# SpatialData-DB collections, shard 8
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.
## Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.
- Page: /collections/doi-10-1038-s42003-021-02810-x/
- Kind: comparison
- Datasets: 3
- Reference: 10.1038/s42003-021-02810-x
- Members: [visium-spatial-gene-expression-skeletal-muscle-tissue-ej51zwnralziscrk0000](/datasets/md/2e.md#visium-spatial-gene-expression-skeletal-muscle-tissue-ej51zwnralziscrk0000), [visium-spatial-gene-expression-skeletal-muscle-tissue-2so1ap03ti6w1lj10000](/datasets/md/20.md#visium-spatial-gene-expression-skeletal-muscle-tissue-2so1ap03ti6w1lj10000), [visium-spatial-gene-expression-skeletal-muscle-tissue-c5lpru3emha4kday0000](/datasets/md/dc.md#visium-spatial-gene-expression-skeletal-muscle-tissue-c5lpru3emha4kday0000)
## Spatial transcriptomic profiling of the aging mouse brain [spatial scRNA-seq]
- Page: /collections/geo-gse193107/
- Kind: time course
- Datasets: 8
- Reference: PMID:38372175
- Design: 8 slices from young (2 months old) and old mice (28 months old) (strain C57BL/6J) were prepared according to Visium spatial protocols of tissue preparation guide (10x genomics). The brains were rapidly extracted from the cranial cavity, and immediately submerged in ice-cold artificial cerebrospinal fluid. The brains were then blotted to remove excess liquid. The brains were subsequently embedded in Optimal Cutting Temperature compound (OCT) and frozen in isopentane (2-methylbutane, Sigma) precooled with dry ice and liquid nitrogen. The brains were cut into 10-um sections.
- Members: [visium-spatial-gene-expression-brain-4svppqskkrn36i4p0000](/datasets/md/a9.md#visium-spatial-gene-expression-brain-4svppqskkrn36i4p0000), [visium-spatial-gene-expression-brain-uxqf7u2vrypah7q20000](/datasets/md/e0.md#visium-spatial-gene-expression-brain-uxqf7u2vrypah7q20000), [visium-spatial-gene-expression-brain-rbaqywaztdb0cym90000](/datasets/md/6f.md#visium-spatial-gene-expression-brain-rbaqywaztdb0cym90000), [visium-spatial-gene-expression-brain-pjiaha584odqzibf0000](/datasets/md/74.md#visium-spatial-gene-expression-brain-pjiaha584odqzibf0000), [visium-spatial-gene-expression-brain-ve6uuzig7xt8yfb20000](/datasets/md/bf.md#visium-spatial-gene-expression-brain-ve6uuzig7xt8yfb20000), [visium-spatial-gene-expression-brain-6p0ypzd9h2cyqazi0000](/datasets/md/15.md#visium-spatial-gene-expression-brain-6p0ypzd9h2cyqazi0000), [visium-spatial-gene-expression-brain-geuvxdpblgf6y4uz0000](/datasets/md/ce.md#visium-spatial-gene-expression-brain-geuvxdpblgf6y4uz0000), [visium-spatial-gene-expression-brain-gyk7qdablkfqz8hn0000](/datasets/md/47.md#visium-spatial-gene-expression-brain-gyk7qdablkfqz8hn0000)
## geo-gse342738
- Page: /collections/geo-gse342738/
- Kind: replicates
- Datasets: 5
- Members: [visium-hd-medial-amygdaloid-nucleus-mirbajjsybaxbvyw0000](/datasets/md/6b.md#visium-hd-medial-amygdaloid-nucleus-mirbajjsybaxbvyw0000), [visium-hd-central-amygdaloid-nucleus-r5vyxrq5qdleejwb0000](/datasets/md/9f.md#visium-hd-central-amygdaloid-nucleus-r5vyxrq5qdleejwb0000), [visium-hd-intercalated-amygdaloid-nuclei-j7i9bsfotzxbwl5a0000](/datasets/md/65.md#visium-hd-intercalated-amygdaloid-nuclei-j7i9bsfotzxbwl5a0000), [visium-hd-medial-amygdaloid-nucleus-qcdnhuijzokr9wb10000](/datasets/md/bb.md#visium-hd-medial-amygdaloid-nucleus-qcdnhuijzokr9wb10000), [visium-hd-central-amygdaloid-nucleus-iexsoumfnyq4zl8r0000](/datasets/md/88.md#visium-hd-central-amygdaloid-nucleus-iexsoumfnyq4zl8r0000)
## Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment
- Page: /collections/geo-gse203612/
- Kind: other
- Datasets: 12
- Reference: PMID:35931863
- Design: Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment
- Members: [visium-spatial-gene-expression-skin-of-body-spxmbn3quowdsh000000](/datasets/md/9b.md#visium-spatial-gene-expression-skin-of-body-spxmbn3quowdsh000000), [visium-spatial-gene-expression-ovary-yceh40r74oaor1ow0000](/datasets/md/84.md#visium-spatial-gene-expression-ovary-yceh40r74oaor1ow0000), [visium-spatial-gene-expression-mammary-gland-oubf3tkdnjrrahqh0000](/datasets/md/6a.md#visium-spatial-gene-expression-mammary-gland-oubf3tkdnjrrahqh0000), [visium-spatial-gene-expression-endometrium-4lojs3pxf3zps3rq0000](/datasets/md/c1.md#visium-spatial-gene-expression-endometrium-4lojs3pxf3zps3rq0000), [visium-spatial-gene-expression-mammary-gland-ilwc40uzyr96ams40000](/datasets/md/61.md#visium-spatial-gene-expression-mammary-gland-ilwc40uzyr96ams40000), [visium-spatial-gene-expression-unknown-byycbxsnawdoscqh0000](/datasets/md/1b.md#visium-spatial-gene-expression-unknown-byycbxsnawdoscqh0000), [visium-spatial-gene-expression-ovary-ov3fhasvnetyr3ae0000](/datasets/md/ed.md#visium-spatial-gene-expression-ovary-ov3fhasvnetyr3ae0000), [visium-spatial-gene-expression-mammary-gland-clyhb1wl33hf1plb0000](/datasets/md/55.md#visium-spatial-gene-expression-mammary-gland-clyhb1wl33hf1plb0000), [visium-spatial-gene-expression-stomach-5rzuahinspyevscw0000](/datasets/md/21.md#visium-spatial-gene-expression-stomach-5rzuahinspyevscw0000), [visium-spatial-gene-expression-stomach-rlqfmhjkbqnstnwd0000](/datasets/md/95.md#visium-spatial-gene-expression-stomach-rlqfmhjkbqnstnwd0000), [visium-spatial-gene-expression-liver-o3nlio87nq4q6zkv0000](/datasets/md/59.md#visium-spatial-gene-expression-liver-o3nlio87nq4q6zkv0000), [visium-spatial-gene-expression-skin-of-body-u4htkhq5rpu0nmbn0000](/datasets/md/d6.md#visium-spatial-gene-expression-skin-of-body-u4htkhq5rpu0nmbn0000)
## Spatial transcriptomics of triple negative breast cancer
- Page: /collections/geo-gse210616/
- Kind: other
- Datasets: 43
- Reference: PMID:36283023
- Design: 28 tissue sections representing 14 primary TNBC tumors were subject to spatial transcriptomics using the 10x Genomics Visium platform, followed by high throughput sequencing. Raw data not submitted due to patient privacy concerns.
- Members: [visium-spatial-gene-expression-breast-ew0zqc4vm9evnmok0000](/datasets/md/36.md#visium-spatial-gene-expression-breast-ew0zqc4vm9evnmok0000), [visium-spatial-gene-expression-breast-om8v2fbi4jcgbtwb0000](/datasets/md/f8.md#visium-spatial-gene-expression-breast-om8v2fbi4jcgbtwb0000), [visium-spatial-gene-expression-breast-kzz4cez4lcz1hss30000](/datasets/md/73.md#visium-spatial-gene-expression-breast-kzz4cez4lcz1hss30000), [visium-spatial-gene-expression-breast-hib2aecedzfpmqut0000](/datasets/md/92.md#visium-spatial-gene-expression-breast-hib2aecedzfpmqut0000), [visium-spatial-gene-expression-breast-shdeh96qeodcuhan0000](/datasets/md/72.md#visium-spatial-gene-expression-breast-shdeh96qeodcuhan0000), [visium-spatial-gene-expression-breast-nbujjgnsfqmmi8vg0000](/datasets/md/e8.md#visium-spatial-gene-expression-breast-nbujjgnsfqmmi8vg0000), [visium-spatial-gene-expression-breast-aksr7vixrexbje740000](/datasets/md/3b.md#visium-spatial-gene-expression-breast-aksr7vixrexbje740000), [visium-spatial-gene-expression-breast-aguiqanmbi90joqr0000](/datasets/md/61.md#visium-spatial-gene-expression-breast-aguiqanmbi90joqr0000), [visium-spatial-gene-expression-breast-qz5pbsjfs4mxv3cm0000](/datasets/md/a8.md#visium-spatial-gene-expression-breast-qz5pbsjfs4mxv3cm0000), [visium-spatial-gene-expression-breast-hlk0uwhcr1mogn5i0000](/datasets/md/06.md#visium-spatial-gene-expression-breast-hlk0uwhcr1mogn5i0000), [visium-spatial-gene-expression-breast-ck5mcu86s1nroz890000](/datasets/md/67.md#visium-spatial-gene-expression-breast-ck5mcu86s1nroz890000), [visium-spatial-gene-expression-breast-zhdkr6cakcbhzhc90000](/datasets/md/e0.md#visium-spatial-gene-expression-breast-zhdkr6cakcbhzhc90000), [visium-spatial-gene-expression-breast-wraoxirj7af1czhx0000](/datasets/md/eb.md#visium-spatial-gene-expression-breast-wraoxirj7af1czhx0000), [visium-spatial-gene-expression-breast-xg9btcmybp1ifrgx0000](/datasets/md/ac.md#visium-spatial-gene-expression-breast-xg9btcmybp1ifrgx0000), [visium-spatial-gene-expression-breast-hagwiyyfoornay7p0000](/datasets/md/3c.md#visium-spatial-gene-expression-breast-hagwiyyfoornay7p0000), [visium-spatial-gene-expression-breast-ffi1vabnqfad5spn0000](/datasets/md/21.md#visium-spatial-gene-expression-breast-ffi1vabnqfad5spn0000), [visium-spatial-gene-expression-breast-sppv7zb1j6zenuc90000](/datasets/md/f7.md#visium-spatial-gene-expression-breast-sppv7zb1j6zenuc90000), [visium-spatial-gene-expression-breast-prrkys28bjtp3xed0000](/datasets/md/0d.md#visium-spatial-gene-expression-breast-prrkys28bjtp3xed0000), [visium-spatial-gene-expression-breast-myp5fnxnm8cun9wc0000](/datasets/md/8b.md#visium-spatial-gene-expression-breast-myp5fnxnm8cun9wc0000), [visium-spatial-gene-expression-breast-10aovotl2cnefbxa0000](/datasets/md/ad.md#visium-spatial-gene-expression-breast-10aovotl2cnefbxa0000), [visium-spatial-gene-expression-breast-ruoupezafihjoqdc0000](/datasets/md/6f.md#visium-spatial-gene-expression-breast-ruoupezafihjoqdc0000), [visium-spatial-gene-expression-breast-epvks6v7z3xizfkj0000](/datasets/md/6c.md#visium-spatial-gene-expression-breast-epvks6v7z3xizfkj0000), [visium-spatial-gene-expression-breast-qqkxdxme9ay0qgmt0000](/datasets/md/cc.md#visium-spatial-gene-expression-breast-qqkxdxme9ay0qgmt0000), [visium-spatial-gene-expression-breast-fliofzlkkvwg9m0w0000](/datasets/md/e1.md#visium-spatial-gene-expression-breast-fliofzlkkvwg9m0w0000), [visium-spatial-gene-expression-breast-ufm6xwaskywp1qvz0000](/datasets/md/b1.md#visium-spatial-gene-expression-breast-ufm6xwaskywp1qvz0000), [visium-spatial-gene-expression-breast-gjfavhhlrqr3ojfs0000](/datasets/md/67.md#visium-spatial-gene-expression-breast-gjfavhhlrqr3ojfs0000), [visium-spatial-gene-expression-breast-euiaipsahe9itpik0000](/datasets/md/68.md#visium-spatial-gene-expression-breast-euiaipsahe9itpik0000), [visium-spatial-gene-expression-breast-zqakwnk6xr4idrei0000](/datasets/md/61.md#visium-spatial-gene-expression-breast-zqakwnk6xr4idrei0000), [visium-spatial-gene-expression-breast-9ln3acfpohynlxx70000](/datasets/md/1c.md#visium-spatial-gene-expression-breast-9ln3acfpohynlxx70000), [visium-spatial-gene-expression-breast-pzqo2leg1hbp1xrh0000](/datasets/md/6b.md#visium-spatial-gene-expression-breast-pzqo2leg1hbp1xrh0000), [visium-spatial-gene-expression-breast-x1116xwf9jkxf2ss0000](/datasets/md/8b.md#visium-spatial-gene-expression-breast-x1116xwf9jkxf2ss0000), [visium-spatial-gene-expression-breast-0wqovvjgagajm5aa0000](/datasets/md/9a.md#visium-spatial-gene-expression-breast-0wqovvjgagajm5aa0000), [visium-spatial-gene-expression-breast-2kmq7ph1byv04lat0000](/datasets/md/a6.md#visium-spatial-gene-expression-breast-2kmq7ph1byv04lat0000), [visium-spatial-gene-expression-breast-leenr36l2z5zjsdv0000](/datasets/md/88.md#visium-spatial-gene-expression-breast-leenr36l2z5zjsdv0000), [visium-spatial-gene-expression-breast-vtaa6bpnesqpvsmv0000](/datasets/md/ef.md#visium-spatial-gene-expression-breast-vtaa6bpnesqpvsmv0000), [visium-spatial-gene-expression-breast-9mggchaipsuiklx50000](/datasets/md/88.md#visium-spatial-gene-expression-breast-9mggchaipsuiklx50000), [visium-spatial-gene-expression-breast-aso5nchbmegnyc3y0000](/datasets/md/cc.md#visium-spatial-gene-expression-breast-aso5nchbmegnyc3y0000), [visium-spatial-gene-expression-breast-wp8r9hacusngpy6h0000](/datasets/md/af.md#visium-spatial-gene-expression-breast-wp8r9hacusngpy6h0000), [visium-spatial-gene-expression-breast-ajsldvfphawocifw0000](/datasets/md/b7.md#visium-spatial-gene-expression-breast-ajsldvfphawocifw0000), [visium-spatial-gene-expression-breast-fczwy21dgpxuxxy90000](/datasets/md/ff.md#visium-spatial-gene-expression-breast-fczwy21dgpxuxxy90000), [visium-spatial-gene-expression-breast-c4mqjkpdkhryfmgw0000](/datasets/md/fa.md#visium-spatial-gene-expression-breast-c4mqjkpdkhryfmgw0000), [visium-spatial-gene-expression-breast-77w0uqputqnuzdww0000](/datasets/md/fb.md#visium-spatial-gene-expression-breast-77w0uqputqnuzdww0000), [visium-spatial-gene-expression-breast-hj68blsz1jxxqdpr0000](/datasets/md/3b.md#visium-spatial-gene-expression-breast-hj68blsz1jxxqdpr0000)
## Liver metastases originating from 4 colorectal cancer patients (CRC-LM).
- Page: /collections/geo-gse217414/
- Kind: other
- Datasets: 4
- Reference: PMID:37144485
- Design: We performed Spatial Transcriptomics using 10X Genomics Visium in these four different cancer patients and focused on ligand receptor interactions. For some patients, we were also able to perform validations by immunofluorescence. All patients were treated with neo-adjuvant chemotherapy prior to surgery and sample collection.
- Members: [visium-spatial-gene-expression-liver-cqrmubsdes8v3djo0000](/datasets/md/b8.md#visium-spatial-gene-expression-liver-cqrmubsdes8v3djo0000), [visium-spatial-gene-expression-liver-05motgbmjmunyc0j0000](/datasets/md/69.md#visium-spatial-gene-expression-liver-05motgbmjmunyc0j0000), [visium-spatial-gene-expression-liver-zwww2tcb7e3hmrkp0000](/datasets/md/08.md#visium-spatial-gene-expression-liver-zwww2tcb7e3hmrkp0000), [visium-spatial-gene-expression-liver-91yozw36haclbs640000](/datasets/md/93.md#visium-spatial-gene-expression-liver-91yozw36haclbs640000)
## Orthotopic 4T1 tumors spatial transcriptomics
- Page: /collections/geo-gse230098/
- Kind: other
- Datasets: 4
- Reference: PMID:40670787
- Design: FFPE tissue blocks were cut down to approximately 6.5 mm x 6.5 mm in size and sectioned onto the capture areas of the Visium slide according to 10X Genomics Tissue Preparation Guide CG000408. Slides were then deparaffinized and H&E-stained according to the 10X Genomics Demonstrated Protocol CG000409 and imaged at the Animal & Tissue Imaging Core Facility at CSHL. After imaging, the tissue was decrosslinked and probe hybridization with the Visium Mouse Transcriptome Probe Kit (PN-1000365, 10X Genomics) was performed overnight at 50°C. Probe ligation, probe release and extension, and library preparation were performed according to manufacturer’s instructions, and final libraries were sequenced on a NextSeq 500 to target 20,000 reads per spot. Sequencing data were processed with Space Ranger version 2.0.0 (10X Genomics).
- Members: [visium-spatial-gene-expression-mammary-gland-mkzlaehzvq80fdx40000](/datasets/md/d2.md#visium-spatial-gene-expression-mammary-gland-mkzlaehzvq80fdx40000), [visium-spatial-gene-expression-mammary-gland-joxvohsuupsk5itt0000](/datasets/md/82.md#visium-spatial-gene-expression-mammary-gland-joxvohsuupsk5itt0000), [visium-spatial-gene-expression-mammary-gland-3m90ctl5dudaqydf0000](/datasets/md/67.md#visium-spatial-gene-expression-mammary-gland-3m90ctl5dudaqydf0000), [visium-spatial-gene-expression-mammary-gland-8milh1khu0eddgoc0000](/datasets/md/ed.md#visium-spatial-gene-expression-mammary-gland-8milh1khu0eddgoc0000)
## Synovial Th17 transdifferentiation into exTh17 sustains chronic IL-17-independent inflammatory arthritis [Visium]
- Page: /collections/geo-gse232734/
- Kind: other
- Datasets: 2
- Reference: PMID:41202149
- Design: Spatial Transcriptomic (Visium 10X) on Rheumatoid Arthritis (RA) Human Synovium from ACPA and RF positive RA patients with active disease
- Members: [visium-spatial-gene-expression-synovial-membrane-of-synovial-joint-3vwroivzdeehtcgo0000](/datasets/md/d9.md#visium-spatial-gene-expression-synovial-membrane-of-synovial-joint-3vwroivzdeehtcgo0000), [visium-spatial-gene-expression-synovial-membrane-of-synovial-joint-rnkdbbgxyaqollof0000](/datasets/md/b6.md#visium-spatial-gene-expression-synovial-membrane-of-synovial-joint-rnkdbbgxyaqollof0000)
## geo-gse349411
- Page: /collections/geo-gse349411/
- Kind: other
- Datasets: 1
- Members: [vizgen-merscope-brain-zvg3vcnjze55pl1y0000](/datasets/md/fc.md#vizgen-merscope-brain-zvg3vcnjze55pl1y0000)
## Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of BRAF-mutant melanoma
- Page: /collections/geo-gse245582/
- Kind: time course
- Datasets: 23
- Reference: PMID:39700408
- Design: The two WISTAR PDX models, immunotherapy-treated WM4237-1 and treatment-naive WM4007, are BRAF V600E mutant metastatic melanomas of a subcutaneously implanted solid tumor on NSG mice. Twenty mice per model were used in the longitudinal experiment. When the tumors reached 300 mm3, measured biweekly, the continuous dose treatment of mice via chow with either a dual BRAF/MEK inhibitor or vehicle was initiated. One untreated mouse per model was sacrificed at time point T0, day 0. One vehicle-treated mouse per model was sacrificed at time point TC, days 42 and 38, WM4237-1 and WM4007, respectively. The tumors of therapy-treated sacrificed mice, one tumor tissue block per mouse per model per time point, were harvested at time points T1 (day 14), T2 (days 42 and 44), T3 (days 70 and 73), and T4 (days 94 and 133). We analyzed two near adjacent tissue sections from each tumor tissue block for each model and time point using 10x Visium Spatial Gene Expression.
- Members: [visium-spatial-gene-expression-skin-of-body-kk4dwtlmbxw3e51p0000](/datasets/md/8a.md#visium-spatial-gene-expression-skin-of-body-kk4dwtlmbxw3e51p0000), [visium-spatial-gene-expression-skin-of-body-jw4wkdpuuma41wz30000](/datasets/md/a0.md#visium-spatial-gene-expression-skin-of-body-jw4wkdpuuma41wz30000), [visium-spatial-gene-expression-skin-of-body-bczrhzpg3ksbmx4y0000](/datasets/md/76.md#visium-spatial-gene-expression-skin-of-body-bczrhzpg3ksbmx4y0000), [visium-spatial-gene-expression-skin-of-body-bh3vnch1jwm8bnxd0000](/datasets/md/46.md#visium-spatial-gene-expression-skin-of-body-bh3vnch1jwm8bnxd0000), [visium-spatial-gene-expression-skin-of-body-nniou1zkuknezwrg0000](/datasets/md/05.md#visium-spatial-gene-expression-skin-of-body-nniou1zkuknezwrg0000), [visium-spatial-gene-expression-skin-of-body-uahwl4butryaldmb0000](/datasets/md/c2.md#visium-spatial-gene-expression-skin-of-body-uahwl4butryaldmb0000), [visium-spatial-gene-expression-skin-of-body-yjua9rtum0oxywkf0000](/datasets/md/ff.md#visium-spatial-gene-expression-skin-of-body-yjua9rtum0oxywkf0000), [visium-spatial-gene-expression-skin-of-body-6kejtl57ie1o8ps50000](/datasets/md/19.md#visium-spatial-gene-expression-skin-of-body-6kejtl57ie1o8ps50000), [visium-spatial-gene-expression-skin-of-body-zan2sbvagimlkatc0000](/datasets/md/b9.md#visium-spatial-gene-expression-skin-of-body-zan2sbvagimlkatc0000), [visium-spatial-gene-expression-skin-of-body-3z2dntbdk4mtl45f0000](/datasets/md/28.md#visium-spatial-gene-expression-skin-of-body-3z2dntbdk4mtl45f0000), [visium-spatial-gene-expression-skin-of-body-6dtyrlynf7zrindg0000](/datasets/md/71.md#visium-spatial-gene-expression-skin-of-body-6dtyrlynf7zrindg0000), [visium-spatial-gene-expression-skin-of-body-myol1xqadw5fvcag0000](/datasets/md/6c.md#visium-spatial-gene-expression-skin-of-body-myol1xqadw5fvcag0000), [visium-spatial-gene-expression-skin-of-body-x3a1bbkjr5td18lu0000](/datasets/md/74.md#visium-spatial-gene-expression-skin-of-body-x3a1bbkjr5td18lu0000), [visium-spatial-gene-expression-skin-of-body-adrbkz9lsemvhy9g0000](/datasets/md/d1.md#visium-spatial-gene-expression-skin-of-body-adrbkz9lsemvhy9g0000), [visium-spatial-gene-expression-skin-of-body-hvbetwnmet0djyiq0000](/datasets/md/ef.md#visium-spatial-gene-expression-skin-of-body-hvbetwnmet0djyiq0000), [visium-spatial-gene-expression-skin-of-body-emkgpcblcacjns8b0000](/datasets/md/de.md#visium-spatial-gene-expression-skin-of-body-emkgpcblcacjns8b0000), [visium-spatial-gene-expression-skin-of-body-qaszxpgxu4vsnmoj0000](/datasets/md/e8.md#visium-spatial-gene-expression-skin-of-body-qaszxpgxu4vsnmoj0000), [visium-spatial-gene-expression-skin-of-body-lbgdsiwjzgimnymn0001](/datasets/md/ea.md#visium-spatial-gene-expression-skin-of-body-lbgdsiwjzgimnymn0001), [visium-spatial-gene-expression-skin-of-body-ojht1qr0jpene0o80000](/datasets/md/99.md#visium-spatial-gene-expression-skin-of-body-ojht1qr0jpene0o80000), [visium-spatial-gene-expression-skin-of-body-mrzyok9idwjjbe2n0000](/datasets/md/d4.md#visium-spatial-gene-expression-skin-of-body-mrzyok9idwjjbe2n0000), [visium-spatial-gene-expression-skin-of-body-uafvolysrwkenwu40000](/datasets/md/06.md#visium-spatial-gene-expression-skin-of-body-uafvolysrwkenwu40000), [visium-spatial-gene-expression-skin-of-body-6rhc4ny41aq3lfvc0000](/datasets/md/49.md#visium-spatial-gene-expression-skin-of-body-6rhc4ny41aq3lfvc0000), [visium-spatial-gene-expression-skin-of-body-ovzyhu6j4qgmye8x0000](/datasets/md/00.md#visium-spatial-gene-expression-skin-of-body-ovzyhu6j4qgmye8x0000)
## Spatial transcriptomics to dissect molecular signature of cardiac fibroblasts in experimental autoimmune myocarditis
- Page: /collections/geo-gse248347/
- Kind: time course
- Datasets: 2
- Reference: PMID:41341993
- Design: Spatial transcriptomic data of mouse heart at different stages of experimental autoimmune myocarditis. 6-8-week-old BALB/c mice were immunized with αMyHC peptide together with Complete Freunds’ Adjuvant to induce EAM. Heart tissues were isolated, embedded in OTC, sectioned into 10 µm-thick fragments, and placed on a 10x Genomics Visium Gene Expression Slide. Single-cell spatial libraries were prepared using 10x Genomics Visium protocols, and the sequencing was performed using Illumina Chemistry. Single-cell RNA sequencing data was analyzed using RStudio software.
- Members: [visium-spatial-gene-expression-heart-23yfvmrwrytpy8gq0000](/datasets/md/12.md#visium-spatial-gene-expression-heart-23yfvmrwrytpy8gq0000), [visium-spatial-gene-expression-heart-quqpik9r69lx03ft0000](/datasets/md/be.md#visium-spatial-gene-expression-heart-quqpik9r69lx03ft0000)
## Deconvolution of regulatory T cell heterogeneity identifies cycling precursors as conductors of immune escape during breast carcinoma progression [Visium]
- Page: /collections/geo-gse253585/
- Kind: comparison
- Datasets: 20
- Reference: PMID:41997138
- Design: Dataset 4: Visium of outbred Sprague Dawley rat untreated/NMU-treated mammary glands (MG) and NMU-treated tumors. Frozen sections of MG and rat tissues from rat treated with 50mg/kg NMU (twice, 7 days apart) were cryosectioned serially at 10um thickness. The middle sections with the best morphology was fixed, peremabilized and stained with H&E using standard protocol and processed via the 10X Visium Spatial Gene Expression Reagent Kits (Dual-Index Kit TT, PN-1000184). The sections were mounted onto eight 6.5mm x 6.5mm capture areas surrounding by 8mm x 8mm fiducial frame, enabling at least 2000x2000 pixel portion total and ~5000 gene expression per spot. Image for each sample was captured on a brightfield Zeiss Axio microscope, and these images were used later to map gene expression patterns back onto tissues. Afterward, more permeabilization was performed and capturing was enabled by 30nt poly(dT) probes in the presence of nucleotides, spatial barcodes, and 12nt UMIs (Read 1). Reverse transcription was allowed to occur in situ on the slide followed by template-switching Oligo via the Second Strand Mix and cDNA was amplified together with the spatial barcodes. Visium spatial library construction was initiated following enzymatic fragmentation and end-repair with P5 and P7 sample indices and TruSeq Read 2, enabling Illumina sequencing via HiSeq. Note: Same image set for 4 samples : 1NMFPC, 1RMFPC, 2LMFPC, 1LMFPC Same image set for 4 samples : 7L, 7R, 5L, 6N Same image set for 4 samples : 2NMFPC, 3RMFPC, 4LMFPC, 4NMFPC Same image set for 4 samples : 3LB, 3NC, 4RA, 4RC Same image set for 4 samples : 5RA, 5NC, 6LD, 6RC
- Members: [visium-spatial-gene-expression-mammary-gland-su4lzn2lqhuybtgm0000](/datasets/md/78.md#visium-spatial-gene-expression-mammary-gland-su4lzn2lqhuybtgm0000), [visium-spatial-gene-expression-mammary-gland-5eneisiscx4yxe9g0000](/datasets/md/9a.md#visium-spatial-gene-expression-mammary-gland-5eneisiscx4yxe9g0000), [visium-spatial-gene-expression-mammary-gland-ezrt2hrjasj91m5n0000](/datasets/md/e8.md#visium-spatial-gene-expression-mammary-gland-ezrt2hrjasj91m5n0000), [visium-spatial-gene-expression-mammary-gland-jq6srw6yiz3vawrb0000](/datasets/md/92.md#visium-spatial-gene-expression-mammary-gland-jq6srw6yiz3vawrb0000), [visium-spatial-gene-expression-mammary-gland-xeoqk08rssppj4l70000](/datasets/md/f4.md#visium-spatial-gene-expression-mammary-gland-xeoqk08rssppj4l70000), [visium-spatial-gene-expression-mammary-gland-ih3tm26tjcgdvdqa0000](/datasets/md/7e.md#visium-spatial-gene-expression-mammary-gland-ih3tm26tjcgdvdqa0000), [visium-spatial-gene-expression-mammary-gland-qcclmzefulkqblls0000](/datasets/md/17.md#visium-spatial-gene-expression-mammary-gland-qcclmzefulkqblls0000), [visium-spatial-gene-expression-mammary-gland-hm1fzwstlltgxuiz0000](/datasets/md/17.md#visium-spatial-gene-expression-mammary-gland-hm1fzwstlltgxuiz0000), [visium-spatial-gene-expression-mammary-gland-tz54hgpvky9cmha30000](/datasets/md/b8.md#visium-spatial-gene-expression-mammary-gland-tz54hgpvky9cmha30000), [visium-spatial-gene-expression-mammary-gland-gur4lldnnpfm5c6e0000](/datasets/md/df.md#visium-spatial-gene-expression-mammary-gland-gur4lldnnpfm5c6e0000), [visium-spatial-gene-expression-mammary-gland-7fynhe1u7nqs9vi80000](/datasets/md/ec.md#visium-spatial-gene-expression-mammary-gland-7fynhe1u7nqs9vi80000), [visium-spatial-gene-expression-mammary-gland-vv2p0crv1pkxfxc10000](/datasets/md/1f.md#visium-spatial-gene-expression-mammary-gland-vv2p0crv1pkxfxc10000), [visium-spatial-gene-expression-mammary-gland-ud6pmtpfvd1anjjz0000](/datasets/md/80.md#visium-spatial-gene-expression-mammary-gland-ud6pmtpfvd1anjjz0000), [visium-spatial-gene-expression-mammary-gland-sts7i0syfeisih880000](/datasets/md/51.md#visium-spatial-gene-expression-mammary-gland-sts7i0syfeisih880000), [visium-spatial-gene-expression-mammary-gland-ngcyoponx3ws8uuz0000](/datasets/md/c0.md#visium-spatial-gene-expression-mammary-gland-ngcyoponx3ws8uuz0000), [visium-spatial-gene-expression-mammary-gland-vwph6ukka10v0tse0000](/datasets/md/00.md#visium-spatial-gene-expression-mammary-gland-vwph6ukka10v0tse0000), [visium-spatial-gene-expression-mammary-gland-cpstufxmejp8aoa50000](/datasets/md/52.md#visium-spatial-gene-expression-mammary-gland-cpstufxmejp8aoa50000), [visium-spatial-gene-expression-mammary-gland-fwhzlatitwkkirdq0000](/datasets/md/4a.md#visium-spatial-gene-expression-mammary-gland-fwhzlatitwkkirdq0000), [visium-spatial-gene-expression-mammary-gland-pvimylzvramd1pwr0000](/datasets/md/7e.md#visium-spatial-gene-expression-mammary-gland-pvimylzvramd1pwr0000), [visium-spatial-gene-expression-mammary-gland-mtwgjddgogndtniy0000](/datasets/md/01.md#visium-spatial-gene-expression-mammary-gland-mtwgjddgogndtniy0000)
## Analysis of Spatial Transcriptomics for Unveiling the novel molecular characteristics of Recurrent and Non-Recurrent High-Grade Serous Ovarian Cancer
- Page: /collections/geo-gse263920/
- Kind: comparison
- Datasets: 8
- Reference: PMID:39135097
- Design: We obtained ovarian cancer tissues from eight treatment-naïve patients who underwent cytoreductive surgery. Visium spatial transcriptomics analysis was performed on the eight patients with HGSOC: five in recurrent (R) and three in non-recurrent (NR) groups.
- Members: [visium-spatial-gene-expression-ovary-nl2jjqb1zv1lqlku0000](/datasets/md/55.md#visium-spatial-gene-expression-ovary-nl2jjqb1zv1lqlku0000), [visium-spatial-gene-expression-ovary-brxbci2ahagatlpn0000](/datasets/md/88.md#visium-spatial-gene-expression-ovary-brxbci2ahagatlpn0000), [visium-spatial-gene-expression-ovary-s9ohp58eglwyvnch0000](/datasets/md/0a.md#visium-spatial-gene-expression-ovary-s9ohp58eglwyvnch0000), [visium-spatial-gene-expression-ovary-lqo4xi4sz7cfhnha0000](/datasets/md/7f.md#visium-spatial-gene-expression-ovary-lqo4xi4sz7cfhnha0000), [visium-spatial-gene-expression-ovary-6ader8iy0huhrflb0000](/datasets/md/b9.md#visium-spatial-gene-expression-ovary-6ader8iy0huhrflb0000), [visium-spatial-gene-expression-ovary-irgrxigbe1epixj50000](/datasets/md/0c.md#visium-spatial-gene-expression-ovary-irgrxigbe1epixj50000), [visium-spatial-gene-expression-ovary-t9zq7z4tycztapdu0000](/datasets/md/91.md#visium-spatial-gene-expression-ovary-t9zq7z4tycztapdu0000), [visium-spatial-gene-expression-ovary-9nemekdceaz6b1gm0000](/datasets/md/0f.md#visium-spatial-gene-expression-ovary-9nemekdceaz6b1gm0000)
## Single-nucleus and spatial transcriptomics of human ovary: Molecular insights into signaling pathways underlying primary ovarian insufficiency in classic galactosemia [Spatial transcriptomics]
- Page: /collections/geo-gse268523/
- Kind: comparison
- Datasets: 6
- Reference: PMID:39440457
- Design: CG and control ovarian FFPE sections were processed for Visium spatial transcriptomic protocol (10x Genomics).
- Members: [visium-spatial-gene-expression-ovary-rx1s0dufh65wtel10000](/datasets/md/f6.md#visium-spatial-gene-expression-ovary-rx1s0dufh65wtel10000), [visium-spatial-gene-expression-ovary-eljppdw0my5rnq9c0000](/datasets/md/ec.md#visium-spatial-gene-expression-ovary-eljppdw0my5rnq9c0000), [visium-spatial-gene-expression-ovary-grqew8pegcy6vqw50000](/datasets/md/b2.md#visium-spatial-gene-expression-ovary-grqew8pegcy6vqw50000), [visium-spatial-gene-expression-ovary-vluj9ylrjen2urva0000](/datasets/md/10.md#visium-spatial-gene-expression-ovary-vluj9ylrjen2urva0000), [visium-spatial-gene-expression-ovary-ugtp8rrjgqlbdlsl0000](/datasets/md/68.md#visium-spatial-gene-expression-ovary-ugtp8rrjgqlbdlsl0000), [visium-spatial-gene-expression-ovary-0v6jjeq8xbhhawnd0000](/datasets/md/c4.md#visium-spatial-gene-expression-ovary-0v6jjeq8xbhhawnd0000)
## Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma [Spatial Transcriptomics]
- Page: /collections/geo-gse272236/
- Kind: comparison
- Datasets: 8
- Reference: PMID:41339360
- Design: High-grade gliomas were initiated by stereotactically delivering the glioma oncogenic drivers PDGFB and shp53 into the subventricular zone of transgenic adult Ntv-a mice that were either pericyte-poor (Pdgfbret/ret) or control (Pdgfbret/+). 4 Pdgfbret/+ and 4 Pdgfbret/ret mice were sacrificed when displaying severe symptoms. Spatial transcriptomics sequencing was performed using the 10X Genomics Visium system.
- Members: [visium-spatial-gene-expression-brain-rw04rawdhpcv3llh0000](/datasets/md/a3.md#visium-spatial-gene-expression-brain-rw04rawdhpcv3llh0000), [visium-spatial-gene-expression-brain-g0lznfcqdznezjvc0000](/datasets/md/d6.md#visium-spatial-gene-expression-brain-g0lznfcqdznezjvc0000), [visium-spatial-gene-expression-brain-ucyfkcgffcswbcnp0000](/datasets/md/73.md#visium-spatial-gene-expression-brain-ucyfkcgffcswbcnp0000), [visium-spatial-gene-expression-brain-ptiioiiyhb2drlyp0000](/datasets/md/9d.md#visium-spatial-gene-expression-brain-ptiioiiyhb2drlyp0000), [visium-spatial-gene-expression-brain-2aduuq0vx08jxtko0000](/datasets/md/5c.md#visium-spatial-gene-expression-brain-2aduuq0vx08jxtko0000), [visium-spatial-gene-expression-brain-2ikd1hx60caa3ieo0000](/datasets/md/05.md#visium-spatial-gene-expression-brain-2ikd1hx60caa3ieo0000), [visium-spatial-gene-expression-brain-u2szdynzremfuxhg0000](/datasets/md/7e.md#visium-spatial-gene-expression-brain-u2szdynzremfuxhg0000), [visium-spatial-gene-expression-brain-m4nkjticerbryw1y0000](/datasets/md/cb.md#visium-spatial-gene-expression-brain-m4nkjticerbryw1y0000)
## Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn’s Disease
- Page: /collections/geo-gse277387/
- Kind: comparison
- Datasets: 6
- Reference: PMID:40608410
- Design: Single-cell RNA-seq was performed on idiopathic and Crohn's perianal fistula biopsies (N = 6 and 9, respectively) using the 10X Chromium 5' protocol. Spatial transcriptomics was performed using 10X Visium on idiopathic and Crohn's perianal fistula (N = 3/group).
- Members: [visium-spatial-gene-expression-perianal-skin-cu6uavq2qqdx8cxz0000](/datasets/md/a9.md#visium-spatial-gene-expression-perianal-skin-cu6uavq2qqdx8cxz0000), [visium-spatial-gene-expression-perianal-skin-matnd2vnubwueeur0000](/datasets/md/ba.md#visium-spatial-gene-expression-perianal-skin-matnd2vnubwueeur0000), [visium-spatial-gene-expression-perianal-skin-3y06ryu7gyxvtnk90000](/datasets/md/86.md#visium-spatial-gene-expression-perianal-skin-3y06ryu7gyxvtnk90000), [visium-spatial-gene-expression-perianal-skin-txuz4jrne9eprv1l0000](/datasets/md/1c.md#visium-spatial-gene-expression-perianal-skin-txuz4jrne9eprv1l0000), [visium-spatial-gene-expression-perianal-skin-co6ckp83mt77eofb0000](/datasets/md/0e.md#visium-spatial-gene-expression-perianal-skin-co6ckp83mt77eofb0000), [visium-spatial-gene-expression-perianal-skin-vkwi9lbxpvqtf55k0000](/datasets/md/8b.md#visium-spatial-gene-expression-perianal-skin-vkwi9lbxpvqtf55k0000)
## Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [Spatial transcriptomics]
- Page: /collections/geo-gse279676/
- Kind: other
- Datasets: 4
- Reference: PMID:39610085
- Design: Spatial transcriptomics of the adult mouse cortex after CRISPR mediated deletion of Sox9, Trps1 (by injection of g-Control, g-Sox9, g-Trps1 or g-Sox9+Trps1 Mok-LVs) at 7 days post injection (7dpi)
- Members: [visium-spatial-gene-expression-cerebral-cortex-7iu72tr3ufo3jdq90001](/datasets/md/ae.md#visium-spatial-gene-expression-cerebral-cortex-7iu72tr3ufo3jdq90001), [visium-spatial-gene-expression-cerebral-cortex-7lx8qxhbt9eacwei0000](/datasets/md/fa.md#visium-spatial-gene-expression-cerebral-cortex-7lx8qxhbt9eacwei0000), [visium-spatial-gene-expression-cerebral-cortex-gg0jokggxwhu4vu20000](/datasets/md/63.md#visium-spatial-gene-expression-cerebral-cortex-gg0jokggxwhu4vu20000), [visium-spatial-gene-expression-cerebral-cortex-wbzw554aehbzdykp0000](/datasets/md/4b.md#visium-spatial-gene-expression-cerebral-cortex-wbzw554aehbzdykp0000)
## Spatial component of: CELSR3 deficiency leads to tic-related behaviors and dopaminergic alterations in the striatum
- Page: /collections/geo-gse280709/
- Kind: comparison
- Datasets: 4
- Reference: PMID:40155412
- Design: Coronal sections from 4 distinct mice ( 2 from each group: Celsr3 WT and HZ) from FFPE preserved samples were analyzed by Visium Cytassist
- Members: [visium-spatial-gene-expression-brain-8nbnxboz2hfmmkzj0000](/datasets/md/6a.md#visium-spatial-gene-expression-brain-8nbnxboz2hfmmkzj0000), [visium-spatial-gene-expression-brain-pu9vqi2naq8grdg80000](/datasets/md/39.md#visium-spatial-gene-expression-brain-pu9vqi2naq8grdg80000), [visium-spatial-gene-expression-brain-l3qzvlglklntfu7j0000](/datasets/md/08.md#visium-spatial-gene-expression-brain-l3qzvlglklntfu7j0000), [visium-spatial-gene-expression-brain-ckuvsuoehq9oajqa0000](/datasets/md/3a.md#visium-spatial-gene-expression-brain-ckuvsuoehq9oajqa0000)
## Cellular cartography reveals mouse prostate organization and determinants of castration resistance [Spatial Transcriptomics]
- Page: /collections/geo-gse284571/
- Kind: comparison
- Datasets: 8
- Reference: PMID:39763898
- Design: Four serial sections of prostates from sham operated or castrated mice were sequenced by 10x Visium to test for differential spatial gene expression after castration.
- Members: [visium-spatial-gene-expression-prostate-gland-ehi3evp4odv5ywgh0000](/datasets/md/cd.md#visium-spatial-gene-expression-prostate-gland-ehi3evp4odv5ywgh0000), [visium-spatial-gene-expression-prostate-gland-ervhfzjycakcg4na0000](/datasets/md/5b.md#visium-spatial-gene-expression-prostate-gland-ervhfzjycakcg4na0000), [visium-spatial-gene-expression-prostate-gland-wkw77j8xqctkzetq0000](/datasets/md/ff.md#visium-spatial-gene-expression-prostate-gland-wkw77j8xqctkzetq0000), [visium-spatial-gene-expression-prostate-gland-yiywx0wuqkfw9ymp0000](/datasets/md/f3.md#visium-spatial-gene-expression-prostate-gland-yiywx0wuqkfw9ymp0000), [visium-spatial-gene-expression-prostate-gland-bqwcvewhoo0hevtn0000](/datasets/md/d6.md#visium-spatial-gene-expression-prostate-gland-bqwcvewhoo0hevtn0000), [visium-spatial-gene-expression-prostate-gland-wn9rhjwzymlkcfyj0000](/datasets/md/2b.md#visium-spatial-gene-expression-prostate-gland-wn9rhjwzymlkcfyj0000), [visium-spatial-gene-expression-prostate-gland-iytp4nr9xpudtfud0000](/datasets/md/56.md#visium-spatial-gene-expression-prostate-gland-iytp4nr9xpudtfud0000), [visium-spatial-gene-expression-prostate-gland-qza4jigbinueewgn0000](/datasets/md/50.md#visium-spatial-gene-expression-prostate-gland-qza4jigbinueewgn0000)
## Eosinophils drive intestinal remodelling and innate defence in reproduction.
- Page: /collections/geo-gse296053/
- Kind: comparison
- Datasets: 8
- Reference: 10.1038/s41586-026-10531-6
- Design: Xenium spatial transcriptomics of mouse small intestine for nulliparous and lactating mice. The first 10 cm of small intestine were collected, fresh-frozen with isopentane, and embedded in OCT. Tissues cryosectioned at 10 μm were analyzed using the Xenium Prime 5k Mouse Panel. Samples were taken from two nulliparous and two lactating mice, with one nulliparous and one lactating sample placed on the same Xenium slide.
- Members: [10x-xenium-small-intestine-nyo8qnduqklzcyer0000](/datasets/md/0a.md#10x-xenium-small-intestine-nyo8qnduqklzcyer0000), [10x-xenium-small-intestine-pvueryq49fgkcf0v0000](/datasets/md/b7.md#10x-xenium-small-intestine-pvueryq49fgkcf0v0000), [10x-xenium-small-intestine-lkf3kilfjuhafjjm0000](/datasets/md/2e.md#10x-xenium-small-intestine-lkf3kilfjuhafjjm0000), [10x-xenium-small-intestine-8pqrcuvlftyobkpy0000](/datasets/md/df.md#10x-xenium-small-intestine-8pqrcuvlftyobkpy0000), [10x-xenium-small-intestine-eq3nmroz2dapatoz0000](/datasets/md/8a.md#10x-xenium-small-intestine-eq3nmroz2dapatoz0000), [10x-xenium-small-intestine-jxzuq4jwrvvpbq950000](/datasets/md/8a.md#10x-xenium-small-intestine-jxzuq4jwrvvpbq950000), [10x-xenium-small-intestine-gzdu0ipyqtsrh7g90000](/datasets/md/e0.md#10x-xenium-small-intestine-gzdu0ipyqtsrh7g90000), [10x-xenium-small-intestine-gu1uzxjqjqvdq5rx0000](/datasets/md/a0.md#10x-xenium-small-intestine-gu1uzxjqjqvdq5rx0000)
## Polyamines regulate adaptive antitumor immunity by functional specialization of regulatory T cells [Visium]
- Page: /collections/geo-gse296660/
- Kind: comparison
- Datasets: 2
- Reference: PMID:40749666
- Design: 2x105 B16.F10 cells were inoculated in wild-type mice (WT; Csnk2bfl/fl) and Foxp3-Cre × CK2b-fl/fl (KO; Csnk2bTreg-/-) mice (8–16 weeks old). B16.F10 tumors of comparable size were isolated on day 15 after inoculation B16.F10 tumors of comparable size were isolated on day 15 after inoculation, fixed in formalin and embedded in paraffin. Tissue sections were analyzed using spatial transcriptomics.
- Members: [visium-spatial-gene-expression-skin-of-body-uzzc5ai0chp2nag60000](/datasets/md/88.md#visium-spatial-gene-expression-skin-of-body-uzzc5ai0chp2nag60000), [visium-spatial-gene-expression-skin-of-body-cvpyvrp2s1jq9vsz0000](/datasets/md/6e.md#visium-spatial-gene-expression-skin-of-body-cvpyvrp2s1jq9vsz0000)
## Targeting circulating mechanoresponsive monocytes and macrophages to reduce fibrosis
- Page: /collections/geo-gse297064/
- Kind: other
- Datasets: 2
- Reference: PMID:41120571
- Design: scRNA-seq was performed on murine cells collected from skin, scar, or wounds. Cells labeled as GFP+ were isolated and sequenced to analyze cells in the circulation that hone to the wound upon treatment.
- Members: [visium-spatial-gene-expression-skin-of-body-wldmwskeciucijnd0001](/datasets/md/2c.md#visium-spatial-gene-expression-skin-of-body-wldmwskeciucijnd0001), [visium-spatial-gene-expression-skin-of-body-dhm8o9zthvnutdth0000](/datasets/md/8b.md#visium-spatial-gene-expression-skin-of-body-dhm8o9zthvnutdth0000)
## Spatial transcriptomics reveals injury-responsive compartments and coordinated immune–fibrotic signaling in ANCA-associated renal vasculitis
- Page: /collections/geo-gse302677/
- Kind: comparison
- Datasets: 3
- Reference: PMID:42602048
- Design: For spatial transcriptomics, cryopreserved kidney tissue sections from patients with ANCA-associated vasculities (biopsies) and control patients with hematuria (biopsies containing non-diseased regions) were mounted on Visium (10X Genomics) slides and processed according to the manufacturer's instructions. *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. ***************************************************************
- Members: [visium-spatial-gene-expression-cortex-of-kidney-qdcpkrvyqxawitwu0001](/datasets/md/ba.md#visium-spatial-gene-expression-cortex-of-kidney-qdcpkrvyqxawitwu0001), [visium-spatial-gene-expression-cortex-of-kidney-qfhsjeeoyype6yup0000](/datasets/md/62.md#visium-spatial-gene-expression-cortex-of-kidney-qfhsjeeoyype6yup0000), [visium-spatial-gene-expression-cortex-of-kidney-njwcy2qj4cka18zz0000](/datasets/md/d1.md#visium-spatial-gene-expression-cortex-of-kidney-njwcy2qj4cka18zz0000)
## Spatial transcriptional features of MYCN niche in liver tumorigenesis.
- Page: /collections/geo-gse302815/
- Kind: time course
- Datasets: 4
- Reference: PMID:41706888
- Design: Spatial transcriptomics using the 10× Genomics Visium platform in a metabolic HCC mouse model STAM (STAM16w, STAM20w), which mimics MASH and type I diabetes, and in a fibrotic HCC mouse model DEN+CCL4 (DEN22w, DEN30w), which mimics DNA damage–driven and fibrosis-promoting tumor evolution.
- Members: [visium-spatial-gene-expression-liver-9bkg1vdzi2ptpark0000](/datasets/md/38.md#visium-spatial-gene-expression-liver-9bkg1vdzi2ptpark0000), [visium-spatial-gene-expression-liver-xmemg7qv7hqgdisn0000](/datasets/md/f4.md#visium-spatial-gene-expression-liver-xmemg7qv7hqgdisn0000), [visium-spatial-gene-expression-liver-lz8nnqzdrklpbpo90000](/datasets/md/c5.md#visium-spatial-gene-expression-liver-lz8nnqzdrklpbpo90000), [visium-spatial-gene-expression-liver-mylps7q00i7ute9e0000](/datasets/md/a5.md#visium-spatial-gene-expression-liver-mylps7q00i7ute9e0000)
## A novel CAF population coordinates hyper-suppressive regulatory T cell recruitment and localization in lung cancer [Spatial Transcriptomics]
- Page: /collections/geo-gse303162/
- Kind: other
- Datasets: 2
- Reference: PMID:42581185
- Design: C57B6/JN mice (n=3) were intravenously injected with 1.5e5 LLC-GFP cells. After 17 days, lungs of mice were harvested and flash frozen in OCT. Lungs were then sectioned at 8um thickness onto the 10X visium slide
- Members: [visium-spatial-gene-expression-lung-k5l1phwvjxnkbfun0000](/datasets/md/3e.md#visium-spatial-gene-expression-lung-k5l1phwvjxnkbfun0000), [visium-spatial-gene-expression-lung-ovukdubowqfmlf980000](/datasets/md/ef.md#visium-spatial-gene-expression-lung-ovukdubowqfmlf980000)
## Integrated Spatial Transcriptomics and Single-Cell RNA Sequencing Reveal Lars2-Mediated Spatiotemporal Dynamics of Myocardial Remodeling in a Mouse Model of Transverse Aortic Constriction (TAC)
- Page: /collections/geo-gse308859/
- Kind: comparison
- Datasets: 3
- Reference: PMID:41859105
- Design: Eight-week-old male C57BL/6J mice (25–27 g) were randomly assigned to sham or transverse aortic constriction (TAC) groups. Hearts were harvested at 2, 4, and 6 weeks after surgery. Cardiac tissues were processed for both spatial transcriptomics (10x Genomics Visium) and single-cell RNA sequencing (10x Genomics Chromium 3’ v3.1). Sequencing was performed on the Illumina NovaSeq 6000 platform. This design enabled the integration of temporal, spatial, and single-cell transcriptomic data to characterize myocardial remodeling under pressure overload.
- Members: [visium-spatial-gene-expression-heart-s1uqrhpkkpzkrabm0000](/datasets/md/e3.md#visium-spatial-gene-expression-heart-s1uqrhpkkpzkrabm0000), [visium-spatial-gene-expression-heart-gdinatk9sdmws53t0000](/datasets/md/4d.md#visium-spatial-gene-expression-heart-gdinatk9sdmws53t0000), [visium-spatial-gene-expression-heart-akzfaqm58sakrdgv0000](/datasets/md/4a.md#visium-spatial-gene-expression-heart-akzfaqm58sakrdgv0000)
## Mapping the Secondary Response to Traumatic Brain Injury Using Spatial Transcriptomics Shows Acute 4-aminopyridine Treatment Mitigates Axonal and Molecular Pathology
- Page: /collections/geo-gse319409/
- Kind: comparison
- Datasets: 24
- Reference: PMID:41508250
- Design: At 8 weeks of age, 24 male C57BL/6J mice received TBI (non-penetrating closed-skull impact, centered at bregma) or sham procedures, followed by 4-AP (0.5 mg/kg) or saline vehicle injections (i.p., b.i.d.) until analyses at 7 days post-injury. To identify comprehensive molecular changes resulting from acute 4-AP treatment in relation to TBI-induced pathology, genome-wide spatial transcriptomic (Visium CytAssist) and complementary adjacent immunohistochemical analyses of 7 µm thick FFPE coronal brain tissue sections were conducted under the impact site in cortical gray and corpus callosum white matter regions of interest.
- Members: [visium-spatial-gene-expression-brain-gphvvxv7cgbkscep0000](/datasets/md/5b.md#visium-spatial-gene-expression-brain-gphvvxv7cgbkscep0000), [visium-spatial-gene-expression-brain-v45w3tay9vlq3bkr0000](/datasets/md/50.md#visium-spatial-gene-expression-brain-v45w3tay9vlq3bkr0000), [visium-spatial-gene-expression-brain-tab3yih8fdmekjuo0000](/datasets/md/2e.md#visium-spatial-gene-expression-brain-tab3yih8fdmekjuo0000), [visium-spatial-gene-expression-brain-vlhla6brzjfeemmt0000](/datasets/md/8b.md#visium-spatial-gene-expression-brain-vlhla6brzjfeemmt0000), [visium-spatial-gene-expression-brain-utn4gs2en65k8xym0000](/datasets/md/9b.md#visium-spatial-gene-expression-brain-utn4gs2en65k8xym0000), [visium-spatial-gene-expression-brain-qr3f7c3jrrcjkqm90000](/datasets/md/1e.md#visium-spatial-gene-expression-brain-qr3f7c3jrrcjkqm90000), [visium-spatial-gene-expression-brain-hkd9oa67tosjjnyn0000](/datasets/md/35.md#visium-spatial-gene-expression-brain-hkd9oa67tosjjnyn0000), [visium-spatial-gene-expression-brain-azt24u0jswbknmzt0000](/datasets/md/57.md#visium-spatial-gene-expression-brain-azt24u0jswbknmzt0000), [visium-spatial-gene-expression-brain-ss7bkqbvat24zom80000](/datasets/md/d0.md#visium-spatial-gene-expression-brain-ss7bkqbvat24zom80000), [visium-spatial-gene-expression-brain-kg89opbf9anntnxa0000](/datasets/md/8d.md#visium-spatial-gene-expression-brain-kg89opbf9anntnxa0000), [visium-spatial-gene-expression-brain-murufcvxjcbstzl20000](/datasets/md/0f.md#visium-spatial-gene-expression-brain-murufcvxjcbstzl20000), [visium-spatial-gene-expression-brain-lizwvvx4ckeuokij0000](/datasets/md/17.md#visium-spatial-gene-expression-brain-lizwvvx4ckeuokij0000), [visium-spatial-gene-expression-brain-m30dal7e5pjs55hk0000](/datasets/md/8f.md#visium-spatial-gene-expression-brain-m30dal7e5pjs55hk0000), [visium-spatial-gene-expression-brain-elzlm4pwffrduifv0000](/datasets/md/75.md#visium-spatial-gene-expression-brain-elzlm4pwffrduifv0000), [visium-spatial-gene-expression-brain-ewog72rgk8uoeycr0000](/datasets/md/dc.md#visium-spatial-gene-expression-brain-ewog72rgk8uoeycr0000), [visium-spatial-gene-expression-brain-rcskvdtyakcwjaek0000](/datasets/md/78.md#visium-spatial-gene-expression-brain-rcskvdtyakcwjaek0000), [visium-spatial-gene-expression-brain-rc7d5fkwklogqbfm0000](/datasets/md/9f.md#visium-spatial-gene-expression-brain-rc7d5fkwklogqbfm0000), [visium-spatial-gene-expression-brain-rxmebkomieflmrk70000](/datasets/md/4d.md#visium-spatial-gene-expression-brain-rxmebkomieflmrk70000), [visium-spatial-gene-expression-brain-hfusfm1zmkr2cges0000](/datasets/md/43.md#visium-spatial-gene-expression-brain-hfusfm1zmkr2cges0000), [visium-spatial-gene-expression-brain-twudvmn3kiy0vmmn0000](/datasets/md/1e.md#visium-spatial-gene-expression-brain-twudvmn3kiy0vmmn0000), [visium-spatial-gene-expression-brain-lrxg4vsj4d3qx6sa0000](/datasets/md/68.md#visium-spatial-gene-expression-brain-lrxg4vsj4d3qx6sa0000), [visium-spatial-gene-expression-brain-g8d8r70ein8fu73g0000](/datasets/md/d8.md#visium-spatial-gene-expression-brain-g8d8r70ein8fu73g0000), [visium-spatial-gene-expression-brain-w66xhcttlyb8nou90000](/datasets/md/f0.md#visium-spatial-gene-expression-brain-w66xhcttlyb8nou90000), [visium-spatial-gene-expression-brain-gnhwquoe2fhekwbx0000](/datasets/md/98.md#visium-spatial-gene-expression-brain-gnhwquoe2fhekwbx0000)
## Spatial transcriptomic profiling of TOP2B-driven anthracycline-induced cardiotoxicity in mouse hearts
- Page: /collections/geo-gse319842/
- Kind: comparison
- Datasets: 2
- Reference: PMID:42102394
- Design: Mouse hearts were collected from control α-MHC-MerCreMer mice, cardiomyocyte-specific TOP2B transgenic mice induced by tamoxifen mice. Formalin-fixed paraffin-embedded (FFPE) heart sections were processed using the 10x Genomics Visium CytAssist Spatial Gene Expression platform. H&E-stained sections were imaged prior to probe hybridization and library construction. Spatial transcriptomic libraries were sequenced on Illumina NovaSeq. Differential spatial gene expression analyses were performed to identify cardiac remodeling, metabolic, and heart failure–associated signatures linked to TOP2B overexpression and anthracycline exposure.
- Members: [visium-spatial-gene-expression-heart-fdlkflr3oxjccdhw0000](/datasets/md/95.md#visium-spatial-gene-expression-heart-fdlkflr3oxjccdhw0000), [visium-spatial-gene-expression-heart-u4z6zqy5vkttyegx0000](/datasets/md/51.md#visium-spatial-gene-expression-heart-u4z6zqy5vkttyegx0000)
## Accelerated cerebromicrovascular senescence contributes to cognitive decline in a mouse model of paclitaxel (Taxol)-induced chemobrain [Spatial Transcriptomics]
- Page: /collections/geo-gse325554/
- Kind: comparison
- Datasets: 7
- Reference: PMID:37243381
- Design: The authors performed spatial transcriptomics to assess the anatomical distribution of senescent cells in the brains of paclitaxel (PTX)-treated p16-3MR mice. Mice were treated with PTX or vehicle and, following a 6-month post-treatment period with or without senolytic interventions (GCV or ABT263), brains were collected and sectioned for spatially resolved transcriptomic analysis. Tissue sections were processed to capture whole-transcriptome mRNA expression while preserving histological context, enabling the mapping of senescence-associated gene expression (e.g., Cdkn2a) to specific brain regions. This approach allowed comparison of the spatial distribution and abundance of senescent cells across experimental groups, including cortex, white matter, and hippocampus.
- Members: [visium-spatial-gene-expression-brain-hyjdbnhunzuw24cp0000](/datasets/md/fa.md#visium-spatial-gene-expression-brain-hyjdbnhunzuw24cp0000), [visium-spatial-gene-expression-brain-aulritribe8fotne0000](/datasets/md/48.md#visium-spatial-gene-expression-brain-aulritribe8fotne0000), [visium-spatial-gene-expression-brain-idsh2ljpuqbmmotr0000](/datasets/md/82.md#visium-spatial-gene-expression-brain-idsh2ljpuqbmmotr0000), [visium-spatial-gene-expression-brain-oz8zniniuspp7uns0000](/datasets/md/56.md#visium-spatial-gene-expression-brain-oz8zniniuspp7uns0000), [visium-spatial-gene-expression-brain-eivafo4ibtjphsbb0000](/datasets/md/85.md#visium-spatial-gene-expression-brain-eivafo4ibtjphsbb0000), [visium-spatial-gene-expression-brain-lvullj7d0fnhopdz0000](/datasets/md/b2.md#visium-spatial-gene-expression-brain-lvullj7d0fnhopdz0000), [visium-spatial-gene-expression-brain-dsxsp5788ujnynry0000](/datasets/md/e1.md#visium-spatial-gene-expression-brain-dsxsp5788ujnynry0000)
## Glioma-intrinsic MAPK/ERK signaling promotes immunotherapy efficacy through T cell infiltration and interferon responses
- Page: /collections/geo-gse331374/
- Kind: comparison
- Datasets: 4
- Reference: PMID:42350396
- Design: This repository contains spatial transcriptomics (Visium) with paired single-nucleus RNA-seq data generated in this study from a BRAF V600E-mutant glioblastoma, including primary, recurrent, temozolomide-treated, and targeted therapy-treated samples. *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. ***************************************************************
- Members: [visium-spatial-gene-expression-brain-q76kzyulcj62of1w0000](/datasets/md/e1.md#visium-spatial-gene-expression-brain-q76kzyulcj62of1w0000), [visium-spatial-gene-expression-brain-rgievlopkhxon1ow0000](/datasets/md/16.md#visium-spatial-gene-expression-brain-rgievlopkhxon1ow0000), [visium-spatial-gene-expression-brain-nunabrfjsclnymhe0000](/datasets/md/63.md#visium-spatial-gene-expression-brain-nunabrfjsclnymhe0000), [visium-spatial-gene-expression-brain-abpm1ao5d9ifwp1v0000](/datasets/md/29.md#visium-spatial-gene-expression-brain-abpm1ao5d9ifwp1v0000)
## Epicardial fat drives macrophage response in atrial cardiomyopathy
- Page: /collections/geo-gse331446/
- Kind: other
- Datasets: 4
- Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE331446
- Design: FFPE human right atrial sections representing different degrees of fibro-fatty remodeling were processed using 10x Genomics Visium Spatial Gene Expression technology.
- Members: [visium-spatial-gene-expression-right-atrium-auricular-region-bybi8litrdfvzmjw0000](/datasets/md/1a.md#visium-spatial-gene-expression-right-atrium-auricular-region-bybi8litrdfvzmjw0000), [visium-spatial-gene-expression-right-atrium-auricular-region-09ikm0ytcchlhhwa0000](/datasets/md/5d.md#visium-spatial-gene-expression-right-atrium-auricular-region-09ikm0ytcchlhhwa0000), [visium-spatial-gene-expression-right-atrium-auricular-region-gusm31tkt6rwksmt0000](/datasets/md/99.md#visium-spatial-gene-expression-right-atrium-auricular-region-gusm31tkt6rwksmt0000), [visium-spatial-gene-expression-right-atrium-auricular-region-qchkejobhfoamzwm0000](/datasets/md/5e.md#visium-spatial-gene-expression-right-atrium-auricular-region-qchkejobhfoamzwm0000)
## Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.
- Page: /collections/geo-gsm9238734/
- Kind: publication
- Datasets: 7
- Reference: 10.1038/s41467-025-64990-y
- Members: [vizgen-merscope-unknown-x8epzesw37wvxd620000](/datasets/md/9c.md#vizgen-merscope-unknown-x8epzesw37wvxd620000), [vizgen-merscope-unknown-ngo9baymrztxtduk0000](/datasets/md/f2.md#vizgen-merscope-unknown-ngo9baymrztxtduk0000), [vizgen-merscope-unknown-tlhvb4tugplqksqt0000](/datasets/md/75.md#vizgen-merscope-unknown-tlhvb4tugplqksqt0000), [vizgen-merscope-unknown-lffdrpoudgqo2mpm0000](/datasets/md/47.md#vizgen-merscope-unknown-lffdrpoudgqo2mpm0000), [vizgen-merscope-unknown-qkudzolq8uzxm4wb0000](/datasets/md/0f.md#vizgen-merscope-unknown-qkudzolq8uzxm4wb0000), [vizgen-merscope-unknown-mujyi91cdu1j1zxp0000](/datasets/md/23.md#vizgen-merscope-unknown-mujyi91cdu1j1zxp0000), [vizgen-merscope-unknown-hrgb1d8j0agj6tq70000](/datasets/md/08.md#vizgen-merscope-unknown-hrgb1d8j0agj6tq70000)
## zenodo-17617626
- Page: /collections/zenodo-17617626/
- Kind: publication
- Datasets: 1
- Reference: 10.5281/zenodo.17617626
- Members: [stereo-seq-skin-of-body-l7mjzf7mvnnchrlx0000](/datasets/md/19.md#stereo-seq-skin-of-body-l7mjzf7mvnnchrlx0000)