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soil metagenome (5)
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hot springs metagenome (3)
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Repository

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Disease

Disease free (3)
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Technology Type

Mass Spectrometry (84)
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Affinity purification coupled with mass spectrometry proteomics (8)
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MSE (3)
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Illumina HiSeq 2000, Illumina HumanOmni2-5M-8v1-1_B (1)
Illumina HiSeq 2000, Illumina HumanOmni2-5_8v1_A (1)
Illumina Human Omni Express Bead Chip-24 v1.0 (1)
Illumina HumanOmni1-Quad-Illumina GenomeStudio (1)
Illumina HumanOmni2.5-8 (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
HDMSE (1)
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SRM/MRM (1)
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Instrument Platform

Illumina HiSeq 2000 (14)
Illumina HiSeq 2500 (9)
NextSeq 500 (6)
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Q Exactive (4)
Axon- GenePix4000B (3)
Illumina NovaSeq 6000 (3)
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STAR (1)
Single Cell/Low Input RNA Library Prep Kit for Illumina (#E6420S, New England Biolabs) (1)
RNA Micro Kit (Qiagen). (1)
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- (1)
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Unknown (1)

Publication Date

2013 (116)
2015 (102)
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2012 (81)
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2018 (40)
2008 (33)
2007 (15)
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2005 (2)

UNIPROT ID/AC

Q940U6 (2)
Q9XFM0 (2)
P05067 (1)
P49677 (1)
Q570C0 (1)
Q9LPW7 (1)
Q9LW29 (1)
Q9NZ42 (1)
Q9ZR12 (1)

CHEBI ID

CHEBI:116314 (3)
CHEBI:15746 (3)
CHEBI:15756 (3)
CHEBI:16547 (3)
CHEBI:17351 (3)
CHEBI:18012 (3)
CHEBI:27997 (3)
CHEBI:28875 (3)
CHEBI:30769 (3)
CHEBI:30805 (3)
CHEBI:30887 (3)
CHEBI:37024 (3)
CHEBI:64483 (3)
CHEBI:64549 (3)
CHEBI:64561 (3)
CHEBI:64563 (3)
CHEBI:64566 (3)
CHEBI:72736 (3)
CHEBI:72737 (3)
CHEBI:73853 (3)
CHEBI:131988 (2)
CHEBI:134761 (2)
CHEBI:136619 (2)
CHEBI:139458 (2)
CHEBI:142219 (2)
CHEBI:145243 (2)
CHEBI:145247 (2)
CHEBI:145255 (2)
CHEBI:15318 (2)
CHEBI:86193 (1)

Metabolite Name

Fumaric acid (3)
Linoleic acid (3)
Palmitic acid (3)
Spermidine (3)
Spermine (3)
Succinic acid (3)
1-Eicosanol (2)
1-Linoleoylglycerol (2)
1-Oleoyl-Sn-Glycerol (2)
1-alpha-Linolenoyl-glycerol (2)
11-Octadecanoic acid (Vaccenic acid) (2)
13S-Hydroperoxy-9Z,11E-octadecadienoic acid (2)
13S-Hydroxy-9Z,11E,15Z-octadecatrienoic acid (2)
2-Aminoisobutyric acid (2)
2-Hydroxyisobutyric acid (2)
2-Hydroxyisocaproic acid (2)
2-Linoleoylglycerol (2)
2-alpha-Linolenoyl-glycerol (2)
3-Dehydroshikimic acid (2)
3-Hydroxybutyric acid (2)
3-Hydroxyoctadecanoic Acid (2)
4-Aminobenzoic acid (2)
4-Hydroxybenzoic acid (2)
5-Aminovaleric acid (2)
9,10,13-Trihydroxy-11-Octadecenoic Acid (2)
9-Hydroperoxy-10E,12,15Z-octadecatrienoic acid (2)
9S-Hydroxy-10E,12Z-octadecadienoic acid (2)
Adenine (2)
Adenosine (2)
Agmatine (2)

First Public Date

2025 (151)
2013 (138)
2024 (135)
2023 (135)
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2020 (106)
2026 (105)
2014 (101)
2019 (96)
2018 (88)
2017 (86)
2022 (85)
2016 (60)
2015 (58)
2012 (3)
2011 (2)
2010 (2)

Modelling Approach

Ordinary differential equation model (5)
Differential equation model (1)

Study status

Completed (1)
Terminated (1)
Withdrawn (1)

Lab affiliation

Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands (2)
Globe Institute, University of Copenhagen (2)
Globe Institute, University of Copenhagen, Denmark (2)
University Regensburg Biochemistry I Mass Spectrometry group (2)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (2)
Laboratoire MSAP UAR 3290 CNRS Bâtiment C4 Avenue Paul Langevin Cité Scientifique 59655 Villeneuve D'ascq 03 20 33 71 12 https://msap-lab.fr/ (2)
Assistant Professor, Department of Chemistry Assistant Professor, Department of Biology (by courtesy) Assistant Professor, Thomas C. Jenkins Department of Biophysics (by courtesy) Preceptor, Chemistry-Biology Interface (CBI) Program (1)
Assistant Professor, Department of Chemistry Assistant Professor, Thomas C. Jenkins Department of Biophysics (by courtesy) (1)
Assistant Professor, RTGR (Tomato building), Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046. (1)
Associate Professor of Chemistry Dow Early Career Professor of Chemistry Associate Director of the Program in Chemical Biology Co-Director the Chemical Biology Interface Training Program University of Michigan 930 N University Ann Arbor, MI 48109 (1)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (1)
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) Technical University Munich (TUM) Gregor-Mendel-Straße 4 85354 Freising GERMANY (1)
Berlin Institute for Medical System Biology @ Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association Hannoversche Str. 28, 10115 Berlin Germanyt (1)
BioArCh, University of York, UK (1)
Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of NSW Australia (1)
Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Canada (1)
Biology Department, University of Massachusetts Boston, Boston, MA, USA (1)
Biomolecular characterization unit, Center for Sustainable Resource Science, RIKEN (1)
CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France, and Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France (1)
Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching b. München 85747, Germany; Chair of Organic Chemistry II, Technische Universität München, Garching b. München 85747, Germany (1)
Centre for Advanced Technology/ Adam Mickiewicz University, Poznań, Poland (1)
Centre for Bioinformatics and Computational Biology, University of Stellenbosch, South Africa (1)
Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain (1)
Centre scientifique de Monaco, Monaco (1)
Chemistry Department, University of Minnesota (1)
Clinical and Diagnostic Immunology, Department Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium (1)
Cornell University (1)
Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, 04023-901, Brazil; Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, 05503-900, Brazil (1)
Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. (1)
Department of Biochemistry and Molecular Biology, University of British Columbia, Canada (1)

Keyword

Endoscopic en-bloc resection (1)
Endoscopic submucosal dissection (ESD) (1)
Metastatic Cancer (1)
Peritoneal Perfusion (1)
Piecemeal endoscopic mucosal resection (EMR) (1)
Piecemeal polypectomy (1)
Rectal Cancer (1)

IsPrivate

False (7)

Model Flag

Non Kinetic (1)

Classification

bacteria (12)
fungi (7)
protozoa (3)
helminths (2)
viruses (1)

Study type

Transcription profiling by array (187)
RNA-seq of non coding RNA (158)
RNA-seq of coding RNA (91)
Other (33)
ChIP-seq (21)
Comparative genomic hybridization by array (8)
Methylation profiling by high throughput sequencing (7)
RIP-seq (5)
Unknown experiment type (4)
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Genotyping by array (4)
MicroRNA profiling by high-throughput sequencing (3)
ChIP-chip by tiling array (3)
CLIP-seq (3)
MicroRNA profiling by high throughput sequencing (3)
DNA-seq (3)
RNA-seq of coding RNA from single cells (3)
Transcription profiling by tiling array (2)
ChIP-chip by array (2)
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Interventional (2)
RIP-chip by array (1)
Plant - High-throughput sequencing (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
MicroRNA profiling by array (1)
Methylation profiling by array (1)
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Observational (1)

Release Date

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2020 (976)
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2000 (19)
1998 (16)
1999 (13)
1997 (7)

Location

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Germany (1)
United Kingdom (1)
United States (1)

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Ago-RIP-Seq Analysis to Identify miR-375 Targets in Human Macrophages

miR-375 is not expression in human macrophages, however there is an enhanced accumulation of miR-375 in macrophages upon coculture with breast cancer cells. The target landscape of this miR in macrophages is not known. Ago-RIP-Seq was aimed to identify miR-375 targets in human macrophages.

ORGANISM(S): Homo sapiens

2019-02-08 | E-MTAB-6943 | biostudies-arrayexpress

Ago HITS-CLIP in KSHV-infected primary effusion lymphoma (PEL) cell lines BCBL-1 and BC-3

We performed Ago HITS-CLIP to identify targets of viral and human miRNAs in latently KSHV-infected PEL cells Ago HITS-CLIP was performed in two latently infected PEL cell lines, BCBL-1 and BC-3; Argonaute-immunoprecipitation of UV cross-linked Ago-miRNA-mRNA complexes, followed by RNA isolation, lib...

ORGANISM(S): Homo sapiens

2012-10-05 | E-GEOD-41357 | biostudies-arrayexpress

Identification of microRNAs and microRNA targets in Xenopus ectoderm

Purpose: The establishment of cell lineages occurs via a dynamic progression of gene regulatory networks that underlie developmental commitment and differentiation. To investigate how microRNAs (miRs) function in this process, we compared miRs and miR targets at the initiation of the two major ectod...

ORGANISM(S): Xenopus laevis

2016-06-28 | E-GEOD-83784 | biostudies-arrayexpress

High-throughput sequencing of AGO-immunoprecipitating miRs in human senescent fibroblast WI-38

In humans, there are four Ago proteins (Ago1M-bM-^@M-^S4) and AGO1- and 2 were previously implicated in TGS induced by exogenous siRNAs and microRNAs (miRs) directed against gene promoter transcripts via promotion of changes in histone covalent modifications and DNA methylation. Not-with-standing, m...

ORGANISM(S): Homo sapiens

2011-12-17 | E-GEOD-34494 | biostudies-arrayexpress

Roles and Programming of Arabidopsis ARGONAUTE Proteins During Turnip Mosaic Virus Infection

AGO protein immunoprecipitation was combined with high-throughput sequencing of associated small RNAs. AGO2, AGO10, and to a lesser extent AGO1 were shown to associate with siRNAs derived from silencing suppressor (HC-Pro)-deficient TuMV-AS9, but not with siRNAs derived from wild-type TuMV. Co-immun...

ORGANISM(S): Arabidopsis thaliana

2015-04-06 | E-GEOD-64911 | biostudies-arrayexpress

Ago-APP: a GW peptide-based Argonaute affinity capture strategy

During microRNA (miRNA)-guided gene silencing, Argonaute (Ago) proteins interact with a member of the TNRC6/GW protein family. Here we used a short GW protein-derived peptide fused to GST and demonstrate that it binds to Ago proteins with high affinity. This allows for the simultaneous isolation of ...

ORGANISM(S): Arabidopsis thaliana

2015-09-08 | E-GEOD-70553 | biostudies-arrayexpress

A broad RNA virus survey reveals dependence on host miRNAs and specific sequestration modulating the cellular transcriptome

Small non-coding RNAs have emerged as key players in modulation of viral infection. A unique example is the critical dependence of hepatitis C virus (HCV) on the liver-specific microRNA (miRNA), miR-122, which has surfaced as therapeutic target. Here, we used crosslinking immunoprecipitation (CLIP) ...

ORGANISM(S): Bos taurus

2016-01-20 | E-GEOD-76967 | biostudies-arrayexpress

Characterization of AGO1-/AGO4-associated smRNAs

To fully characterize smRNAs associated with AGO1 and AGO4, we developed a two-step protocol to purify AGO/smRNA complexes from flowers, leaves, roots and seedlings with enhanced purity, and sequenced the smRNAs by IlluminaM-CM-"M-BM-^@M-BM-^Ys technology. We identified some additional miRNAs, colla...

ORGANISM(S): Arabidopsis thaliana

2011-04-19 | E-GEOD-28591 | biostudies-arrayexpress

High throughput sequencing of endogenous small RNAs from AGO pathway mutants

High-throughput pyrosequencing of endogenous small RNAs from >95% male enriched populations of alg-3(tm1155);alg-4(ok1041);fog-2(q71) and fog-2(q71) worms as well as purified spermatids from fem-3(q20) adult worms. Gametogenesis is thermosensitive in numerous metazoa ranging from worms to man. In C...

ORGANISM(S): Caenorhabditis elegans

2010-02-24 | E-GEOD-18729 | biostudies-arrayexpress

Isolation and sequencing of AGO-bound RNAs reveals characteristics of stem-loop processing in vivo

MicroRNA precursors (pre-miRNAs) are short hairpin RNAs that are rapidly processed into mature microRNAs (miRNAs) in the cytoplasm. Due to their low abundance in cells, sequencing-based studies of pre-miRNAs have been limited. We successfully enriched for and deep sequenced pre-miRNAs in human cells...

ORGANISM(S): Homo sapiens

2016-07-30 | E-GEOD-71710 | biostudies-arrayexpress

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