Spatial organization

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Mus musculus (584)
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groundwater metagenome (3)
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Organisms

Homo sapiens (336)
Mus musculus (331)
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human oral metagenome (2)
Mus musculus musculus x Mus musculus castaneus (1)
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Technology Type

Mass Spectrometry (82)
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Instrument Platform

Illumina NovaSeq 6000 (25)
Illumina HiSeq 2500 (15)
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NextSeq 500 (10)
Illumina HiSeq 4000 (7)
N/A (6)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (4)
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Scanning of was performed on an Axon 4000B scanner (1)
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Linux Beowulf cluster (1)

Publication Date

2026 (282)
2025 (147)
2024 (123)
2013 (121)
2014 (105)
2012 (99)
2010 (90)
2022 (88)
2021 (88)
2015 (85)
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2011 (70)
2019 (57)
2017 (54)
2016 (54)
2020 (51)
2009 (46)
2008 (43)
2018 (32)
2007 (29)
2005 (15)
2006 (12)
2004 (7)

CHEBI ID

CHEBI:1014 (1)
CHEBI:133325 (1)
CHEBI:134236 (1)
CHEBI:134237 (1)
CHEBI:134490 (1)
CHEBI:136225 (1)
CHEBI:136235 (1)
CHEBI:136239 (1)
CHEBI:136257 (1)
CHEBI:136489 (1)
CHEBI:141589 (1)
CHEBI:15356 (1)
CHEBI:156190 (1)
CHEBI:15698 (1)
CHEBI:15741 (1)
CHEBI:15756 (1)
CHEBI:15971 (1)
CHEBI:16024 (1)
CHEBI:16335 (1)
CHEBI:16449 (1)
CHEBI:16485 (1)
CHEBI:16551 (1)
CHEBI:165564 (1)
CHEBI:16919 (1)
CHEBI:16958 (1)
CHEBI:16996 (1)
CHEBI:170068 (1)
CHEBI:170122 (1)
CHEBI:170156 (1)
CHEBI:170157 (1)

Metabolite Name

1-octadecyl-sn-glycero-3-phosphoinositol-3-phosphate (1)
11(12)-EET (1)
11,12,15-THET (1)
11,12-DHET (1)
11-HEPE (1)
11-dehydrocorticosterone (1)
12(13)-EpOME (1)
12,13-DiHOME (1)
12-HETE (1)
13-HDoHE (1)
13-HODE (1)
13-oxo-ODE (1)
14(15)-EET (1)
14,15-dihydroxyeicosatrienoic acid (1)
14,15-dihydroxyeicosatrienoic acid (14,15-DHET) (1)
15-HETE (1)
15-deoxyPGJ2 (1)
15-oxo-ETE (1)
18-hydroxycorticosterone (1)
19-HETE (1)
2-hydroxyoctanoic acid (1)
20-HETE (1)
5(6)-EET (1)
5,6-DHET (1)
5-oxo-ETE (1)
8,9-DHET (1)
8-HETE (1)
8-iso-PGE2 (1)
8-iso-PGF2alpha (1)
9(10)-EpOME (1)

First Public Date

2026 (278)
2025 (143)
2024 (124)
2021 (80)
2023 (77)
2022 (63)
2019 (61)
2017 (46)
2020 (45)
2014 (44)
2013 (30)
2018 (21)
2016 (14)
2015 (14)
2012 (1)
2010 (1)

Modelling Approach

Agent-based model (1)
Logical model (1)
Ordinary differential equation model (1)

Lab affiliation

Carnegie Mass Spectrometry Facility (2)
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic (2)
1.Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA 2.Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. Netherlands Proteomic Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands. (1)
Biomolecular Mass Spectrometry and Proteomics, BijvoetCenter for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands (1)
Cambridge University (1)
Carnegie Science Institution at Stanford (1)
College of chemistry and molecular engineering, Peking University (1)
College of chemistry and molecular engineering, Peking University. (1)
Core Facility Proteomics, Department of Clinical Medicine, University Medical Center Goettingen, Germany (1)
Core Facilitz Proteomics, Department of Clinical Chemistry, University Medical Center Goettingen (1)
DIMEVET- Unversità degli Studi di Milano (1)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg im Breisgau, Germany (1)
Department of Biochemistry, University of Cambridge, UK (1)
Department of Biochemistry, University of Cambridge, United Kingdom (1)
Department of Bioengineering, Stanford University, Stanford, CA, USA (1)
Department of Biology, Technical University of Darmstadt, Darmstadt, Germany (1)
Department of Cell Biology and Immunnology (1)
Department of Cellular Biology, University of Georgia, Athens, GA 30602 (1)
Department of Human Structure and Repair, Laboratory of Experimental Cancer Research, Ghent University, Belgium3. Cancer Research Institute Ghent (CRIG), Ghent University, Belgium (1)
Department of Laboratory Medicine and Pathology Mayo Clinic, Rochester USA (1)
Department of Molecular Biology, Princeton University, Princeton, NJ, USA (1)
Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA. (1)
Department of Psychiatry, Oregon Health & Science University, Portland, OR (1)
Dept. of Bioloy, University of Rome Tor Vergata (1)
Division of Blood Cells and Blood Cancer The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville Victoria, Australia, 3050 (1)
Division of Vascular Oncology and Metastasis Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany. (1)
Division of Vascular Oncology and Metastasis Research,German Cancer Research Center (DKFZ), Heidelberg, Germany. European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany. (1)
Duke University Eye Center (1)
European Institute of Oncology (1)

IsPrivate

False (3)

Submitter Keywords

TransQST (1)

Classification

bacteria (14)
protozoa (7)
helminths (2)
viruses (2)
fungi (1)

Modification

-17.026549 (1)
15.994915 (1)
31.989829 (1)
42.010565 (1)
57.021464 (1)
79.966331 (1)
N6 (1)
Not available (1)

Study type

Transcription profiling by array (351)
ChIP-seq (114)
RNA-seq of coding RNA (77)
Other (49)
ChIP-chip by tiling array (25)
Comparative genomic hybridization by array (24)
Unknown experiment type (12)
ChIP-chip by array (11)
RNA-seq of coding RNA from single cells (11)
Methylation profiling by high throughput sequencing (11)
Spatial transcriptomics by high-throughput sequencing (8)
DNA-seq (8)
RNA-seq of non coding RNA (8)
Methylation profiling by array (7)
Single nucleus RNA sequencing (5)
RNA-seq of total RNA (4)
Animal - One-color microarray (3)
Genotyping by array (3)
High-throughput sequencing (2)
Animal - High-throughput sequencing (2)
Cell line - High-throughput sequencing (2)
Transcription profiling by tiling array (2)
Bisulfite-seq (2)
Hi-C (2)
ScATAC-seq (2)
MicroRNA profiling by array (2)
Proteomic profiling by array (2)
Baseline (1)
RNA-seq of non coding RNA from single cells (1)
Human - Two-color microarray (1)

Release Date

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2007 (57)
2006 (36)
2005 (30)
2004 (21)
2000 (9)
2001 (7)
2002 (4)
2003 (3)
1999 (1)
1998 (1)
1997 (1)

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Chromosomal translocations are guided by the spatial organization of the genome

The extent to which the three-dimensional organization of the genome contributes to chromosomal translocations is an important question in cancer genomics. We now have generated a high-resolution Hi-C spatial organization map of the G1-arrested mouse pro-B cell genome and mapped translocations from...

ORGANISM(S): Mus musculus

2012-02-16 | E-GEOD-35519 | biostudies-arrayexpress

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

Though important for gene regulation most studies of genome organisation use either fluorescence in situ hybridisation (FISH) or chromosome conformation capture (3C) methods. FISH directly visualises the spatial relationship of sequences, but is usually applied to a few loci at a time. The frequency...

ORGANISM(S): Mus musculus

2015-01-02 | E-GEOD-61814 | biostudies-arrayexpress

Spatial organization of transcribed eukaryotic genes (ChIP-seq)

The nuclear organization of the genome is accepted as an important feature of gene expression regulation. However, it has remained unknown what the spatial organization of a single transcribed gene is. Here, we made use of several long highly expressed mammalian genes to describe their structure and...

ORGANISM(S): Mus musculus

2021-12-06 | E-MTAB-9060 | biostudies-arrayexpress

Spatial Organization of Transcribed Eukaryotic Genes

PRJNA633182 | ENA

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 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

Distinct spatial organization governs oral mucosal immunity

PRJNA1259397 | ENA

Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

Understanding the topological configurations of chromatin can reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor...

ORGANISM(S): Mus musculus

2013-05-24 | E-GEOD-36203 | biostudies-arrayexpress

Spatial organization of transcribed eukaryotic genes (ChIP-seq)

PRJEB38291 | ENA

Surface topography guides morphology and spatial patterning of induced pluripotent stem cell colonies

The relevance of topographic cues for commitment of induced pluripotent stem cells (iPSCs) is largely unknown. In this study, we demonstrate that groove-ridge structures with a periodicity in the submicrometer range induce elongation of iPSC colonies, guide the orientation of apical actin fibers, an...

ORGANISM(S): Homo sapiens

2018-10-31 | E-MTAB-7327 | biostudies-arrayexpress

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