# SpatialData-DB collections, shard 6 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. ## Zika virus co-opts microRNA networks to persist in placental niches detected by spatial transcriptomics. - Page: /collections/doi-10-1016-j-ajog-2023-08-012/ - Kind: comparison - Datasets: 8 - Reference: 10.1016/j.ajog.2023.08.012 - Members: [visium-spatial-gene-expression-uterus-g2fpaigejaupydig0001](/datasets/md/40.md#visium-spatial-gene-expression-uterus-g2fpaigejaupydig0001), [visium-spatial-gene-expression-uterus-jiqwxz0a2zv9ahey0000](/datasets/md/31.md#visium-spatial-gene-expression-uterus-jiqwxz0a2zv9ahey0000), [visium-spatial-gene-expression-uterus-p9f7tgtig4h4jgka0000](/datasets/md/c1.md#visium-spatial-gene-expression-uterus-p9f7tgtig4h4jgka0000), [visium-spatial-gene-expression-uterus-pn7c0op7peb1zf160000](/datasets/md/86.md#visium-spatial-gene-expression-uterus-pn7c0op7peb1zf160000), [visium-spatial-gene-expression-uterus-6bltulwavasecj7r0000](/datasets/md/f0.md#visium-spatial-gene-expression-uterus-6bltulwavasecj7r0000), [visium-spatial-gene-expression-placenta-jzsydnilya5qptrd0000](/datasets/md/54.md#visium-spatial-gene-expression-placenta-jzsydnilya5qptrd0000), [visium-spatial-gene-expression-uterus-ymbrkzfhndayz2ix0000](/datasets/md/ed.md#visium-spatial-gene-expression-uterus-ymbrkzfhndayz2ix0000), [visium-spatial-gene-expression-uterus-xevbudemwvus6ucy0000](/datasets/md/91.md#visium-spatial-gene-expression-uterus-xevbudemwvus6ucy0000) ## SARS-CoV-2 niches in human placenta revealed by spatial transcriptomics. - Page: /collections/doi-10-1016-j-medj-2023-06-003/ - Kind: comparison - Datasets: 15 - Reference: 10.1016/j.medj.2023.06.003 - Members: [visium-spatial-gene-expression-placenta-w3rgxmap6qjjqoyv0000](/datasets/md/79.md#visium-spatial-gene-expression-placenta-w3rgxmap6qjjqoyv0000), [visium-spatial-gene-expression-placenta-fhern6yv1ymjqpzv0000](/datasets/md/f4.md#visium-spatial-gene-expression-placenta-fhern6yv1ymjqpzv0000), [visium-spatial-gene-expression-placenta-t7vmo6d3pbaiqo8w0000](/datasets/md/5c.md#visium-spatial-gene-expression-placenta-t7vmo6d3pbaiqo8w0000), [visium-spatial-gene-expression-placenta-mqcroun3psmyy0ra0000](/datasets/md/96.md#visium-spatial-gene-expression-placenta-mqcroun3psmyy0ra0000), [visium-spatial-gene-expression-placenta-iwbxz1k7wuolbk7d0000](/datasets/md/64.md#visium-spatial-gene-expression-placenta-iwbxz1k7wuolbk7d0000), [visium-spatial-gene-expression-placenta-nkldow3diiwduzp20000](/datasets/md/13.md#visium-spatial-gene-expression-placenta-nkldow3diiwduzp20000), [visium-spatial-gene-expression-placenta-6cu9tmjkwxbqkut30000](/datasets/md/e1.md#visium-spatial-gene-expression-placenta-6cu9tmjkwxbqkut30000), [visium-spatial-gene-expression-placenta-mtxzssff95wp3tfy0000](/datasets/md/d8.md#visium-spatial-gene-expression-placenta-mtxzssff95wp3tfy0000), [visium-spatial-gene-expression-placenta-y2wb0o2mdw4ipawo0000](/datasets/md/ff.md#visium-spatial-gene-expression-placenta-y2wb0o2mdw4ipawo0000), [visium-spatial-gene-expression-placenta-ivdwpyiexwxb5usw0000](/datasets/md/64.md#visium-spatial-gene-expression-placenta-ivdwpyiexwxb5usw0000), [visium-spatial-gene-expression-placenta-6ty1ubkxnyfocq4e0000](/datasets/md/47.md#visium-spatial-gene-expression-placenta-6ty1ubkxnyfocq4e0000), [visium-spatial-gene-expression-placenta-2lcm5qzqln50bppl0000](/datasets/md/68.md#visium-spatial-gene-expression-placenta-2lcm5qzqln50bppl0000), [visium-spatial-gene-expression-placenta-rzs9yt5r5odhin240000](/datasets/md/ff.md#visium-spatial-gene-expression-placenta-rzs9yt5r5odhin240000), [visium-spatial-gene-expression-placenta-l4c1zvsbbjjkskba0000](/datasets/md/71.md#visium-spatial-gene-expression-placenta-l4c1zvsbbjjkskba0000), [visium-spatial-gene-expression-placenta-dztxaoy7ezszgnts0000](/datasets/md/4a.md#visium-spatial-gene-expression-placenta-dztxaoy7ezszgnts0000) ## Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions. - Page: /collections/doi-10-1038-s41467-021-26271-2/ - Kind: replicates - Datasets: 36 - Reference: 10.1038/s41467-021-26271-2 - Members: [spatial-transcriptomics-breast-gzyl5xoplo28vmd00000](/datasets/md/21.md#spatial-transcriptomics-breast-gzyl5xoplo28vmd00000), [spatial-transcriptomics-breast-drpc4n34kf3aapeo0000](/datasets/md/5a.md#spatial-transcriptomics-breast-drpc4n34kf3aapeo0000), [spatial-transcriptomics-breast-njehbpdvmas2754g0000](/datasets/md/a0.md#spatial-transcriptomics-breast-njehbpdvmas2754g0000), [spatial-transcriptomics-breast-qsftmxhhzlukps7o0000](/datasets/md/a3.md#spatial-transcriptomics-breast-qsftmxhhzlukps7o0000), [spatial-transcriptomics-breast-6r0awvlngq8duch90000](/datasets/md/9c.md#spatial-transcriptomics-breast-6r0awvlngq8duch90000), [spatial-transcriptomics-breast-vdbgczlnvpmp0bsl0000](/datasets/md/6f.md#spatial-transcriptomics-breast-vdbgczlnvpmp0bsl0000), [spatial-transcriptomics-breast-hj8sinxmcwkxfekp0001](/datasets/md/2d.md#spatial-transcriptomics-breast-hj8sinxmcwkxfekp0001), [spatial-transcriptomics-breast-pusurqj3a6vds4zc0000](/datasets/md/0e.md#spatial-transcriptomics-breast-pusurqj3a6vds4zc0000), [spatial-transcriptomics-breast-oemexqu4fzqqc4xf0000](/datasets/md/3c.md#spatial-transcriptomics-breast-oemexqu4fzqqc4xf0000), [spatial-transcriptomics-breast-6wvrukspdt8t4gpg0000](/datasets/md/ea.md#spatial-transcriptomics-breast-6wvrukspdt8t4gpg0000), [spatial-transcriptomics-breast-nd1ikqbcpnbcqqms0000](/datasets/md/59.md#spatial-transcriptomics-breast-nd1ikqbcpnbcqqms0000), [spatial-transcriptomics-breast-mdhsoizz1eqsrugi0000](/datasets/md/c0.md#spatial-transcriptomics-breast-mdhsoizz1eqsrugi0000), [spatial-transcriptomics-breast-cawydzvzom8pe0hv0001](/datasets/md/de.md#spatial-transcriptomics-breast-cawydzvzom8pe0hv0001), [spatial-transcriptomics-breast-738nw0kgsdcjvmvw0000](/datasets/md/90.md#spatial-transcriptomics-breast-738nw0kgsdcjvmvw0000), [spatial-transcriptomics-breast-ll8tdz0levhasasq0000](/datasets/md/67.md#spatial-transcriptomics-breast-ll8tdz0levhasasq0000), [spatial-transcriptomics-breast-3e0wrfsge3mli3yp0000](/datasets/md/6b.md#spatial-transcriptomics-breast-3e0wrfsge3mli3yp0000), [spatial-transcriptomics-breast-mtnbvyb6pjrt44oq0000](/datasets/md/81.md#spatial-transcriptomics-breast-mtnbvyb6pjrt44oq0000), [spatial-transcriptomics-breast-dj0vcfzv4bziygii0001](/datasets/md/e7.md#spatial-transcriptomics-breast-dj0vcfzv4bziygii0001), [spatial-transcriptomics-breast-wbygycxu7iex09on0001](/datasets/md/45.md#spatial-transcriptomics-breast-wbygycxu7iex09on0001), [spatial-transcriptomics-breast-pnfofvpxffu6sktb0000](/datasets/md/1c.md#spatial-transcriptomics-breast-pnfofvpxffu6sktb0000), [spatial-transcriptomics-breast-lw1dzss5b0zmjwva0000](/datasets/md/ac.md#spatial-transcriptomics-breast-lw1dzss5b0zmjwva0000), [spatial-transcriptomics-breast-1scsz7w8zenq2cve0000](/datasets/md/17.md#spatial-transcriptomics-breast-1scsz7w8zenq2cve0000), [spatial-transcriptomics-breast-evlh7o5m2vfiwsls0000](/datasets/md/6d.md#spatial-transcriptomics-breast-evlh7o5m2vfiwsls0000), [spatial-transcriptomics-breast-jqaafysbq5rempp20000](/datasets/md/6c.md#spatial-transcriptomics-breast-jqaafysbq5rempp20000), [spatial-transcriptomics-breast-e6umtmbkdbrdby2c0000](/datasets/md/fc.md#spatial-transcriptomics-breast-e6umtmbkdbrdby2c0000), [spatial-transcriptomics-breast-zo2ftmroal96vc3j0000](/datasets/md/d8.md#spatial-transcriptomics-breast-zo2ftmroal96vc3j0000), [spatial-transcriptomics-breast-xec6f039va0tasql0000](/datasets/md/ef.md#spatial-transcriptomics-breast-xec6f039va0tasql0000), [spatial-transcriptomics-breast-eywnq1j738xsrvw60000](/datasets/md/48.md#spatial-transcriptomics-breast-eywnq1j738xsrvw60000), [spatial-transcriptomics-breast-rosdvqvrdawwpahm0000](/datasets/md/f9.md#spatial-transcriptomics-breast-rosdvqvrdawwpahm0000), [spatial-transcriptomics-breast-apevcdfqrcjxemay0000](/datasets/md/81.md#spatial-transcriptomics-breast-apevcdfqrcjxemay0000), [spatial-transcriptomics-breast-nucbgly6e4dao6700000](/datasets/md/2d.md#spatial-transcriptomics-breast-nucbgly6e4dao6700000), [spatial-transcriptomics-breast-au2f8vagm9yu14pq0000](/datasets/md/db.md#spatial-transcriptomics-breast-au2f8vagm9yu14pq0000), [spatial-transcriptomics-breast-zs3pl1mfaap5xuup0000](/datasets/md/1a.md#spatial-transcriptomics-breast-zs3pl1mfaap5xuup0000), [spatial-transcriptomics-breast-7wtbyi2uzymzamsl0000](/datasets/md/ea.md#spatial-transcriptomics-breast-7wtbyi2uzymzamsl0000), [spatial-transcriptomics-breast-pun25r1vw3m56abl0000](/datasets/md/8d.md#spatial-transcriptomics-breast-pun25r1vw3m56abl0000), [spatial-transcriptomics-breast-tkftyhvsvqxqt9sj0000](/datasets/md/35.md#spatial-transcriptomics-breast-tkftyhvsvqxqt9sj0000) ## Spatial transcriptomics reveal unnresolved wound repair as potential driver of PFA Ependymoma progression - Page: /collections/doi-10-1093-neuonc-noac079-165/ - Kind: replicates - Datasets: 14 - Reference: 10.1093/neuonc/noac079.165 - Members: [visium-spatial-gene-expression-brain-xxgxse38ihh0ibmx0000](/datasets/md/f7.md#visium-spatial-gene-expression-brain-xxgxse38ihh0ibmx0000), [visium-spatial-gene-expression-brain-f7yhxldrhs32b8fb0000](/datasets/md/a4.md#visium-spatial-gene-expression-brain-f7yhxldrhs32b8fb0000), [visium-spatial-gene-expression-brain-u8asqicmrdeufkbk0000](/datasets/md/5c.md#visium-spatial-gene-expression-brain-u8asqicmrdeufkbk0000), [visium-spatial-gene-expression-brain-3isjkam6p1sncek60000](/datasets/md/5b.md#visium-spatial-gene-expression-brain-3isjkam6p1sncek60000), [visium-spatial-gene-expression-brain-pfst2rswtkuvfyok0000](/datasets/md/1b.md#visium-spatial-gene-expression-brain-pfst2rswtkuvfyok0000), [visium-spatial-gene-expression-brain-ykut8yyyhpw50jjd0000](/datasets/md/aa.md#visium-spatial-gene-expression-brain-ykut8yyyhpw50jjd0000), [visium-spatial-gene-expression-brain-jynfcr8djyr2dwb20000](/datasets/md/a6.md#visium-spatial-gene-expression-brain-jynfcr8djyr2dwb20000), [visium-spatial-gene-expression-brain-hynjoejdoszt1izy0000](/datasets/md/35.md#visium-spatial-gene-expression-brain-hynjoejdoszt1izy0000), [visium-spatial-gene-expression-brain-cvjpc4akpbo0rhux0000](/datasets/md/2c.md#visium-spatial-gene-expression-brain-cvjpc4akpbo0rhux0000), [visium-spatial-gene-expression-brain-4wepcp6jwxr6xyqz0000](/datasets/md/9d.md#visium-spatial-gene-expression-brain-4wepcp6jwxr6xyqz0000), [visium-spatial-gene-expression-brain-a5ffddq8m8wgto8j0000](/datasets/md/a1.md#visium-spatial-gene-expression-brain-a5ffddq8m8wgto8j0000), [visium-spatial-gene-expression-brain-r39duszohn56tang0000](/datasets/md/06.md#visium-spatial-gene-expression-brain-r39duszohn56tang0000), [visium-spatial-gene-expression-brain-qgwvgy34c0y2tuqw0000](/datasets/md/61.md#visium-spatial-gene-expression-brain-qgwvgy34c0y2tuqw0000), [visium-spatial-gene-expression-brain-hkhrgahegu5mxxsl0000](/datasets/md/69.md#visium-spatial-gene-expression-brain-hkhrgahegu5mxxsl0000) ## Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGFβ signaling - Page: /collections/geo-gse174313/ - Kind: other - Datasets: 4 - Reference: PMID:34663698 - Design: P0 calvaria were isolated from TrkAF592A homozygous (mutant) and heterozygous (control) mice in which mothers were treated with 1NMPP1 via their drinking water from the time of conception through birth. Sagittal sutures and flanking parietal bones were dissected out, stacked and fresh frozen in OCT. Frozen sections were applied to the 10X Visium spatial transcriptomics gene expression platform and processed according to manufacturers protocols. Following sequencing, alignment and image registration was conducted using SpaceRanger. - Members: [visium-spatial-gene-expression-sagittal-suture-bhrxsptvxllmscl50000](/datasets/md/23.md#visium-spatial-gene-expression-sagittal-suture-bhrxsptvxllmscl50000), [visium-spatial-gene-expression-sagittal-suture-ckivapgca1yqqmxc0000](/datasets/md/23.md#visium-spatial-gene-expression-sagittal-suture-ckivapgca1yqqmxc0000), [visium-spatial-gene-expression-sagittal-suture-mcqdcnxgwtstihxq0000](/datasets/md/18.md#visium-spatial-gene-expression-sagittal-suture-mcqdcnxgwtstihxq0000), [visium-spatial-gene-expression-sagittal-suture-0noex8eg79p9irjo0000](/datasets/md/0d.md#visium-spatial-gene-expression-sagittal-suture-0noex8eg79p9irjo0000) ## Integrated spatial multi-omics reveals fibroblast fate during tissue repair - Page: /collections/geo-gse178758/ - Kind: time course - Datasets: 4 - Reference: PMID:34620713 - Design: Mouse wound tissue transcriptomes were profiles using RNA bulk and single cell RNA sequencing, single cell ATAC sequencing, and Visium spatial transcriptomics. For bulk RNA sequencing, RNA was obtained from mouse inner wound region and outer wound region, as well as uninjured control fibroblasts at post-operative day (POD) #7 and #14, as well as inner wound region and outer wound region fibroblasts from POD #14 treated with a small molecule FAK inhibitor. For single-cell RNA sequencing, FACS-isolated Rainbow mouse inner wound region and outer wound region fibroblasts harvested at 3 timepoints over the course of wound healing (POD #2, #7, and #14) and single cell sorted for plate-seq. For single-cell ATAC sequencing, Rainbow mouse wound fibroblasts were FACS-isolated from inner and outer wound regions at the same 3 timepoints as single-cell RNA sequencing. For Visium spatial transcriptomics, mouse wound tissue sections were mounted and sequenced from POD #2, #7, and #14 as well as uninjured skin. - Members: [visium-spatial-gene-expression-skin-of-body-gsehr94nqd8gfggf0000](/datasets/md/c6.md#visium-spatial-gene-expression-skin-of-body-gsehr94nqd8gfggf0000), [visium-spatial-gene-expression-skin-of-body-x2gsdx6wbi7ugn3z0000](/datasets/md/6e.md#visium-spatial-gene-expression-skin-of-body-x2gsdx6wbi7ugn3z0000), [visium-spatial-gene-expression-skin-of-body-5nfc813jugjrbdpz0000](/datasets/md/29.md#visium-spatial-gene-expression-skin-of-body-5nfc813jugjrbdpz0000), [visium-spatial-gene-expression-skin-of-body-i4t1xonkvbreuayp0000](/datasets/md/84.md#visium-spatial-gene-expression-skin-of-body-i4t1xonkvbreuayp0000) ## Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection [Spatial transcriptomics] - Page: /collections/geo-gse207205/ - Kind: other - Datasets: 8 - Reference: PMID:36741401 - Design: Human thymic tissue samples (N = 8) were collected from paediatric donors (<2 years) undergoing corrective cardiac surgery. Spatial transcriptomics was performed by the 10x visium solution. ***Raw data for human samples not available due to patient privacy concerns*** - Members: [visium-spatial-gene-expression-thymus-eubykxkkuh2ozvx80000](/datasets/md/19.md#visium-spatial-gene-expression-thymus-eubykxkkuh2ozvx80000), [visium-spatial-gene-expression-thymus-c2fl97bowr2lsirw0000](/datasets/md/02.md#visium-spatial-gene-expression-thymus-c2fl97bowr2lsirw0000), [visium-spatial-gene-expression-thymus-swamdvs9xbpsyocg0000](/datasets/md/87.md#visium-spatial-gene-expression-thymus-swamdvs9xbpsyocg0000), [visium-spatial-gene-expression-thymus-wonoobycaex7art30000](/datasets/md/95.md#visium-spatial-gene-expression-thymus-wonoobycaex7art30000), [visium-spatial-gene-expression-thymus-vs36eewyvrxohf0t0000](/datasets/md/ab.md#visium-spatial-gene-expression-thymus-vs36eewyvrxohf0t0000), [visium-spatial-gene-expression-thymus-zzv5mqjfnl7gagsy0000](/datasets/md/f3.md#visium-spatial-gene-expression-thymus-zzv5mqjfnl7gagsy0000), [visium-spatial-gene-expression-thymus-lmwxlgg9b6tcelb10000](/datasets/md/18.md#visium-spatial-gene-expression-thymus-lmwxlgg9b6tcelb10000), [visium-spatial-gene-expression-thymus-m5pgjntgnscxvn8u0000](/datasets/md/b0.md#visium-spatial-gene-expression-thymus-m5pgjntgnscxvn8u0000) ## Spatial RNA sequencing of bleomycin-treated young and old mice lungs at day 14 and day 28 post injection - Page: /collections/geo-gse234198/ - Kind: time course - Datasets: 8 - Reference: PMID:40769983 - Design: Young (7 weeks) or old (18 months) mice were injected with PBS or bleomycin to induce transient alveolar damages. At the bleomycin-induced fibrotic response peak at day 14 and during the resolution phase at day 28 post injection, their lungs were embedded in OCT and stored at -80°C. OCT blocks were cryosectioned at 10µm thickness on capture areas of Visium 10 Genomics slide. - Members: [visium-spatial-gene-expression-lung-udg3mrimfxucmgz60000](/datasets/md/f8.md#visium-spatial-gene-expression-lung-udg3mrimfxucmgz60000), [visium-spatial-gene-expression-lung-bb2rkid3emziw9o90000](/datasets/md/f2.md#visium-spatial-gene-expression-lung-bb2rkid3emziw9o90000), [visium-spatial-gene-expression-lung-q94rrs0kfhvg5qoq0000](/datasets/md/32.md#visium-spatial-gene-expression-lung-q94rrs0kfhvg5qoq0000), [visium-spatial-gene-expression-lung-zup24cecqlpbkour0000](/datasets/md/75.md#visium-spatial-gene-expression-lung-zup24cecqlpbkour0000), [visium-spatial-gene-expression-lung-odxtsxehdyyuv5og0000](/datasets/md/55.md#visium-spatial-gene-expression-lung-odxtsxehdyyuv5og0000), [visium-spatial-gene-expression-lung-omsccjps3tvdsz5v0000](/datasets/md/e8.md#visium-spatial-gene-expression-lung-omsccjps3tvdsz5v0000), [visium-spatial-gene-expression-lung-qhtsfuwfc9xe5wy80000](/datasets/md/3d.md#visium-spatial-gene-expression-lung-qhtsfuwfc9xe5wy80000), [visium-spatial-gene-expression-lung-9lfnowvm4yhbv8lu0000](/datasets/md/0d.md#visium-spatial-gene-expression-lung-9lfnowvm4yhbv8lu0000) ## High-resolution analysis of mononuclear phagocytes reveals clinically relevant markers in human colo-rectal liver metastasis - Visium Spatial Transcriptomics - Page: /collections/geo-gse254364/ - Kind: other - Datasets: 2 - Reference: PMID:36652202 - Design: Four-μm FFPE tissue sections were stained with hematoxylin and eosin (H&E) and the appropriate tissue regions (inclusive of tumor and IM) were selected for further processing. - Members: [visium-spatial-gene-expression-liver-opug41ncpaorkzyg0000](/datasets/md/83.md#visium-spatial-gene-expression-liver-opug41ncpaorkzyg0000), [visium-spatial-gene-expression-liver-km7jlmcvcgh8gtoz0000](/datasets/md/16.md#visium-spatial-gene-expression-liver-km7jlmcvcgh8gtoz0000) ## Single cell approached deine forebrain neural stem cell niches and identify microglial ligands that enhance precursor-mediated remyelination (Xenium) - Page: /collections/geo-gse266689/ - Kind: other - Datasets: 19 - Reference: PMID:39823226 - Design: Multiplexed in situ hybridization-based spatial transcriptomics using the 10X genomics Xenium platform was used to analyze coronal adult (P100) CD-1 mouse forebrain sections containing the V-SVZ and corpus callosum, with a probeset that included marker genes for relevant cell types, ligands and receptors. We analyzed a region of interest that included the V-SVZ and corpus callosum from four different brains from mice which had been exposed to either a control or cuprizone-rapamycin (cup-rap) protocol (2 control, and 2 cup-rap). Replicates are indicated at the end of each sample name (i.e. Adult_Control_Forebrain_Xenium_Biol1, Adult_CupRap_Forebrain_Xenium_Biol1 ). Multiplexed in situ hybridization-based spatial transcriptomics using the 10X genomics Xenium platform was used to analyze coronal adult (P100) CD-1 mouse forebrain sections containing the V-SVZ and corpus callosum, with a probeset that included marker genes for relevant cell types, ligands and receptors. We analyzed a region of interest that included the V-SVZ and corpus callosum from four different brains from mice which had been exposed to either a control or cuprizone-rapamycin (cup-rap) protocol and were given no recovery after treatment cessation. Replicates are indicated at the end of each sample name (i.e. Adult_Control_NoRecovery_Xenium_Biol1, Adult_CupRap_NoRecovery_Xenium_Biol1 ). We also collected tissue from adult CD1 mice which were fitted with osmotic minipumps to infused ligands into the right lateral ventricle. Animals were then either infused with 0.1% BSA-PBS (control) or 204ng OSM in 0.1% BSA-PBS for 7 days, with a delivery rate of 0.5ul per hour. - Members: [10x-xenium-brain-bv9ny0swhygjihq40001](/datasets/md/43.md#10x-xenium-brain-bv9ny0swhygjihq40001), [10x-xenium-brain-w79nahvvnd6zkjk40001](/datasets/md/74.md#10x-xenium-brain-w79nahvvnd6zkjk40001), [10x-xenium-brain-yajsbgrgznvfde8e0000](/datasets/md/ba.md#10x-xenium-brain-yajsbgrgznvfde8e0000), [10x-xenium-brain-wdue5bnioyxejczv0000](/datasets/md/b8.md#10x-xenium-brain-wdue5bnioyxejczv0000), [10x-xenium-brain-dnaqzla5xyzfkq7j0000](/datasets/md/c9.md#10x-xenium-brain-dnaqzla5xyzfkq7j0000), [10x-xenium-brain-um0suu7w2yjbjprx0000](/datasets/md/ae.md#10x-xenium-brain-um0suu7w2yjbjprx0000), [10x-xenium-brain-xlnawdtjensscfch0000](/datasets/md/eb.md#10x-xenium-brain-xlnawdtjensscfch0000), [10x-xenium-brain-e6xkfepmyrfcfdfj0000](/datasets/md/48.md#10x-xenium-brain-e6xkfepmyrfcfdfj0000), [10x-xenium-brain-sdw0lxj4h8ojkee10000](/datasets/md/1e.md#10x-xenium-brain-sdw0lxj4h8ojkee10000), [10x-xenium-brain-9mees1jthwmznmm10000](/datasets/md/be.md#10x-xenium-brain-9mees1jthwmznmm10000), [10x-xenium-brain-mjjcbvgrpc8rejvk0000](/datasets/md/0b.md#10x-xenium-brain-mjjcbvgrpc8rejvk0000), [10x-xenium-brain-56aqeu6o7b5l2eac0000](/datasets/md/2c.md#10x-xenium-brain-56aqeu6o7b5l2eac0000), [10x-xenium-brain-zt6xqs8wtzfjpuo00000](/datasets/md/90.md#10x-xenium-brain-zt6xqs8wtzfjpuo00000), [10x-xenium-brain-t8cvk08ubzrwt9vv0000](/datasets/md/f2.md#10x-xenium-brain-t8cvk08ubzrwt9vv0000), [10x-xenium-brain-ys7hqoaf49muafpe0000](/datasets/md/47.md#10x-xenium-brain-ys7hqoaf49muafpe0000), [10x-xenium-brain-yt4uonuog1o39xbz0000](/datasets/md/a0.md#10x-xenium-brain-yt4uonuog1o39xbz0000), [10x-xenium-brain-zkcoc91rskq0hkrb0000](/datasets/md/83.md#10x-xenium-brain-zkcoc91rskq0hkrb0000), [10x-xenium-brain-wix9q2zf9g4wcwtn0000](/datasets/md/8b.md#10x-xenium-brain-wix9q2zf9g4wcwtn0000), [10x-xenium-brain-xewkhkfd2oxbm3ix0000](/datasets/md/5e.md#10x-xenium-brain-xewkhkfd2oxbm3ix0000) ## Identification of perturbation-responsive regions and genes in comparative spatial transcriptomics atlases - Page: /collections/geo-gse268779/ - Kind: comparison - Datasets: 7 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE268779 - Design: We used spatial transcriptomics to profile the mid thoracic spinal cord in young SCI mice, old SCI mice and old mice treated with regeneration therapy. - Members: [visium-spatial-gene-expression-spinal-cord-tr7ba86cgwlhac6a0000](/datasets/md/a8.md#visium-spatial-gene-expression-spinal-cord-tr7ba86cgwlhac6a0000), [visium-spatial-gene-expression-spinal-cord-v285h08ns5mgbltm0000](/datasets/md/0d.md#visium-spatial-gene-expression-spinal-cord-v285h08ns5mgbltm0000), [visium-spatial-gene-expression-spinal-cord-qya1mae2xxeiim9y0000](/datasets/md/18.md#visium-spatial-gene-expression-spinal-cord-qya1mae2xxeiim9y0000), [visium-spatial-gene-expression-spinal-cord-adyxhnuxihuljwtj0000](/datasets/md/05.md#visium-spatial-gene-expression-spinal-cord-adyxhnuxihuljwtj0000), [visium-spatial-gene-expression-spinal-cord-zvzfcwd5xgpjnrsk0000](/datasets/md/44.md#visium-spatial-gene-expression-spinal-cord-zvzfcwd5xgpjnrsk0000), [visium-spatial-gene-expression-spinal-cord-6ccg8xvvybpc05r80000](/datasets/md/23.md#visium-spatial-gene-expression-spinal-cord-6ccg8xvvybpc05r80000), [visium-spatial-gene-expression-spinal-cord-bfwjvjx7fahqdkax0000](/datasets/md/f8.md#visium-spatial-gene-expression-spinal-cord-bfwjvjx7fahqdkax0000) ## Spatial characterization of the transcriptome of the adult healthy and mutant FUS mouse spinal cords [Spatial transcriptomics] - Page: /collections/geo-gse269377/ - Kind: other - Datasets: 4 - Reference: PMID:41430470 - Design: Eight 10-um thick sections of spinal cord tissue (4 controls and 4 mutant FUS samples) were layered on the proprietary Visium Spatial Gene Expression Slide (10X Genomics, Cat#PN-2000233) and further processed. - Members: [visium-spatial-gene-expression-spinal-cord-q03ioxmet35qemga0000](/datasets/md/71.md#visium-spatial-gene-expression-spinal-cord-q03ioxmet35qemga0000), [visium-spatial-gene-expression-spinal-cord-n3z7pagnepakdpxc0000](/datasets/md/c1.md#visium-spatial-gene-expression-spinal-cord-n3z7pagnepakdpxc0000), [visium-spatial-gene-expression-spinal-cord-e1ciikjdujachcax0000](/datasets/md/89.md#visium-spatial-gene-expression-spinal-cord-e1ciikjdujachcax0000), [visium-spatial-gene-expression-spinal-cord-msfx4yrc8f8zhx3h0000](/datasets/md/d5.md#visium-spatial-gene-expression-spinal-cord-msfx4yrc8f8zhx3h0000) ## Mid-Lobular Hepatocytes Exhibit Transient Proliferation Pause and Stress Response through Atf4-Ddit3 axis in Early Acute Liver Injury (10x Visium) - Page: /collections/geo-gse272564/ - Kind: other - Datasets: 4 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE272564 - Design: To understand the temporal spatial response to acute APAP injury, liver sections from wild-type mice treated with APAP for 0 h to 72 h were subjected to spatial transcriptomics (ST) using the Visium (10 × Genomics) platform. - Members: [visium-spatial-gene-expression-liver-1i7fm72j5ydinuzz0000](/datasets/md/a1.md#visium-spatial-gene-expression-liver-1i7fm72j5ydinuzz0000), [visium-spatial-gene-expression-liver-gw8hn5ue3czr0thm0000](/datasets/md/6d.md#visium-spatial-gene-expression-liver-gw8hn5ue3czr0thm0000), [visium-spatial-gene-expression-liver-zszv7kh23t6ywhpk0000](/datasets/md/02.md#visium-spatial-gene-expression-liver-zszv7kh23t6ywhpk0000), [visium-spatial-gene-expression-liver-bh45t7okrojqh9es0000](/datasets/md/26.md#visium-spatial-gene-expression-liver-bh45t7okrojqh9es0000) ## Multi-omic analysis reveals retinoic acid molecular drivers for fibrosis and regenerative repair in skin fibrosis [Spatial transcriptomics] - Page: /collections/geo-gse278169/ - Kind: other - Datasets: 5 - Reference: PMID:40816279 - Design: Mouse wound tissue transcriptomes were profiles using single cell RNA sequencing, single cell ATAC sequencing, and Visium spatial transcriptomics. For single-cell RNA sequencing, wound cells were harvested at 3 timepoints over the course of wound healing (POD 12, 21, 28) and normal skin as a control. For single-cell ATAC sequencing and visium similiar time points were harvested. For single cell RNA sequencing, cells treated with a cyp26b1 inhibitor were also assessed referred to as POD 12 + TREATMENT. - Members: [visium-spatial-gene-expression-skin-of-body-2rz8eqhorxlkdh020000](/datasets/md/16.md#visium-spatial-gene-expression-skin-of-body-2rz8eqhorxlkdh020000), [visium-spatial-gene-expression-skin-of-body-1e884toec1zbftth0000](/datasets/md/b5.md#visium-spatial-gene-expression-skin-of-body-1e884toec1zbftth0000), [visium-spatial-gene-expression-skin-of-body-il5cwjfjtb2llinu0000](/datasets/md/8a.md#visium-spatial-gene-expression-skin-of-body-il5cwjfjtb2llinu0000), [visium-spatial-gene-expression-skin-of-body-mdjufegffvnlnxrh0000](/datasets/md/36.md#visium-spatial-gene-expression-skin-of-body-mdjufegffvnlnxrh0000), [visium-spatial-gene-expression-skin-of-body-awygpuiv0nkxlfq60000](/datasets/md/0d.md#visium-spatial-gene-expression-skin-of-body-awygpuiv0nkxlfq60000) ## Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [Xenium] - Page: /collections/geo-gse280069/ - Kind: comparison - Datasets: 4 - Reference: PMID:39480496 - Design: Formalin-fixed, paraffin-embedded murine skin (healthy or POD4-wounds, Control and PITX1+) or buccal mucosa (healthy Control) was processed for Xenium in situ analysis to determine spatial localization and expression of selected mRNA transcripts. - Members: [10x-xenium-skin-of-back-mt10cwkfiohkaasz0000](/datasets/md/41.md#10x-xenium-skin-of-back-mt10cwkfiohkaasz0000), [10x-xenium-skin-of-back-cz1ctokidcxou1y40000](/datasets/md/eb.md#10x-xenium-skin-of-back-cz1ctokidcxou1y40000), [10x-xenium-skin-of-back-bcxzyyxqyvhxb3xw0000](/datasets/md/5d.md#10x-xenium-skin-of-back-bcxzyyxqyvhxb3xw0000), [10x-xenium-buccal-mucosa-sebdr3awnrowtima0000](/datasets/md/a3.md#10x-xenium-buccal-mucosa-sebdr3awnrowtima0000) ## single-cell multiomics data for the developing human pelvic girdle [spatial] - Page: /collections/geo-gse281317/ - Kind: replicates - Datasets: 28 - Reference: PMID:40866708 - Design: Fresh ilium samples were dissected out (along with the soft tissues surrounding them), flash frozen in OCT, and were processed using 10X Genomics visium spatial transcriptomics protocol. Each 10X genomics visium run has raw fatq files and input files - Members: [visium-spatial-gene-expression-ilium-0rhxib6lhdiytzsp0001](/datasets/md/1a.md#visium-spatial-gene-expression-ilium-0rhxib6lhdiytzsp0001), [visium-spatial-gene-expression-ilium-mpwpojffpcygswdm0000](/datasets/md/83.md#visium-spatial-gene-expression-ilium-mpwpojffpcygswdm0000), [visium-spatial-gene-expression-ilium-qg3e70rdngoot0ux0000](/datasets/md/fd.md#visium-spatial-gene-expression-ilium-qg3e70rdngoot0ux0000), [visium-spatial-gene-expression-ilium-t0orkzdaocf08kds0001](/datasets/md/9a.md#visium-spatial-gene-expression-ilium-t0orkzdaocf08kds0001), [visium-spatial-gene-expression-ilium-aylvefsm60vfit6z0000](/datasets/md/3f.md#visium-spatial-gene-expression-ilium-aylvefsm60vfit6z0000), [visium-spatial-gene-expression-ilium-hfcrcmuhxrdcsakl0000](/datasets/md/47.md#visium-spatial-gene-expression-ilium-hfcrcmuhxrdcsakl0000), [visium-spatial-gene-expression-ilium-24u9a4syklrta47i0000](/datasets/md/e9.md#visium-spatial-gene-expression-ilium-24u9a4syklrta47i0000), [visium-spatial-gene-expression-ilium-abwq7ualtmvwgzqm0000](/datasets/md/3a.md#visium-spatial-gene-expression-ilium-abwq7ualtmvwgzqm0000), [visium-spatial-gene-expression-ilium-hd8k1dlebowzlvgp0000](/datasets/md/51.md#visium-spatial-gene-expression-ilium-hd8k1dlebowzlvgp0000), [visium-spatial-gene-expression-ilium-sddcfctyxjraft8s0000](/datasets/md/dc.md#visium-spatial-gene-expression-ilium-sddcfctyxjraft8s0000), [visium-spatial-gene-expression-ilium-dhtqzyvqy5dttx0d0000](/datasets/md/be.md#visium-spatial-gene-expression-ilium-dhtqzyvqy5dttx0d0000), [visium-spatial-gene-expression-ilium-dp0v4tfiunqsrqpr0000](/datasets/md/3b.md#visium-spatial-gene-expression-ilium-dp0v4tfiunqsrqpr0000), [visium-spatial-gene-expression-ilium-kdnzcz81vsgb4nkn0001](/datasets/md/ab.md#visium-spatial-gene-expression-ilium-kdnzcz81vsgb4nkn0001), [visium-spatial-gene-expression-ilium-r9rhjwswdowjidgv0000](/datasets/md/6c.md#visium-spatial-gene-expression-ilium-r9rhjwswdowjidgv0000), [visium-spatial-gene-expression-ilium-auhbyglctk2hqlsu0000](/datasets/md/8e.md#visium-spatial-gene-expression-ilium-auhbyglctk2hqlsu0000), [visium-spatial-gene-expression-ilium-q2cvcazoaazlfotn0000](/datasets/md/e4.md#visium-spatial-gene-expression-ilium-q2cvcazoaazlfotn0000), [visium-spatial-gene-expression-ilium-er0pv3zkuzsh1e6z0000](/datasets/md/59.md#visium-spatial-gene-expression-ilium-er0pv3zkuzsh1e6z0000), [visium-spatial-gene-expression-ilium-ty567earb8ozvqyf0000](/datasets/md/c9.md#visium-spatial-gene-expression-ilium-ty567earb8ozvqyf0000), [visium-spatial-gene-expression-ilium-3wemqbqtxzlrboyh0000](/datasets/md/57.md#visium-spatial-gene-expression-ilium-3wemqbqtxzlrboyh0000), [visium-spatial-gene-expression-ilium-xxzv8wtkihpspyb00000](/datasets/md/e1.md#visium-spatial-gene-expression-ilium-xxzv8wtkihpspyb00000), [visium-spatial-gene-expression-ilium-vwnva7rqhzkl7uwo0000](/datasets/md/39.md#visium-spatial-gene-expression-ilium-vwnva7rqhzkl7uwo0000), [visium-spatial-gene-expression-ilium-us5hnkjzbjfsbw2d0000](/datasets/md/48.md#visium-spatial-gene-expression-ilium-us5hnkjzbjfsbw2d0000), [visium-spatial-gene-expression-ilium-6sluxr8abebhwgau0000](/datasets/md/91.md#visium-spatial-gene-expression-ilium-6sluxr8abebhwgau0000), [visium-spatial-gene-expression-ilium-mamgis4jpa9e2flj0000](/datasets/md/61.md#visium-spatial-gene-expression-ilium-mamgis4jpa9e2flj0000), [visium-spatial-gene-expression-ilium-qdjjfnily7lhpp410000](/datasets/md/91.md#visium-spatial-gene-expression-ilium-qdjjfnily7lhpp410000), [visium-spatial-gene-expression-ilium-ow1k1dxdqb5esize0000](/datasets/md/7d.md#visium-spatial-gene-expression-ilium-ow1k1dxdqb5esize0000), [visium-spatial-gene-expression-ilium-nn2hzjh4k9rpzwrd0000](/datasets/md/b5.md#visium-spatial-gene-expression-ilium-nn2hzjh4k9rpzwrd0000), [visium-spatial-gene-expression-ilium-xx8rsebsjsnsxgl00000](/datasets/md/30.md#visium-spatial-gene-expression-ilium-xx8rsebsjsnsxgl00000) ## Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients - Page: /collections/geo-gse288607/ - Kind: other - Datasets: 9 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288607 - Design: Lung tissue from 9 sarcoidosis patients - Members: [visium-spatial-gene-expression-lung-pst4kavz8dc8axnk0001](/datasets/md/d9.md#visium-spatial-gene-expression-lung-pst4kavz8dc8axnk0001), [visium-spatial-gene-expression-lung-ki6r6odt2c8xc9em0000](/datasets/md/5c.md#visium-spatial-gene-expression-lung-ki6r6odt2c8xc9em0000), [visium-spatial-gene-expression-lung-xxie1j6w0yhuahex0000](/datasets/md/49.md#visium-spatial-gene-expression-lung-xxie1j6w0yhuahex0000), [visium-spatial-gene-expression-lung-cttsvn92q2sg6ltv0000](/datasets/md/be.md#visium-spatial-gene-expression-lung-cttsvn92q2sg6ltv0000), [visium-spatial-gene-expression-lung-dhn12rdph1mgbdol0000](/datasets/md/22.md#visium-spatial-gene-expression-lung-dhn12rdph1mgbdol0000), [visium-spatial-gene-expression-lung-dcgw3hmb34fcnulk0000](/datasets/md/21.md#visium-spatial-gene-expression-lung-dcgw3hmb34fcnulk0000), [visium-spatial-gene-expression-lung-sw3ihiaghxsvouej0000](/datasets/md/a6.md#visium-spatial-gene-expression-lung-sw3ihiaghxsvouej0000), [visium-spatial-gene-expression-lung-xhzfhmtn20ydaltv0000](/datasets/md/2a.md#visium-spatial-gene-expression-lung-xhzfhmtn20ydaltv0000), [visium-spatial-gene-expression-lung-hgrq0lkilqjkfubj0000](/datasets/md/e8.md#visium-spatial-gene-expression-lung-hgrq0lkilqjkfubj0000) ## Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover [VisiumHD] - Page: /collections/geo-gse293042/ - Kind: other - Datasets: 2 - Reference: PMID:42711427 - Design: We isolated biopsies from dissected adrenal glands from mouse adults and subjected them to spatial transcriptomics sequencing using 10x Genomics Visium HD approach. - Members: [visium-hd-adrenal-gland-ezvbxllunyzgpmsp0000](/datasets/md/95.md#visium-hd-adrenal-gland-ezvbxllunyzgpmsp0000), [visium-hd-adrenal-gland-lc6byzxxxkf0saxu0000](/datasets/md/7e.md#visium-hd-adrenal-gland-lc6byzxxxkf0saxu0000) ## HMG Box-Containing Protein 1 (HBP1) Protects Against Pancreatic Injury in Acute Pancreatitis but Promotes Neoplastic Progression - Page: /collections/geo-gse296582/ - Kind: comparison - Datasets: 6 - Reference: PMID:40404099 - Design: Spatial transcriptomic analysis was performed on pancreata from three HBP1 WT and three HBP1 CKO mice on days 1 and 2 post-cerulein treatment. Pancreatitis areas were mounted on 10x Genomics Visium slides, with 5000 barcoded 55 µm spots capturing 1–10 cells per spot, each containing millions of probes for 20,551 mouse genes via CytAssist28. Sequencing (25k read pairs/spot) generated FASTQ files, which were mapped to H&E images and feature-barcode matrices using Spaceranger. - Members: [visium-spatial-gene-expression-pancreas-sm6kizc61wuaoltk0000](/datasets/md/94.md#visium-spatial-gene-expression-pancreas-sm6kizc61wuaoltk0000), [visium-spatial-gene-expression-pancreas-rz4fitz8d09vwfe10000](/datasets/md/29.md#visium-spatial-gene-expression-pancreas-rz4fitz8d09vwfe10000), [visium-spatial-gene-expression-pancreas-cblrv9ivnu1gveto0000](/datasets/md/09.md#visium-spatial-gene-expression-pancreas-cblrv9ivnu1gveto0000), [visium-spatial-gene-expression-pancreas-yrgpc82aljpcsowe0000](/datasets/md/71.md#visium-spatial-gene-expression-pancreas-yrgpc82aljpcsowe0000), [visium-spatial-gene-expression-pancreas-bjajgsrwh3pxpcjh0000](/datasets/md/f1.md#visium-spatial-gene-expression-pancreas-bjajgsrwh3pxpcjh0000), [visium-spatial-gene-expression-pancreas-csxbtrif5siczbgz0000](/datasets/md/54.md#visium-spatial-gene-expression-pancreas-csxbtrif5siczbgz0000) ## IL-17A Neutralization Prevents Immune Checkpoint Inhibitor-Associated Myocarditis and Synergistically Enhances Immune Checkpoint Blockade Therapy - Page: /collections/geo-gse297745/ - Kind: other - Datasets: 2 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE297745 - Design: FVB/NJ mice were immunized with MyHCα peptide and treated with either dual ICIs alone or dual ICIs plus IL-17A neutralizing antibody. Heart tissues from both groups were collected and analyzed using 10x Genomics Visium Spatial Transcriptomics. Two samples per group were used to assess spatial immune infiltration, fibrosis, and transcriptional responses. - Members: [visium-spatial-gene-expression-heart-c07phah6dapr3afx0000](/datasets/md/19.md#visium-spatial-gene-expression-heart-c07phah6dapr3afx0000), [visium-spatial-gene-expression-heart-epvfc851jklw7ti30000](/datasets/md/e6.md#visium-spatial-gene-expression-heart-epvfc851jklw7ti30000) ## Spatial gene expression profiling of aortitis samples. - Page: /collections/geo-gse306150/ - Kind: comparison - Datasets: 10 - Reference: PMID:41948935 - Design: We performed spatial profiling (10X Xenium in-situ spatial platform) on ascending aorta samples resected from three subjects with giant cell aortitis (denoted as GCA1, GCA2 and GCA3), one subject with IgG4-related aortitis and three subjects with aortic stenosis (denoted as AS1, AS2 and AS3). Two tissue sections (denoted as R1 and R2) were processed from each giant cell aortitis subject. - Members: [10x-xenium-ascending-aorta-rorfut8gqomjlx2r0000](/datasets/md/bb.md#10x-xenium-ascending-aorta-rorfut8gqomjlx2r0000), [10x-xenium-ascending-aorta-np4mhg6uwrny6zec0000](/datasets/md/6d.md#10x-xenium-ascending-aorta-np4mhg6uwrny6zec0000), [10x-xenium-ascending-aorta-x6bsmsbydryclxbo0000](/datasets/md/42.md#10x-xenium-ascending-aorta-x6bsmsbydryclxbo0000), [10x-xenium-ascending-aorta-by5t5q86dgtuh3z60000](/datasets/md/82.md#10x-xenium-ascending-aorta-by5t5q86dgtuh3z60000), [10x-xenium-ascending-aorta-3expjcmfrxabbtth0000](/datasets/md/ff.md#10x-xenium-ascending-aorta-3expjcmfrxabbtth0000), [10x-xenium-ascending-aorta-btprgq5qw25ikqja0000](/datasets/md/20.md#10x-xenium-ascending-aorta-btprgq5qw25ikqja0000), [10x-xenium-ascending-aorta-gjs0gpw3oq3gm1ma0000](/datasets/md/00.md#10x-xenium-ascending-aorta-gjs0gpw3oq3gm1ma0000), [10x-xenium-ascending-aorta-qpiaeynnww3anvux0000](/datasets/md/43.md#10x-xenium-ascending-aorta-qpiaeynnww3anvux0000), [10x-xenium-ascending-aorta-tqbmzjoaligqwsmn0000](/datasets/md/e5.md#10x-xenium-ascending-aorta-tqbmzjoaligqwsmn0000), [10x-xenium-ascending-aorta-ntzfyqrcmxo5jsbx0000](/datasets/md/fc.md#10x-xenium-ascending-aorta-ntzfyqrcmxo5jsbx0000) ## Single-cell-scale spatial transcriptome of the developing and adult mouse ovary - Page: /collections/geo-gse307688/ - Kind: other - Datasets: 8 - Reference: PMID:42804628 - Design: Ovaries from wild-type CD-1 mice at 4 fetal timepoints: E12.5 - E14.5 - E16.5 - E18.5; and 4 postnatal timepoints: P0 - P3 - P21 - P90. Each section contains ovaries from multiple litters or individuals. Sections were analyzed using spatial transcriptomics with 10x Genomics Visium HD technology. - Members: [visium-hd-ovary-w5kl5ya2kl2pramp0000](/datasets/md/c5.md#visium-hd-ovary-w5kl5ya2kl2pramp0000), [visium-hd-ovary-1rob6hx6yhbwzd2z0000](/datasets/md/ba.md#visium-hd-ovary-1rob6hx6yhbwzd2z0000), [visium-hd-ovary-zp7icgrzzewng42l0000](/datasets/md/e3.md#visium-hd-ovary-zp7icgrzzewng42l0000), [visium-hd-ovary-plgp263zt6248din0000](/datasets/md/6d.md#visium-hd-ovary-plgp263zt6248din0000), [visium-hd-ovary-dmvryhxhmnmncxcg0000](/datasets/md/ea.md#visium-hd-ovary-dmvryhxhmnmncxcg0000), [visium-hd-ovary-joruajyzwvtcewzr0000](/datasets/md/8f.md#visium-hd-ovary-joruajyzwvtcewzr0000), [visium-hd-ovary-yfkfcyg6teptzxxj0000](/datasets/md/41.md#visium-hd-ovary-yfkfcyg6teptzxxj0000), [visium-hd-ovary-0veiya6iog6dviao0000](/datasets/md/c0.md#visium-hd-ovary-0veiya6iog6dviao0000) ## Spatial and single cell transcriptomics in the human Entorhinal Cortex across diverse risk of Alzheimer’s disease [Visium] - Page: /collections/geo-gse307990/ - Kind: other - Datasets: 31 - Reference: PMID:41332786 - Design: We obtained tissue blocks of postmortem human brain entorhinal cortex (ERC) from 31 neurotypical adult brain donors carrying either E2 or E4 APOE alleles from both African and European ancestry. For each donor, a sample was generated for both spatially resolved transcriptomics with 10x Visium, and single nucleus RNA-seq with 10x Chromium. Visium data showed 9 transcriptional distinct spatial domains. snRNA-seq data was clustered into 38 fine subtypes across 8 broad cell types. Differential expression between APOE carrier status (E2+ vs. E4+) was performed at the cluster level in both data types. *************************************************************** 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-entorhinal-cortex-1qviqhcfleyumqz10000](/datasets/md/8c.md#visium-spatial-gene-expression-entorhinal-cortex-1qviqhcfleyumqz10000), [visium-spatial-gene-expression-entorhinal-cortex-sewl70jeh6y0qixx0000](/datasets/md/a5.md#visium-spatial-gene-expression-entorhinal-cortex-sewl70jeh6y0qixx0000), [visium-spatial-gene-expression-entorhinal-cortex-wkhd18gtaqypdbdt0000](/datasets/md/1c.md#visium-spatial-gene-expression-entorhinal-cortex-wkhd18gtaqypdbdt0000), [visium-spatial-gene-expression-entorhinal-cortex-wn7bh3alormftuvq0000](/datasets/md/f3.md#visium-spatial-gene-expression-entorhinal-cortex-wn7bh3alormftuvq0000), [visium-spatial-gene-expression-entorhinal-cortex-alqteyisrnzzoip50000](/datasets/md/5c.md#visium-spatial-gene-expression-entorhinal-cortex-alqteyisrnzzoip50000), [visium-spatial-gene-expression-entorhinal-cortex-z6zryllgmpobcggo0000](/datasets/md/15.md#visium-spatial-gene-expression-entorhinal-cortex-z6zryllgmpobcggo0000), [visium-spatial-gene-expression-entorhinal-cortex-pffzg1jdqrwrhxpb0000](/datasets/md/ec.md#visium-spatial-gene-expression-entorhinal-cortex-pffzg1jdqrwrhxpb0000), [visium-spatial-gene-expression-entorhinal-cortex-xep9jyqmhddrzagv0000](/datasets/md/66.md#visium-spatial-gene-expression-entorhinal-cortex-xep9jyqmhddrzagv0000), [visium-spatial-gene-expression-entorhinal-cortex-ffnyevyxlcvspedu0000](/datasets/md/15.md#visium-spatial-gene-expression-entorhinal-cortex-ffnyevyxlcvspedu0000), [visium-spatial-gene-expression-entorhinal-cortex-ecbdgg91pddxkub00000](/datasets/md/cb.md#visium-spatial-gene-expression-entorhinal-cortex-ecbdgg91pddxkub00000), [visium-spatial-gene-expression-entorhinal-cortex-rxv74ntlosgxg8pi0000](/datasets/md/6c.md#visium-spatial-gene-expression-entorhinal-cortex-rxv74ntlosgxg8pi0000), [visium-spatial-gene-expression-entorhinal-cortex-gikpnse2bkywljs60000](/datasets/md/49.md#visium-spatial-gene-expression-entorhinal-cortex-gikpnse2bkywljs60000), [visium-spatial-gene-expression-entorhinal-cortex-iewxf1s6l72vcfm40000](/datasets/md/ad.md#visium-spatial-gene-expression-entorhinal-cortex-iewxf1s6l72vcfm40000), [visium-spatial-gene-expression-entorhinal-cortex-mhogerdx4klcatgj0000](/datasets/md/c4.md#visium-spatial-gene-expression-entorhinal-cortex-mhogerdx4klcatgj0000), [visium-spatial-gene-expression-entorhinal-cortex-8lhwwc8xfvg21rth0000](/datasets/md/9f.md#visium-spatial-gene-expression-entorhinal-cortex-8lhwwc8xfvg21rth0000), [visium-spatial-gene-expression-entorhinal-cortex-82vpcz9mdveiopks0000](/datasets/md/40.md#visium-spatial-gene-expression-entorhinal-cortex-82vpcz9mdveiopks0000), [visium-spatial-gene-expression-entorhinal-cortex-gjmvnhklio1vewnz0000](/datasets/md/fb.md#visium-spatial-gene-expression-entorhinal-cortex-gjmvnhklio1vewnz0000), [visium-spatial-gene-expression-entorhinal-cortex-gffcez5yq8jlxaz50000](/datasets/md/6b.md#visium-spatial-gene-expression-entorhinal-cortex-gffcez5yq8jlxaz50000), [visium-spatial-gene-expression-entorhinal-cortex-lsxbkez4tuxudj9p0000](/datasets/md/d5.md#visium-spatial-gene-expression-entorhinal-cortex-lsxbkez4tuxudj9p0000), [visium-spatial-gene-expression-entorhinal-cortex-rvqqrii2fdzcaoby0000](/datasets/md/98.md#visium-spatial-gene-expression-entorhinal-cortex-rvqqrii2fdzcaoby0000), [visium-spatial-gene-expression-entorhinal-cortex-sip34jpjclmurdtr0000](/datasets/md/88.md#visium-spatial-gene-expression-entorhinal-cortex-sip34jpjclmurdtr0000), [visium-spatial-gene-expression-entorhinal-cortex-vsmskat2ft4ql36h0000](/datasets/md/56.md#visium-spatial-gene-expression-entorhinal-cortex-vsmskat2ft4ql36h0000), [visium-spatial-gene-expression-entorhinal-cortex-0idukqkvitua7w280000](/datasets/md/6d.md#visium-spatial-gene-expression-entorhinal-cortex-0idukqkvitua7w280000), [visium-spatial-gene-expression-entorhinal-cortex-k8ykmeinfqtdimbs0000](/datasets/md/87.md#visium-spatial-gene-expression-entorhinal-cortex-k8ykmeinfqtdimbs0000), [visium-spatial-gene-expression-entorhinal-cortex-dbabr8l5fis2yvlr0000](/datasets/md/03.md#visium-spatial-gene-expression-entorhinal-cortex-dbabr8l5fis2yvlr0000), [visium-spatial-gene-expression-entorhinal-cortex-36jaadspdaz82zy60000](/datasets/md/e9.md#visium-spatial-gene-expression-entorhinal-cortex-36jaadspdaz82zy60000), [visium-spatial-gene-expression-entorhinal-cortex-fwhqawrgv5drva0k0000](/datasets/md/75.md#visium-spatial-gene-expression-entorhinal-cortex-fwhqawrgv5drva0k0000), [visium-spatial-gene-expression-entorhinal-cortex-wrappwev0eohk0bs0000](/datasets/md/24.md#visium-spatial-gene-expression-entorhinal-cortex-wrappwev0eohk0bs0000), [visium-spatial-gene-expression-entorhinal-cortex-uowatqsy2djjvdma0000](/datasets/md/b8.md#visium-spatial-gene-expression-entorhinal-cortex-uowatqsy2djjvdma0000), [visium-spatial-gene-expression-entorhinal-cortex-szynuzmpdqucygox0000](/datasets/md/aa.md#visium-spatial-gene-expression-entorhinal-cortex-szynuzmpdqucygox0000), [visium-spatial-gene-expression-entorhinal-cortex-bxr2wvju8wifgbxr0000](/datasets/md/fb.md#visium-spatial-gene-expression-entorhinal-cortex-bxr2wvju8wifgbxr0000) ## Translational profiling of ET-insensitive cell populations in ER+ breast cancer reveals new therapeutic vulnerabilities - Page: /collections/geo-gse310362/ - Kind: comparison - Datasets: 4 - Reference: PMID:42780132 - Design: Spatial RNA sequencing of UIC013 and UIC020 primary breast tumors and assosiated PDXs. - Members: [visium-spatial-gene-expression-breast-ef2qhxaimialuigz0000](/datasets/md/c1.md#visium-spatial-gene-expression-breast-ef2qhxaimialuigz0000), [visium-spatial-gene-expression-breast-nxcenswg0jy1jkm30000](/datasets/md/f5.md#visium-spatial-gene-expression-breast-nxcenswg0jy1jkm30000), [visium-spatial-gene-expression-breast-7g5nzsqif58mrtpo0000](/datasets/md/01.md#visium-spatial-gene-expression-breast-7g5nzsqif58mrtpo0000), [visium-spatial-gene-expression-breast-jvvsyfd0bkrpi1yp0000](/datasets/md/29.md#visium-spatial-gene-expression-breast-jvvsyfd0bkrpi1yp0000) ## A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer [Spatial Transcriptomics] - Page: /collections/geo-gse316402/ - Kind: time course - Datasets: 12 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE316402 - Design: FFPE tissues from patients with biliary tract cancer, collected pre-GM-CSF and post-pembrolizumab ("pre" biopsy) and post-combined GM-CSF and pembrolizumab ("post" biopsy). - Members: [visium-spatial-gene-expression-bile-duct-lhf9hw3o0mumh6j40001](/datasets/md/40.md#visium-spatial-gene-expression-bile-duct-lhf9hw3o0mumh6j40001), [visium-spatial-gene-expression-bile-duct-yfv2at4xus4hfesh0001](/datasets/md/1a.md#visium-spatial-gene-expression-bile-duct-yfv2at4xus4hfesh0001), [visium-spatial-gene-expression-bile-duct-j2zo74gzka9p0gqt0001](/datasets/md/49.md#visium-spatial-gene-expression-bile-duct-j2zo74gzka9p0gqt0001), [visium-spatial-gene-expression-bile-duct-2oio0zpv6z41ci5z0001](/datasets/md/f5.md#visium-spatial-gene-expression-bile-duct-2oio0zpv6z41ci5z0001), [visium-spatial-gene-expression-bile-duct-aaxybyy1ovvjpsh10001](/datasets/md/d0.md#visium-spatial-gene-expression-bile-duct-aaxybyy1ovvjpsh10001), [visium-spatial-gene-expression-bile-duct-fyletkxspuxoacjk0001](/datasets/md/4a.md#visium-spatial-gene-expression-bile-duct-fyletkxspuxoacjk0001), [visium-spatial-gene-expression-bile-duct-lsxdmnzsc2siehos0001](/datasets/md/35.md#visium-spatial-gene-expression-bile-duct-lsxdmnzsc2siehos0001), [visium-spatial-gene-expression-bile-duct-3wohbgry5ndkf9jj0001](/datasets/md/8d.md#visium-spatial-gene-expression-bile-duct-3wohbgry5ndkf9jj0001), [visium-spatial-gene-expression-bile-duct-tyd6dohoqygcdgcx0001](/datasets/md/87.md#visium-spatial-gene-expression-bile-duct-tyd6dohoqygcdgcx0001), [visium-spatial-gene-expression-bile-duct-fuhqbvt5onqumxcv0001](/datasets/md/c0.md#visium-spatial-gene-expression-bile-duct-fuhqbvt5onqumxcv0001), [visium-spatial-gene-expression-bile-duct-xazvmqczzpcum5oa0001](/datasets/md/22.md#visium-spatial-gene-expression-bile-duct-xazvmqczzpcum5oa0001), [visium-spatial-gene-expression-bile-duct-uncjlgwtfz4duedu0001](/datasets/md/31.md#visium-spatial-gene-expression-bile-duct-uncjlgwtfz4duedu0001) ## Spatial Transcriptomics Reveals Compartment-Specific Cytotoxic T cells Crosstalk with AT2 and Goblet cells in Advanced COPD - Page: /collections/geo-gse318039/ - Kind: comparison - Datasets: 8 - Reference: PMID:42351239 - Design: Using Fresh Frozen 10X Visium Spatial Transcriptomics v1 3' Gene Expression, archived frozen lung tissues from human, healthy, unused donor and COPD were cut to 10 µm thickness crysections and then placed into the Visium Spatial Gene Expression Slides. The slides were fixed in methanol at -20°C and stained with H&E. The brightfield images were taken on Olympus VS120 Slide Scanner (Olympus, Japan) at 40X resolution. Tissues were permeabilized for 12 minutes at 37°C. cDNA was synthesized, amplified, and libraries were constructed (250-600 bp) according to Visium Spatial Gene Expression protocol. Samples were sequenced on Illumina NovaSeq S1 Full Flow Cell. - Members: [visium-spatial-gene-expression-lung-esa5qbdxy5tx9av70000](/datasets/md/b8.md#visium-spatial-gene-expression-lung-esa5qbdxy5tx9av70000), [visium-spatial-gene-expression-lung-etbothyt9ju7o4mt0000](/datasets/md/37.md#visium-spatial-gene-expression-lung-etbothyt9ju7o4mt0000), [visium-spatial-gene-expression-lung-idwuwzhpidhyb0iv0001](/datasets/md/0a.md#visium-spatial-gene-expression-lung-idwuwzhpidhyb0iv0001), [visium-spatial-gene-expression-lung-qxh8yhkwaem3khpy0000](/datasets/md/d9.md#visium-spatial-gene-expression-lung-qxh8yhkwaem3khpy0000), [visium-spatial-gene-expression-lung-dq7wumnbeulpurbw0000](/datasets/md/33.md#visium-spatial-gene-expression-lung-dq7wumnbeulpurbw0000), [visium-spatial-gene-expression-lung-ozidaghhakr2kuhk0000](/datasets/md/b8.md#visium-spatial-gene-expression-lung-ozidaghhakr2kuhk0000), [visium-spatial-gene-expression-lung-ir8wapddv0ng0vvt0000](/datasets/md/5e.md#visium-spatial-gene-expression-lung-ir8wapddv0ng0vvt0000), [visium-spatial-gene-expression-lung-nu3v9eyuuycx6ba30000](/datasets/md/a8.md#visium-spatial-gene-expression-lung-nu3v9eyuuycx6ba30000) ## Targeting the lipid metabolism proteins FASN and GPAM in alveolar type II cells decreases lung metastasis - Page: /collections/geo-gse318532/ - Kind: comparison - Datasets: 2 - Reference: PMID:41778850 - Design: 6–8-week-old female Balb/c mice were inoculated with 4T1 (1 x 10^6) cells in the mammary fat pad. Mice were euthanized after 21-23 days. Lungs from either tumour-bearing or control mice were taken for the analysis. Visium spatial transcriptomics analysis was carried out according to the manufacturer’s instructions (10x Genomics) with the following parameters: Fresh-frozen mouse either control or metastatic lung tissues derived from 4T1 m.f.p. injection model was processed for spatial gene expression profiling using the 10x Genomics Visium Spatial Gene Expression platform (Visium Slide PN-2000233, SN: V13J17-305). Tissue sections were mounted on a Visium Spatial Gene Expression Slide with four capture areas, each containing ~5,000 spatially barcoded spots. Following fixation and hematoxylin and eosin (H&E) staining, tissue permeabilization was performed for 18 minutes—a duration determined through prior tissue optimization using the 10x Genomics Tissue Optimization protocol (CG000238). mRNA released from permeabilized tissue was hybridized to oligonucleotides on the slide, and reverse transcription was carried out in situ to generate spatially barcoded cDNA. Subsequent library preparation followed the manufacturer's protocol (Visium Spatial Gene Expression Reagent Kits User Guide, CG000239 Rev F), including second-strand synthesis, cDNA amplification, enzymatic fragmentation, end repair, adaptor ligation, and sample index PCR. Libraries were sequenced on an Illumina platform (NovaSeq 6000) using paired-end sequencing (Read 1: 28 bp, Read 2: 90 bp) at a target depth of (50k reads per cell/spot). - Members: [visium-spatial-gene-expression-lung-cxacyygpbnrzffpu0000](/datasets/md/d2.md#visium-spatial-gene-expression-lung-cxacyygpbnrzffpu0000), [visium-spatial-gene-expression-lung-c6cdz8ski1vy2ktz0000](/datasets/md/d4.md#visium-spatial-gene-expression-lung-c6cdz8ski1vy2ktz0000) ## Spatial Transcriptomics Analysis of inflamed versus healthy Dental Pulps - Page: /collections/geo-gse322883/ - Kind: comparison - Datasets: 4 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE322883 - Design: To evaluate the inflammatory profile of several degrees of dental pulpitis beyond clinical diagnosis, we analysed dental pulp samples by spatial transcriptomics. Our samples were one healthy pulp, one clinically diagnosed reversible pulpitis and two clinically diagnosed irreversible pulpitis. - Members: [visium-spatial-gene-expression-dental-pulp-li8fhwwq7ku9qezk0000](/datasets/md/dc.md#visium-spatial-gene-expression-dental-pulp-li8fhwwq7ku9qezk0000), [visium-spatial-gene-expression-dental-pulp-khuzzjthru0lhmxe0000](/datasets/md/ac.md#visium-spatial-gene-expression-dental-pulp-khuzzjthru0lhmxe0000), [visium-spatial-gene-expression-dental-pulp-ov2imx5y1kcxho2r0000](/datasets/md/9b.md#visium-spatial-gene-expression-dental-pulp-ov2imx5y1kcxho2r0000), [visium-spatial-gene-expression-dental-pulp-ybhmop7tfl5y3bvz0000](/datasets/md/37.md#visium-spatial-gene-expression-dental-pulp-ybhmop7tfl5y3bvz0000) ## Spatial transcriptomic analysis of mouse liver in a high-fat diet model with kimchi supplementation - Page: /collections/geo-gse326636/ - Kind: comparison - Datasets: 4 - Reference: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE326636 - Design: Male C57BL/6J mouse liver samples from dietary intervention groups were analyzed using 10x Genomics Visium Spatial Gene Expression. Each sample represents one liver section profiled as an independent Visium library. The four samples correspond to the following conditions: Liv_N-3, ND; Liv_H-4, HFD; Liv_K-4, S-K; and Liv_S2-7, LMS-K. The study was designed to compare spatially resolved hepatic transcriptional patterns among dietary groups, with emphasis on zonation-associated differences across the portal-to-central axis. - Members: [visium-spatial-gene-expression-liver-ifnhvmkfitdrhknd0001](/datasets/md/1b.md#visium-spatial-gene-expression-liver-ifnhvmkfitdrhknd0001), [visium-spatial-gene-expression-liver-cggjcq6nhn40kcgb0000](/datasets/md/b1.md#visium-spatial-gene-expression-liver-cggjcq6nhn40kcgb0000), [visium-spatial-gene-expression-liver-mdpzpqw8qad5dip30000](/datasets/md/c0.md#visium-spatial-gene-expression-liver-mdpzpqw8qad5dip30000), [visium-spatial-gene-expression-liver-vqsktoponk35txux0000](/datasets/md/20.md#visium-spatial-gene-expression-liver-vqsktoponk35txux0000) ## Integrated multimodal cell atlas of Alzheimer's disease. - Page: /collections/seaad-mtg-merfish/ - Kind: replicates - Datasets: 64 - Reference: 10.1038/s41593-024-01774-5 - Members: [vizgen-merscope-middle-temporal-gyrus-ysxhr8jijzi7ybhe0000](/datasets/md/9e.md#vizgen-merscope-middle-temporal-gyrus-ysxhr8jijzi7ybhe0000), [vizgen-merscope-middle-temporal-gyrus-lgak75mrxjch2rql0000](/datasets/md/3d.md#vizgen-merscope-middle-temporal-gyrus-lgak75mrxjch2rql0000), [vizgen-merscope-middle-temporal-gyrus-3g5bghfijqak1q2h0000](/datasets/md/6b.md#vizgen-merscope-middle-temporal-gyrus-3g5bghfijqak1q2h0000), [vizgen-merscope-middle-temporal-gyrus-wttfzbtldnalda5s0000](/datasets/md/ef.md#vizgen-merscope-middle-temporal-gyrus-wttfzbtldnalda5s0000), [vizgen-merscope-middle-temporal-gyrus-4dzf48eh0mqeyue10000](/datasets/md/07.md#vizgen-merscope-middle-temporal-gyrus-4dzf48eh0mqeyue10000), [vizgen-merscope-middle-temporal-gyrus-pdrqlfbvyny1yjd60000](/datasets/md/9a.md#vizgen-merscope-middle-temporal-gyrus-pdrqlfbvyny1yjd60000), [vizgen-merscope-middle-temporal-gyrus-lq3bpv0u0ssjheog0000](/datasets/md/45.md#vizgen-merscope-middle-temporal-gyrus-lq3bpv0u0ssjheog0000), [vizgen-merscope-middle-temporal-gyrus-3gibmpo4njiyiebo0000](/datasets/md/76.md#vizgen-merscope-middle-temporal-gyrus-3gibmpo4njiyiebo0000), [vizgen-merscope-middle-temporal-gyrus-frdf0cun8jje89wt0000](/datasets/md/6a.md#vizgen-merscope-middle-temporal-gyrus-frdf0cun8jje89wt0000), [vizgen-merscope-middle-temporal-gyrus-4vcbppplltk933vj0000](/datasets/md/d5.md#vizgen-merscope-middle-temporal-gyrus-4vcbppplltk933vj0000), [vizgen-merscope-middle-temporal-gyrus-k3ixw7of9jfnikr20000](/datasets/md/ef.md#vizgen-merscope-middle-temporal-gyrus-k3ixw7of9jfnikr20000), [vizgen-merscope-middle-temporal-gyrus-upatb7ks7sloduw70000](/datasets/md/b3.md#vizgen-merscope-middle-temporal-gyrus-upatb7ks7sloduw70000), [vizgen-merscope-middle-temporal-gyrus-vrdheas9ipdjpvs90000](/datasets/md/5b.md#vizgen-merscope-middle-temporal-gyrus-vrdheas9ipdjpvs90000), [vizgen-merscope-middle-temporal-gyrus-2fktb9tbydr3va0n0000](/datasets/md/cd.md#vizgen-merscope-middle-temporal-gyrus-2fktb9tbydr3va0n0000), [vizgen-merscope-middle-temporal-gyrus-rkxakggqvpsoahiw0000](/datasets/md/b4.md#vizgen-merscope-middle-temporal-gyrus-rkxakggqvpsoahiw0000), [vizgen-merscope-middle-temporal-gyrus-kepcuyh6utmizhjc0000](/datasets/md/8a.md#vizgen-merscope-middle-temporal-gyrus-kepcuyh6utmizhjc0000), [vizgen-merscope-middle-temporal-gyrus-hb67fbgag615o9va0000](/datasets/md/c8.md#vizgen-merscope-middle-temporal-gyrus-hb67fbgag615o9va0000), [vizgen-merscope-middle-temporal-gyrus-6lvjsv5ico5gc9by0000](/datasets/md/a7.md#vizgen-merscope-middle-temporal-gyrus-6lvjsv5ico5gc9by0000), [vizgen-merscope-middle-temporal-gyrus-e3lqmbsibrkvcar70000](/datasets/md/bc.md#vizgen-merscope-middle-temporal-gyrus-e3lqmbsibrkvcar70000), [vizgen-merscope-middle-temporal-gyrus-jdhdq93cnqsmuzqk0000](/datasets/md/0e.md#vizgen-merscope-middle-temporal-gyrus-jdhdq93cnqsmuzqk0000), [vizgen-merscope-middle-temporal-gyrus-c66vtv6oq58o3syw0000](/datasets/md/a1.md#vizgen-merscope-middle-temporal-gyrus-c66vtv6oq58o3syw0000), [vizgen-merscope-middle-temporal-gyrus-r8zrwm6zg2tajwet0000](/datasets/md/e2.md#vizgen-merscope-middle-temporal-gyrus-r8zrwm6zg2tajwet0000), [vizgen-merscope-middle-temporal-gyrus-h3rycrc32vo3vvqe0000](/datasets/md/23.md#vizgen-merscope-middle-temporal-gyrus-h3rycrc32vo3vvqe0000), [vizgen-merscope-middle-temporal-gyrus-ryg5xjmta2df21bd0000](/datasets/md/b9.md#vizgen-merscope-middle-temporal-gyrus-ryg5xjmta2df21bd0000), [vizgen-merscope-middle-temporal-gyrus-qoznselagyapviz20000](/datasets/md/df.md#vizgen-merscope-middle-temporal-gyrus-qoznselagyapviz20000), [vizgen-merscope-middle-temporal-gyrus-0qux4yucp8s5buc20000](/datasets/md/df.md#vizgen-merscope-middle-temporal-gyrus-0qux4yucp8s5buc20000), [vizgen-merscope-middle-temporal-gyrus-ajgs1iei9r1torwy0000](/datasets/md/53.md#vizgen-merscope-middle-temporal-gyrus-ajgs1iei9r1torwy0000), [vizgen-merscope-middle-temporal-gyrus-hosv6bkbkhptbl8g0000](/datasets/md/5d.md#vizgen-merscope-middle-temporal-gyrus-hosv6bkbkhptbl8g0000), [vizgen-merscope-middle-temporal-gyrus-wjy2g11d4d4difgu0000](/datasets/md/44.md#vizgen-merscope-middle-temporal-gyrus-wjy2g11d4d4difgu0000), [vizgen-merscope-middle-temporal-gyrus-7lucr7c0wtncpryy0000](/datasets/md/60.md#vizgen-merscope-middle-temporal-gyrus-7lucr7c0wtncpryy0000), [vizgen-merscope-middle-temporal-gyrus-3krcpo4uahznb1om0000](/datasets/md/91.md#vizgen-merscope-middle-temporal-gyrus-3krcpo4uahznb1om0000), [vizgen-merscope-middle-temporal-gyrus-efvazqdcek6wvtos0000](/datasets/md/98.md#vizgen-merscope-middle-temporal-gyrus-efvazqdcek6wvtos0000), [vizgen-merscope-middle-temporal-gyrus-eya7kmtvix7aeoz90000](/datasets/md/0b.md#vizgen-merscope-middle-temporal-gyrus-eya7kmtvix7aeoz90000), [vizgen-merscope-middle-temporal-gyrus-xfnizs8fv6lnhwjy0000](/datasets/md/14.md#vizgen-merscope-middle-temporal-gyrus-xfnizs8fv6lnhwjy0000), [vizgen-merscope-middle-temporal-gyrus-b8jnjavpgiwgrxoe0000](/datasets/md/52.md#vizgen-merscope-middle-temporal-gyrus-b8jnjavpgiwgrxoe0000), [vizgen-merscope-middle-temporal-gyrus-0yetdjey77wfw4io0000](/datasets/md/9c.md#vizgen-merscope-middle-temporal-gyrus-0yetdjey77wfw4io0000), [vizgen-merscope-middle-temporal-gyrus-ty8pfptp6n8chcxf0000](/datasets/md/8e.md#vizgen-merscope-middle-temporal-gyrus-ty8pfptp6n8chcxf0000), [vizgen-merscope-middle-temporal-gyrus-qf38bfxgd9xyccvn0000](/datasets/md/05.md#vizgen-merscope-middle-temporal-gyrus-qf38bfxgd9xyccvn0000), [vizgen-merscope-middle-temporal-gyrus-bxhiv0oa5qn60mef0000](/datasets/md/4e.md#vizgen-merscope-middle-temporal-gyrus-bxhiv0oa5qn60mef0000), [vizgen-merscope-middle-temporal-gyrus-re0lvbvratirsewz0000](/datasets/md/61.md#vizgen-merscope-middle-temporal-gyrus-re0lvbvratirsewz0000), [vizgen-merscope-middle-temporal-gyrus-1eexmwwkybwvzpl50000](/datasets/md/cb.md#vizgen-merscope-middle-temporal-gyrus-1eexmwwkybwvzpl50000), [vizgen-merscope-middle-temporal-gyrus-cezoi9vi94x0i6jt0000](/datasets/md/ce.md#vizgen-merscope-middle-temporal-gyrus-cezoi9vi94x0i6jt0000), [vizgen-merscope-middle-temporal-gyrus-oof3nxkhjdglspua0000](/datasets/md/6c.md#vizgen-merscope-middle-temporal-gyrus-oof3nxkhjdglspua0000), [vizgen-merscope-middle-temporal-gyrus-ix900ag4fmsfdrao0000](/datasets/md/bf.md#vizgen-merscope-middle-temporal-gyrus-ix900ag4fmsfdrao0000), [vizgen-merscope-middle-temporal-gyrus-yfxuzk0cfpz8sjcd0000](/datasets/md/16.md#vizgen-merscope-middle-temporal-gyrus-yfxuzk0cfpz8sjcd0000), [vizgen-merscope-middle-temporal-gyrus-ob77d84fzaag3md30000](/datasets/md/14.md#vizgen-merscope-middle-temporal-gyrus-ob77d84fzaag3md30000), [vizgen-merscope-middle-temporal-gyrus-tyecd61cifmmkjhk0000](/datasets/md/30.md#vizgen-merscope-middle-temporal-gyrus-tyecd61cifmmkjhk0000), [vizgen-merscope-middle-temporal-gyrus-89zzotqicvnbr6or0000](/datasets/md/3d.md#vizgen-merscope-middle-temporal-gyrus-89zzotqicvnbr6or0000), [vizgen-merscope-middle-temporal-gyrus-lkuayfnnct2uktbo0000](/datasets/md/fa.md#vizgen-merscope-middle-temporal-gyrus-lkuayfnnct2uktbo0000), [vizgen-merscope-middle-temporal-gyrus-hvc6s4tel8jxw2a00000](/datasets/md/d7.md#vizgen-merscope-middle-temporal-gyrus-hvc6s4tel8jxw2a00000), [vizgen-merscope-middle-temporal-gyrus-kpjryeequsxpifmb0000](/datasets/md/87.md#vizgen-merscope-middle-temporal-gyrus-kpjryeequsxpifmb0000), [vizgen-merscope-middle-temporal-gyrus-jsizpv0jejirm7oc0000](/datasets/md/5e.md#vizgen-merscope-middle-temporal-gyrus-jsizpv0jejirm7oc0000), [vizgen-merscope-middle-temporal-gyrus-xd97gfsckliwushi0000](/datasets/md/4b.md#vizgen-merscope-middle-temporal-gyrus-xd97gfsckliwushi0000), [vizgen-merscope-middle-temporal-gyrus-c2x6emdjhnwcfj490000](/datasets/md/e6.md#vizgen-merscope-middle-temporal-gyrus-c2x6emdjhnwcfj490000), [vizgen-merscope-middle-temporal-gyrus-ukc0zusff6yxfwjq0000](/datasets/md/b0.md#vizgen-merscope-middle-temporal-gyrus-ukc0zusff6yxfwjq0000), [vizgen-merscope-middle-temporal-gyrus-f3nfyidw1dp6zgyf0000](/datasets/md/d0.md#vizgen-merscope-middle-temporal-gyrus-f3nfyidw1dp6zgyf0000), [vizgen-merscope-middle-temporal-gyrus-rf6dj7st07jewvor0000](/datasets/md/22.md#vizgen-merscope-middle-temporal-gyrus-rf6dj7st07jewvor0000), [vizgen-merscope-middle-temporal-gyrus-0ocoguvr5gtrmeqg0000](/datasets/md/91.md#vizgen-merscope-middle-temporal-gyrus-0ocoguvr5gtrmeqg0000), [vizgen-merscope-middle-temporal-gyrus-hldbmzy8nsoxk0wq0000](/datasets/md/27.md#vizgen-merscope-middle-temporal-gyrus-hldbmzy8nsoxk0wq0000), [vizgen-merscope-middle-temporal-gyrus-l7ajkbsnetufb9wy0000](/datasets/md/81.md#vizgen-merscope-middle-temporal-gyrus-l7ajkbsnetufb9wy0000), [vizgen-merscope-middle-temporal-gyrus-hufyphoavt50gckm0000](/datasets/md/81.md#vizgen-merscope-middle-temporal-gyrus-hufyphoavt50gckm0000), [vizgen-merscope-middle-temporal-gyrus-gzx1bxegnjnlmjqr0000](/datasets/md/83.md#vizgen-merscope-middle-temporal-gyrus-gzx1bxegnjnlmjqr0000), [vizgen-merscope-middle-temporal-gyrus-ur1773jfa1lxsfpb0000](/datasets/md/d5.md#vizgen-merscope-middle-temporal-gyrus-ur1773jfa1lxsfpb0000), [vizgen-merscope-middle-temporal-gyrus-ldn98idsu61covak0000](/datasets/md/bc.md#vizgen-merscope-middle-temporal-gyrus-ldn98idsu61covak0000) ## Molecularly defined and spatially resolved cell atlas of the whole mouse brain. - Page: /collections/abc-zhuang-abca-3/ - Kind: publication - Datasets: 23 - Reference: 10.1038/s41586-023-06808-9 - Members: [merfish-brain-kxw9f3gimkpdldrx0000](/datasets/md/8d.md#merfish-brain-kxw9f3gimkpdldrx0000), [merfish-brain-ymgnkqsvkxbsefku0000](/datasets/md/ac.md#merfish-brain-ymgnkqsvkxbsefku0000), [merfish-brain-7bwqwnnop2vlnxyr0000](/datasets/md/c8.md#merfish-brain-7bwqwnnop2vlnxyr0000), [merfish-brain-naoqi7fzmwpdmzwl0000](/datasets/md/54.md#merfish-brain-naoqi7fzmwpdmzwl0000), [merfish-brain-j6eoqh1ruvu1dcm20000](/datasets/md/24.md#merfish-brain-j6eoqh1ruvu1dcm20000), [merfish-brain-xriyas046coy7m9v0000](/datasets/md/cd.md#merfish-brain-xriyas046coy7m9v0000), [merfish-brain-prrnwedqbucfp7gf0000](/datasets/md/1b.md#merfish-brain-prrnwedqbucfp7gf0000), [merfish-brain-6dzgjqri87y1zxpd0000](/datasets/md/da.md#merfish-brain-6dzgjqri87y1zxpd0000), [merfish-brain-8xk9xw1c5teju8tk0000](/datasets/md/b1.md#merfish-brain-8xk9xw1c5teju8tk0000), [merfish-brain-nf4yqqj0blrgj6kg0000](/datasets/md/6c.md#merfish-brain-nf4yqqj0blrgj6kg0000), [merfish-brain-xzte0yys38w3pfwh0000](/datasets/md/47.md#merfish-brain-xzte0yys38w3pfwh0000), [merfish-brain-j3hvdocc8ycv7lky0000](/datasets/md/96.md#merfish-brain-j3hvdocc8ycv7lky0000), [merfish-brain-ztjpibcqm7rg0e9i0000](/datasets/md/8f.md#merfish-brain-ztjpibcqm7rg0e9i0000), [merfish-brain-rjg7kzljygqccuvv0000](/datasets/md/4f.md#merfish-brain-rjg7kzljygqccuvv0000), [merfish-brain-zfydf4b6xzioqbv60000](/datasets/md/a7.md#merfish-brain-zfydf4b6xzioqbv60000), [merfish-brain-f4otamqyajqtm5hu0000](/datasets/md/c4.md#merfish-brain-f4otamqyajqtm5hu0000), [merfish-brain-dtas94trncp0mm5p0000](/datasets/md/7f.md#merfish-brain-dtas94trncp0mm5p0000), [merfish-brain-q9erfvyytome2wec0000](/datasets/md/f7.md#merfish-brain-q9erfvyytome2wec0000), [merfish-brain-cep8tebcgsodk0eh0000](/datasets/md/d5.md#merfish-brain-cep8tebcgsodk0eh0000), [merfish-brain-vfjpzbrqemxmazr90000](/datasets/md/2d.md#merfish-brain-vfjpzbrqemxmazr90000), [merfish-brain-tayzbn4sgneloiuh0000](/datasets/md/0e.md#merfish-brain-tayzbn4sgneloiuh0000), [merfish-brain-lihtbhylu2yyuxhi0000](/datasets/md/df.md#merfish-brain-lihtbhylu2yyuxhi0000), [merfish-brain-xtjnbw8z6ugnldbz0000](/datasets/md/c5.md#merfish-brain-xtjnbw8z6ugnldbz0000)