Low Benjamin B - OmicsDI

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Unknown (181)
Transcriptomics (145)
Proteomics (48)
Genomics (36)
Metabolomics (8)
Models (2)
Multiomics (1)

Organisms

Homo sapiens (88)
Mus musculus (62)
Saccharomyces cerevisiae (7)
Rhodospirillum rubrum (6)
Rattus norvegicus (6)
Folsomia candida (5)
Danio rerio (5)
Drosophila melanogaster (4)
Arabidopsis thaliana (4)
Mycobacterium tuberculosis (3)
Cupriavidus metallidurans CH34 (2)
Aspergillus niger (2)
synthetic construct (2)
Apis mellifera (2)
Bos taurus (2)
Desmodus rotundus (2)
Schizosaccharomyces pombe (1)
Ascaris suum (1)
Pyrus pyrifolia (1)
Pinus radiata (1)
Pseudomonas synxantha (1)
Dictyostelium discoideum (1)
Phaeodactylum tricornutum (1)
Fundulus heteroclitus (1)
Daphnia magna (1)
Mesocricetus auratus (1)
Escherichia coli K-12 (1)
Escherichia coli (1)
Gallus gallus (1)
Carica papaya (1)

Repository

biostudies-arrayexpress (166)
pride (37)
EGA (15)
MassIVE (10)
MetaboLights (8)
BioModels (2)
iProX (1)

Tissue

Brain (6)
Cell culture (6)
Blood plasma (4)
Blood serum (4)
Epithelial cell (4)
Cell suspension culture (3)
Hepatocyte (2)
Lymphocyte of B lineage (2)
Plant cell (2)
Astrocyte of the cerebral cortex (1)
B cell (1)
Barrett's esophagus (1)
Blood cell (1)
Colon (1)
Cotyledon (1)
HeLa cell (1)
Heart (1)
Leaf (1)
Microglial cell (1)
Multipotent stem cell (1)
Muscle (1)
Myotube (1)
Neuron of cerebral cortex (1)
Permanent cell line cell (1)
Somatic embryo (1)
Thymus (1)

Disease

Breast cancer (2)
Alzheimer's disease (2)
Cervix carcinoma (2)
Prostate adenocarcinoma (2)
Benign glioma (1)
Breast adenocarcinoma (1)
HCV-MC (1)
Normal (1)
Barrett's esophagus (1)
Cardiomyopathy (1)
Dementia (1)
Disease free (1)
Lymphoma (1)
Neurodegenerative disease (1)

Technology Type

Mass Spectrometry (37)
Shotgun proteomics (20)
Mass spectrometry (7)
Bottom-up proteomics (7)
SWATH MS (5)
Affinity purification coupled with mass spectrometry proteomics (3)
Data-dependent acquisition (2)
Top-down proteomics (2)
Illumina Genome Analyzer IIx, Illumina HiSeq 2000 (1)
Mass spectrometry assay (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
Data-independent acquisition (1)
HDMSE (1)
Mass spectrometry imaging (1)
SRM/MRM (1)

Instrument Platform

Illumina HiSeq 2500 (5)
Q Exactive (5)
Illumina HiSeq 2000 (3)
428 [Affymetrix] (2)
Illumina HiSeq 4000 (2)
NextSeq 500 (2)
LTQ Orbitrap Elite (2)
LTQ Orbitrap Velos (2)
Q Exactive HF (2)
FACSAria (BD) (1)
NanoDrop (1)
Bellco roll-in incubator (1)
G2565BA DNA microarray scanner [Agilent] (1)
Illumina Genome Analyzer II (1)
Axon GenePix 4000B scanning hardware (1)
Vortex (1)
NextSeq 2000 (1)
MinION (1)
Illumina HiSeq 1500 (1)
Illumina NovaSeq 6000 (1)
Orbitrap Eclipse (1)
Orbitrap Exploris 240 (1)
Orbitrap Fusion (1)
Orbitrap Fusion Lumos (1)
Q Exactive HF-X (1)
Q Exactive Plus (1)
TimsTOF (1)
TripleTOF 5600 (1)
TripleTOF 6600 (1)
Xevo G2-XS TOF (1)

Publication Date

2015 (23)
2014 (21)
2013 (21)
2010 (21)
2011 (18)
2016 (16)
2012 (15)
2024 (11)
2021 (10)
2020 (10)
2026 (8)
2009 (8)
2025 (7)
2019 (7)
2008 (6)
2022 (5)
2017 (5)
2006 (4)
2023 (3)
2004 (2)
2018 (2)
2003 (1)

UNIPROT ID/AC

P04695 (1)
P62873 (1)
P63211 (1)

CHEBI ID

CHEBI:15354 (2)
CHEBI:15891 (2)
CHEBI:15940 (2)
CHEBI:16113 (2)
CHEBI:16235 (2)
CHEBI:16244 (2)
CHEBI:16335 (2)
CHEBI:16566 (2)
CHEBI:16610 (2)
CHEBI:16708 (2)
CHEBI:16919 (2)
CHEBI:17154 (2)
CHEBI:17368 (2)
CHEBI:17750 (2)
CHEBI:17964 (2)
CHEBI:24809 (2)
CHEBI:27592 (2)
CHEBI:30769 (2)
CHEBI:35280 (2)
CHEBI:46961 (2)
CHEBI:72998 (2)
CHEBI:85533 (2)
CHEBI:15996 (1)
CHEBI:17552 (1)
CHEBI:18367 (1)
CHEBI:28445 (1)
CHEBI:71417 (1)
CHEBI:10072 (1)
CHEBI:10362 (1)
CHEBI:111517 (1)

Metabolite Name

Adenine (2)
Cholesterol (2)
Quinate (2)
Taurine (2)
(14:0) 1-myristoyl-sn-glycero-3-phosphocholine (1)
(16:0) 1-palmitoyl-sn-glycero-3-phosphocholine (1)
(2R)-2,3-Dihydroxypropanoic acid (1)
1-(1-enyl-palmitoyl)-GPE (P-16:0)* (1)
1-(1-enyl-stearoyl)-2-linoleoyl-GPE (P-18:0/18:2)* (1)
1-(1-enyl-stearoyl)-GPE (P-18:0)* (1)
1-O-dodecylglycerol (1)
1-linoleoyl-2-arachidonoyl-GPC (18:2/20:4n6)* (1)
1-linoleoyl-GPC (18:2) (1)
1-linoleoyl-GPE (18:2)* (1)
1-methyl-4-imidazoleacetate (1)
1-methyladenine (1)
1-methylguanidine (1)
1-methylhistamine (1)
1-methylhistidine (1)
1-methylnicotinamide (1)
1-methylurate (1)
1-methylxanthine (1)
1-oleoyl-2-linoleoyl-GPC (18:1/18:2)* (1)
1-oleoyl-GPI (18:1)* (1)
1-palmitoyl-2-docosahexaenoyl-GPC (16:0/22:6) (1)
1-palmitoyl-2-linoleoyl-GPC (16:0/18:2) (1)
1-palmitoyl-2-linoleoyl-GPE (16:0/18:2) (1)
1-palmitoyl-2-oleoyl-GPC (16:0/18:1) (1)
1-palmitoyl-2-palmitoleoyl-GPC (16:0/16:1)* (1)
1-palmitoyl-2-stearoyl-GPC (16:0/18:0) (1)

IsPrivate

False (2)

Modelling Approach

Ordinary differential equation model (2)

Study type

Transcription profiling by array (96)
RNA-seq of coding RNA (27)
ChIP-seq (17)
RNA-seq of non coding RNA (5)
ChIP-chip by tiling array (4)
Methylation profiling by high throughput sequencing (4)
ChIP-chip by array (2)
Comparative genomic hybridization by array (2)
Other (2)
Human - High-throughput sequencing (1)
Cell line - One-color microarray (1)
Whole chromosome random sequencing (1)
Hi-C (1)
Single nucleus RNA sequencing (1)
RNA-seq of coding RNA from single cells (1)
RNA-seq of total RNA (1)

Release Date

2015 (28)
2013 (28)
2014 (26)
2010 (24)
2012 (23)
2016 (22)
2011 (22)
2025 (20)
2021 (20)
2024 (20)
2022 (19)
2023 (19)
2018 (15)
2019 (13)
2020 (12)
2009 (11)
2008 (8)
2017 (5)
2006 (4)
2026 (2)
2004 (2)
2003 (2)
2007 (1)

Lab affiliation

Department of Chemistry, Scripps Research (2)
Laboratory of Molecular Basis of Synaptic Plasticity Centre of New Technologies, University of Warsaw (2)
National Institute of Standards and Technology (2)
Department of Chemistry, Imperial College London, UK Chemical Glycobiology Laboratory, The Francis Crick Institute, London, UK (1)
Department of Chemistry, Imperial College London, UK; Chemical Glycobiology Laboratory, The Francis Crick Institute, London (1)
Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA (lab head) (1)
Director, NCI-Designated Cancer Center Professor, Cancer Metabolism and Microenvironment Program Sanford Burnham Prebys Medical Discovery Institute 10901 North Torrey Pines Road La Jolla, CA 92037 (1)
Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania (1)
Institute Krems Bioanalytics, IMC University of Applied Sciences, 3500, Krems, Austria (1)
Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland (1)
Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia Universidade Estadual do Norte Fluminense Darcy Ribeiro Av. Alberto Lamego 2000 Campos dos Goytacazes-RJ, Brazil 28013-602 (1)
Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brasil (1)
MRC Laboratory of Molecular Biology, Neurobiology division, Cambridge, UK (1)
Maastricht MultiModal Molecular Imaging institute (M4i), Maastricht University, The Netherlands (1)
Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK (1)
Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH (1)
NIST Charleston (1)
National Institute of Standards and Technology, Charleston, South Carolina, USA (1)
Professor in Translational Oncology Director of Postgraduate Teaching and Learning, School of Medicine Principal Investigator, Cancer Chemoradiation Research Group Department of Surgery, Trinity Translational Medicine Institute Trinity College Dublin, St. James’s Hospital, Dublin (1)
Professor in Translational Oncology Director of Postgraduate Teaching and Learning, School of Medicine Principal Investigator, Cancer Chemoradiation Research Group Department of Surgery, Trinity Translational Medicine Institute, Trinity St. James’s Cancer Institute, Rm 1.20, Trinity Centre for Health Sciences, Trinity College Dublin, St. James’s Hospital, Dublin 8, D08 W9RT, Ireland. (1)
Proteomic Platform Necker, INSERM US24, SFR Necker Université de Paris (1)
Roskamp Institute, Neurodegenerative Disease and Proteomics Lab, Sarasota, FL (1)
School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Queensland, Australia. (1)
School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD, Australia, 4072 (lab head) (1)
School of Chemistry and Molecular Biosciences, University of Queensland, Australia (1)
Scripps Research (1)
Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China (1)
Shanghai Jiao Tong University (1)
The University of Melbourne (1)
The University of Sydney (1)

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Molecular analysis of clonal B cells in hepatitis C virus related-lymphoproliferation

Comparison of molecular pathways in clonal and non-clonal marginal zone B cells in Hepatitis C virus patients

ORGANISM(S): Homo sapiens

2011-02-15 | E-MTAB-521 | biostudies-arrayexpress

Transcription profiling of four mouse bone marrow hematopoietic stem cells (HSC) early B lineage stages(MLP, CLP, Fr.A, Fr.B) to identify coordinately regulated gene as cells progress down the B cell development pathway

Differentiation from hematopoietic stem cells (HSC) to early B-lineage cells proceeds through a series of intermediate stages, during which cells are thought to become progressively more restricted in their developmental potential. RNAs were prepared from four early B lineage stages(MLP, CLP, Fr.A, ...

ORGANISM(S): Mus musculus

2006-12-16 | E-MEXP-559 | biostudies-arrayexpress

Transformation of Cardiology and Cardiothoracic Services at Benjamin Mkapa Hospital, Tanzania: Findings and Experiences from 1,313 Cardiovascular Procedures in Five Years.

Not available

S-EPMC12533416 | biostudies-literature

Ribba2012 - Low-grade gliomas, tumour growth inhibition model

Ribba2012 - Low-grade gliomas, tumour growth inhibition model Using longitudinal mean tumour diameter (MTD) data, this model describe the size evolution of low-grade glioma (LGG) in patients treated with chemotherapy or radiotherapy. This model is...

2024-09-02 | BIOMD0000000521 | BioModels

Transcription profiling of colon mucosa from HLAB27 transgenic rats fed apple-supplemented diets with low or high levels of proanthocyanidins

Transcription profiling in rats fed modified AIN76 diet, high fat/low fibre, (controls) and rats fed apple-supplemented diets, contained 7.6% of lyophilized apples with low (Golden) or high (Marie Mï¿½nard) proanthocyanidins.

ORGANISM(S): Rattus norvegicus

2009-06-16 | E-TABM-514 | biostudies-arrayexpress

Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a (CMS bisulfite-seq)

Gains and losses in DNA methylation are prominent genomic features of all mammalian cell types. To gain insight into mechanisms that could promote shifts in DNA 5-hydroxymethylation (5hmc) patterns and thus contribute to cell fate, including malignant transformation, we performed genome-wide mappin...

ORGANISM(S): Mus musculus

2014-01-22 | E-GEOD-53742 | biostudies-arrayexpress

Involvement of low molecular weight tyrosine acid phosphatase in abscisic acid signaling in Arabidopsis

Low molecular weight protein tyrosine phosphatase (LWM-PTP) is highly conserved tyrosine phosphatase from plants to animals. The function and putative targets of plant LWM-PTP homolog is not reported yet. Here, we revealed that Arabidopsis LWM-PTP homolog APH is a functional tyrosine phosphatase. AP...

ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress)

2022-10-14 | PXD029650 | Pride

Transcription profiling of human breast cancers to define clinically distinct molecular subtypes in estrogen receptor positive breast carcinomas using genomic grade

Purpose: A number of microarray studies have reported distinct molecular profiles of breast cancers (BC): basal-like, ErbB2-like and two to three luminal-like subtypes. These were associated with different clinical outcomes. However, although the basal and the ErbB2 subtypes are repeatedly recognize...

ORGANISM(S): Homo sapiens

2008-06-20 | E-GEOD-6532 | biostudies-arrayexpress

Prophylactic rituximab after allogeneic transplantation decreases B-cell alloimmunity with low chronic GVHD incidence.