spatial transcriptomics

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Transcriptomics (9506)
Unknown (2837)
Genomics (2721)
Other (929)
Proteomics (98)
Models (32)
Metabolomics (12)
Methylation profiling (4)
Multiomics (2)

Organisms

Homo sapiens (3899)
Mus musculus (3212)
Arabidopsis thaliana (495)
Rattus norvegicus (298)
Saccharomyces cerevisiae (260)
Drosophila melanogaster (240)
Danio rerio (128)
Caenorhabditis elegans (97)
Sus scrofa (92)
Bos taurus (84)
Gallus gallus (80)
Schizosaccharomyces pombe (69)
Oryza sativa (62)
Escherichia coli (55)
Zea mays (51)
Macaca mulatta (45)
Streptomyces coelicolor (42)
Salmonella enterica subsp. enterica serovar Typhimurium (38)
Plasmodium falciparum (29)
Solanum lycopersicum (28)
Medicago truncatula (25)
Triticum aestivum (25)
Escherichia coli str. K-12 substr. MG1655 (23)
Candida albicans (22)
Glycine max (20)
Oryza sativa Japonica Group (19)
Ovis aries (19)
Apis mellifera (18)
Hordeum vulgare (16)
Gossypium hirsutum (14)

Organisms

Homo sapiens (1032)
Mus musculus (916)
Rattus norvegicus (26)
Gallus gallus (12)
Danio rerio (11)
Arabidopsis thaliana (11)
Ambystoma mexicanum (6)
Canis lupus familiaris (6)
Sus scrofa (6)
Drosophila melanogaster (5)
Xenopus laevis (4)
Mesocricetus auratus (4)
Macaca fascicularis (4)
Triticum aestivum (4)
Mus (4)
Macaca mulatta (4)
unidentified (4)
Nematostella vectensis (3)
Caenorhabditis elegans (3)
Solanum lycopersicum (3)
Bos taurus (3)
Anableps anableps (2)
Daucus carota (2)
Picea abies (2)
Glycine soja (2)
Populus trichocarpa (2)
Oryctolagus cuniculus (2)
Medicago truncatula (2)
Apis mellifera (2)
Oryza sativa (2)

Repository

biostudies-arrayexpress (6423)
geo (4098)
ENA (2572)
EGA (61)
pride (52)
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MassIVE (30)
iProX (14)
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NODE (10)
PeptideAtlas (2)

Tissue

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Liver (4)
Cell culture (4)
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Malignant cell (2)
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Neuron (2)
Blood serum (2)
Heart (2)
Cell suspension culture (2)
Stem cell (2)
Fibroblast (2)
B cell (2)
Monocyte (2)
Pancreatic tumor (1)
Palate (1)
Orallips (1)
Floor of the mouth (1)
Tongue (1)
Mammary gland (1)
Whole embryo (1)
Cheek (1)
Pancreas (1)
Lymph node (1)
Embryo (1)
Ovarian low malignant potential tumor cell (1)
GSC cell line (1)

Disease

Normal (32)
Rheumatoid arthritis (4)
Prostate cancer (4)
Infiltrating ductal carcinoma (3)
Chronic myeloid leukemia (3)
Head and neck squamous cell carcinoma (3)
Ovarian cancer (3)
Breast cancer (3)
HHV-6B infected (2)
Chronic lymphocytic leukemia (2)
Melanoma (2)
Colorectal adenocarcinoma (2)
None (2)
Wilms tumour (2)
Neuroblastoma (2)
Idiopathic pulmonary fibrosis (2)
Oral squamous cell carcinoma (2)
Astrocytoma (1)
Myelodysplasia (1)
Non tumoral reference sample (1)
Toxicity (1)
HPV positive (1)
Uninjured (1)
High grade glioblastoma (1)
Insulitis and diabetes (1)
Ovarian carcinoma (1)
Malignant testicular germ cell tumor (1)
Wounded; tumour (1)
CVB3 infected (1)
Pseudomonas aeruginosa rsmA mutant infected (1)

Technology Type

Mass Spectrometry (52)
Bottom-up proteomics (26)
Data-independent acquisition (15)
Shotgun proteomics (13)
Mass spectrometry (7)
Data-dependent acquisition (7)
Mass spectrometry assay (5)
Mass spectrometry imaging (3)
SWATH MS (2)
Top-down proteomics (2)
ILLUMINA, Illumina HiSeq 2500, NextSeq 500, Nanostring (1)
NextSeq 500, ILLUMINA (1)
Illumina Genome Analyzer, Illumina HiSeq 2000, Illumina MiSeq, Affymetrix_U133plus2- (1)
DiaPASEF (1)
Affinity purification coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (176)
NextSeq 500 (97)
Illumina HiSeq 2500 (88)
Illumina HiSeq 4000 (80)
Illumina HiSeq 2000 (73)
Axon GenePix 4000B scanning hardware (23)
NextSeq 550 (23)
Illumina Genome Analyzer IIx (13)
Axon- GenePix4000B (9)
Illumina NovaSeq X (9)
DNBSEQ-G400 (9)
Illumina HiSeq 3000 (9)
GenePix 4000B [Axon Instruments] (8)
Scanning hardware (8)
Affymetrix GeneChip(R) HT Scanner (7)
G2500A Hewlett Packard (7)
ScanArray 5000 [PerkinElmer] (7)
Affymetrix Fluidics Station 400 (7)
Illumina MiSeq (7)
GenePix 4000A [Axon Instruments] (6)
N/A (6)
Agilent 2100 Bioanalyzer (5)
Generation III Array Scanner [Amersham] (5)
G2565BA DNA microarray scanner [Agilent] (5)
Vortex (5)
NextSeq 2000 (5)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (4)
Fluidigm C1 (4)
Illumina HiScanSQ (4)
ScanArray Express HT [PerkinElmer] (4)

Publication Date

2026 (1098)
2010 (971)
2025 (920)
2013 (823)
2024 (716)
2012 (700)
2014 (651)
2011 (609)
2023 (557)
2015 (534)
2008 (438)
2022 (389)
2016 (382)
2009 (363)
2021 (282)
2007 (222)
2020 (191)
2018 (140)
2005 (139)
2017 (136)
2019 (128)
2006 (119)
2004 (118)
2003 (29)
2002 (1)

UNIPROT ID/AC

Z4YJZ7 (2)
V9GXM1 (2)
S4R2L4 (2)
Q9Z329 (2)
Q9Z2X8 (2)
Q9Z2U2 (2)
Q9Z2E1 (2)
Q9Z2D1 (2)
Q9Z2C9 (2)
Q9Z1P6 (2)
Q9Z148-2 (2)
Q9Z0Z7 (2)
Q9Z0Z4 (2)
Q9Z0Y1 (2)
Q9Z0S9 (2)
Q9Z0S5 (2)
Q9Z0J0 (2)
Q9Z0H1 (2)
Q9Z0F4 (2)
Q9WVH4 (2)
Q9WVA2 (2)
Q9WV98 (2)
Q9WV96 (2)
Q9WV52 (2)
Q9WUU9 (2)
Q9WU62 (2)
Q9R257 (2)
Q9R207 (2)
Q9R1Z7 (2)
Q9R1K9 (2)

ENSEMBL ID

ENSMUSP00000141637 (2)
ENSMUSG00000096410 (2)
ENSMUSG00000095442 (2)
ENSMUSG00000094797 (2)
ENSMUSG00000094075 (2)
ENSMUSG00000093896 (2)
ENSMUSG00000027651 (2)
ENSMUSG00000021039 (2)
ENSMUSG00000094930 (2)
ENSMUSP00000141097 (2)
ENSMUSG00000098557 (2)
ENSMUSG00000103290 (1)
ENSMUSG00000096326 (1)
ENSMUSG00000095753 (1)
ENSMUSG00000095416 (1)
ENSMUSG00000094689 (1)
ENSMUSG00000094509 (1)
ENSMUSG00000094502 (1)
ENSMUSG00000094356 (1)
ENSMUSG00000093894 (1)
ENSMUSG00000076532 (1)
ENSMUSG00000076508 (1)
ENSMUSG00000095210 (1)
ENSMUSG00000076731 (1)
ENSMUSG00000098814 (1)
ENSMUSG00000094652 (1)
ENSMUSG00000094546 (1)
ENSMUSG00000076695 (1)
ENSMUSG00000076586 (1)
ENSMUSG00000072849 (1)

CHEBI ID

CHEBI:3110 (32)
CHEBI:16874 (32)
CHEBI:16565 (32)
CHEBI:27515 (32)
CHEBI:36528 (32)
CHEBI:15958 (32)
CHEBI:17927 (32)
CHEBI:28101 (32)
CHEBI:28865 (32)
CHEBI:17687 (32)
CHEBI:36274 (32)
CHEBI:16675 (32)
CHEBI:28058 (32)
CHEBI:17292 (32)
CHEBI:16091 (32)
CHEBI:28648 (32)
CHEBI:28175 (32)
CHEBI:18163 (32)
CHEBI:17798 (32)
CHEBI:17364 (32)
CHEBI:17474 (32)
CHEBI:27870 (32)
CHEBI:27910 (32)
CHEBI:17500 (32)
CHEBI:17737 (32)
CHEBI:15700 (32)
CHEBI:17123 (32)
CHEBI:17864 (32)
CHEBI:16797 (32)
CHEBI:16427 (32)

Metabolite Name

LysoPA(20:4(8Z,11Z,14Z,17Z)/0:0) (3)
3-hydroxyoctanoyl carnitine (3)
D-Pipecolic acid (3)
MG(18:3(6Z,9Z,12Z)/0:0/0:0) (3)
P,P-Dioctyldiphenylamine (3)
Linoleamide (3)
Pentadecanoic acid (3)
Benzaldehyde (3)
9-OxoODE (3)
12-Hydroxydodecanoic acid (3)
Adenosine (3)
Cytidine (3)
Inosine (3)
Hypoxanthine (3)
Oxidized Latia luciferin (2)
Cyclopentanone (2)
Boschnialactone (2)
Trihexosylceramide (d18:1/12:0) (2)
PGP(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:2(11Z,14Z)) (2)
Oleanolic acid 3-[rhamnosyl-(1->4)-glucosyl-(1->6)-glucoside] (2)
Neogitogenin 3-[glucosyl-(1->2)-glucosyl-(1->4)-galactoside] (2)
Glycerol 2-(9Z,12Z-octadecadienoate) 1-hexadecanoate 3-O-[alpha-D-galactopyranosyl-(1->6)-beta-D-galactopyranoside] (2)
Agavasaponin C (2)
CDP-DG(i-12:0/i-17:0) (2)
Hebevinoside XIII (2)
PI(20:4(5Z,8Z,11Z,14Z)/20:1(11Z)) (2)
PGP(18:0/22:4(7Z,10Z,13Z,16Z)) (2)
Alpha-Solamarine (2)
Glycerol 1-(9Z-octadecenoate) 2-hexadecanoate 3-octadecanoate (2)
PC(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:5(5Z,8Z,11Z,14Z,17Z)) (2)

First Public Date

2026 (842)
2025 (687)
2024 (478)
2023 (258)
2022 (144)
2021 (78)
2020 (45)
2019 (22)
2018 (6)
2017 (5)
2014 (4)
2015 (2)
2016 (1)

Lab affiliation

Department of Oncology-Pathology, Karolinska Institute and Scilifelab, Solna, Sweden (2)
Zhengzhou University (2)
Biomarker Assay Development 1 Novo Nordisk Park 1 Måløv, Denmark (1)
Figueiredo Lab, Instituto de Medicina Molecular, Lisbon, Portugal (1)
Pathology and Laboratory Medicine Kansas University Medical Center (1)
Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education (1)
Histone Modifications Group Zentrallabor für Proteinanalytik BioMedical Center Faculty of Medicine Ludwig-Maximilians-University of Munich Großhadernerstr. 9 82152 Planegg-Martinsried GERMANY (1)
Washington University, St. Louis (1)
Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (1)
Center for Alzheimer’s Disease and Related Dementias (CARD) National Institutes of Health (NIH) (1)
Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan (1)
Department of Animal Biosciences (HBIO), Swedish University of Agricultural Sciences, Uppsala, SWEDEN (1)
Department of Microbiology, University of Oslo and Oslo University Hospital, Norway (1)
Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany. (1)
Laboratory of Animal Physiology, Department of Biology, FI-20014 University of Turku, Finland (1)
CNRS, Inserm, Nantes Université, Univ Angers, CRIC2NA, Nantes, France (1)
QTAS, or previously DMPK, Abbvie Bioresearch Center (1)
Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA (1)
Max Planck Institute of Biophysics and Max Planck Institute for Brain Research (1)
Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven (1)
UNIL | University of Lausanne Faculty of Biology and Medicine Department of Biomedical Sciences Rue du Bugnon 7 CH-1005 Lausanne (1)
Research & Development, AbbVie, North Chicago, IL, 60064 (1)
Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (1)
Biological Engineering, MIT (1)
Head of Proteomics & Metabolomics Facility (1)
Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (CSIC/USAL/IBSAL). Avda. Universidad de Coimbra, S/N, 37007 Salamanca, Spain. Phone: +34 923294811 Fax: +34 923294743 (1)
Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY (1)
Deutsches Zentrum für Neurodegeneration (DZNE) Technische Universität München (1)
Biomedical Research Institute, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece (1)
Medical University of South Carolina, Department of Cell and Molecular Pharmacology, Charleston, SC 29425, United States (1)

IsPrivate

False (32)

Model Flag

Non Kinetic (32)

Classification

bacteria (3)
viruses (1)
protozoa (1)

Modification

15.994915 (1)
57.021464 (1)

Study type

Transcription profiling by array (3499)
RNA-seq of coding RNA (949)
Comparative genomic hybridization by array (306)
Unknown experiment type (227)
Other (207)
ChIP-chip by tiling array (203)
RNA-seq of non coding RNA (185)
ChIP-chip by array (138)
Methylation profiling by array (124)
RNA-seq of coding RNA from single cells (120)
Transcription profiling by tiling array (82)
Spatial transcriptomics by high-throughput sequencing (60)
Genotyping by array (39)
RNA-seq of total RNA (23)
ATAC-seq (22)
Cell line - High-throughput sequencing (18)
ChIP-seq (15)
MicroRNA profiling by array (15)
Human - High-throughput sequencing (14)
High-throughput sequencing (12)
Animal - High-throughput sequencing (12)
RNAi profiling by array (12)
MicroRNA profiling by high throughput sequencing (12)
Single nucleus RNA sequencing (12)
ScATAC-seq (9)
Transcription profiling by RT-PCR (8)
Transcription profiling by SAGE (7)
CLIP-seq (6)
Human - Single-cell sequencing (5)
Bisulfite-seq (5)

Release Date

2025 (1193)
2010 (946)
2013 (790)
2012 (678)
2024 (669)
2014 (621)
2011 (581)
2023 (552)
2015 (467)
2008 (418)
2009 (343)
2016 (330)
2022 (323)
2026 (247)
2007 (208)
2021 (189)
2005 (137)
2020 (115)
2004 (115)
2006 (106)
2018 (75)
2017 (74)
2019 (72)
2003 (10)
2002 (1)

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Single-Cell and Spatial Multi-Omics Reveal Mechanical Stress Driving Heterogeneous Xylem Development in Populus [Spatial metabolomics_MALDI imaging]

Xylem, the predominant tissue for structural support, forms tension wood with G-layer-rich fibers under mechanical stress. Despite being recognized over a century ago, three key biological questions remained unclear: (1) Are fibers in normal and tension wood distinct cells due to morphological diffe...

2025-06-16 | MTBLS12601 | MetaboLights

Spatial Transcriptomics of the human musculotendinous unit, the myotendinous junction

Identification of cell types in the interphase between muscle and tendon by Visium Spatial Transcriptomics of four human semitendinous muscle-tendon biopsies. Cell types identified by single nuclei RNA seq on similar tissue were localized in situ with the use of Spatial Transcriptomics.

ORGANISM(S): Homo sapiens

2023-03-02 | E-MTAB-12530 | biostudies-arrayexpress

Single-Cell and Spatial Multi-Omics Reveal Mechanical Stress Driving Heterogeneous Xylem Development in Populus [Spatial metabolomics_LCM]

2025-06-16 | MTBLS12561 | MetaboLights

Spatial transcriptomics of human heart development

This experiment uses 10x Genomics Visium HD spatial transcriptomics to characterise the cellular and molecular organisation of the developing human heart.

ORGANISM(S): Homo sapiens

2026-09-23 | E-MTAB-17440 | biostudies-arrayexpress

Single-nucleus RNA-seq (10x Genomics Flex) of wild-type C57BL/6J mouse spleen following Plasmodium berghei ANKA infection, generated as a transcriptome-wide reference for the SpatialBench spatial transcriptomics benchmark

This dataset provides single-nucleus RNA-sequencing (snRNA-seq) profiles of wild-type mouse spleen, generated as a matched, transcriptome-wide reference for the SpatialBench resource benchmarking high-resolution spatial transcriptomics platforms (Visium HD, Xenium and MERSCOPE). Spleens were collect...

ORGANISM(S): Mus musculus

2026-07-07 | E-MTAB-17245 | biostudies-arrayexpress

spatial transcriptomics (10x Visium) of first and second trimester human reproductive tract

spatial transcriptomics by means of 10x Visium of first and second trimester human reproductive tract (including female and male internal and external genitalia)

ORGANISM(S): Homo sapiens

2025-08-06 | E-MTAB-15471 | biostudies-arrayexpress

Spatial transcriptomics of the axolotl forebrain

To investigate spatial heterogeneities in the axolotl forebrain, a coronal section of it was obtained for spatial transcriptomics using Visium V1.

ORGANISM(S): Ambystoma mexicanum

2022-07-20 | E-MTAB-11665 | biostudies-arrayexpress

A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche - Visium

Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microen...

ORGANISM(S): Homo sapiens

2022-01-06 | E-MTAB-11640 | biostudies-arrayexpress

Spatial transcriptomics of human colorectal cancer liver metastatic samples

These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Spatial transcriptomics was performed using 10x Genomics Visium on colorectal cancer liver metastatic patient samples.

ORGANISM(S): Homo sapiens

2025-04-22 | E-MTAB-13655 | biostudies-arrayexpress

Spatial transcriptomics of 8 whole opisthosomas samples from adult female L. sclopetarius spiders

This dataset comprises spatial transcriptomics of 8 whole opisthosomas samples isolated from adult female L. sclopetarius spiders.

ORGANISM(S): Larinioides sclopetarius

2024-06-01 | E-MTAB-14082 | biostudies-arrayexpress

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