-tof-brain-we6xesvx1sq9diqh0000](/datasets/md/9f.md#mibi-tof-brain-we6xesvx1sq9diqh0000), [mibi-tof-brain-sdrnieshdapvoya40000](/datasets/md/67.md#mibi-tof-brain-sdrnieshdapvoya40000), [mibi-tof-brain-fwbdqpx99jboyrzk0000](/datasets/md/c3.md#mibi-tof-brain-fwbdqpx99jboyrzk0000), [mibi-tof-brain-ewv4sgjkhovxm5ye0000](/datasets/md/f4.md#mibi-tof-brain-ewv4sgjkhovxm5ye0000), [mibi-tof-brain-cnzdfcwftmkfhzdi0000](/datasets/md/9f.md#mibi-tof-brain-cnzdfcwftmkfhzdi0000), [mibi-tof-brain-brndvtznvw2avu820000](/datasets/md/96.md#mibi-tof-brain-brndvtznvw2avu820000), [mibi-tof-brain-tv3dnbvmps6z4m1y0000](/datasets/md/82.md#mibi-tof-brain-tv3dnbvmps6z4m1y0000), [mibi-tof-brain-kaotrhoyzciy350r0000](/datasets/md/9b.md#mibi-tof-brain-kaotrhoyzciy350r0000), [mibi-tof-brain-nh0yv78gemptwooe0000](/datasets/md/71.md#mibi-tof-brain-nh0yv78gemptwooe0000), [mibi-tof-brain-1l1gao2lmkuswz1b0000](/datasets/md/49.md#mibi-tof-brain-1l1gao2lmkuswz1b0000), [mibi-tof-brain-j0bd1fio3eq118cu0000](/datasets/md/11.md#mibi-tof-brain-j0bd1fio3eq118cu0000), [mibi-tof-brain-wveuqotqilu4cyth0000](/datasets/md/f7.md#mibi-tof-brain-wveuqotqilu4cyth0000)