Allen A A - OmicsDI

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Unknown (12665)
Transcriptomics (248)
Genomics (208)
Proteomics (122)
Metabolomics (38)
Genomic (14)
Models (6)
Other (6)
Clinical (1)
Methylation profiling (1)

Organisms

Homo sapiens (188)
Mus musculus (81)
Rattus norvegicus (20)
Saccharomyces cerevisiae (16)
Arabidopsis thaliana (9)
Drosophila mojavensis (5)
Emiliania huxleyi (5)
Phaeodactylum tricornutum (5)
Picea glauca (3)
Medicago truncatula (3)
Oryza sativa (3)
Nicotiana tabacum (3)
Daphnia magna (2)
Vitis vinifera (2)
Escherichia coli str. K-12 substr. MG1655 (2)
Danio rerio (2)
Thalassiosira pseudonana CCMP1335 (2)
Rhabdomys pumilio (1)
Ictalurus punctatus x Ictalurus furcatus (1)
Drosophila serrata (1)
Vitis labrusca x Vitis vinifera (1)
Ralstonia solanacearum UW551 (1)
Cafeteria roenbergensis virus BV-PW1 (1)
marine metagenome (1)
Thalassiosira pseudonana (1)
Salmonella enterica (1)
Anolis carolinensis (1)
Macaca mulatta (1)
Loxodonta africana (1)
Ectocarpus siliculosus (1)

Organisms

Homo sapiens (56)
Mus musculus (37)
Eretmochelys imbricata (3)
Macaca nemestrina (3)
Urocitellus parryii (3)
Dasypus novemcinctus (3)
Saimiri boliviensis (3)
Monodelphis domestica (3)
Methylotuvimicrobium buryatense (2)
Python regius (2)
Ralstonia solanacearum (2)
Haemophilus influenzae 3655 (1)
Fusobacterium vincentii 4_1_13 (1)
Microtus ochrogaster (1)
Fusobacterium animalis (1)
Fusobacterium nucleatum (1)
Trichiurus japonicus (1)
ice metagenome (1)
Corynebacterium ulcerans (1)
Ralstonia pseudosolanacearum (1)
Macaca mulatta (1)
Theobroma cacao (1)
Triticum aestivum (1)

Repository

biostudies-arrayexpress (243)
ENA (154)
pride (98)
EGA (41)
MetaboLights (30)
MassIVE (24)
geo (20)
dbGaP (14)
GNPS (8)
BioModels (5)
PanoramaPublic (4)
jPOST (2)
Cell Collective (1)

Tissue

Cell culture (20)
Brain (7)
Epithelial cell (7)
Photosynthetic cell (5)
Blood plasma (4)
Lung (4)
B cell (3)
Blood (3)
Blood platelet (3)
Macrophage (3)
Extracellular vesicle (2)
Leukocyte (2)
Neuron (2)
Platelet (2)
Whole body (2)
Acute myeloid leukemia cell line (1)
Adrenal gland (1)
Astrocyte (1)
Blood cell (1)
Bone marrow (1)
Cell suspension culture (1)
Cerebellar neuron (1)
Cervical epithelial cell (1)
Cotyledon (1)
Culture fluid (1)
Early embryonic cell (1)
HeLa cell (1)
LCL-721 cell (1)
LNCaP cell (1)
T cell (1)

Disease

Colorectal cancer (3)
Colorectal Carcinoma (2)
Cervix carcinoma (2)
Severe acute respiratory syndrome (2)
Colon cancer (1)
Normal (1)
The participants enrolled in this study will all undergo major upper abdominal surgery (i.e. mostly Pylorus Preserving Pancreatico Duodenectomy or whipple procedure) mostly for pancreatic cancer, papillary carcinoma or pancreatitis. However, the indication for which the IMP is administered is intestinal ischemia and reperfusion. (1)
Acquired immunodeficiency syndrome (1)
Acute leukemia (1)
Acute myeloid leukemia (1)
Autoimmune disease (1)
Breast cancer (1)
Cardiovascular system disease (1)
Castration-resistant prostate carcinoma (1)
Colorectal carcinoma (1)
Disease free (1)
Fibrolamellar carcinoma (1)
Glaucoma (1)
Inflammation (1)
Influenza (1)
Lung cancer (1)
Lung squamous cell carcinoma (1)
Neuroblastoma (1)
Neurodegenerative disease (1)
Neurofibromatosis 1 (1)
Pancreatic ductal adenocarcinoma (1)
Parasitic helminthiasis infectious disease (1)
Parasitic infectious disease (1)
Pulmonary fibrosis (1)
Small cell carcinoma (1)

Technology Type

Mass Spectrometry (98)
Shotgun proteomics (56)
Mass spectrometry (25)
Affinity purification coupled with mass spectrometry proteomics (13)
Bottom-up proteomics (13)
Data-dependent acquisition (11)
Gel-based experiment (10)
NMR spectroscopy (5)
Data-independent acquisition (4)
Top-down proteomics (4)
Illumina HiSeq 2000 (3)
SWATH MS (3)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
MSE (2)
Affymetrix 6.0, Illumina_670k - Illuminus, Illumina 1.2M (1)
Illumina Genome Analyzer II (1)
Illumina HiSeq 2000, Illumina HiSeq 2500, ILLUMINA (1)
Illumina MiSeq (1)
Infinium_370k - GenomeStudio (1)
Mass spectrometry assay (1)
Mass spectrometry imaging (1)

Instrument Platform

Illumina NovaSeq 6000 (9)
Q Exactive (9)
Illumina HiSeq 2000 (5)
Illumina HiSeq 4000 (3)
Q Exactive HF (3)
Q Exactive Plus (3)
Orbitrap Exploris 480 (3)
NextSeq 500 (2)
Agilent 6530 Accurate Mass Q-TOF (2)
Hydro reverse-phase (RP) high-performance liquid chromatography (HPLC) followed by ionization by electrospray in negative mode on an Orbitrap mass spectrometer (2)
Vanquish UHPLC plumbed directly to a Q Exactive Plus mass spectrometer (Thermo Scientific) (2)
Bruker Avance 600 MHz NMR spectrometer (2)
Orbitrap Eclipse (2)
Orbitrap Fusion (2)
Agilent Tapestation 4200 (1)
FastPrep-24 5G bead beater, Qubit Fluorometer (1)
12 well TC-treated plate, LETs buffer, dry ice (1)
GeneChip Scanner 3000 [Affymetrix] (1)
DNA Microarray Scanner BA [Agilent Technologies] (1)
Scanning hardware (1)
Illumina HiSeq X (1)
N/A (1)
NextSeq 550 (1)
Illumina HiSeq 2500 (1)
6530 Quadrupole Time of Flight MS (Agilent Instrument) (1)
Orbitrap Exploris 240 (1)
LTQ Orbitrap Elite (1)
LTQ Orbitrap Velos (1)
LTQ Velos (1)
Orbitrap Fusion Lumos (1)

Publication Date

2023 (32)
2014 (31)
2022 (30)
2015 (29)
2008 (28)
2013 (26)
2010 (26)
2016 (25)
2024 (24)
2012 (24)
2021 (22)
2011 (21)
2025 (19)
2019 (15)
2017 (14)
2009 (14)
2026 (13)
2007 (13)
2020 (10)
2018 (5)
2006 (4)
2005 (1)
2004 (1)

CHEBI ID

CHEBI:16704 (12)
CHEBI:18237 (12)
CHEBI:28044 (12)
CHEBI:17368 (11)
CHEBI:15741 (10)
CHEBI:15891 (10)
CHEBI:16335 (10)
CHEBI:18186 (10)
CHEBI:15354 (9)
CHEBI:16919 (9)
CHEBI:17568 (9)
CHEBI:17596 (9)
CHEBI:27897 (9)
CHEBI:16750 (8)
CHEBI:17154 (8)
CHEBI:17858 (8)
CHEBI:18012 (8)
CHEBI:25017 (8)
CHEBI:28842 (8)
CHEBI:29016 (8)
CHEBI:30769 (8)
CHEBI:16196 (7)
CHEBI:16449 (7)
CHEBI:16708 (7)
CHEBI:16811 (7)
CHEBI:16856 (7)
CHEBI:17562 (7)
CHEBI:17750 (7)
CHEBI:25094 (7)
CHEBI:28300 (7)

Metabolite Name

Hypoxanthine (7)
Inosine (7)
Adenosine (6)
Choline (6)
L-Lactic acid (6)
Phenylalanine (6)
Succinic acid (6)
Uridine (6)
Alanine (5)
Citric acid (5)
Creatine (5)
Cytidine (5)
Guanosine (5)
L-Tyrosine (5)
Taurine (5)
Uracil (5)
Valine (5)
Xanthine (5)
ADP (4)
AMP (4)
Adenine (4)
Betaine (4)
Creatinine (4)
Glutamine (4)
Glycine (4)
L-Aspartic acid (4)
L-Cysteine (4)
L-Isoleucine (4)
L-Methionine (4)
L-Phenylalanine (4)

First Public Date

2025 (23)
2026 (22)
2023 (22)
2024 (19)
2017 (14)
2021 (9)
2019 (9)
2014 (9)
2016 (8)
2013 (5)
2022 (4)
2018 (4)
2020 (3)
2015 (3)

Modelling Approach

Constraint-based model (2)
Ordinary differential equation model (2)
Computational model (1)

Study status

Ongoing (1)

Lab affiliation

Pacific Northwest National Laboratory (4)
IBERS, Aberystwyth University (2)
Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA (2)
School of Biotechnology and Biomolecular Sciences The University of NSW Sydney NSW 2052 Australia (2)
Scripps Institution of Oceanography, University of California (2)
The Institute of Cancer Research (2)
University of the Pacific (2)
Virginia Tech, Department of Biochemistry (2)
Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry Department (2)
1 - i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; 2 - Cancer Drug Resistance Group, IPATIMUP – Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal; 3 - Department of Biological Sciences, FFUP – Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal (1)
1. Division of Radiation Health, 2. Department of Pharmaceutical Sciences, 3. Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR (1)
1. Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA 2. Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA (1)
1Division of Radiation Health, 2Department of Pharmaceutical Sciences, 3Neurobiology & Developmental Sciences, (1)
Agios Pharmaceuticals 88 Sidney Street Cambridge MA 02139 USA (1)
Associate Professor Biology, Dalhousie University (1)
Associate Professor Systems Virology Department of Translation medicine Faculty of Medicine Lund University Sweden (1)
CMU, University of Geneva (1)
Calico Life Sciences (1)
Case Western Reserve University, Department of Genetics and Genome Sciences, School of Medicine (1)
Center for Neuroscience and Cell Biology (1)
Centre For Eye Research Australia(CERA) (1)
Centre Médical Universitaire, University of Geneva (1)
Children's Medical Research Institute. Telomere Length Regulation Unit. (1)
Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia (1)
Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University (1)
Department of Biochemistry, Monash University, Clayton,3168, Australia (1)
Department of Biochemistry, University of Oxford (1)
Department of Biological Sciences, Tomida Lab, University of North Carolina at Charlotte, USA (1)
Department of Biology, Dalhousie University, Halifax Nova Scotia Canada B3H-4R2 (1)
Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada (1)

Keyword

Doxycycline (1)
Tranexmic acid (1)

IsPrivate

False (5)

Model Flag

Non Kinetic (1)

Submitter Keywords

FAIR-AIML (1)
FROG (1)
Machine Learning Model (1)

Classification

bacteria (5)

Study type

Transcription profiling by array (148)
RNA-seq of coding RNA (27)
Unknown experiment type (11)
ChIP-seq (10)
RNA-seq of coding RNA from single cells (7)
RNA-seq of non coding RNA (7)
Comparative genomic hybridization by array (6)
Transcription profiling by SAGE (3)
Transcription profiling by tiling array (3)
Genotyping by array (3)
Other (3)
ChIP-chip by tiling array (2)
RNAi profiling by array (2)
Transcription profiling by RT-PCR (2)
Differential (1)
Animal - One-color microarray (1)
High-throughput sequencing (1)
RIP-seq (1)
DNA-seq (1)
Methylation profiling by array (1)
Methylation profiling by high throughput sequencing (1)
RNA-seq of total RNA (1)
Interventional (1)

Release Date

2022 (1286)
2023 (1281)
2021 (1230)
2024 (1152)
2025 (1101)
2020 (1063)
2019 (923)
2018 (855)
2017 (712)
2016 (585)
2015 (553)
2014 (451)
2013 (287)
2012 (261)
2011 (247)
2010 (201)
2026 (189)
2009 (146)
2008 (121)
2007 (78)
2006 (58)
2004 (30)
2005 (28)
2002 (19)
2001 (11)
2000 (11)
2003 (9)
1999 (9)
1998 (6)
1997 (2)

Location

Netherlands (1)

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Metabolomic and Metataxonomic Fingerprinting of Human Milk Suggests Compositional Stability over a Natural Term of Breastfeeding to 24 Months

Sparse data exist regarding the normal range of composition of maternal milk beyond the first postnatal weeks. This single timepoint, observational study in collaboration with the 'Parenting Science Gang' citizen science group evaluated the metabolite and bacterial composition of human milk from 62 ...

2022-02-11 | MTBLS1370 | MetaboLights

Identification of genetic markers for cortical areas using a Random Forest classification routine and the Allen Mouse Brain Atlas.

Not available

S-EPMC6726226 | biostudies-literature

Sharing neurophysiology data from the Allen Brain Observatory.

Not available

S-EPMC10335829 | biostudies-literature

LC-HRMS Metabolomics for Untargeted Diagnostic Screening in Clinical Laboratories: A Feasibility Study

Today's high-resolution mass spectrometers (HRMS) allow bioanalysts to perform untargeted/global determinations that can reveal unexpected compounds or concentrations in a patient’s sample. This could be performed for preliminary diagnosis attempts when usual diagnostic processes and targeted ...

2019-06-06 | MTBLS476 | MetaboLights

Metabolic phenotyping of urine from a dementia research cohort

To better understand the molecular mechanisms underpinning physiological variation in human populations, metabolic phenotyping approaches are increasingly being applied to studies involving hundreds and thousands of biofluid samples. Hyphenated ultra-performance liquid chromatography-mass spectromet...

2022-03-01 | MTBLS719 | MetaboLights

A Course-Based Research Experience Using the Allen Brain Map: From Research Question to Poster Session.

Not available

S-EPMC8437365 | biostudies-literature

Positional Enrichment by Proton Analysis (PEPA): a One-Dimensional 1H-NMR Approach for 13C Stable Isotope Tracer Studies in Metabolomics

A novel metabolomics approach for NMR-based stable isotope tracer studies called PEPA is presented, and its performance validated using human cancer cells. PEPA detects the position of carbon label in isotopically enriched metabolites and quantifies fractional enrichment by indirect determination of...

2017-02-23 | MTBLS247 | MetaboLights

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.

Not available

S-EPMC8152789 | biostudies-literature

Self-reported COVID-19 severity among persons with tuberculosis infection in western Kenya, 2021.

Not available

S-EPMC12043119 | biostudies-literature

Treatment of lean and diet-induced obesity (DIO) mice with a novel stable obestatin analogue alters plasma metabolite levels as detected by untargeted LC-MS metabolomics

Introduction: Obestatin is a controversial gastrointestinal peptide purported to have metabolic actions. Objectives: This study investigated whether treatment with a stable obestatin analogue (PEG-OB(Cys10, Cys13) changed plasma metabolite levels firstly in lean and subsequently in diet-induced obes...

2017-07-25 | MTBLS334 | MetaboLights

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