Microscopy - OmicsDI

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Genomics (2686)
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Organisms

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Aliivibrio salmonicida LFI1238 (4)
Lupinus angustifolius (3)
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Legionella pneumophila (3)

Organisms

Homo sapiens (551)
Mus musculus (454)
Rattus norvegicus (42)
Danio rerio (26)
Saccharomyces cerevisiae (23)
Escherichia coli (23)
Drosophila melanogaster (22)
Arabidopsis thaliana (19)
Staphylococcus aureus (13)
Caenorhabditis elegans (12)
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Oryctolagus cuniculus (7)
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Gallus gallus (7)
activated sludge metagenome (6)
Plasmodium falciparum (5)
Candida albicans (5)
Schizosaccharomyces pombe (5)
marine metagenome (5)
Chlamydia trachomatis (4)
Escherichia coli str. K-12 substr. MG1655 (4)
Vibrio cholerae (4)
Bacillus subtilis (4)
Zea mays (4)
Paracentrotus lividus (3)
Bacillus subtilis PY79 (3)
Salmo salar (3)
Leishmania donovani (3)

Repository

ENA (2319)
geo (1332)
pride (970)
biostudies-arrayexpress (843)
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iProX (116)
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PeptideAtlas (4)
dbGaP (3)
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FAIRDOMHub (1)

Tissue

Cell culture (159)
Epithelial cell (43)
Brain (41)
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Cell suspension culture (18)
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Whole body (13)
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T cell (11)
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Disease

Disease free (25)
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Normal (5)
Not Available (5)
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Colorectal Tumor Colorectal Cancer (1)
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VEGF-Targeted Near-Infrared Fluorescence imaging in Peritoneal Carcinomatosis (1)
Peritoneal carcinomatosis of colorectal cancer (1)
Monkeypox (1)
Carcinoma (1)
Malignant neoplasm of colon (1)
Glioblastoma (1)

Technology Type

Mass Spectrometry (970)
Shotgun proteomics (432)
Bottom-up proteomics (243)
Data-dependent acquisition (136)
Affinity purification coupled with mass spectrometry proteomics (83)
Chemical cross-linking coupled with mass spectrometry proteomics (70)
Data-independent acquisition (69)
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Fluorescence intensity (38)
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Fluorescence imaging (28)
SWATH MS (27)
HDMSE (23)
Top-down proteomics (20)
MEMA (10)
Illumina HiSeq 2000 (7)
NMR spectroscopy (6)
Illumina HiSeq 2500, ILLUMINA (2)
Illumina HiSeq 2500 (2)
HiSeq X Five, ILLUMINA (1)
Illumina MiSeq, ILLUMINA (1)
Illumina HiSeq 4000, ILLUMINA (1)
Illumina HiSeq 2500 (ILLUMINA) (1)
ILLUMINA, Illumina MiSeq (1)
NextSeq 500, Illumina HiSeq 2500, AB 5500xl Genetic Analyzer, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2000 (1)
Illumina HiSeq 2000, Illumina HiSeq 2500 (1)
Illumina MiSeq (1)
NMR spectroscopy assay (1)

Instrument Platform

Illumina NovaSeq 6000 (63)
NextSeq 500 (40)
Illumina HiSeq 4000 (14)
Illumina HiSeq 2500 (14)
Illumina HiSeq 2000 (10)
Illumina NovaSeq X (9)
NextSeq 2000 (4)
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GenePix 4000B [Axon Instruments] (3)
NA (3)
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10x Genomics Chromium Controller (2)
DNBSEQ-G400 (2)
Illumina HiSeq 1500 (2)
Chromium X instrument (10x Genomics); GEM-X FX Chips (10x Genomics); Agilent TapeStation D1000; qPCR (library quantification kit for Illumina platforms) (1)
Chromium X instrument (10x Genomics); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781); Human Gene Expression Probe Set v1.0.1 (10x Genomics) (1)
Countess 3 FL Automated Cell Counter (Thermo Fisher Scientific; AMQAF2000); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781) (1)
TruSeq Stranded Total RNA kit (Illumina) (1)
FACSAria III (BD Sciences) (1)
Chromium Controller with Chromium Next GEM Single Cell 5’ and V(D)J (kits v1.1) (1)
RiboErase Roche (1)
Qiagen RNaesy kit (1)
NextSeq 500, 75 bp single end lane (1)
BD Rhapsody Express Instrument (1)
Nanodrop 2000c spectrophotometer (1)
Linux Bash Scripting (1)
NEBNext Ultra II Directional RNA Library Prep (1)
Qiagen RNeasy Mini Kit (1)
With L-glutamine supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% penicillin-streptomycin (10,000 units/mL penicillin and 10 mg/mL streptomycin) (Gibco). (1)

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2019 (153)
2012 (130)
2015 (122)
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2011 (100)
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2013 (95)
2017 (91)
2008 (73)
2009 (60)
2007 (32)
2006 (20)
2005 (15)
2004 (5)
2003 (2)

UNIPROT ID/AC

M0X228_HORVV (4)
M0US35_HORVV (4)
M0XYT2_HORVV (4)
A0A287W0Q2_HORVV (4)
A0A287T624_HORVV (4)
4513.MLOC_7329.1 (4)
A0A287J4L4_HORVV (4)
A0A287GM49_HORVV (4)
M0YEZ0_HORVV (4)
A0A287X8X1_HORVV (4)
M0WZT8_HORVV (4)
A0A287KE24_HORVV (4)
A0A287EE26_HORVV (4)
A0A287JJ36_HORVV (4)
Q8K4S1 (1)
O43526 (1)
O88944 (1)
O95257 (1)
P24522 (1)
O75293 (1)
P38936 (1)
P29992 (1)
P0DP23 (1)
Q13315 (1)
Q16539 (1)
P04049 (1)
Q02750 (1)
P28482 (1)
P04637 (1)
Q00987 (1)

ENSEMBL ID

ENSG00000170477 (4)
ENSG00000247315 (2)
ENSG00000229353 (1)

CHEBI ID

CHEBI:30769 (18)
CHEBI:16335 (17)
CHEBI:15422 (7)
CHEBI:16595 (2)
CHEBI:18348 (2)
CHEBI:16991 (2)
CHEBI:43000 (1)
CHEBI:30111 (1)
CHEBI:38322 (1)
CHEBI:38309 (1)
CHEBI:5235 (1)
CHEBI:35868 (1)
CHEBI:35610 (1)
CHEBI:25000 (1)
CHEBI:70727 (1)
CHEBI:63632 (1)
CHEBI:28874 (1)
CHEBI:30212 (1)
CHEBI:32635 (1)
CHEBI:46195 (1)
CHEBI:25107 (1)
CHEBI:39124 (1)
CHEBI:26523 (1)
CHEBI:26034 (1)
CHEBI:18420 (1)
CHEBI:18035 (1)
CHEBI:17526 (1)
CHEBI:16749 (1)
CHEBI:15996 (1)
CHEBI:17552 (1)

Metabolite Name

Adenosine (15)
Hypoxanthine (13)
Creatine (13)
L-Tyrosine (12)
Uracil (12)
Adenine (12)
Guanine (11)
Pantothenic acid (10)
Phenylalanine (10)
Palmitic acid (10)
L-Histidine (10)
Choline (10)
L-Phenylalanine (10)
L-Glutamine (10)
Inosine (10)
Histidine (9)
Thymine (9)
4-Hydroxybenzaldehyde (9)
Citric acid (9)
Riboflavin (9)
Cytosine (9)
Creatinine (9)
Taurine (9)
Xanthine (9)
Leucine (8)
Succinic acid (8)
Fumaric acid (8)
L-Tryptophan (8)
Hexadecanedioic acid (8)
Glutamine (8)

First Public Date

2025 (411)
2026 (344)
2024 (272)
2014 (223)
2023 (202)
2022 (172)
2021 (151)
2020 (124)
2019 (112)
2018 (101)
2017 (76)
2016 (50)
2015 (49)
2013 (31)
2012 (1)

Modelling Approach

Ordinary differential equation model (9)
Constraint-based model (2)

Study status

Recruiting (5)
Not yet recruiting (2)
Completed (2)
Withdrawn (1)
Not provided (1)

Lab affiliation

iBET – Instituto de Biologia Experimental e Tecnológica, Av. da República, Oeiras, 2780-157, Portugal (14)
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (10)
Protein Biogenesis Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT (4)
German Cancer Consortium (DKTK), partner site Freiburg German Cancer Research Center (DKFZ) Foundation under Public Law c/o Department of Urology Zentrale Klinische Forschung (ZKF) Medical Center-University of Freiburg Breisacher Str. 66, 79106 Freiburg, Germany (4)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (4)
USDA-ARS (4)
University of Alabama at Birmingham, Department of Pathology, Division MCP, O'Neal Comprehensive Cancer Center (4)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (4)
Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria (3)
Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy,Chicago,IL,USA Richard and Loan Hill Department of Biomedical Engineering, University of Illinois College of Engineering,Chicago, IL,USA University of Illinois Cancer Center,Chicago, IL,USA (3)
Human Technopole, 20157, Milan, Italy (3)
1VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium 2Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium (3)
NovAliX, Department of Biophysics, 16 Rue d’Ankara, 67000, Strasbourg, France; orcid.org/0000-0001-6229-4524 (3)
The Rockefeller University (3)
University Medical Center Goettingen, Department of Clinical Chemistry, Core Facility Proteomics (3)
Chair of Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany (3)
Biomolecular characterization unit, Center for Sustainable Resource Science, RIKEN (3)
Functional Proteomics, ICR (3)
University of Bremen, Faculty 2 Biology / Chemistry (2)
Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland (2)
Plant Biology (2)
King's College London, Chemistry Department, 7 Trinity Street, London, SE1 1DB, UK (2)
Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan International Institute for Sustainability with Knotted Chiral Meta Matter (SKCM2), Hiroshima University, Hiroshima, 739-8511, Japan (2)
UC Berkeley (2)
Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India (2)
National Center for Biotechnology (CNB-CSIC), Department of Macromolecular Structures) (2)
School of Integrative Plant Science Plant Biology Section, Cornell University (2)
Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, 66421 Homburg, Germany (2)
Department of Biochemistry Biophysics and Structural Biology, Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri, United States (2)
Systems Arbovirology, Leibniz Institute of Virology, Hamburg, Germany (2)

Keyword

Fluorescence Sigmoidoscopy (1)
PDD (1)
Nearinfrared (1)
Probe-based imaging of GI pre-malignant or malignant lesions (1)
Epigenetic landscape (1)
Perfusion (1)
Tumor heterogeneity (1)
Differential expression of gene (1)
Immunohistochemical staining (1)
Tumor microenvironment (1)
Artificial intelligence (1)
Anastomosis (1)
Peritoneal carcinomatosis (1)
Colorectal surgery (1)

IsPrivate

False (11)

Classification

bacteria (102)
protozoa (15)
viruses (13)
fungi (8)
helminths (5)

Modification

Not available (3)
N6 (1)
4 (1)

Study type

Transcription profiling by array (491)
RNA-seq of coding RNA (128)
ChIP-seq (53)
RNA-seq of coding RNA from single cells (38)
Other (12)
RNA-seq of non coding RNA (11)
Unknown experiment type (9)
Comparative genomic hybridization by array (7)
DNA-seq (7)
Transcription profiling by SAGE (6)
Transcription profiling by tiling array (6)
Methylation profiling by array (6)
RNA-seq of total RNA (6)
ChIP-chip by tiling array (5)
Animal - High-throughput sequencing (5)
Spatial transcriptomics by high-throughput sequencing (5)
Cell line - High-throughput sequencing (4)
RNAi profiling by array (3)
Transcription profiling by RT-PCR (3)
Hi-C (3)
MicroRNA profiling by array (3)
CUT&RUN (3)
Cell line - Single-cell sequencing (2)
Human - High-throughput sequencing (2)
High-throughput sequencing (2)
ChIP-chip by array (2)
MicroRNA profiling by high throughput sequencing (2)
ATAC-seq (2)
RIP-seq (2)
ScATAC-seq (2)

Release Date

2022 (9248)
2025 (9039)
2023 (8663)
2021 (8225)
2024 (7607)
2020 (7224)
2019 (6088)
2018 (5400)
2017 (4440)
2016 (3863)
2015 (3276)
2014 (2609)
2013 (1940)
2012 (1620)
2011 (1405)
2026 (1347)
2010 (1184)
2009 (996)
2008 (820)
2007 (518)
2006 (421)
2005 (355)
2004 (247)
2002 (189)
2003 (174)
2001 (143)
2000 (118)
1999 (97)
1998 (93)
1997 (19)

Location

Netherlands (2)
France (2)
Ireland (1)
Australia (1)
China (1)
Germany (1)
Japan (1)
United States (1)

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Spatial Transcriptomics correlated Electron Microscopy [MERFISH]

PRJNA836863 | ENA

Spatial Transcriptomics correlated Electron Microscopy [scRNA-Seq]

PRJNA836864 | ENA

Spatial Transcriptomics correlated Electron Microscopy

PRJNA836860 | ENA

Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy.

Not available

S-EPMC4757415 | biostudies-literature

Expansion microscopy for the analysis of centrioles and cilia.

Not available

S-EPMC6972531 | biostudies-literature

Primary ciliary dyskinesia without obvious electron microscopy defects

PRJNA635175 | ENA

Primary ciliary dyskinesia without obvious electron microscopy defects

PRJNA635176 | ENA

Identification of new regulators of the three dimensional Polycomb organization by a microscopy-based genome-wide RNAi screen

Polycomb group (PcG) proteins dynamically define cellular identities through epigenetic repression of key developmental genes. PcG target gene repression can be stabilized through the interaction in the nucleus at PcG foci. Here, we report the results of a high-resolution microscopy genome-wide RNAi...

ORGANISM(S): Drosophila melanogaster

2014-04-03 | E-GEOD-55303 | biostudies-arrayexpress

Diagnostic electron microscopy in human infectious diseases - Methods and applications.

Not available

S-EPMC12352021 | biostudies-literature

Transcription profiling of microdissected global and orbital layers of the rectus extraocular muscle (EOM) from adult Sprague-Dawley rats

Adult rat global and orbital layers of rectal extraocular muscles microdissected using Arcturus Pixcell II LCM are gene profiled here using affymetrix rat RAE230A gene chip. www.med.upenn.edu/cellbio/faculty/rubinstein/; www.uphs.upenn.edu/pmi/members/khurana/lab%20page.htm

ORGANISM(S): Rattus norvegicus

2007-10-31 | E-GEOD-1374 | biostudies-arrayexpress

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92680 Results

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