# SpatialData-DB collections, shard 9
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.
## Charting spatial ligand-target activity using Renoir.
- Page: /collections/geo-gse319617/
- Kind: publication
- Datasets: 2
- Reference: 10.1038/s41467-026-72388-7
- Design: Two fetal liver samples (FFPE) were used for the generation of 10x Genomics Visium HD datasets.
- Members: [visium-hd-liver-j1dr8zbhmubb6ozg0000](/datasets/md/98.md#visium-hd-liver-j1dr8zbhmubb6ozg0000), [visium-hd-liver-fl8gdod8fd8rgqzy0000](/datasets/md/1a.md#visium-hd-liver-fl8gdod8fd8rgqzy0000)
## Spatial transcriptomic analyses highlight distinct erythroid niches in mice and humans.
- Page: /collections/geo-gse271824/
- Kind: publication
- Datasets: 3
- Reference: 10.1038/s41588-026-02671-2
- Design: Formalin-Fixed Paraffin-Embedded (FFPE) blocks of diverse human hematopoietic organs including embryonic 16 weeks (gestational age, GA) fetal liver, adult bone marrow from healthy donor and MDS patient were used for the analysis. These FFPE block samples were analyzed using spatial transcriptomics.
- Members: [10x-xenium-bone-marrow-igxqqsomuffzkbwp0000](/datasets/md/2f.md#10x-xenium-bone-marrow-igxqqsomuffzkbwp0000), [10x-xenium-bone-marrow-0w9hdkmt5xvkii9m0000](/datasets/md/80.md#10x-xenium-bone-marrow-0w9hdkmt5xvkii9m0000), [10x-xenium-liver-w3zppeofvctddlbv0000](/datasets/md/32.md#10x-xenium-liver-w3zppeofvctddlbv0000)
## Spatiotemporally deciphering the mysterious mechanism of persistent HPV-induced malignant transition and immune remodelling from HPV-infected normal cervix, precancer to cervical cancer: Integrating single-cell RNA-sequencing and spatial transcriptome.
- Page: /collections/doi-10-1002-ctm2-1219/
- Kind: comparison
- Datasets: 4
- Reference: 10.1002/ctm2.1219
- Members: [visium-spatial-gene-expression-uterine-cervix-smgjlbpj43jpamzf0000](/datasets/md/ed.md#visium-spatial-gene-expression-uterine-cervix-smgjlbpj43jpamzf0000), [visium-spatial-gene-expression-uterine-cervix-qlx8f7kk5fhqos7p0000](/datasets/md/26.md#visium-spatial-gene-expression-uterine-cervix-qlx8f7kk5fhqos7p0000), [visium-spatial-gene-expression-uterine-cervix-u5vyqoc0wa97cp3g0000](/datasets/md/7b.md#visium-spatial-gene-expression-uterine-cervix-u5vyqoc0wa97cp3g0000), [visium-spatial-gene-expression-uterine-cervix-jgcramtoluyc0nux0000](/datasets/md/0f.md#visium-spatial-gene-expression-uterine-cervix-jgcramtoluyc0nux0000)
## Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples.
- Page: /collections/doi-10-1038-s41467-023-36071-5/
- Kind: comparison
- Datasets: 35
- Reference: 10.1038/s41467-023-36071-5
- Members: [visium-spatial-gene-expression-lung-49ipachz6xc0igpv0000](/datasets/md/73.md#visium-spatial-gene-expression-lung-49ipachz6xc0igpv0000), [visium-spatial-gene-expression-prostate-gland-lrgv8yysdlu577fp0000](/datasets/md/98.md#visium-spatial-gene-expression-prostate-gland-lrgv8yysdlu577fp0000), [visium-spatial-gene-expression-intestine-dvtov07l6pufejgj0000](/datasets/md/2f.md#visium-spatial-gene-expression-intestine-dvtov07l6pufejgj0000), [visium-spatial-gene-expression-prostate-gland-x6osmy5sphfussvo0000](/datasets/md/85.md#visium-spatial-gene-expression-prostate-gland-x6osmy5sphfussvo0000), [visium-spatial-gene-expression-brain-nfuj5xnh7kgvvs1r0000](/datasets/md/36.md#visium-spatial-gene-expression-brain-nfuj5xnh7kgvvs1r0000), [visium-spatial-gene-expression-brain-hut8yvy8cunlvvbn0000](/datasets/md/62.md#visium-spatial-gene-expression-brain-hut8yvy8cunlvvbn0000), [visium-spatial-gene-expression-prostate-gland-vzlhqnwecbo8pwuu0000](/datasets/md/2e.md#visium-spatial-gene-expression-prostate-gland-vzlhqnwecbo8pwuu0000), [visium-spatial-gene-expression-brain-l1d6xdvuxbro95kd0000](/datasets/md/1c.md#visium-spatial-gene-expression-brain-l1d6xdvuxbro95kd0000), [visium-spatial-gene-expression-intestine-jiehoix9p7mqagos0000](/datasets/md/17.md#visium-spatial-gene-expression-intestine-jiehoix9p7mqagos0000), [visium-spatial-gene-expression-prostate-gland-db2e2jj3rpvgwitu0000](/datasets/md/9e.md#visium-spatial-gene-expression-prostate-gland-db2e2jj3rpvgwitu0000), [visium-spatial-gene-expression-bone-element-dckxkuceohwmbh6p0000](/datasets/md/6a.md#visium-spatial-gene-expression-bone-element-dckxkuceohwmbh6p0000), [visium-spatial-gene-expression-brain-3mqm6rqls1bmnqmi0000](/datasets/md/fc.md#visium-spatial-gene-expression-brain-3mqm6rqls1bmnqmi0000), [visium-spatial-gene-expression-brain-kniuuo356eheez3q0000](/datasets/md/53.md#visium-spatial-gene-expression-brain-kniuuo356eheez3q0000), [visium-spatial-gene-expression-brain-lii9sqcpsrlvx4mf0000](/datasets/md/3d.md#visium-spatial-gene-expression-brain-lii9sqcpsrlvx4mf0000), [visium-spatial-gene-expression-brain-8w65g8uuamrqlvbq0000](/datasets/md/db.md#visium-spatial-gene-expression-brain-8w65g8uuamrqlvbq0000), [visium-spatial-gene-expression-bone-element-awfh9nbgd950hjdp0000](/datasets/md/29.md#visium-spatial-gene-expression-bone-element-awfh9nbgd950hjdp0000), [visium-spatial-gene-expression-bone-element-wvbqrltseyu9mawc0000](/datasets/md/00.md#visium-spatial-gene-expression-bone-element-wvbqrltseyu9mawc0000), [visium-spatial-gene-expression-brain-wvn2zqpzpqleviqm0000](/datasets/md/3c.md#visium-spatial-gene-expression-brain-wvn2zqpzpqleviqm0000), [visium-spatial-gene-expression-intestine-jwjth450pg9hrjjm0000](/datasets/md/96.md#visium-spatial-gene-expression-intestine-jwjth450pg9hrjjm0000), [visium-spatial-gene-expression-lung-sjj3udxkmj0wv3mw0000](/datasets/md/fb.md#visium-spatial-gene-expression-lung-sjj3udxkmj0wv3mw0000), [visium-spatial-gene-expression-brain-nfs3zakfiqlemvu30000](/datasets/md/15.md#visium-spatial-gene-expression-brain-nfs3zakfiqlemvu30000), [visium-spatial-gene-expression-bone-element-rviiwwjljurgevlf0000](/datasets/md/0f.md#visium-spatial-gene-expression-bone-element-rviiwwjljurgevlf0000), [visium-spatial-gene-expression-brain-dxpmieosifkavwxt0000](/datasets/md/81.md#visium-spatial-gene-expression-brain-dxpmieosifkavwxt0000), [visium-spatial-gene-expression-intestine-dfqihmss0cnxiogj0000](/datasets/md/50.md#visium-spatial-gene-expression-intestine-dfqihmss0cnxiogj0000), [visium-spatial-gene-expression-lung-mizxg1w8wzoku5qt0000](/datasets/md/ba.md#visium-spatial-gene-expression-lung-mizxg1w8wzoku5qt0000), [visium-spatial-gene-expression-intestine-yscb68d8nfslpu1g0000](/datasets/md/7c.md#visium-spatial-gene-expression-intestine-yscb68d8nfslpu1g0000), [visium-spatial-gene-expression-lung-ndxruszhdizodz550000](/datasets/md/f2.md#visium-spatial-gene-expression-lung-ndxruszhdizodz550000), [visium-spatial-gene-expression-lung-ojsjpfnhv617unbe0000](/datasets/md/d5.md#visium-spatial-gene-expression-lung-ojsjpfnhv617unbe0000), [visium-spatial-gene-expression-brain-oikbvsrk2re2e6hg0000](/datasets/md/c2.md#visium-spatial-gene-expression-brain-oikbvsrk2re2e6hg0000), [visium-spatial-gene-expression-bone-element-lk73ziolshxu4asd0000](/datasets/md/5a.md#visium-spatial-gene-expression-bone-element-lk73ziolshxu4asd0000), [visium-spatial-gene-expression-brain-rbcex5fygwquxk3y0000](/datasets/md/7b.md#visium-spatial-gene-expression-brain-rbcex5fygwquxk3y0000), [visium-spatial-gene-expression-lung-rbl1hjjmk76hlzpc0000](/datasets/md/3a.md#visium-spatial-gene-expression-lung-rbl1hjjmk76hlzpc0000), [visium-spatial-gene-expression-bone-element-uhqhqatenmanjxuk0000](/datasets/md/6e.md#visium-spatial-gene-expression-bone-element-uhqhqatenmanjxuk0000), [visium-spatial-gene-expression-brain-s9bhqtmverbm1bow0000](/datasets/md/d4.md#visium-spatial-gene-expression-brain-s9bhqtmverbm1bow0000), [visium-spatial-gene-expression-brain-dugljrscsuvb0bfj0000](/datasets/md/4f.md#visium-spatial-gene-expression-brain-dugljrscsuvb0bfj0000)
## A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.
- Page: /collections/doi-10-1038-s41588-022-01243-4/
- Kind: publication
- Datasets: 20
- Reference: 10.1038/s41588-022-01243-4
- Members: [visium-spatial-gene-expression-lung-kehsjvgj8gclnqcb0000](/datasets/md/d7.md#visium-spatial-gene-expression-lung-kehsjvgj8gclnqcb0000), [visium-spatial-gene-expression-lung-tabimqjgzkvmwosb0000](/datasets/md/82.md#visium-spatial-gene-expression-lung-tabimqjgzkvmwosb0000), [visium-spatial-gene-expression-lung-pg7qfd5iln6gdxbv0000](/datasets/md/47.md#visium-spatial-gene-expression-lung-pg7qfd5iln6gdxbv0000), [visium-spatial-gene-expression-lung-zctgslawiiyicroj0000](/datasets/md/99.md#visium-spatial-gene-expression-lung-zctgslawiiyicroj0000), [visium-spatial-gene-expression-lung-4cq5mdqvlfs1lsqm0000](/datasets/md/d6.md#visium-spatial-gene-expression-lung-4cq5mdqvlfs1lsqm0000), [visium-spatial-gene-expression-lung-oqrfnuxh1tcrjzri0000](/datasets/md/fa.md#visium-spatial-gene-expression-lung-oqrfnuxh1tcrjzri0000), [visium-spatial-gene-expression-lung-c0hyxkialbz1zq7e0000](/datasets/md/4b.md#visium-spatial-gene-expression-lung-c0hyxkialbz1zq7e0000), [visium-spatial-gene-expression-lung-ecrd3y4yjahr2u8c0000](/datasets/md/26.md#visium-spatial-gene-expression-lung-ecrd3y4yjahr2u8c0000), [visium-spatial-gene-expression-lung-t4gpfhpprpb5ytjx0000](/datasets/md/e6.md#visium-spatial-gene-expression-lung-t4gpfhpprpb5ytjx0000), [visium-spatial-gene-expression-lung-ve4rab7tkmho1zry0000](/datasets/md/79.md#visium-spatial-gene-expression-lung-ve4rab7tkmho1zry0000), [visium-spatial-gene-expression-lung-ue4t38ctya7rsdgd0000](/datasets/md/1e.md#visium-spatial-gene-expression-lung-ue4t38ctya7rsdgd0000), [visium-spatial-gene-expression-lung-da5y3neil70r5xdx0000](/datasets/md/bd.md#visium-spatial-gene-expression-lung-da5y3neil70r5xdx0000), [visium-spatial-gene-expression-lung-vkrn8sz5kmamk0hm0000](/datasets/md/4d.md#visium-spatial-gene-expression-lung-vkrn8sz5kmamk0hm0000), [visium-spatial-gene-expression-lung-etrfbc76wolxosdd0000](/datasets/md/dc.md#visium-spatial-gene-expression-lung-etrfbc76wolxosdd0000), [visium-spatial-gene-expression-lung-xymw5kjyeodzl6cu0000](/datasets/md/29.md#visium-spatial-gene-expression-lung-xymw5kjyeodzl6cu0000), [visium-spatial-gene-expression-lung-ftay393cgtaw8esm0000](/datasets/md/e0.md#visium-spatial-gene-expression-lung-ftay393cgtaw8esm0000), [visium-spatial-gene-expression-lung-olxb93kcusynmg9p0000](/datasets/md/13.md#visium-spatial-gene-expression-lung-olxb93kcusynmg9p0000), [visium-spatial-gene-expression-lung-dqpzj1fwkmzxodoo0000](/datasets/md/b0.md#visium-spatial-gene-expression-lung-dqpzj1fwkmzxodoo0000), [visium-spatial-gene-expression-lung-pjyi5ipkoffnuj380000](/datasets/md/a3.md#visium-spatial-gene-expression-lung-pjyi5ipkoffnuj380000), [visium-spatial-gene-expression-lung-ao1ev5x79sswkmqh0000](/datasets/md/4f.md#visium-spatial-gene-expression-lung-ao1ev5x79sswkmqh0000)
## Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain
- Page: /collections/geo-gse182127/
- Kind: comparison
- Datasets: 7
- Reference: PMID:34793930
- Design: Spatial transcriptome analysis of mouse brain using the 10X genomics Visium spatial gene expression kit after stereotactic injections.
- Members: [visium-spatial-gene-expression-brain-sfbpsq3yvkqtud8j0000](/datasets/md/78.md#visium-spatial-gene-expression-brain-sfbpsq3yvkqtud8j0000), [visium-spatial-gene-expression-brain-iddillx2hvdelw5r0000](/datasets/md/ac.md#visium-spatial-gene-expression-brain-iddillx2hvdelw5r0000), [visium-spatial-gene-expression-brain-jb1s7yo87fkxheh90000](/datasets/md/c4.md#visium-spatial-gene-expression-brain-jb1s7yo87fkxheh90000), [visium-spatial-gene-expression-brain-q72wncoprobjdui60000](/datasets/md/f5.md#visium-spatial-gene-expression-brain-q72wncoprobjdui60000), [visium-spatial-gene-expression-brain-4lf7nx5eqbis23yh0000](/datasets/md/bb.md#visium-spatial-gene-expression-brain-4lf7nx5eqbis23yh0000), [visium-spatial-gene-expression-brain-4n1mcnuge77smwno0000](/datasets/md/0c.md#visium-spatial-gene-expression-brain-4n1mcnuge77smwno0000), [visium-spatial-gene-expression-brain-6k82lzvyj3ysa4mp0000](/datasets/md/4b.md#visium-spatial-gene-expression-brain-6k82lzvyj3ysa4mp0000)
## Reconstruction of 3-dimensional tissue organization at the single-cell resolution [ST]
- Page: /collections/geo-gse220572/
- Kind: other
- Datasets: 2
- Reference: PMID:36711844
- Design: Human foreskin samples were fixed using FFPE protocol and then sectioned and analyzed using 10X Visium v1 FFPE ST protocol
- Members: [visium-spatial-gene-expression-prepuce-of-penis-nddj4n9igwbve91g0000](/datasets/md/58.md#visium-spatial-gene-expression-prepuce-of-penis-nddj4n9igwbve91g0000), [visium-spatial-gene-expression-prepuce-of-penis-e9eagk7osnbeto8v0000](/datasets/md/61.md#visium-spatial-gene-expression-prepuce-of-penis-e9eagk7osnbeto8v0000)
## Time-series spatial transcriptomic analysis of murine small intestine (SI) undergoing irradiation induced injury-repair with and without LXR activation
- Page: /collections/geo-gse227742/
- Kind: comparison
- Datasets: 4
- 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. Ten days after diet, mice were exposed to 10Gy total body irradiation (TBI) and SI Swiss rolls (starting from distal SI) were collected on day3 after irradiation (3 dpi), processed and submitted for sequencing. SI Swiss rolls from mice fed with either standard or GW3965 diet but no irradiation (0 dpi) were used as control.
- Members: [visium-spatial-gene-expression-small-intestine-aq0wgpvycxfpnh7k0000](/datasets/md/70.md#visium-spatial-gene-expression-small-intestine-aq0wgpvycxfpnh7k0000), [visium-spatial-gene-expression-small-intestine-9zntt2bypc2uunay0000](/datasets/md/33.md#visium-spatial-gene-expression-small-intestine-9zntt2bypc2uunay0000), [visium-spatial-gene-expression-small-intestine-or3h9nij2st9w4pn0000](/datasets/md/76.md#visium-spatial-gene-expression-small-intestine-or3h9nij2st9w4pn0000), [visium-spatial-gene-expression-small-intestine-unn2r1eb9bs8six60000](/datasets/md/c8.md#visium-spatial-gene-expression-small-intestine-unn2r1eb9bs8six60000)
## Spatiotemporal trajectory analysis and validation of microglia activation in traumatic brain injury
- Page: /collections/geo-gse236171/
- Kind: comparison
- Datasets: 2
- Reference: PMID:38007580
- Design: We conducted an experimental study to investigate the spatio-temporal dynamics of microglia in the mouse brain following injury. The Visium ST data were acquired from the mouse brain at 3 days post-injury. To segment the brain regions, we employed stSME-based clustering, fine-tuning the clustering parameters using the Allen Mouse Brain Atlas. Next, we identified microglia-containing spots by examining the expression of marker genes, specifically Fcrls and Tmem119. To analyze the transcriptional dissimilarity between the injury site and different brain regions, we applied the PSeudo-Time-Space (PSTS) algorithm, which assigned a PTS score. Our analysis revealed that the hypothalamus region exhibited the greatest transcriptional dissimilarity compared to the injury site. To visualize the spatial trajectory of microglia activation, we utilized the PSTS algorithm to predict the minimum spanning tree connecting the damaged site and the hypothalamus. The resulting trajectory displayed the activation of microglia along the dorsoventral axis of the injured brain, with the directionality of transcriptional changes indicated by the arrows. Additionally, we compared the results with the mouse naive brain as a control to provide evidence for the spatio-temporal dynamics of microglia.
- Members: [visium-spatial-gene-expression-brain-0vpypxrf1xct9aim0000](/datasets/md/0d.md#visium-spatial-gene-expression-brain-0vpypxrf1xct9aim0000), [visium-spatial-gene-expression-brain-tphuk3csxhjk6dfl0000](/datasets/md/bc.md#visium-spatial-gene-expression-brain-tphuk3csxhjk6dfl0000)
## Spatial mapping of RNA turnover kinetics in the mouse brain [Spatial NT-seq]
- Page: /collections/geo-gse249403/
- Kind: time course
- Datasets: 19
- Reference: PMID:42675226
- Design: To spatially co-map RNA abundance and turnover in intact tissues, we developed spatially resolved New RNA Tagging Sequencing technology (spatial NT-Seq). The newly synthesized RNAs in postnatal day 7 (P7) or 56 (P56) mouse brains were labeled by intraperitoneally injecting 4-thiouridine (4sU), and whole brains were dissected and embedded in OCT for spatial NT-seq analysis. This method combines transgenesis-free in vivo 4sU labeling, fresh frozen tissue sectioning, methanol fixation, and histological staining with an optimized in situ SLAM reaction to chemically recode 4sU-labeled new mRNAs directly within tissue sections. This strategy is broadly compatible with sequencing-based spatial transcriptomics (ST) methods, including the Visium patform used in this study, which contains spatially barcoded mRNA capture oligonucleotides. After tissue permeabilization, modified reverse transcription (RT) and second-strand synthesis reactions were used to efficiently capture newly synthesized (“new”) and pre-existing (“old”) transcriptomes from the same tissue section.
- Members: [visium-spatial-gene-expression-brain-4qnhpmzstlpkz0de0000](/datasets/md/8f.md#visium-spatial-gene-expression-brain-4qnhpmzstlpkz0de0000), [visium-spatial-gene-expression-brain-wognxou2pbeqxu6i0000](/datasets/md/08.md#visium-spatial-gene-expression-brain-wognxou2pbeqxu6i0000), [visium-spatial-gene-expression-brain-ydrkz1sjxvtbgtrd0000](/datasets/md/59.md#visium-spatial-gene-expression-brain-ydrkz1sjxvtbgtrd0000), [visium-spatial-gene-expression-brain-1ohufj03sauedhhb0000](/datasets/md/07.md#visium-spatial-gene-expression-brain-1ohufj03sauedhhb0000), [visium-spatial-gene-expression-brain-yb3taiavbdxwxgq70000](/datasets/md/d9.md#visium-spatial-gene-expression-brain-yb3taiavbdxwxgq70000), [visium-spatial-gene-expression-brain-9hmw8yakdeqz5vzc0000](/datasets/md/4d.md#visium-spatial-gene-expression-brain-9hmw8yakdeqz5vzc0000), [visium-spatial-gene-expression-brain-3d71rldxwk8tuhvc0001](/datasets/md/e2.md#visium-spatial-gene-expression-brain-3d71rldxwk8tuhvc0001), [visium-spatial-gene-expression-brain-wcgnzpktudjnn8gv0000](/datasets/md/40.md#visium-spatial-gene-expression-brain-wcgnzpktudjnn8gv0000), [visium-spatial-gene-expression-brain-xs1wcu0nvymdwgvs0000](/datasets/md/92.md#visium-spatial-gene-expression-brain-xs1wcu0nvymdwgvs0000), [visium-spatial-gene-expression-brain-t3nrskeopyxzqzln0000](/datasets/md/d4.md#visium-spatial-gene-expression-brain-t3nrskeopyxzqzln0000), [visium-spatial-gene-expression-brain-njupu6piprd7nmrx0000](/datasets/md/d6.md#visium-spatial-gene-expression-brain-njupu6piprd7nmrx0000), [visium-spatial-gene-expression-brain-tmaasinicqpwnxbk0000](/datasets/md/2f.md#visium-spatial-gene-expression-brain-tmaasinicqpwnxbk0000), [visium-spatial-gene-expression-brain-z2k3iebrsdrzhuvv0000](/datasets/md/01.md#visium-spatial-gene-expression-brain-z2k3iebrsdrzhuvv0000), [visium-spatial-gene-expression-brain-ai1r4xqaew8fjmzo0000](/datasets/md/45.md#visium-spatial-gene-expression-brain-ai1r4xqaew8fjmzo0000), [visium-spatial-gene-expression-brain-dsv81bgu2jpnbsxg0000](/datasets/md/d4.md#visium-spatial-gene-expression-brain-dsv81bgu2jpnbsxg0000), [visium-spatial-gene-expression-brain-q1lhhemmhgbht0qx0000](/datasets/md/51.md#visium-spatial-gene-expression-brain-q1lhhemmhgbht0qx0000), [visium-spatial-gene-expression-brain-evanhrwipaf9cqkx0000](/datasets/md/e2.md#visium-spatial-gene-expression-brain-evanhrwipaf9cqkx0000), [visium-spatial-gene-expression-brain-siwel4etzhkzy8xt0000](/datasets/md/6d.md#visium-spatial-gene-expression-brain-siwel4etzhkzy8xt0000), [visium-spatial-gene-expression-brain-pf7x5hr5ymvohvg40000](/datasets/md/af.md#visium-spatial-gene-expression-brain-pf7x5hr5ymvohvg40000)
## Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis [Spatial Transcriptomics]
- Page: /collections/geo-gse253199/
- Kind: other
- Datasets: 12
- Reference: PMID:39919907
- Design: Spatial transcriptomics sequencing libraries were constructed for 12 infrapatellar fat pad (IFP) of knee OA samples using the 10X Genomics Visium CytAssist Spatial Gene Expression Reagent Kits to spatially resolve the celltypes in the IFP tissue using bioinformatics analysis.
- Members: [visium-spatial-gene-expression-infrapatellar-fat-pad-hp1sxxzqypzerd040000](/datasets/md/5f.md#visium-spatial-gene-expression-infrapatellar-fat-pad-hp1sxxzqypzerd040000), [visium-spatial-gene-expression-infrapatellar-fat-pad-i3rv3r8u3mwc4erj0000](/datasets/md/84.md#visium-spatial-gene-expression-infrapatellar-fat-pad-i3rv3r8u3mwc4erj0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-f6jgwsinw0ecua5g0000](/datasets/md/84.md#visium-spatial-gene-expression-infrapatellar-fat-pad-f6jgwsinw0ecua5g0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-4sbnhjapwfe4yw8z0000](/datasets/md/fb.md#visium-spatial-gene-expression-infrapatellar-fat-pad-4sbnhjapwfe4yw8z0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-bxl4j55dkjytlhpj0000](/datasets/md/a9.md#visium-spatial-gene-expression-infrapatellar-fat-pad-bxl4j55dkjytlhpj0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-sbru3taahclq6cad0000](/datasets/md/42.md#visium-spatial-gene-expression-infrapatellar-fat-pad-sbru3taahclq6cad0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-ifa4spqhpaqw5irr0000](/datasets/md/ab.md#visium-spatial-gene-expression-infrapatellar-fat-pad-ifa4spqhpaqw5irr0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-hbhnduvnuombsjoj0000](/datasets/md/18.md#visium-spatial-gene-expression-infrapatellar-fat-pad-hbhnduvnuombsjoj0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-54o0eov1xqkqen2m0000](/datasets/md/b4.md#visium-spatial-gene-expression-infrapatellar-fat-pad-54o0eov1xqkqen2m0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-pbessdcr5zkkrjhz0000](/datasets/md/54.md#visium-spatial-gene-expression-infrapatellar-fat-pad-pbessdcr5zkkrjhz0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-qt6bdtkevmopakfb0000](/datasets/md/8f.md#visium-spatial-gene-expression-infrapatellar-fat-pad-qt6bdtkevmopakfb0000), [visium-spatial-gene-expression-infrapatellar-fat-pad-zuavdszaguo2moc30000](/datasets/md/5b.md#visium-spatial-gene-expression-infrapatellar-fat-pad-zuavdszaguo2moc30000)
## CH6824025, potent and selective DDR1 inhibitor, reduces kidney fibrosis in UUO mice
- Page: /collections/geo-gse273978/
- Kind: comparison
- Datasets: 8
- Reference: PMID:39379147
- Design: After the allocation of mice, the oral once daily administration of vehicle or CH6824025 was started. Seven days after the surgery of UUO, mice were subjected to analysis. FFPE blocks of kidneys from each group (Sham n=1, UUO Vehicle group n=3, UUO CH6824025 200 mg/kg group n=4) were used.
- Members: [visium-spatial-gene-expression-kidney-rihsh9qnu5dtqbdq0000](/datasets/md/0b.md#visium-spatial-gene-expression-kidney-rihsh9qnu5dtqbdq0000), [visium-spatial-gene-expression-kidney-q4wom49upiu3nq6o0000](/datasets/md/f2.md#visium-spatial-gene-expression-kidney-q4wom49upiu3nq6o0000), [visium-spatial-gene-expression-kidney-lk6ojhhluq2kjxjq0000](/datasets/md/b3.md#visium-spatial-gene-expression-kidney-lk6ojhhluq2kjxjq0000), [visium-spatial-gene-expression-kidney-cvomz8bw6tion1tq0000](/datasets/md/a8.md#visium-spatial-gene-expression-kidney-cvomz8bw6tion1tq0000), [visium-spatial-gene-expression-kidney-4h5ljzyfb1mnbw1w0000](/datasets/md/cb.md#visium-spatial-gene-expression-kidney-4h5ljzyfb1mnbw1w0000), [visium-spatial-gene-expression-kidney-f0wrvay9gjv0vgrl0000](/datasets/md/1d.md#visium-spatial-gene-expression-kidney-f0wrvay9gjv0vgrl0000), [visium-spatial-gene-expression-kidney-zqvui2qmumcqeovj0000](/datasets/md/a5.md#visium-spatial-gene-expression-kidney-zqvui2qmumcqeovj0000), [visium-spatial-gene-expression-kidney-s2bgd9uqmhk6ieev0000](/datasets/md/ee.md#visium-spatial-gene-expression-kidney-s2bgd9uqmhk6ieev0000)
## Spatial transcriptomics of HIV-associated non-Hodgkin lymphomas by EBV status and cell of origin
- Page: /collections/geo-gse274051/
- Kind: comparison
- Datasets: 10
- Reference: PMID:41279969
- Design: FFPE sections from ten different HIV-associated non-Hodgkin lymphoma (HIV-NHL) biopsies were analyzed with the 10x Genomics Visium V2 platform in this study. Five of the biopsied tumors were positive for Epstein-Barr virus (EBV) and five were EBV-negative. Tumors from different cells of origin (e.g., germinal center B cells, plasmablasts) were incldued in both EBV-postiive and EBV-negative sample subsets.
- Members: [visium-spatial-gene-expression-lymphoid-tissue-k4yqpmlbbiwz8uig0000](/datasets/md/a9.md#visium-spatial-gene-expression-lymphoid-tissue-k4yqpmlbbiwz8uig0000), [visium-spatial-gene-expression-lymphoid-tissue-byfgwxghxwpfhx1x0000](/datasets/md/f4.md#visium-spatial-gene-expression-lymphoid-tissue-byfgwxghxwpfhx1x0000), [visium-spatial-gene-expression-lymphoid-tissue-h7aafjsfowfcazec0000](/datasets/md/00.md#visium-spatial-gene-expression-lymphoid-tissue-h7aafjsfowfcazec0000), [visium-spatial-gene-expression-lymphoid-tissue-14timpvzfr3sgdoz0000](/datasets/md/ec.md#visium-spatial-gene-expression-lymphoid-tissue-14timpvzfr3sgdoz0000), [visium-spatial-gene-expression-lymphoid-tissue-ukiq5wqqbanitlnz0000](/datasets/md/85.md#visium-spatial-gene-expression-lymphoid-tissue-ukiq5wqqbanitlnz0000), [visium-spatial-gene-expression-lymphoid-tissue-zyvnfgq3fquoif1e0000](/datasets/md/64.md#visium-spatial-gene-expression-lymphoid-tissue-zyvnfgq3fquoif1e0000), [visium-spatial-gene-expression-lymphoid-tissue-hsgzgqxfl7ew0xwe0000](/datasets/md/23.md#visium-spatial-gene-expression-lymphoid-tissue-hsgzgqxfl7ew0xwe0000), [visium-spatial-gene-expression-lymphoid-tissue-7ykjs51nk6sl5ikw0000](/datasets/md/e7.md#visium-spatial-gene-expression-lymphoid-tissue-7ykjs51nk6sl5ikw0000), [visium-spatial-gene-expression-lymphoid-tissue-6pepmkkykw7i7nja0000](/datasets/md/27.md#visium-spatial-gene-expression-lymphoid-tissue-6pepmkkykw7i7nja0000), [visium-spatial-gene-expression-lymphoid-tissue-rmervn8vhq4dfcfv0000](/datasets/md/3e.md#visium-spatial-gene-expression-lymphoid-tissue-rmervn8vhq4dfcfv0000)
## Deciphering head and neck cancer microenvironment: Single‐cell and spatial transcriptomics reveals human papillomavirus‐associated differences
- Page: /collections/geo-gse281978/
- Kind: comparison
- Datasets: 5
- Reference: PMID:38235919
- Design: Six samples for spatial transcriptomics (ST), composed of matched primary tumors (PT) and lymph node metastases (LNMT), were collected from both HPV-negative (HPV−) and HPV-positive (HPV+) patients using the 10x Genomics Visium platform.
- Members: [visium-spatial-gene-expression-lymph-node-ahg75ot5hyjdky6o0000](/datasets/md/05.md#visium-spatial-gene-expression-lymph-node-ahg75ot5hyjdky6o0000), [visium-spatial-gene-expression-mucosa-pyhcfjdd42wiio320000](/datasets/md/c1.md#visium-spatial-gene-expression-mucosa-pyhcfjdd42wiio320000), [visium-spatial-gene-expression-mucosa-ja2vde6vrvx0ysx00000](/datasets/md/58.md#visium-spatial-gene-expression-mucosa-ja2vde6vrvx0ysx00000), [visium-spatial-gene-expression-lymph-node-fovxwxpoamhgdyyl0000](/datasets/md/8b.md#visium-spatial-gene-expression-lymph-node-fovxwxpoamhgdyyl0000), [visium-spatial-gene-expression-mucosa-fc0rqyphj9sgieky0000](/datasets/md/fd.md#visium-spatial-gene-expression-mucosa-fc0rqyphj9sgieky0000)
## Fibroblast-Derived Thrombospondin 2 Shapes the Immune-Exclusionary Environment at Invasive Fronts in Colorectal Cancer [Visium
- Page: /collections/geo-gse285505/
- Kind: other
- Datasets: 4
- Reference: PMID:41276505
- Design: Four slides from FFPE blocks of surgically resected CRC specimens, which were determined as CMS1/MSI, CMS2, or CMS4 using bulk-RNA-seq data, were analyzed using spatial transcriptomics (ST).
- Members: [visium-spatial-gene-expression-colorectum-wis54w6nwcckpx310000](/datasets/md/10.md#visium-spatial-gene-expression-colorectum-wis54w6nwcckpx310000), [visium-spatial-gene-expression-colorectum-asztbvcdoyofefxh0000](/datasets/md/42.md#visium-spatial-gene-expression-colorectum-asztbvcdoyofefxh0000), [visium-spatial-gene-expression-colorectum-50nmbrnit2dhttpu0000](/datasets/md/b5.md#visium-spatial-gene-expression-colorectum-50nmbrnit2dhttpu0000), [visium-spatial-gene-expression-colorectum-hgiubmbqqa0yi0ap0000](/datasets/md/aa.md#visium-spatial-gene-expression-colorectum-hgiubmbqqa0yi0ap0000)
## Ontogeny-independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis [Spatial Transcriptomics]
- Page: /collections/geo-gse290324/
- Kind: comparison
- Datasets: 7
- Reference: PMID:41862629
- Design: Adult female C57BL/6J mice were maintained and bred at the University of York, UK. The mice were housed in ventilated cages under specified pathogen-free conditions with access to food and water ad libitum. Identification of the mouse colony was confirmed through genetic profiling of microsatellite markers, verifying C57BL/6J genetic background with minor variations at 3 markers. Healthy (6-8 week old females) were infected intravenously with 3x107 amastigotes of the Ethiopian LV9 strain of Leishmania donovani to establish visceral infection. At 28 days post-infection, mice were euthanized by CO2 inhalation followed by cervical dislocation according to Home Office regulations. Livers were harvested after euthanization and the major lobe cut and snap-frozen in liquid nitrogen while bathed in isopenane and then kept in -80 degrees until used. For spatial gene expression, 4 infected and 4 uninfected liver sections from individual mice were processed using 10x Visium.
- Members: [visium-spatial-gene-expression-liver-negla3rph2eqeeml0000](/datasets/md/c7.md#visium-spatial-gene-expression-liver-negla3rph2eqeeml0000), [visium-spatial-gene-expression-liver-9mvmauoxvgzitwvk0000](/datasets/md/56.md#visium-spatial-gene-expression-liver-9mvmauoxvgzitwvk0000), [visium-spatial-gene-expression-liver-alu95wjcuepmyvwu0000](/datasets/md/47.md#visium-spatial-gene-expression-liver-alu95wjcuepmyvwu0000), [visium-spatial-gene-expression-liver-jvagmityvqzjqyz20000](/datasets/md/70.md#visium-spatial-gene-expression-liver-jvagmityvqzjqyz20000), [visium-spatial-gene-expression-liver-arhqdw1e40mzuwmb0000](/datasets/md/ef.md#visium-spatial-gene-expression-liver-arhqdw1e40mzuwmb0000), [visium-spatial-gene-expression-liver-5vsyg2urvz1bboq40000](/datasets/md/da.md#visium-spatial-gene-expression-liver-5vsyg2urvz1bboq40000), [visium-spatial-gene-expression-liver-wh6m0t7pxgqsnblc0000](/datasets/md/a1.md#visium-spatial-gene-expression-liver-wh6m0t7pxgqsnblc0000)
## Impact of Alzheimer’s disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus
- Page: /collections/geo-gse307866/
- Kind: other
- Datasets: 43
- Reference: PMID:41278831
- Design: We obtained tissue blocks of postmortem human brain containing locus coeruleus (LC) from 33 neurotypical adult brain donors, balanced for age, sex, APOE2 and APOE4 carrier status (all donors had at least one copy of one of the two alleles), and predominant genomic ancestry (African Ancestry or European Ancestry). We used the 10x Genomics Visium platform to generate spatial transcriptomics from two sequential tissue sections containing LC for each donor, with a second pair of tissue sections collected for a subset of donors. Data were integrated and clustered, defining a robust LC cluster, two mixed non-LC neuron clusters, and several clusters labeling spots with mixed glial types contents. 77 samples from 30 donors with substantial LC content (≥10 spots per tissue section) were retained for downstream analyses. Differential expression (DE) analyses were then performed for the 5 clusters (of 9 total) with adequate count data, including LC, comparing expression between groups for each Alzheimer's risk variable of interest (sex, genomic ancestry, and APOE genotype). Additional analyses were performed for: 1) spatially variable expression within spots of the LC cluster; 2) comparing neuromelanin (NM)containing LC spots NM-negative LC spots; 3) modeling spot-level NM relationships to spot-level gene expression; 4) nonnegative matrix factorization of LC cluster gene expression to identify discrete expression programs; 5) gene set enrichment analyses of DE genes, NM-associated genes, and factorization-identfied LC gene groups. *************************************************************** 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-locus-ceruleus-vr1awo4v9jgutgs50001](/datasets/md/27.md#visium-spatial-gene-expression-locus-ceruleus-vr1awo4v9jgutgs50001), [visium-spatial-gene-expression-locus-ceruleus-wicqryqgp1i4t8ts0000](/datasets/md/7a.md#visium-spatial-gene-expression-locus-ceruleus-wicqryqgp1i4t8ts0000), [visium-spatial-gene-expression-locus-ceruleus-bfagcawdkcup4no60000](/datasets/md/91.md#visium-spatial-gene-expression-locus-ceruleus-bfagcawdkcup4no60000), [visium-spatial-gene-expression-locus-ceruleus-rxin8lylzenrtwyf0000](/datasets/md/27.md#visium-spatial-gene-expression-locus-ceruleus-rxin8lylzenrtwyf0000), [visium-spatial-gene-expression-locus-ceruleus-qbjjzpn2cva5ibpb0000](/datasets/md/6a.md#visium-spatial-gene-expression-locus-ceruleus-qbjjzpn2cva5ibpb0000), [visium-spatial-gene-expression-locus-ceruleus-q8qjb5pgim39og930000](/datasets/md/b3.md#visium-spatial-gene-expression-locus-ceruleus-q8qjb5pgim39og930000), [visium-spatial-gene-expression-locus-ceruleus-hfc3rc04hiccn0xa0000](/datasets/md/17.md#visium-spatial-gene-expression-locus-ceruleus-hfc3rc04hiccn0xa0000), [visium-spatial-gene-expression-locus-ceruleus-nnh6dcpcu90ouzb80000](/datasets/md/94.md#visium-spatial-gene-expression-locus-ceruleus-nnh6dcpcu90ouzb80000), [visium-spatial-gene-expression-locus-ceruleus-kf4ugskrngdcc8nn0000](/datasets/md/ca.md#visium-spatial-gene-expression-locus-ceruleus-kf4ugskrngdcc8nn0000), [visium-spatial-gene-expression-locus-ceruleus-bb1e42x2ud22ukws0000](/datasets/md/ff.md#visium-spatial-gene-expression-locus-ceruleus-bb1e42x2ud22ukws0000), [visium-spatial-gene-expression-locus-ceruleus-l4ge3h835pvl7vux0000](/datasets/md/dc.md#visium-spatial-gene-expression-locus-ceruleus-l4ge3h835pvl7vux0000), [visium-spatial-gene-expression-locus-ceruleus-lxrsntqfyc1fdjb10000](/datasets/md/74.md#visium-spatial-gene-expression-locus-ceruleus-lxrsntqfyc1fdjb10000), [visium-spatial-gene-expression-locus-ceruleus-jki2c42dcxnjedsv0000](/datasets/md/e9.md#visium-spatial-gene-expression-locus-ceruleus-jki2c42dcxnjedsv0000), [visium-spatial-gene-expression-locus-ceruleus-ra8mw6n0qmqmbzws0000](/datasets/md/a3.md#visium-spatial-gene-expression-locus-ceruleus-ra8mw6n0qmqmbzws0000), [visium-spatial-gene-expression-locus-ceruleus-0p6hcnl6p3prxmcb0000](/datasets/md/f5.md#visium-spatial-gene-expression-locus-ceruleus-0p6hcnl6p3prxmcb0000), [visium-spatial-gene-expression-locus-ceruleus-imnhlip6raivdvjn0000](/datasets/md/57.md#visium-spatial-gene-expression-locus-ceruleus-imnhlip6raivdvjn0000), [visium-spatial-gene-expression-locus-ceruleus-poxzxkrkxyn9dgkg0000](/datasets/md/b8.md#visium-spatial-gene-expression-locus-ceruleus-poxzxkrkxyn9dgkg0000), [visium-spatial-gene-expression-locus-ceruleus-qpivsnaojis8wvg10000](/datasets/md/40.md#visium-spatial-gene-expression-locus-ceruleus-qpivsnaojis8wvg10000), [visium-spatial-gene-expression-locus-ceruleus-phyzxgxhauypz4cn0000](/datasets/md/8d.md#visium-spatial-gene-expression-locus-ceruleus-phyzxgxhauypz4cn0000), [visium-spatial-gene-expression-locus-ceruleus-dud5b0cadcpnlr2z0000](/datasets/md/7c.md#visium-spatial-gene-expression-locus-ceruleus-dud5b0cadcpnlr2z0000), [visium-spatial-gene-expression-locus-ceruleus-7hewy0qemr9yqmsl0000](/datasets/md/03.md#visium-spatial-gene-expression-locus-ceruleus-7hewy0qemr9yqmsl0000), [visium-spatial-gene-expression-locus-ceruleus-sbru8ijmzadghdbp0000](/datasets/md/4a.md#visium-spatial-gene-expression-locus-ceruleus-sbru8ijmzadghdbp0000), [visium-spatial-gene-expression-locus-ceruleus-msj2ursx0i4msjuf0000](/datasets/md/e3.md#visium-spatial-gene-expression-locus-ceruleus-msj2ursx0i4msjuf0000), [visium-spatial-gene-expression-locus-ceruleus-q3akshhggawiimmj0000](/datasets/md/58.md#visium-spatial-gene-expression-locus-ceruleus-q3akshhggawiimmj0000), [visium-spatial-gene-expression-locus-ceruleus-axeure6r5xbpwf6g0000](/datasets/md/bc.md#visium-spatial-gene-expression-locus-ceruleus-axeure6r5xbpwf6g0000), [visium-spatial-gene-expression-locus-ceruleus-agaxgimbmtzasc8r0000](/datasets/md/f8.md#visium-spatial-gene-expression-locus-ceruleus-agaxgimbmtzasc8r0000), [visium-spatial-gene-expression-locus-ceruleus-ihd1ija29bd7oecq0000](/datasets/md/33.md#visium-spatial-gene-expression-locus-ceruleus-ihd1ija29bd7oecq0000), [visium-spatial-gene-expression-locus-ceruleus-ptvbw2zvmlcekovz0000](/datasets/md/a4.md#visium-spatial-gene-expression-locus-ceruleus-ptvbw2zvmlcekovz0000), [visium-spatial-gene-expression-locus-ceruleus-i4aqdqmo9qbc61hh0000](/datasets/md/10.md#visium-spatial-gene-expression-locus-ceruleus-i4aqdqmo9qbc61hh0000), [visium-spatial-gene-expression-locus-ceruleus-6etce8tcllktqwje0000](/datasets/md/12.md#visium-spatial-gene-expression-locus-ceruleus-6etce8tcllktqwje0000), [visium-spatial-gene-expression-locus-ceruleus-kab4bxiqhwnycuy90000](/datasets/md/0c.md#visium-spatial-gene-expression-locus-ceruleus-kab4bxiqhwnycuy90000), [visium-spatial-gene-expression-locus-ceruleus-dwoavfgr6rw8apkh0000](/datasets/md/37.md#visium-spatial-gene-expression-locus-ceruleus-dwoavfgr6rw8apkh0000), [visium-spatial-gene-expression-locus-ceruleus-5pzlksaqtajglgr30000](/datasets/md/6d.md#visium-spatial-gene-expression-locus-ceruleus-5pzlksaqtajglgr30000), [visium-spatial-gene-expression-locus-ceruleus-3nrlpwpzhsww8ygl0000](/datasets/md/c3.md#visium-spatial-gene-expression-locus-ceruleus-3nrlpwpzhsww8ygl0000), [visium-spatial-gene-expression-locus-ceruleus-qrqqo3wwyqkd7dbt0000](/datasets/md/62.md#visium-spatial-gene-expression-locus-ceruleus-qrqqo3wwyqkd7dbt0000), [visium-spatial-gene-expression-locus-ceruleus-3ttjpfbdg1yi8o9d0000](/datasets/md/37.md#visium-spatial-gene-expression-locus-ceruleus-3ttjpfbdg1yi8o9d0000), [visium-spatial-gene-expression-locus-ceruleus-kzj9iejphqf0we0v0000](/datasets/md/65.md#visium-spatial-gene-expression-locus-ceruleus-kzj9iejphqf0we0v0000), [visium-spatial-gene-expression-locus-ceruleus-2ovzd9tfw8ut2cxu0000](/datasets/md/54.md#visium-spatial-gene-expression-locus-ceruleus-2ovzd9tfw8ut2cxu0000), [visium-spatial-gene-expression-locus-ceruleus-d1anqqbfbuyyymbk0000](/datasets/md/5a.md#visium-spatial-gene-expression-locus-ceruleus-d1anqqbfbuyyymbk0000), [visium-spatial-gene-expression-locus-ceruleus-gekk7j8ej5wkw2b90000](/datasets/md/cf.md#visium-spatial-gene-expression-locus-ceruleus-gekk7j8ej5wkw2b90000), [visium-spatial-gene-expression-locus-ceruleus-2x8xgwxb4katdimn0000](/datasets/md/37.md#visium-spatial-gene-expression-locus-ceruleus-2x8xgwxb4katdimn0000), [visium-spatial-gene-expression-locus-ceruleus-ashb1ewyuififgxs0000](/datasets/md/38.md#visium-spatial-gene-expression-locus-ceruleus-ashb1ewyuififgxs0000), [visium-spatial-gene-expression-locus-ceruleus-khl2xufuiwppfknx0000](/datasets/md/fa.md#visium-spatial-gene-expression-locus-ceruleus-khl2xufuiwppfknx0000)
## Spatial Transcriptomics of Human Fetal Lungs
- Page: /collections/geo-gse310610/
- Kind: time course
- Datasets: 12
- Reference: PMID:41484334
- Design: Lung tissue sections were assessed for quality using DV200 criteria, and those with DV200 values greater than 50% were selected for spatial transcriptomics. 5-micron tissue sections from individual samples were placed onto Visium Gene Expression Slides (10X Genomics), stained with H&E using Visium chemistry (v1) and scanned, in two batches. Subsequently, the tissue samples were permeabilized to release ligated probe pairs from the cells, that are bound to the spatially barcoded oligonucleotides present on the spots. The resulting barcoded libraries were sequenced on a NovaSeq 6000 sequencer (Illumina) and aligned to GRCh38-2020-A and quantified using the standard Spaceranger workflow (v2.0.1).
- Members: [visium-spatial-gene-expression-lung-kizdy0c4fvucthnz0000](/datasets/md/96.md#visium-spatial-gene-expression-lung-kizdy0c4fvucthnz0000), [visium-spatial-gene-expression-lung-y30th7ywc5dkdwnt0000](/datasets/md/41.md#visium-spatial-gene-expression-lung-y30th7ywc5dkdwnt0000), [visium-spatial-gene-expression-lung-nio5ibzncwyjofa00000](/datasets/md/2f.md#visium-spatial-gene-expression-lung-nio5ibzncwyjofa00000), [visium-spatial-gene-expression-lung-mholiffz3xnlyg5i0000](/datasets/md/c1.md#visium-spatial-gene-expression-lung-mholiffz3xnlyg5i0000), [visium-spatial-gene-expression-lung-f2imzuavxichgxcx0000](/datasets/md/51.md#visium-spatial-gene-expression-lung-f2imzuavxichgxcx0000), [visium-spatial-gene-expression-lung-0bthpfm4wtczn9z80000](/datasets/md/3b.md#visium-spatial-gene-expression-lung-0bthpfm4wtczn9z80000), [visium-spatial-gene-expression-lung-ql0soa8rmgwczzgv0000](/datasets/md/23.md#visium-spatial-gene-expression-lung-ql0soa8rmgwczzgv0000), [visium-spatial-gene-expression-lung-jhjqfa4yk9f8ueno0000](/datasets/md/22.md#visium-spatial-gene-expression-lung-jhjqfa4yk9f8ueno0000), [visium-spatial-gene-expression-lung-jwf3fnbcbwpkqsqg0000](/datasets/md/a9.md#visium-spatial-gene-expression-lung-jwf3fnbcbwpkqsqg0000), [visium-spatial-gene-expression-lung-oylykuokxgfmc4mc0000](/datasets/md/85.md#visium-spatial-gene-expression-lung-oylykuokxgfmc4mc0000), [visium-spatial-gene-expression-lung-6lknqzwrwg43mdhz0000](/datasets/md/93.md#visium-spatial-gene-expression-lung-6lknqzwrwg43mdhz0000), [visium-spatial-gene-expression-lung-xizycdkyxa4dpzvb0000](/datasets/md/3f.md#visium-spatial-gene-expression-lung-xizycdkyxa4dpzvb0000)
## High-resolution spatial transcriptomics of human liver with VisiumHD
- Page: /collections/geo-gse311383/
- Kind: other
- Datasets: 3
- Reference: PMID:42342734
- Design: We applied 10x Genomics Visium HD to liver tissue from three healthy human donors to generate subcellular-resolution spatial transcriptomic profiles. Adjacent sections were imaged and sequenced to identify spatially distinct cell signatures and map the organization of the healthy liver.
- Members: [visium-hd-caudate-lobe-of-liver-fvj5oqtkecvgkkt50000](/datasets/md/a4.md#visium-hd-caudate-lobe-of-liver-fvj5oqtkecvgkkt50000), [visium-hd-caudate-lobe-of-liver-mccxtksaaa7nti440000](/datasets/md/72.md#visium-hd-caudate-lobe-of-liver-mccxtksaaa7nti440000), [visium-hd-right-lobe-of-liver-je9v0tyzpol7vsix0000](/datasets/md/fe.md#visium-hd-right-lobe-of-liver-je9v0tyzpol7vsix0000)
## A targetable developmental program co-regulates angiogenesis and immune evasion [Spatial Transcriptomics]
- Page: /collections/geo-gse311909/
- Kind: other
- Datasets: 2
- Reference: PMID:41631877
- Design: Human acral melanoma samples were processed for Visium 10X spatial transcriptomics.
- Members: [visium-spatial-gene-expression-skin-of-body-yd6klyv8knjfmz1u0000](/datasets/md/72.md#visium-spatial-gene-expression-skin-of-body-yd6klyv8knjfmz1u0000), [visium-spatial-gene-expression-skin-of-body-5dms9xtj8szsbb5w0000](/datasets/md/61.md#visium-spatial-gene-expression-skin-of-body-5dms9xtj8szsbb5w0000)
## Activated Interferon Signaling Suppresses Age-Dependent Liver Cancer [MERFISH]
- Page: /collections/geo-gse313704/
- Kind: time course
- Datasets: 10
- Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE313704
- Design: Age is a major risk factor for liver cancer, as is the case for most adult human cancers. However, the underlying mechanisms are not well defined. A better understanding of the role of aging in liver and other cancers can facilitate approaches for risk assessment, early detection and prevention. We hypothesize that age-driven changes render aged liver more sensitive to oncogenic stress and hence tumorigenesis. To investigate how the liver changes with age, we documented the immune profile, transcriptome and epigenome of healthy livers from both young and aged mice, revealing pronounced alterations with aging. Notably, in aged hepatocytes, we identified heightened interferon (IFN) signaling, as well as simultaneous tumor suppressor and oncogene signaling at both bulk and single cell level, suggestive of an aged liver that is poised for neoplasia. To challenge this seemingly poised state, we employed adeno-associated virus (AAV)-mediated expression of a c-Myc oncogene in young and aged mouse liver hepatocytes in vivo. Analysis of aged hepatocytes expressing c-Myc revealed further elevated expression of IFN Stimulated Genes (ISGs). This ISG upregulation was evident in multiple models of oncogenic stress and transformation in older mice and also observed in aged humans with Metabolic dysfunction-Associated Steatohepatitis (MASH). We determined that Stat1 is both necessary and sufficient for the age specific elevated ISG expression in old wild type mice. Remarkably, inhibiting Jak/Stat signaling alongside ectopic c-Myc expression led to high-grade hepatocyte dysplasia and tumor formation, selectively in aged mice. Together, these results suggest that an aged liver is in a state of “precarious balance”, due to concurrent activation of oncogenic and tumor suppressor pathways, but protected against neoplastic progression by IFN-signaling. Age-dependent activation of IFN signaling has been observed in many tissues and recent studies have demonstrated its detrimental consequences on aging, raising the question as to why IFN-signaling is activated during aging. We propose that aged tissues are intrinsically at higher risk of cancer and age-dependent activation of IFN-signaling is an adaptive process to protect from tumorigenesis, but one that also has maladaptive consequences.
- Members: [vizgen-merscope-liver-zejy9d76sqtmicts0000](/datasets/md/bb.md#vizgen-merscope-liver-zejy9d76sqtmicts0000), [vizgen-merscope-liver-il93x3irx1cazxs80000](/datasets/md/70.md#vizgen-merscope-liver-il93x3irx1cazxs80000), [vizgen-merscope-liver-ywntul28gu5hg5k40000](/datasets/md/db.md#vizgen-merscope-liver-ywntul28gu5hg5k40000), [vizgen-merscope-liver-74yliu2o9vgpjceu0000](/datasets/md/bf.md#vizgen-merscope-liver-74yliu2o9vgpjceu0000), [vizgen-merscope-liver-ahct8u64p7nmxmhr0000](/datasets/md/7e.md#vizgen-merscope-liver-ahct8u64p7nmxmhr0000), [vizgen-merscope-liver-rcgzjcupe9rbubeu0000](/datasets/md/86.md#vizgen-merscope-liver-rcgzjcupe9rbubeu0000), [vizgen-merscope-liver-arhgiqjqvudgeqib0000](/datasets/md/0c.md#vizgen-merscope-liver-arhgiqjqvudgeqib0000), [vizgen-merscope-liver-xwolgoe2zfapwhcf0000](/datasets/md/08.md#vizgen-merscope-liver-xwolgoe2zfapwhcf0000), [vizgen-merscope-liver-tu1pnp3olsnbofiq0000](/datasets/md/a8.md#vizgen-merscope-liver-tu1pnp3olsnbofiq0000), [vizgen-merscope-liver-ed5bbbiervizmbd40000](/datasets/md/3b.md#vizgen-merscope-liver-ed5bbbiervizmbd40000)
## Spatial transcriptomics of MRGPRX4-driven melanoma
- Page: /collections/geo-gse313828/
- Kind: other
- Datasets: 3
- Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE313828
- Design: TyrCreER;MRGPRX4-ROSA26-stop-flox animals received intraperitoneal injection of tamoxifen (1 mg/40 g) for 3 conxecutive days. Cutaneous melnoma tissue was collected into OCT and flash frozen in liquid nitrogen-cooled isopentane for downstream Visium processing.
- Members: [visium-spatial-gene-expression-skin-of-body-t6gapzndpwveyfss0000](/datasets/md/70.md#visium-spatial-gene-expression-skin-of-body-t6gapzndpwveyfss0000), [visium-spatial-gene-expression-skin-of-body-z6ptac6tuhdnrhvc0000](/datasets/md/e3.md#visium-spatial-gene-expression-skin-of-body-z6ptac6tuhdnrhvc0000), [visium-spatial-gene-expression-skin-of-body-higw7cakuh8cpt8o0000](/datasets/md/5a.md#visium-spatial-gene-expression-skin-of-body-higw7cakuh8cpt8o0000)
## Dendritic cell-mediated antigen presentation regulates tertiary lymphoid structure development in cancer.
- Page: /collections/geo-gse322553/
- Kind: replicates
- Datasets: 7
- Reference: PMID:42462020
- Design: Visium spatial transcriptomics of human colorectal cancer (CRC; n = 4), liver cancer (HCC; n = 1) and lung cancer (NSCLC; n =2)
- Members: [visium-spatial-gene-expression-lung-x2jlvggagsmqlvbh0000](/datasets/md/9d.md#visium-spatial-gene-expression-lung-x2jlvggagsmqlvbh0000), [visium-spatial-gene-expression-colon-eknmykaci3ivml1s0000](/datasets/md/09.md#visium-spatial-gene-expression-colon-eknmykaci3ivml1s0000), [visium-spatial-gene-expression-colon-fuv4mufggcuwi4us0000](/datasets/md/bf.md#visium-spatial-gene-expression-colon-fuv4mufggcuwi4us0000), [visium-spatial-gene-expression-liver-zmfka6uiodiiqfgt0000](/datasets/md/d8.md#visium-spatial-gene-expression-liver-zmfka6uiodiiqfgt0000), [visium-spatial-gene-expression-lung-t0tr8ud9foi1yehe0000](/datasets/md/b9.md#visium-spatial-gene-expression-lung-t0tr8ud9foi1yehe0000), [visium-spatial-gene-expression-colon-poo79pxnxvvmgaq10000](/datasets/md/ed.md#visium-spatial-gene-expression-colon-poo79pxnxvvmgaq10000), [visium-spatial-gene-expression-colon-xobx8m20iil0l2a30000](/datasets/md/98.md#visium-spatial-gene-expression-colon-xobx8m20iil0l2a30000)
## Single-cell and Spatial Transcriptomic Profiling of the Bone Metastatic Microenvironment
- Page: /collections/geo-gse323357/
- Kind: other
- Datasets: 4
- Reference: PMID:42108258
- Design: Mouse bone metastasis samples were generated using an internal iliac artery (IIA) injection model. Mice were maintained under standard laboratory housing conditions with ad libitum access to food and water. Bone metastases were induced by injection of LLC1 tumor cells, and animals were monitored post-procedure until full recovery. Bone tissues were harvested at defined experimental endpoints for downstream single-cell RNA sequencing and spatial transcriptomics analysis. For the details, please refer to Wang, H. et al. The osteogenic niche promotes early-stage bone colonization of disseminated breast cancer cells. Cancer Cell 27, 193-210 (2015).
- Members: [visium-spatial-gene-expression-bone-tissue-9qom4zwmgramu5fc0001](/datasets/md/8b.md#visium-spatial-gene-expression-bone-tissue-9qom4zwmgramu5fc0001), [visium-spatial-gene-expression-bone-tissue-idickmgqnclcus6q0000](/datasets/md/8a.md#visium-spatial-gene-expression-bone-tissue-idickmgqnclcus6q0000), [visium-spatial-gene-expression-bone-tissue-4x2fajbwcbsjtaxk0001](/datasets/md/d8.md#visium-spatial-gene-expression-bone-tissue-4x2fajbwcbsjtaxk0001), [visium-spatial-gene-expression-bone-tissue-utlngkryyztqeaf20001](/datasets/md/1a.md#visium-spatial-gene-expression-bone-tissue-utlngkryyztqeaf20001)
## The Spatial Landscape of Extracellular Matrix Gene Expression in Healthy and Type 2 Diabetic Human Pancreas
- Page: /collections/geo-gse333737/
- Kind: publication
- Datasets: 12
- Reference: 10.64898/2026.06.30.733275
- Members: [vizgen-merscope-pancreas-q32kyvyeqfv26w4p0000](/datasets/md/01.md#vizgen-merscope-pancreas-q32kyvyeqfv26w4p0000), [vizgen-merscope-pancreas-crsfpkqwn4wlnqsg0000](/datasets/md/66.md#vizgen-merscope-pancreas-crsfpkqwn4wlnqsg0000), [vizgen-merscope-pancreas-12guuot31vmjwn600000](/datasets/md/08.md#vizgen-merscope-pancreas-12guuot31vmjwn600000), [vizgen-merscope-pancreas-qfiehbwskxgoijlc0000](/datasets/md/10.md#vizgen-merscope-pancreas-qfiehbwskxgoijlc0000), [vizgen-merscope-pancreas-n3myk7zosjvbxu3y0000](/datasets/md/35.md#vizgen-merscope-pancreas-n3myk7zosjvbxu3y0000), [vizgen-merscope-pancreas-v6wgaivkfpei3fec0000](/datasets/md/77.md#vizgen-merscope-pancreas-v6wgaivkfpei3fec0000), [vizgen-merscope-pancreas-ghtll0miyf3rwoep0000](/datasets/md/99.md#vizgen-merscope-pancreas-ghtll0miyf3rwoep0000), [vizgen-merscope-pancreas-rf0mqqphmlt5ajlw0000](/datasets/md/2c.md#vizgen-merscope-pancreas-rf0mqqphmlt5ajlw0000), [vizgen-merscope-pancreas-7t7dqw2n64frqzmq0000](/datasets/md/51.md#vizgen-merscope-pancreas-7t7dqw2n64frqzmq0000), [vizgen-merscope-pancreas-85qirgvhb3wrspbe0000](/datasets/md/81.md#vizgen-merscope-pancreas-85qirgvhb3wrspbe0000), [vizgen-merscope-pancreas-vlfdu42wj1avjdoe0000](/datasets/md/8e.md#vizgen-merscope-pancreas-vlfdu42wj1avjdoe0000), [vizgen-merscope-pancreas-ujfz8xhsubc04acv0000](/datasets/md/64.md#vizgen-merscope-pancreas-ujfz8xhsubc04acv0000)
## Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.
- Page: /collections/geo-gsm9238732/
- Kind: publication
- Datasets: 7
- Reference: 10.1038/s41467-025-64990-y
- Members: [vizgen-merscope-unknown-fggxurmws6elvm740000](/datasets/md/0f.md#vizgen-merscope-unknown-fggxurmws6elvm740000), [vizgen-merscope-unknown-4zwwkphws26xtmp20000](/datasets/md/09.md#vizgen-merscope-unknown-4zwwkphws26xtmp20000), [vizgen-merscope-unknown-pjy8kii42afjkr2o0000](/datasets/md/d4.md#vizgen-merscope-unknown-pjy8kii42afjkr2o0000), [vizgen-merscope-unknown-hxdc1sdm70odsyqb0000](/datasets/md/7d.md#vizgen-merscope-unknown-hxdc1sdm70odsyqb0000), [vizgen-merscope-unknown-gfrjwgbyobnwehbd0000](/datasets/md/63.md#vizgen-merscope-unknown-gfrjwgbyobnwehbd0000), [vizgen-merscope-unknown-nmbvfod5gv0kuxrv0000](/datasets/md/86.md#vizgen-merscope-unknown-nmbvfod5gv0kuxrv0000), [vizgen-merscope-unknown-ql3xtru9jyugregn0000](/datasets/md/e6.md#vizgen-merscope-unknown-ql3xtru9jyugregn0000)
## QuantCell: machine learning based cell annotation integrating qualitative and quantitative imaging profiles
- Page: /collections/zenodo-23672666/
- Kind: publication
- Datasets: 1
- Reference: 10.64898/2026.02.15.706033
- Members: [phenocycler-bone-marrow-i9vhud5cpfeo3bcx0000](/datasets/md/d3.md#phenocycler-bone-marrow-i9vhud5cpfeo3bcx0000)
## geo-gse276063
- Page: /collections/geo-gse276063/
- Kind: other
- Datasets: 1
- Members: [stereo-seq-liver-m9mf2rpbigadz3jr0000](/datasets/md/b6.md#stereo-seq-liver-m9mf2rpbigadz3jr0000)
## geo-gse274447
- Page: /collections/geo-gse274447/
- Kind: other
- Datasets: 3
- Members: [stereo-seq-brain-gdbpq5ritungchr50000](/datasets/md/86.md#stereo-seq-brain-gdbpq5ritungchr50000), [stereo-seq-brain-a2pyox5nemftstvw0000](/datasets/md/21.md#stereo-seq-brain-a2pyox5nemftstvw0000), [stereo-seq-brain-pscs4urz4cgknqqn0000](/datasets/md/53.md#stereo-seq-brain-pscs4urz4cgknqqn0000)