# SpatialData-DB collections, shard 7
Generated from catalog release catalog-2026-11-01. Each collection has an anchor named after its slug, and every page on the site links its own section. The guide for agents is /llms.txt.
## geo-gse345644
- Page: /collections/geo-gse345644/
- Kind: other
- Datasets: 1
- Members: [10x-xenium-urinary-bladder-pjsqvrgiqcvyqb8y0000](/datasets/md/97.md#10x-xenium-urinary-bladder-pjsqvrgiqcvyqb8y0000)
## Binge ethanol exposure in advanced age elevates neuroinflammation and early indicators of neurodegeneration and cognitive impairment in female mice.
- Page: /collections/doi-10-1016-j-bbi-2023-12-034/
- Kind: comparison
- Datasets: 4
- Reference: 10.1016/j.bbi.2023.12.034
- Members: [visium-spatial-gene-expression-brain-ioqngi6xcxf681fv0000](/datasets/md/23.md#visium-spatial-gene-expression-brain-ioqngi6xcxf681fv0000), [visium-spatial-gene-expression-brain-ndlvhxq2xduawgex0000](/datasets/md/06.md#visium-spatial-gene-expression-brain-ndlvhxq2xduawgex0000), [visium-spatial-gene-expression-brain-t0ugzcrl0gkkvfmn0000](/datasets/md/96.md#visium-spatial-gene-expression-brain-t0ugzcrl0gkkvfmn0000), [visium-spatial-gene-expression-brain-4ubyxhhqpieujkrc0000](/datasets/md/ec.md#visium-spatial-gene-expression-brain-4ubyxhhqpieujkrc0000)
## Multimodal decoding of human liver regeneration.
- Page: /collections/doi-10-1038-s41586-024-07376-2/
- Kind: comparison
- Datasets: 19
- Reference: 10.1038/s41586-024-07376-2
- Members: [visium-spatial-gene-expression-liver-y2pwnosksywf1tre0000](/datasets/md/52.md#visium-spatial-gene-expression-liver-y2pwnosksywf1tre0000), [visium-spatial-gene-expression-liver-bwzbri5sdga2yq0q0000](/datasets/md/dc.md#visium-spatial-gene-expression-liver-bwzbri5sdga2yq0q0000), [visium-spatial-gene-expression-liver-j7vqx5eier0ampow0000](/datasets/md/19.md#visium-spatial-gene-expression-liver-j7vqx5eier0ampow0000), [visium-spatial-gene-expression-liver-n3fvb7vyqosqjeqh0000](/datasets/md/ec.md#visium-spatial-gene-expression-liver-n3fvb7vyqosqjeqh0000), [visium-spatial-gene-expression-liver-iawmppaoeb5uc1mh0000](/datasets/md/22.md#visium-spatial-gene-expression-liver-iawmppaoeb5uc1mh0000), [visium-spatial-gene-expression-liver-tsix7g8juvxi65g20000](/datasets/md/1d.md#visium-spatial-gene-expression-liver-tsix7g8juvxi65g20000), [visium-spatial-gene-expression-liver-ktdedj1khbz68xsh0000](/datasets/md/a0.md#visium-spatial-gene-expression-liver-ktdedj1khbz68xsh0000), [visium-spatial-gene-expression-liver-ly6wmbc6s6yn8jzi0000](/datasets/md/29.md#visium-spatial-gene-expression-liver-ly6wmbc6s6yn8jzi0000), [visium-spatial-gene-expression-liver-clguhctgkzoxmv4l0000](/datasets/md/3d.md#visium-spatial-gene-expression-liver-clguhctgkzoxmv4l0000), [visium-spatial-gene-expression-liver-ef48dhman0xprj4g0000](/datasets/md/f5.md#visium-spatial-gene-expression-liver-ef48dhman0xprj4g0000), [visium-spatial-gene-expression-liver-qp1urcry0ndstm400000](/datasets/md/b0.md#visium-spatial-gene-expression-liver-qp1urcry0ndstm400000), [visium-spatial-gene-expression-liver-tvac6d254mmpjlgk0000](/datasets/md/fa.md#visium-spatial-gene-expression-liver-tvac6d254mmpjlgk0000), [visium-spatial-gene-expression-liver-uzzqi3wqgxaxzqer0000](/datasets/md/63.md#visium-spatial-gene-expression-liver-uzzqi3wqgxaxzqer0000), [visium-spatial-gene-expression-liver-koccep2mimsg0jwa0000](/datasets/md/06.md#visium-spatial-gene-expression-liver-koccep2mimsg0jwa0000), [visium-spatial-gene-expression-liver-ufxzqlh1oj4ufyfq0000](/datasets/md/0b.md#visium-spatial-gene-expression-liver-ufxzqlh1oj4ufyfq0000), [visium-spatial-gene-expression-liver-7taurn6nwtq9esq10000](/datasets/md/d5.md#visium-spatial-gene-expression-liver-7taurn6nwtq9esq10000), [visium-spatial-gene-expression-liver-k4pi1l5tmmvrj8qf0000](/datasets/md/56.md#visium-spatial-gene-expression-liver-k4pi1l5tmmvrj8qf0000), [visium-spatial-gene-expression-liver-n3xazay5erplijzu0000](/datasets/md/97.md#visium-spatial-gene-expression-liver-n3xazay5erplijzu0000), [visium-spatial-gene-expression-liver-3nbgorelud9lnn8l0000](/datasets/md/b4.md#visium-spatial-gene-expression-liver-3nbgorelud9lnn8l0000)
## Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics [spatial]
- Page: /collections/geo-gse188888/
- Kind: time course
- Datasets: 4
- Reference: PMID:35050211
- Design: The cardiac apex was resected at P2, within the regenerative window, and hearts were isolated at indicated timepoints for spatial transcriptomics.
- Members: [visium-spatial-gene-expression-heart-xs7tw92zqag99irp0000](/datasets/md/e5.md#visium-spatial-gene-expression-heart-xs7tw92zqag99irp0000), [visium-spatial-gene-expression-heart-hleqmhjoxygvzr1m0000](/datasets/md/51.md#visium-spatial-gene-expression-heart-hleqmhjoxygvzr1m0000), [visium-spatial-gene-expression-heart-pwnhgjl5plh057q60000](/datasets/md/c8.md#visium-spatial-gene-expression-heart-pwnhgjl5plh057q60000), [visium-spatial-gene-expression-heart-xircl4u8wo3k6kpr0000](/datasets/md/cf.md#visium-spatial-gene-expression-heart-xircl4u8wo3k6kpr0000)
## Spatial sequencing of young and aged lungs following influenza A virus infection
- Page: /collections/geo-gse202322/
- Kind: time course
- Datasets: 6
- Reference: PMID:37852965
- Design: Mice were infected with influenza A/PR8/34 (~50 PFU/mouse) to establish acute infection. Infections were performed by intranasal (i.n.) administration under anesthesia as described before (Sun et al., 2009). Mice were then euthanized and the right ventricle was perfused with 10 mL cold DPBS (Corning). For Visium spatial sequencing, mice were euthanized and lungs were inflated with 500 μL of 50% v/v OCT/PBS (Fisher Healthcare) via an intratracheal catheter. The left lung was excised and the caudal half was placed in a cryomold containing OCT. The mold was frozen in an isopentane (Fisher Scientific) bath chilled by liquid nitrogen. 10 μm sections were generated from frozen inflated left lungs using a cryostat 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. Lung tissue on Visium slides was permeabilized for 14 minutes to extract mRNA. Barcoded cDNA libraries were sequenced on an Illumina NextSeq 500 instrument using a NextSeq 500/550 High Output Kit v2 (150 cycles) (20024907, Illumina) with the following cycle counts: 28 (read 1), 10 (index 1), 10 (index 2), 90 (read 2). Loupe Browser (v5.0, 10x Genomics) was used to identify which spatial sequencing capture area spots were in contact with tissue. Demultiplexing and alignment was performed with Space Ranger (v2.1, 10x Genomics) and the mm10 2020-A reference transcriptome (10x Genomics). Analysis was mainly performed in R using Seurat (v4.0). Visium datasets were integrated using the SCTransform pipeline, and PCA and UMAP were performed using the top 30 principal components. SPOTlight (Elosua-Bayes et al., 2021) was used to demultiplex Visium data with our integrated scRNA-seq data used as a reference.
- Members: [visium-spatial-gene-expression-lung-nxu2cj3ndlypzd5k0000](/datasets/md/22.md#visium-spatial-gene-expression-lung-nxu2cj3ndlypzd5k0000), [visium-spatial-gene-expression-lung-fvqqullcsq13s7xv0000](/datasets/md/cb.md#visium-spatial-gene-expression-lung-fvqqullcsq13s7xv0000), [visium-spatial-gene-expression-lung-anxziilmlyw9exuj0000](/datasets/md/a5.md#visium-spatial-gene-expression-lung-anxziilmlyw9exuj0000), [visium-spatial-gene-expression-lung-bwhjskcd0hjy7jfn0000](/datasets/md/18.md#visium-spatial-gene-expression-lung-bwhjskcd0hjy7jfn0000), [visium-spatial-gene-expression-lung-v5fldm5ytfehsidq0000](/datasets/md/07.md#visium-spatial-gene-expression-lung-v5fldm5ytfehsidq0000), [visium-spatial-gene-expression-lung-8gjudebmikfzacgr0000](/datasets/md/73.md#visium-spatial-gene-expression-lung-8gjudebmikfzacgr0000)
## INPP5D limits plaque formation and glial reactivity in the APP/PS1 mouse model of Alzheimer’s disease
- Page: /collections/geo-gse203424/
- Kind: comparison
- Datasets: 12
- Reference: PMID:36448627
- Design: Spatial Transcriptomics of Inpp5dfl/fl/Cx3cr1CreER/+ crossed to APPKM670/671NL/PSEN1Δexon9 (PSAPP) mice to study the transcriptomics, brain-region resolved effect of removing Inpp5d from microglia in an animal model of Alzheimer's disease
- Members: [visium-spatial-gene-expression-brain-ucqynd3fkyl44qnb0000](/datasets/md/71.md#visium-spatial-gene-expression-brain-ucqynd3fkyl44qnb0000), [visium-spatial-gene-expression-brain-rykis5dqyprkgdzk0000](/datasets/md/f7.md#visium-spatial-gene-expression-brain-rykis5dqyprkgdzk0000), [visium-spatial-gene-expression-brain-8d5olswjlfcjkgic0000](/datasets/md/50.md#visium-spatial-gene-expression-brain-8d5olswjlfcjkgic0000), [visium-spatial-gene-expression-brain-ydip1vfz851fo9fe0000](/datasets/md/40.md#visium-spatial-gene-expression-brain-ydip1vfz851fo9fe0000), [visium-spatial-gene-expression-brain-os9xrgiwumfgy0350000](/datasets/md/34.md#visium-spatial-gene-expression-brain-os9xrgiwumfgy0350000), [visium-spatial-gene-expression-brain-oziqe0fofm9m4cg30000](/datasets/md/0a.md#visium-spatial-gene-expression-brain-oziqe0fofm9m4cg30000), [visium-spatial-gene-expression-brain-jse5usjxcdftnrsh0000](/datasets/md/fd.md#visium-spatial-gene-expression-brain-jse5usjxcdftnrsh0000), [visium-spatial-gene-expression-brain-dixib9tyeoxwoc1z0000](/datasets/md/f3.md#visium-spatial-gene-expression-brain-dixib9tyeoxwoc1z0000), [visium-spatial-gene-expression-brain-jpsiakdkkrc994bo0000](/datasets/md/9f.md#visium-spatial-gene-expression-brain-jpsiakdkkrc994bo0000), [visium-spatial-gene-expression-brain-fntf7jaux5gfpizf0000](/datasets/md/5b.md#visium-spatial-gene-expression-brain-fntf7jaux5gfpizf0000), [visium-spatial-gene-expression-brain-ngkvnyr7pr9m2pxm0000](/datasets/md/25.md#visium-spatial-gene-expression-brain-ngkvnyr7pr9m2pxm0000), [visium-spatial-gene-expression-brain-78uxjj7v6vu1x4pa0000](/datasets/md/d7.md#visium-spatial-gene-expression-brain-78uxjj7v6vu1x4pa0000)
## Shared inflammatory glial cell signature after brain injury, revealed by spatial, temporal and cell-type-specific profiling of the murine cerebral cortex [spatial transcriptomics]
- Page: /collections/geo-gse226208/
- Kind: time course
- Datasets: 2
- Reference: PMID:38570482
- Design: Spatial transcriptomics of the intact and injured mouse cerebral cortex at 3 days post injury (dpi).
- Members: [visium-spatial-gene-expression-cerebral-cortex-87e1jhuh65fo9b4n0000](/datasets/md/68.md#visium-spatial-gene-expression-cerebral-cortex-87e1jhuh65fo9b4n0000), [visium-spatial-gene-expression-cerebral-cortex-xcynojf4gga2cawy0000](/datasets/md/cf.md#visium-spatial-gene-expression-cerebral-cortex-xcynojf4gga2cawy0000)
## In vivo single-cell CRISPR uncovers distinct TNF-α programs in tumor evolution
- Page: /collections/geo-gse235325/
- Kind: other
- Datasets: 4
- Reference: PMID:39020166
- Design: To longitudinally monitor the function of cancer driver genes, we chose the 150 most frequently altered genes in human head and neck (HNSCC) and skin squamous cell carcinomas (sSCC), comprising 134 mutated genes and 16 copy number variations (CNVs). We selected 3 sgRNAs per gene and included 50 non-targeting control sgRNAs, resulting in a CROP-seq library of 500 sgRNAs used for high-titer lentivirus production. Lentiviral library was delivered into E9.5 embryos using ultrasound-guided in utero microinjection to infect the single-layered surface ectoderm, resident immune cells and melanoblasts of constitutively Cas9-expressing mouse embryos and introduce loss-of-function mutations in each of the selected cancer genes. At postnatal day 4 (P4) and 60 (P60), epidermal tissues are collected, sorted for mCherry-positive infected cells, and subjected them to single-cell RNA sequencing (scRNA-seq) to assess gene expression profiles and read out the corresponding sgRNA identity (via dial-out PCR). At P60, chemical carcinogenesis was induced by DMBA/TPA for 12 weeks, then from 30 of thus obtained skin tumors (from 2 animals) single-cell suspensions were sorted for mCherry-positive and negative cells by FACS, and finally sequenced for single-cell transcriptomes. Visium spatial transcriptomics was additionally performed on 4 other DMBA/TPA-induced tumors.
- Members: [visium-spatial-gene-expression-skin-of-body-qzzp9rbeml6zhkg10000](/datasets/md/9e.md#visium-spatial-gene-expression-skin-of-body-qzzp9rbeml6zhkg10000), [visium-spatial-gene-expression-skin-of-body-b0frpk6kic3awl5d0000](/datasets/md/78.md#visium-spatial-gene-expression-skin-of-body-b0frpk6kic3awl5d0000), [visium-spatial-gene-expression-skin-of-body-gyjdjznp863bio7r0000](/datasets/md/0a.md#visium-spatial-gene-expression-skin-of-body-gyjdjznp863bio7r0000), [visium-spatial-gene-expression-skin-of-body-mrwwm9v98prxkplg0000](/datasets/md/41.md#visium-spatial-gene-expression-skin-of-body-mrwwm9v98prxkplg0000)
## Clonal proliferation of smooth muscle cell in human atherosclerosis
- Page: /collections/geo-gse243179/
- Kind: other
- Datasets: 2
- Reference: PMID:37881937
- Design: Spatial transcriptomics analysis. Sample selection for 10X Genomics Visium V1 FFPE assay was based on the erosion plaque phenotypes selected for the detection of BGN using BaseScope (ACD). Adjacent section was selected from two of the coronary artery FFPE blocks corresponding to the erosion phenotypes. Total RNA was isolated from ten 5 µm sections from the FFPE blocks using RNeasy FFPE kit (Qiagen). RNA was analyzed using TapeStation (Agilent) and DV200 of ≥50% was observed for generating successful Visium spatial gene expression libraries. Next, the FFPE blocks for two erosion plaque phenotypes were sectioned at 5-8 µm thickness and mounted within a single 6.5 × 6.5 mm capture area on the Visium v1 spatial gene expression slide. Spatial transcriptomics assay using Visium V1 spatial gene expression slide and reagent kits were used according to instructions outlined by 10X Genomics (Pleasanton, CA). Visium Spatial Gene Expression was performed for FFPE sectioned tissues that produce spatially barcoded, Illumina® sequencer-ready libraries that are dual indexed. The generated libraries were loaded on a NovaSeq 6000 System (Illumina) and sequencing was performed using the following read protocol: read 1, 28 cycles (spatial barcode, UMI); i7 index read, 10 cycles (sample index); i5 index read, 10 cycles (sample index); read 2, 91 cycles (insert). Visium v1 raw data processing: Raw FASTQ files for a given capture area and corresponding capture area histology images were processed with Space Ranger software version 1.3.0 (10X Genomics, Pleasanton CA). Space Ranger Pipeline was used to align Fastq reads to human hg38 reference genome, and the probe set reference file specific only to human FFPE tissues because the synthetic probe DNA was sequenced rather than cDNA of a captured transcript. For FFPE samples, Space Ranger counts oligo ligation events to build the feature-barcode matrix. Gene expression analysis. The data files of raw transcriptomics were posted at NCBI’s Gene Expression Omnibus public database. Sequencing data was then imported into Partek Flow Enterprise Edition software (Partek Inc., Louis, MO). The data was filtered to exclude features where value <= 1.0 in at least 99.0 % of the cells and further normalized to CPM (counts per million) at Add: 1.0, Log: 2.0. A subset of SMCs was selected from the normalized counts by selecting for ACTA2 positive cells. Principle Component analysis (PCA) was then performed on these SMCs and for visualization, dimensionality reduction was performed using Uniform Manifold Approximation and Projection (UMAP) for the top 20 principal components from the graph-based clustering for ACTA2 positive cells. The data was further classified as with attributes for ACTA2 positive cells expressing BGN. We selected two regions each of WT-Clonal, Del-Clonal and non-clonal ROIs from two erosion sections as described in Supplemental Figure S5 (total 6 ROIs/section x2 = 12 ROIs). FDR (false discovery rate) < 0.05 and fold change < -1 or > 1. Marker genes identified were differentially expressed genes (DEGs) identified by one-to-one comparison of each cluster with all other clusters with P-values < 0.05 for regions of no clonality to clonality (Clonal WT + Del) to generate hierarchical cluster mapping (dot plot).
- Members: [visium-spatial-gene-expression-coronary-artery-sehua3wjwfopjrnf0000](/datasets/md/e8.md#visium-spatial-gene-expression-coronary-artery-sehua3wjwfopjrnf0000), [visium-spatial-gene-expression-coronary-artery-xfnllvs3p3mxlswc0000](/datasets/md/47.md#visium-spatial-gene-expression-coronary-artery-xfnllvs3p3mxlswc0000)
## Spatial microniches of IL-2 synergize with IL-10 to drive lung migratory Th2 cells in response to inhaled allergen [Spatial transcriptomics]
- Page: /collections/geo-gse245110/
- Kind: time course
- Datasets: 4
- Reference: PMID:38374265
- Design: 1DER CD45.1 Tg T cells were adoptively transferred to CD45.2 host, followed by intrasnasal immunization with 25ug of house dust mite daily for three days. Mediastinal lymph nodes (mLN) were isolated on day 4 and day 6, snap frozen and embedded in OCT for 10X Genomics Visium Spatial Gene Expression.
- Members: [visium-spatial-gene-expression-mediastinal-lymph-node-myeu3s99wjoospcz0000](/datasets/md/93.md#visium-spatial-gene-expression-mediastinal-lymph-node-myeu3s99wjoospcz0000), [visium-spatial-gene-expression-mediastinal-lymph-node-hxo7iwyculmxwvfi0000](/datasets/md/54.md#visium-spatial-gene-expression-mediastinal-lymph-node-hxo7iwyculmxwvfi0000), [visium-spatial-gene-expression-mediastinal-lymph-node-7whuxwypwsxzqoop0000](/datasets/md/93.md#visium-spatial-gene-expression-mediastinal-lymph-node-7whuxwypwsxzqoop0000), [visium-spatial-gene-expression-mediastinal-lymph-node-ufjov0ejakfzsh1x0000](/datasets/md/91.md#visium-spatial-gene-expression-mediastinal-lymph-node-ufjov0ejakfzsh1x0000)
## Regional and Cell Specific Bioactivity of Injectable ECM Biomaterials in MI through Spatial and Single Nucleus Transcriptomics
- Page: /collections/geo-gse262430/
- Kind: comparison
- Datasets: 9
- Reference: PMID:41285846
- Design: Gene expression profiling of 10x Genomic Chromium single nucleus RNA-Seq or Visium spatial transcriptomics from the left ventricular myocardium ornshort axis sections on injured Sprague Dawley female rats (225-250 g). Injuries include I/R (35 minutes of ischemia followed by reperfusion).
- Members: [visium-spatial-gene-expression-heart-left-ventricle-jpmyppeayak7o1v00000](/datasets/md/95.md#visium-spatial-gene-expression-heart-left-ventricle-jpmyppeayak7o1v00000), [visium-spatial-gene-expression-heart-left-ventricle-qkzwmcz0svy5rdaj0000](/datasets/md/bb.md#visium-spatial-gene-expression-heart-left-ventricle-qkzwmcz0svy5rdaj0000), [visium-spatial-gene-expression-heart-left-ventricle-s0spimismfapunx80000](/datasets/md/d1.md#visium-spatial-gene-expression-heart-left-ventricle-s0spimismfapunx80000), [visium-spatial-gene-expression-heart-left-ventricle-fna2mlzohy8gsgcf0000](/datasets/md/ea.md#visium-spatial-gene-expression-heart-left-ventricle-fna2mlzohy8gsgcf0000), [visium-spatial-gene-expression-heart-left-ventricle-jcnanwfrkphf172m0000](/datasets/md/36.md#visium-spatial-gene-expression-heart-left-ventricle-jcnanwfrkphf172m0000), [visium-spatial-gene-expression-heart-left-ventricle-kitzprddkqmzssnn0000](/datasets/md/11.md#visium-spatial-gene-expression-heart-left-ventricle-kitzprddkqmzssnn0000), [visium-spatial-gene-expression-heart-left-ventricle-3pud0oyhgqkmopg60000](/datasets/md/36.md#visium-spatial-gene-expression-heart-left-ventricle-3pud0oyhgqkmopg60000), [visium-spatial-gene-expression-heart-left-ventricle-0bd32met8wrgtkox0000](/datasets/md/44.md#visium-spatial-gene-expression-heart-left-ventricle-0bd32met8wrgtkox0000), [visium-spatial-gene-expression-heart-left-ventricle-h4qppmjt8f0ed9ue0000](/datasets/md/1e.md#visium-spatial-gene-expression-heart-left-ventricle-h4qppmjt8f0ed9ue0000)
## Spatial transcriptome analysis for placental tissue of preeclampsia
- Page: /collections/geo-gse266604/
- Kind: comparison
- Datasets: 2
- Reference: PMID:41604492
- Design: We used formalin-fixed paraffin embedded (FFPE) tissues of preeclampsia and normal placenta. Accoriding to the Visium FFPE protocol, the spatial transcriptome analysis was conducted by CyberomiX (Kyoto, Japan).
- Members: [visium-spatial-gene-expression-placenta-cbzxp4rkw17obiu70000](/datasets/md/b9.md#visium-spatial-gene-expression-placenta-cbzxp4rkw17obiu70000), [visium-spatial-gene-expression-placenta-dusaxfuqdksl5bb00000](/datasets/md/50.md#visium-spatial-gene-expression-placenta-dusaxfuqdksl5bb00000)
## Spatial Transcriptomics of Lungs Infected with Coccidioides posadasii
- Page: /collections/geo-gse274767/
- Kind: time course
- Datasets: 2
- Reference: PMID:39611685
- Design: Spatial transcriptomics was conducted on lung tissues from mice intranasally infected with Coccidioides posadasii. Samples were taken from a non-infected lung (D0) and an infected lung 14 days post-infection (D14).
- Members: [visium-spatial-gene-expression-lung-whqbpb62mecywbg40000](/datasets/md/6e.md#visium-spatial-gene-expression-lung-whqbpb62mecywbg40000), [visium-spatial-gene-expression-lung-nia2ghsnb9pppu8m0000](/datasets/md/9d.md#visium-spatial-gene-expression-lung-nia2ghsnb9pppu8m0000)
## Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair.
- Page: /collections/geo-gse280515/
- Kind: comparison
- Datasets: 3
- Reference: PMID:39862865
- Design: Single cell RNA Seq = Total liver cells derived from mice following PBS and APAP administration and CD64+F4/80+ macrophages from Trem2 fl/fl mice and CD64CRE Trem2 fl/fl mice. Bulk RNA seq on KCs and LAM-like KCs isolated from livers 48hr post PBS or APAP administration 10 Visium Spatial Seq = mouse liver 48h post PBS or APAP administration.
- Members: [visium-spatial-gene-expression-liver-rrtpdg4sewxgbda60000](/datasets/md/1f.md#visium-spatial-gene-expression-liver-rrtpdg4sewxgbda60000), [visium-spatial-gene-expression-liver-9rsxi2ijeffz1bmm0000](/datasets/md/de.md#visium-spatial-gene-expression-liver-9rsxi2ijeffz1bmm0000), [visium-spatial-gene-expression-liver-0f7ft658lu9q6t7h0000](/datasets/md/0a.md#visium-spatial-gene-expression-liver-0f7ft658lu9q6t7h0000)
## Spatial transcriptomic analysis of developing hearts at embryonic and neonatal stages
- Page: /collections/geo-gse282547/
- Kind: other
- Datasets: 8
- Reference: PMID:42141139
- Design: Visium from 10X genomics and Slide-seq from Curio-bio were used to profile the genome-wide genes expression of heart sections.
- Members: [visium-spatial-gene-expression-heart-t1nc4qqeacd2l9hb0000](/datasets/md/8e.md#visium-spatial-gene-expression-heart-t1nc4qqeacd2l9hb0000), [visium-spatial-gene-expression-heart-mlppcpyvcizxniin0000](/datasets/md/c4.md#visium-spatial-gene-expression-heart-mlppcpyvcizxniin0000), [visium-spatial-gene-expression-heart-10exquomgelmqhhz0000](/datasets/md/73.md#visium-spatial-gene-expression-heart-10exquomgelmqhhz0000), [visium-spatial-gene-expression-heart-na7epyrl6a9sa0s60000](/datasets/md/a8.md#visium-spatial-gene-expression-heart-na7epyrl6a9sa0s60000), [visium-spatial-gene-expression-heart-tqi2wing03y7fhdn0000](/datasets/md/e0.md#visium-spatial-gene-expression-heart-tqi2wing03y7fhdn0000), [visium-spatial-gene-expression-heart-y6bpdams8e0ue7jq0000](/datasets/md/ce.md#visium-spatial-gene-expression-heart-y6bpdams8e0ue7jq0000), [visium-spatial-gene-expression-heart-rftkii3ecmsb6gdj0000](/datasets/md/6b.md#visium-spatial-gene-expression-heart-rftkii3ecmsb6gdj0000), [visium-spatial-gene-expression-heart-dt5srhtiohrscnpv0000](/datasets/md/17.md#visium-spatial-gene-expression-heart-dt5srhtiohrscnpv0000)
## Spatial transcriptomic atlas of aggressive osteosarcomas reveals shared gene surface expression and immune landscape.
- Page: /collections/geo-gse293065/
- Kind: comparison
- Datasets: 26
- Reference: PMID:42399228
- Design: 26 FFPE samples of primary (n=9) and relapse (n=17) osteosarcoma tumors were analyzed by spatial transcriptomics using the Visium V1 FFPE protocol.
- Members: [visium-spatial-gene-expression-bone-element-yy3uwr6jeb6c3jhg0000](/datasets/md/7f.md#visium-spatial-gene-expression-bone-element-yy3uwr6jeb6c3jhg0000), [visium-spatial-gene-expression-bone-element-fzgwwkksxjpzktbb0000](/datasets/md/29.md#visium-spatial-gene-expression-bone-element-fzgwwkksxjpzktbb0000), [visium-spatial-gene-expression-bone-element-w5hvxfqttuki5akf0000](/datasets/md/0e.md#visium-spatial-gene-expression-bone-element-w5hvxfqttuki5akf0000), [visium-spatial-gene-expression-bone-element-dtfdwgoz8ev4spza0000](/datasets/md/2f.md#visium-spatial-gene-expression-bone-element-dtfdwgoz8ev4spza0000), [visium-spatial-gene-expression-bone-element-b5ndyznf2w2gahkn0000](/datasets/md/95.md#visium-spatial-gene-expression-bone-element-b5ndyznf2w2gahkn0000), [visium-spatial-gene-expression-bone-element-ha5zjtnrc9wqkp420000](/datasets/md/e1.md#visium-spatial-gene-expression-bone-element-ha5zjtnrc9wqkp420000), [visium-spatial-gene-expression-bone-element-iqg0wxgoattqoqfu0000](/datasets/md/bc.md#visium-spatial-gene-expression-bone-element-iqg0wxgoattqoqfu0000), [visium-spatial-gene-expression-bone-element-129xe3nzxqrv7snv0000](/datasets/md/43.md#visium-spatial-gene-expression-bone-element-129xe3nzxqrv7snv0000), [visium-spatial-gene-expression-bone-element-x7lnn0mndgdqahu10000](/datasets/md/10.md#visium-spatial-gene-expression-bone-element-x7lnn0mndgdqahu10000), [visium-spatial-gene-expression-bone-element-mtfgirrg7leyaxyp0000](/datasets/md/97.md#visium-spatial-gene-expression-bone-element-mtfgirrg7leyaxyp0000), [visium-spatial-gene-expression-bone-element-qvxbkhym8vcucoto0000](/datasets/md/81.md#visium-spatial-gene-expression-bone-element-qvxbkhym8vcucoto0000), [visium-spatial-gene-expression-bone-element-jsejhnjikbwrqwio0000](/datasets/md/c5.md#visium-spatial-gene-expression-bone-element-jsejhnjikbwrqwio0000), [visium-spatial-gene-expression-bone-element-cvvssfcyw3lw0fqw0000](/datasets/md/96.md#visium-spatial-gene-expression-bone-element-cvvssfcyw3lw0fqw0000), [visium-spatial-gene-expression-bone-element-zqc9cbxajrdkqhj30000](/datasets/md/f0.md#visium-spatial-gene-expression-bone-element-zqc9cbxajrdkqhj30000), [visium-spatial-gene-expression-bone-element-at35fhm3607gdap90000](/datasets/md/ce.md#visium-spatial-gene-expression-bone-element-at35fhm3607gdap90000), [visium-spatial-gene-expression-bone-element-umklkrizg8ec85aj0000](/datasets/md/6f.md#visium-spatial-gene-expression-bone-element-umklkrizg8ec85aj0000), [visium-spatial-gene-expression-bone-element-500mp4c5ml5q1gha0000](/datasets/md/9d.md#visium-spatial-gene-expression-bone-element-500mp4c5ml5q1gha0000), [visium-spatial-gene-expression-bone-element-ciygvbtc6bvxj8jd0000](/datasets/md/68.md#visium-spatial-gene-expression-bone-element-ciygvbtc6bvxj8jd0000), [visium-spatial-gene-expression-bone-element-assktdpctqmyir090000](/datasets/md/a5.md#visium-spatial-gene-expression-bone-element-assktdpctqmyir090000), [visium-spatial-gene-expression-bone-element-8uxncjy6tdsic1xd0000](/datasets/md/45.md#visium-spatial-gene-expression-bone-element-8uxncjy6tdsic1xd0000), [visium-spatial-gene-expression-bone-element-udc2ypaoariaemta0000](/datasets/md/3c.md#visium-spatial-gene-expression-bone-element-udc2ypaoariaemta0000), [visium-spatial-gene-expression-bone-element-2lggpaxlju98m77a0000](/datasets/md/79.md#visium-spatial-gene-expression-bone-element-2lggpaxlju98m77a0000), [visium-spatial-gene-expression-bone-element-hbgyjbjg0pghjein0000](/datasets/md/6f.md#visium-spatial-gene-expression-bone-element-hbgyjbjg0pghjein0000), [visium-spatial-gene-expression-bone-element-ljumqvnch1pfouto0000](/datasets/md/72.md#visium-spatial-gene-expression-bone-element-ljumqvnch1pfouto0000), [visium-spatial-gene-expression-bone-element-rqf5kpd1g1mcsaq90000](/datasets/md/08.md#visium-spatial-gene-expression-bone-element-rqf5kpd1g1mcsaq90000), [visium-spatial-gene-expression-bone-element-sutivcmswyrzismv0000](/datasets/md/9a.md#visium-spatial-gene-expression-bone-element-sutivcmswyrzismv0000)
## Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response [Spatial Transcriptomics]
- Page: /collections/geo-gse293427/
- Kind: comparison
- Datasets: 10
- Reference: PMID:42018669
- Design: We performed spatial transcriptomics profiling using 10x Genomics Visium on mesenteric arteries from non-diabetic and diabetic donors
- Members: [visium-spatial-gene-expression-mesenteric-artery-788jnlyxx23vu3hs0000](/datasets/md/5e.md#visium-spatial-gene-expression-mesenteric-artery-788jnlyxx23vu3hs0000), [visium-spatial-gene-expression-mesenteric-artery-zjxvmu1rnsbzsnen0000](/datasets/md/7d.md#visium-spatial-gene-expression-mesenteric-artery-zjxvmu1rnsbzsnen0000), [visium-spatial-gene-expression-mesenteric-artery-6ofmgvoqzr7ark0b0000](/datasets/md/9f.md#visium-spatial-gene-expression-mesenteric-artery-6ofmgvoqzr7ark0b0000), [visium-spatial-gene-expression-mesenteric-artery-jnloy7c8gvngu1ms0000](/datasets/md/82.md#visium-spatial-gene-expression-mesenteric-artery-jnloy7c8gvngu1ms0000), [visium-spatial-gene-expression-mesenteric-artery-ihvcrzj44itqbhxr0000](/datasets/md/25.md#visium-spatial-gene-expression-mesenteric-artery-ihvcrzj44itqbhxr0000), [visium-spatial-gene-expression-mesenteric-artery-y0inymjtxs4dh9dx0000](/datasets/md/03.md#visium-spatial-gene-expression-mesenteric-artery-y0inymjtxs4dh9dx0000), [visium-spatial-gene-expression-mesenteric-artery-lbsscjikwe12wrfu0000](/datasets/md/88.md#visium-spatial-gene-expression-mesenteric-artery-lbsscjikwe12wrfu0000), [visium-spatial-gene-expression-mesenteric-artery-jecz0wmr6qpuproj0000](/datasets/md/eb.md#visium-spatial-gene-expression-mesenteric-artery-jecz0wmr6qpuproj0000), [visium-spatial-gene-expression-mesenteric-artery-pm5tasjki4cqziic0000](/datasets/md/ab.md#visium-spatial-gene-expression-mesenteric-artery-pm5tasjki4cqziic0000), [visium-spatial-gene-expression-mesenteric-artery-a12eqjbmymia024n0000](/datasets/md/c9.md#visium-spatial-gene-expression-mesenteric-artery-a12eqjbmymia024n0000)
## A skeletal muscle atlas shows neuromuscular junction adaptations to growth and atrophy
- Page: /collections/geo-gse294765/
- Kind: comparison
- Datasets: 6
- Reference: PMID:42019489
- Design: scRNA-seq: Plantaris muscles were harvested from wt mice in basal/unperturbed conditions, as well as at 3- and 7 days post atrophy (denervation, Den) or hypertrophy (overloading, OVL) induction. A single-cell suspension from an average of 10-16 pooled plantaris muscles per condition and time point was subjected to FACS to enrich in minor cell populations in skeletal muscle (muscle stem cells, endothelial cells, Schwann cells and mural cells). The enriched cell suspension was analyzed using scRNA-seq. snRNA-seq: Plantaris muscles were harvested from wt mice in basal/unperturbed conditions, as well as at 3- and 7 days post-atrophy (denervation, Den) or hypertrophy (overloading, OVL) induction. A single-nucleus suspension from 2 pooled plantaris muscles per condition and time point was analyzed using snRNA-seq. Spatial Transcriptomics: Plantaris muscles were harvested from wt mice in basal/unperturbed conditions, as well as at 7 days post-atrophy (denervation, Den) or hypertrophy (overloading, OVL) induction. Two plantaris muscles per condition and time point were analyzed using spatial transcriptomics.
- Members: [visium-spatial-gene-expression-plantaris-8wvdm7tgoj5ln3wo0000](/datasets/md/8c.md#visium-spatial-gene-expression-plantaris-8wvdm7tgoj5ln3wo0000), [visium-spatial-gene-expression-plantaris-ocyaz009aemljrv00000](/datasets/md/93.md#visium-spatial-gene-expression-plantaris-ocyaz009aemljrv00000), [visium-spatial-gene-expression-plantaris-h4fplgv2vrs8lb9w0000](/datasets/md/d3.md#visium-spatial-gene-expression-plantaris-h4fplgv2vrs8lb9w0000), [visium-spatial-gene-expression-plantaris-ofirgkjmozwnfb7s0000](/datasets/md/a9.md#visium-spatial-gene-expression-plantaris-ofirgkjmozwnfb7s0000), [visium-spatial-gene-expression-plantaris-twljycxoyamerlci0000](/datasets/md/64.md#visium-spatial-gene-expression-plantaris-twljycxoyamerlci0000), [visium-spatial-gene-expression-plantaris-wd0giqmh0czwyios0000](/datasets/md/85.md#visium-spatial-gene-expression-plantaris-wd0giqmh0czwyios0000)
## Spatial transcriptomics and scRNA-sequencing on gastrocnemius muscle form B6-mdx and D2-mdx mice
- Page: /collections/geo-gse297388/
- Kind: comparison
- Datasets: 4
- Reference: PMID:42067923
- Design: For spatial transcriptomics, gastrocnemius muscles from 10-week-old C57BL/6J and D2.B10 (DBA/2-congenic) mice were either isolated, embedded in OCT and flash-frozen in liquid nitrogen-cooled isopentane. Embedded muscle was transversely sectioned at 10µm thickness and processed for 10X Genomics Visium analysis. For single-cell RNA-sequencing, FACS-isolated cells of gastrocnemius muscles from 10-week-old C57BL/6J and D2.B10 mice were captured using the 10X Genomics Chromium Platform and sequenced using an Illumina NextSeq 50.
- Members: [visium-spatial-gene-expression-gastrocnemius-atbw83y2xgmmfryf0000](/datasets/md/4d.md#visium-spatial-gene-expression-gastrocnemius-atbw83y2xgmmfryf0000), [visium-spatial-gene-expression-gastrocnemius-mmzbdvh4gcp35xwn0000](/datasets/md/30.md#visium-spatial-gene-expression-gastrocnemius-mmzbdvh4gcp35xwn0000), [visium-spatial-gene-expression-gastrocnemius-hfzkc8g8lxgwsxwq0000](/datasets/md/7e.md#visium-spatial-gene-expression-gastrocnemius-hfzkc8g8lxgwsxwq0000), [visium-spatial-gene-expression-gastrocnemius-kguesih2ol9izlqs0000](/datasets/md/8c.md#visium-spatial-gene-expression-gastrocnemius-kguesih2ol9izlqs0000)
## Spatial transcriptomics of Atg7 knockout mice reveals ATG7’s role in antimicrobial immunity against nontuberculous mycobacteria
- Page: /collections/geo-gse297621/
- Kind: comparison
- Datasets: 2
- Reference: PMID:40730835
- Design: Following the resection of lungs from Mav-infected Atg7 wild type and knock out at 21 dpi. Tissues were dissociated by Liberase TL
- Members: [visium-spatial-gene-expression-lung-kzml10xkkgu9naor0000](/datasets/md/35.md#visium-spatial-gene-expression-lung-kzml10xkkgu9naor0000), [visium-spatial-gene-expression-lung-vx3ap7i2mp8abzxu0000](/datasets/md/a4.md#visium-spatial-gene-expression-lung-vx3ap7i2mp8abzxu0000)
## Molecular pathology of acute spinal cord injury in middle-aged mice
- Page: /collections/geo-gse298545/
- Kind: time course
- Datasets: 4
- Reference: PMID:40653490
- Design: C57Bl/6J mouse contusive spinal cord injury sites were analyzed with single-cell sequencing (10X Chromium v3.1) at uninjured and 3 days-post injury conditions in middle-aged (10-12 months-old) and young (2-4 months-old) mice. 3dpi injury sites in aged and young mice were analyzed with spatial sequencing (10X Visium v1).
- Members: [visium-spatial-gene-expression-spinal-cord-my1vrsgod1rlqtvl0000](/datasets/md/e6.md#visium-spatial-gene-expression-spinal-cord-my1vrsgod1rlqtvl0000), [visium-spatial-gene-expression-spinal-cord-kjyeakcsb2lgtjr40000](/datasets/md/60.md#visium-spatial-gene-expression-spinal-cord-kjyeakcsb2lgtjr40000), [visium-spatial-gene-expression-spinal-cord-mtayiqahq0zuuubw0000](/datasets/md/e1.md#visium-spatial-gene-expression-spinal-cord-mtayiqahq0zuuubw0000), [visium-spatial-gene-expression-spinal-cord-l6oimhxmjrxpnfe80000](/datasets/md/89.md#visium-spatial-gene-expression-spinal-cord-l6oimhxmjrxpnfe80000)
## Immunosuppressive tumor microenvironment of osteosarcoma [Spatial transcriptomics]
- Page: /collections/geo-gse299025/
- Kind: replicates
- Datasets: 2
- Reference: PMID:40647416
- Design: Formalin-fixed, paraffin-embedded (FFPE) samples of two primary OS pre-treatment biopsy tissue samples (Patients A and B) were obtained from CCMC and stored at 4 °C in the dark. Prior to Visium transcriptomics, RNA quality of FFPE samples was determined by DV200 score using Agilent (Santa Clara, California) TapeStation 4200 High Sensitivity DNA ScreenTape. Tissue blocks with DV200 scores above 50% were used for downstream processing. Briefly, FFPE sections were placed on a 10x Visium FFPE Gene Expression slide, deparaffinized, H&E stained, then imaged in brightfield using a NanoZoomer SQ (Hamamatsu Photonics, Shizuoka, Japan) slide scanner, followed by incubation with human-specific probe sets provided by the manufacturer for subsequent mRNA labeling and library generation per the manufacturer's protocol (10x Genomics, CG000407). Libraries were pooled for sequencing on an Illumina NovaSeq 6000 200-cycle S4 flow cell using a 28-10-10-90 read configuration, targeting 100,000 read pairs per spot covered by tissue.
- Members: [visium-spatial-gene-expression-bone-tissue-lpbcdodkyrznsc5y0000](/datasets/md/31.md#visium-spatial-gene-expression-bone-tissue-lpbcdodkyrznsc5y0000), [visium-spatial-gene-expression-bone-tissue-lqb529rrpc5xiocj0000](/datasets/md/1c.md#visium-spatial-gene-expression-bone-tissue-lqb529rrpc5xiocj0000)
## Unveiling Transcriptional Heterogeneity and Discovering Footprints in Pediatric Medulloblastoma via Spatial RNA-Seq and Machine Learning
- Page: /collections/geo-gse306506/
- Kind: comparison
- Datasets: 6
- Reference: PMID:42449993
- Design: We performed a comprehensive analysis of the transcriptional landscape of medulloblastoma (MB) using spatial transcriptomics (stRNA-seq) from five pediatric MB patients (3 MB-SHH, 1 MB-Group 4, and 1 MB-Group 3), including one biological replicate for two patients—one classified as MB-SHH and the other as MB-Group 4. Tissues were paraffin-embedded and sequenced using the 10x Genomics Visium V1 platform and the Illumina HiSeq 2000 system.
- Members: [visium-spatial-gene-expression-cerebellum-9n1bwakv4oqxfryq0000](/datasets/md/d9.md#visium-spatial-gene-expression-cerebellum-9n1bwakv4oqxfryq0000), [visium-spatial-gene-expression-cerebellum-qtu6p8h7qxwasrcg0000](/datasets/md/3f.md#visium-spatial-gene-expression-cerebellum-qtu6p8h7qxwasrcg0000), [visium-spatial-gene-expression-cerebellum-ljechkfsmmizewri0000](/datasets/md/85.md#visium-spatial-gene-expression-cerebellum-ljechkfsmmizewri0000), [visium-spatial-gene-expression-cerebellum-yzoy55tbgeilqqzg0000](/datasets/md/ae.md#visium-spatial-gene-expression-cerebellum-yzoy55tbgeilqqzg0000), [visium-spatial-gene-expression-cerebellum-4cv6hpbvtn43zr5h0000](/datasets/md/b9.md#visium-spatial-gene-expression-cerebellum-4cv6hpbvtn43zr5h0000), [visium-spatial-gene-expression-cerebellum-1dr2soclcqzsxxmu0000](/datasets/md/1f.md#visium-spatial-gene-expression-cerebellum-1dr2soclcqzsxxmu0000)
## Integrated single-cell and spatial transcriptomics of ovarian immune landscape reveal role of distinct macrophages in classic galactosemia associated with premature ovarian insufficiency
- Page: /collections/geo-gse308275/
- Kind: replicates
- Datasets: 2
- Reference: PMID:42226209
- Design: CG and control ovarian FFPE sections were processed for Visium spatial transcriptomic protocol (10x Genomics).
- Members: [visium-spatial-gene-expression-ovary-uqnflb2cmq2ohxv60000](/datasets/md/9e.md#visium-spatial-gene-expression-ovary-uqnflb2cmq2ohxv60000), [visium-spatial-gene-expression-ovary-2amm0at7shgomk5m0000](/datasets/md/00.md#visium-spatial-gene-expression-ovary-2amm0at7shgomk5m0000)
## Blocking the Gut–Liver IgA Axis Attenuates Macrophage-Mediated Inflammation and Injury in Alcohol-Associated Liver Disease [Spatial Transcriptomics]
- Page: /collections/geo-gse320442/
- Kind: comparison
- Datasets: 15
- Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE320442
- Design: FFPE tissue sections were processed on the Visium CytAssist instrument and sequenced on an Illumina platform (paired-end; Read1 contains spatial barcode/UMI and Read2 captures transcript-derived sequence). Data were processed with Space Ranger to generate spatial feature-barcode matrices and QC summaries for each sample.
- Members: [visium-spatial-gene-expression-liver-2twxaw4ydmbjj8em0000](/datasets/md/41.md#visium-spatial-gene-expression-liver-2twxaw4ydmbjj8em0000), [visium-spatial-gene-expression-liver-oeqntngtdyanvg2i0000](/datasets/md/a9.md#visium-spatial-gene-expression-liver-oeqntngtdyanvg2i0000), [visium-spatial-gene-expression-intestine-iidaira8djgbvkqw0000](/datasets/md/93.md#visium-spatial-gene-expression-intestine-iidaira8djgbvkqw0000), [visium-spatial-gene-expression-liver-5kqtvqdnqvkbvfyd0000](/datasets/md/84.md#visium-spatial-gene-expression-liver-5kqtvqdnqvkbvfyd0000), [visium-spatial-gene-expression-liver-djvoghdpuwrqo0ii0000](/datasets/md/2f.md#visium-spatial-gene-expression-liver-djvoghdpuwrqo0ii0000), [visium-spatial-gene-expression-liver-45u4puvdc6py4z1n0000](/datasets/md/5c.md#visium-spatial-gene-expression-liver-45u4puvdc6py4z1n0000), [visium-spatial-gene-expression-liver-5se6wimi9woak0hj0000](/datasets/md/f0.md#visium-spatial-gene-expression-liver-5se6wimi9woak0hj0000), [visium-spatial-gene-expression-liver-jgzxlcgevxcgmmlr0000](/datasets/md/99.md#visium-spatial-gene-expression-liver-jgzxlcgevxcgmmlr0000), [visium-spatial-gene-expression-liver-yunuee5a0xwe0ffh0000](/datasets/md/b0.md#visium-spatial-gene-expression-liver-yunuee5a0xwe0ffh0000), [visium-spatial-gene-expression-intestine-eoyjcos76zxktod70000](/datasets/md/f0.md#visium-spatial-gene-expression-intestine-eoyjcos76zxktod70000), [visium-spatial-gene-expression-liver-rbvygtvok4yhehsd0000](/datasets/md/1c.md#visium-spatial-gene-expression-liver-rbvygtvok4yhehsd0000), [visium-spatial-gene-expression-intestine-aiswteeehoudzs440000](/datasets/md/6d.md#visium-spatial-gene-expression-intestine-aiswteeehoudzs440000), [visium-spatial-gene-expression-intestine-uaxtejjwdys4i32n0000](/datasets/md/0e.md#visium-spatial-gene-expression-intestine-uaxtejjwdys4i32n0000), [visium-spatial-gene-expression-intestine-euhbhnnyllugqoi70000](/datasets/md/32.md#visium-spatial-gene-expression-intestine-euhbhnnyllugqoi70000), [visium-spatial-gene-expression-intestine-npipklgkfrhmjqgu0000](/datasets/md/0c.md#visium-spatial-gene-expression-intestine-npipklgkfrhmjqgu0000)
## Integration of spatial and single cell transcriptomics localizes epithelial-immune cross-talk in kidney injury
- Page: /collections/hest-integration-of-spatial-and-single-cell-transcriptomics-localizes-epithelial-immune-cross-talk-in-kidney-injury/
- Kind: comparison
- Datasets: 3
- Members: [visium-spatial-gene-expression-kidney-agdrf8dv9vyqa0si0000](/datasets/md/d0.md#visium-spatial-gene-expression-kidney-agdrf8dv9vyqa0si0000), [visium-spatial-gene-expression-kidney-1ewiyjxa6qpuxqh20000](/datasets/md/86.md#visium-spatial-gene-expression-kidney-1ewiyjxa6qpuxqh20000), [visium-spatial-gene-expression-kidney-wzsaovlcsjkiwf2c0000](/datasets/md/b3.md#visium-spatial-gene-expression-kidney-wzsaovlcsjkiwf2c0000)
## Aging-Related Cellular and Molecular Changes Reveal a Role for Bglap3+ Neurons in MEC Spatial Cognition
- Page: /collections/geo-gse347650/
- Kind: other
- Datasets: 14
- Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE347650
- Design: Spatial gene expression profiling of sagittal brain sections containing the medial entorhinal cortex (MEC) from two young and two old C57BL/6J mice using 10x Genomics Visium. Four capture-area libraries (s1-s4) were prepared per mouse: Old1, Old2, Young1 and Young2, for 16 libraries in total. Each Old2 library contains two brain tissue sections (8 sections across 4 libraries); each of the other 12 libraries contains one brain tissue section. Thus, 20 brain tissue sections were profiled in 16 libraries from 4 biological replicates (2 per age group). Libraries from the same mouse are within-animal section samples, not independent biological replicates. s1-s4 follows medial-to-lateral MEC order. Analyses compare old versus young in whole brain sections, the whole MEC, and superficial, intermediate and deep MEC subregions.
- Members: [visium-spatial-gene-expression-entorhinal-cortex-kbxabmpgfe2zshh50000](/datasets/md/37.md#visium-spatial-gene-expression-entorhinal-cortex-kbxabmpgfe2zshh50000), [visium-spatial-gene-expression-entorhinal-cortex-90jcvjojkl1efwad0000](/datasets/md/1a.md#visium-spatial-gene-expression-entorhinal-cortex-90jcvjojkl1efwad0000), [visium-spatial-gene-expression-entorhinal-cortex-yht0uxur0wmudnr30000](/datasets/md/87.md#visium-spatial-gene-expression-entorhinal-cortex-yht0uxur0wmudnr30000), [visium-spatial-gene-expression-entorhinal-cortex-hsxzwaynwfm62cyf0000](/datasets/md/f2.md#visium-spatial-gene-expression-entorhinal-cortex-hsxzwaynwfm62cyf0000), [visium-spatial-gene-expression-entorhinal-cortex-nrcdpewfccmec3yn0000](/datasets/md/18.md#visium-spatial-gene-expression-entorhinal-cortex-nrcdpewfccmec3yn0000), [visium-spatial-gene-expression-entorhinal-cortex-ocaa34zu1iez1cyq0000](/datasets/md/74.md#visium-spatial-gene-expression-entorhinal-cortex-ocaa34zu1iez1cyq0000), [visium-spatial-gene-expression-entorhinal-cortex-4jmm4pbxqexjngct0000](/datasets/md/85.md#visium-spatial-gene-expression-entorhinal-cortex-4jmm4pbxqexjngct0000), [visium-spatial-gene-expression-entorhinal-cortex-uxq9xs171h221jia0000](/datasets/md/16.md#visium-spatial-gene-expression-entorhinal-cortex-uxq9xs171h221jia0000), [visium-spatial-gene-expression-entorhinal-cortex-nzknazb8tth8isuy0000](/datasets/md/65.md#visium-spatial-gene-expression-entorhinal-cortex-nzknazb8tth8isuy0000), [visium-spatial-gene-expression-entorhinal-cortex-qma7jka95ejhvqsy0000](/datasets/md/0a.md#visium-spatial-gene-expression-entorhinal-cortex-qma7jka95ejhvqsy0000), [visium-spatial-gene-expression-entorhinal-cortex-shzge500ntrakpp30000](/datasets/md/08.md#visium-spatial-gene-expression-entorhinal-cortex-shzge500ntrakpp30000), [visium-spatial-gene-expression-entorhinal-cortex-jw01ns0wqscvbg5s0000](/datasets/md/95.md#visium-spatial-gene-expression-entorhinal-cortex-jw01ns0wqscvbg5s0000), [visium-spatial-gene-expression-entorhinal-cortex-qa92csnslhw1f4bq0000](/datasets/md/c1.md#visium-spatial-gene-expression-entorhinal-cortex-qa92csnslhw1f4bq0000), [visium-spatial-gene-expression-entorhinal-cortex-gorro86ruijvgh6k0000](/datasets/md/e2.md#visium-spatial-gene-expression-entorhinal-cortex-gorro86ruijvgh6k0000)
## Spatial analysis reveals cellular microenvironments and mechanisms of inflammation and injury in acute interstitial nephritis.
- Page: /collections/bia-s-biad3694/
- Kind: publication
- Datasets: 9
- Reference: 10.1038/s41467-026-77210-y
- Members: [imaging-mass-cytometry-kidney-q7p9hkfqe1tmt6iv0000](/datasets/md/91.md#imaging-mass-cytometry-kidney-q7p9hkfqe1tmt6iv0000), [imaging-mass-cytometry-kidney-epwomli5jdprjlpi0000](/datasets/md/f7.md#imaging-mass-cytometry-kidney-epwomli5jdprjlpi0000), [imaging-mass-cytometry-kidney-kilizmglwwzlny4c0000](/datasets/md/92.md#imaging-mass-cytometry-kidney-kilizmglwwzlny4c0000), [imaging-mass-cytometry-kidney-31no7u1wvtwpletx0000](/datasets/md/72.md#imaging-mass-cytometry-kidney-31no7u1wvtwpletx0000), [imaging-mass-cytometry-kidney-khf91mepgs46yzul0000](/datasets/md/ca.md#imaging-mass-cytometry-kidney-khf91mepgs46yzul0000), [imaging-mass-cytometry-kidney-rlkqe0ns6kmthvlv0000](/datasets/md/7f.md#imaging-mass-cytometry-kidney-rlkqe0ns6kmthvlv0000), [imaging-mass-cytometry-kidney-knywku1i4lubgulm0000](/datasets/md/79.md#imaging-mass-cytometry-kidney-knywku1i4lubgulm0000), [imaging-mass-cytometry-kidney-xlurktr11pneyeqz0000](/datasets/md/d4.md#imaging-mass-cytometry-kidney-xlurktr11pneyeqz0000), [imaging-mass-cytometry-kidney-ykkcdchodgn1tpow0000](/datasets/md/d9.md#imaging-mass-cytometry-kidney-ykkcdchodgn1tpow0000)