Mrna turnover - OmicsDI

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Organisms

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Oncorhynchus nerka (1)
Shewanella oneidensis MR-1 (1)
Bombyx mori (1)
Loxodonta africana (1)
Trypanosoma brucei brucei (1)

Organisms

Homo sapiens (91)
Mus musculus (79)
Saccharomyces cerevisiae (25)
Arabidopsis thaliana (14)
Drosophila melanogaster (12)
Staphylococcus aureus (5)
Schizosaccharomyces pombe (4)
Caenorhabditis elegans (4)
Bacillus subtilis (4)
Escherichia coli (4)
Staphylococcus aureus subsp. aureus str. JKD6008 (3)
Schmidtea mediterranea (3)
Danio rerio (3)
Rattus norvegicus (3)
Prochlorococcus marinus subsp. pastoris str. CCMP1986 (2)
Saccharolobus solfataricus (2)
Synechocystis sp. PCC 6803 (2)
Trypanosoma brucei (2)
Saccharomyces cerevisiae BY4741 (2)
Bacillus subtilis subsp. subtilis str. 168 (2)
Yersinia pseudotuberculosis YPIII (1)
Plasmodium yoelii yoelii 17XNL (1)
Halobacterium salinarum NRC-1 (1)
Salmo trutta (1)
Auxenochlorella protothecoides (1)
Escherichia coli str. K-12 substr. MG1655 (1)
Saccharomyces cerevisiae BY4743 (1)
Saccharomyces cerevisiae S288C (1)
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Corynebacterium diphtheriae (1)

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Disease

Colon cancer (4)
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Cervix carcinoma (1)
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Technology Type

Mass Spectrometry (40)
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Bottom-up proteomics (4)
Mass spectrometry (3)
Data-dependent acquisition (3)
Gel-based experiment (3)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
SRM/MRM (2)
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SWATH MS (1)
Top-down proteomics (1)

Instrument Platform

NextSeq 550 (4)
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Illumina HiSeq 2000 (2)
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Geniom (1)
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HPLC-LTQ-MS (1)

Publication Date

2014 (48)
2012 (44)
2010 (43)
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2016 (32)
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2013 (28)
2022 (28)
2019 (27)
2020 (25)
2008 (24)
2023 (23)
2011 (21)
2021 (17)
2009 (17)
2006 (17)
2007 (13)
2018 (12)
2017 (12)
2005 (10)
2004 (1)
2003 (1)

UNIPROT ID/AC

A0A4V6 (1)
A0JLQ7 (1)
A0JNY3 (1)
A0JNY7 (1)
A0MNP4 (1)
A1A553 (1)
A1ILG8 (1)
A1L0U3 (1)
A1L0U6 (1)
A1L317 (1)
A1L347 (1)
A1L361 (1)
A1L366 (1)
A1L3B6 (1)
A1L3B8 (1)
A2A432 (1)
A2A4P0 (1)
A2A4Z0 (1)
A2A547 (1)
A2A5N2 (1)
A2A5R2 (1)
A2A5V4 (1)
A2A7A7 (1)
A2A7S7 (1)
A2A7Z6 (1)
A2A838 (1)
A2A8L1 (1)
A2A8V9 (1)
A2A9M5 (1)
A2A9Q2 (1)

ENSEMBL ID

ENSMUSG00000021039 (1)
ENSMUSG00000027651 (1)
ENSMUSP00000141097 (1)

CHEBI ID

CHEBI:4348 (1)
CHEBI:47764 (1)
CHEBI:116311 (1)
CHEBI:8453 (1)
CHEBI:3444 (1)
CHEBI:116537 (1)
CHEBI:585244 (1)
CHEBI:3721 (1)
CHEBI:5452 (1)
CHEBI:116289 (1)
CHEBI:3717 (1)
CHEBI:75 (1)
CHEBI:56558 (1)
CHEBI:8815 (1)
CHEBI:4968 (1)
CHEBI:10066 (1)
CHEBI:2231 (1)
CHEBI:8610 (1)
CHEBI:4523 (1)
CHEBI:4552 (1)
CHEBI:2351 (1)
CHEBI:3285 (1)
CHEBI:7707 (1)
CHEBI:2008 (1)
CHEBI:5915 (1)
CHEBI:10573 (1)
CHEBI:7372 (1)
CHEBI:1408 (1)
CHEBI:4124 (1)
CHEBI:8736 (1)

Metabolite Name

N6-acetyl-L-lysine (1)
3-Aminopropanoic acid (1)
1,6-Anhydroglucose (1)
[PE (18:0/18:0)] 1,2-dioctadecanoyl-sn-glycero-3-phosphoethanolamine (1)
[FA (4:2/20:4)] N-butyl-5Z,8Z,11Z,14Z-eicosatetraenoyl amine (1)
Trans-Hexadec-2-enoyl-CoA (1)
[PR] Casbene (1)
[FA ethyl(20:4)] N-ethyl-5Z,8Z,11Z,14Z-eicosatetraenoyl amine (1)
Hexadec-7Z-enoic acid (1)
[SP (14:0)] 1-deoxy-tetradecasphing-13-enine (1)
[FA hydroxy(20:4)] eicosatetraenoyl amine (1)
[FA (20:3)] N-(8Z,11Z,14Z-eicosatrienoyl)-ethanolamine (1)
[FA hydroxy(22:0)] 13-hydroxy-docosanoic acid (1)
[SP (14:0)] 1-deoxy-tetradecasphinganine (1)
[PR] Tretinoin/All-Trans Retinoic Acid (1)
Cis,cis-dodeca-3,6-dienoic acid (1)
7-methyl-3-oxooctanoic acid (1)
Methionine S-oxide (1)
Anthranilic acid (1)
[FA (25:0)] pentacosanoic acid (1)
[FA (23:0)] tricosanoic acid (1)
FA (20:0) (1)
FA (17:0) (1)
FA methyl(14:0) (1)
FA (14:1) tetradecenoic acid (1)
FA (12:1) dodecenoic acid (1)
2-Aminopimelic acid (1)
O-butanoyl-L-carnitine (1)
Decanoyl-CoA (1)
3-Aminoisobutyric acid (1)

First Public Date

2014 (56)
2024 (37)
2025 (34)
2019 (27)
2026 (26)
2020 (26)
2022 (21)
2023 (20)
2021 (18)
2016 (16)
2015 (16)
2017 (12)
2013 (12)
2018 (8)
2012 (2)

Modelling Approach

Ordinary differential equation model (1)

Lab affiliation

Institute for Genetics, University of Cologne, 50674 Cologne, Germany (2)
Max Planck Institute of Immunobiology and Epigenetics Proteomics Unit Stuebeweg 51 79108 Freiburg, Germany (2)
Senior Director, Dynamic Omics, CGR, One Medimmune Way Gaithersburg, MD 20878 (2)
1-Department of protein Science, KTH Royal Institute of Technology, Stockholm, Sweden 2-Science for Life Laboratory, Stockholm, Sweden (1)
Bar-Ilan university, Israel (1)
Biology department, Washington Univeristy in St. Louis (1)
Biology department, Washington University in Saint Louis, Saint Louis, MO, USA (1)
CABIMER (1)
Center for Malaria Research, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802 (1)
College of Dental Medicine, Oral Health Sciences, Medical Univeristy of South Carolina, USA (1)
Department of Biology, Stanford University (1)
Department of Molecular Biology, Princeton University, USA (1)
Department of Plant Molecular Biology, University of Lausanne, Biophore Building, DBMV, CH-1015 Lausanne, Switzerland (1)
Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany (1)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD/NIH) Section on Cell Cycle Regulation Building 49, Room 5A30 49 Convent Drive Bethesda, MD 20892-4480 (1)
Head, Section on Nutrient Control of Gene Expression Building 6, Room 230 6 Center Drive Bethesda, MD 20892 Phone: 301-496-4480 (1)
Institute for Genetics, University of Cologne, Cologne, Germany (1)
Institute for Genetics, UzK, Cologne, Germany (1)
Institute for Research in Biomedicine, Università della Svizzera italiana, Switzerland (1)
Institute of Biomedicine, University of Turku and Department of Pathology, Turku University Hospital Medisiina D, 5th floor Kiinamyllynkatu 10 20520 Turku Finland (1)
Institute of Biophysics, Chinese Academy of Sciences (1)
Institute of Molecular Biology (IMB), Mainz, Germany (1)
Jens Nielsen, PhD, Dr. Tech. Professor Director of Systems and Synthetic Biology Chief Scientific Officer Novo Nordisk Foundation Center for Biosustainability Systems and Synthetic Biology Chalmers University of Technology Kemivägen 10 SE-412 96 Göteborg SWEDEN (1)
KAUST Smart-Health Initiative(KSHI)and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia. Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, H3G1Y6, Canada. Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC, H3A1A3, Canada. (1)
Keck MS & Proteomics Resource Yale School of Medicine (1)
MRC Toxicology Unit, University of Cambridge, UK (1)
Marburg University (1)
Microbial Individuality and Infection Group, Institut Pasteur, Paris, France (1)
Principle Investigator (1)
Proteome Analytics Leibniz Institute of Plant Biochemistry (1)

IsPrivate

False (1)

Classification

bacteria (16)
protozoa (5)
fungi (2)

Study type

Transcription profiling by array (168)
RNA-seq of coding RNA (56)
Unknown experiment type (11)
RNA-seq of non coding RNA (11)
Other (7)
ChIP-seq (7)
Transcription profiling by tiling array (3)
CUT&TAG (1)
Transcription profiling by SAGE (1)
Cell line - One-color microarray (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
RNAi profiling by array (1)
ChIP-chip by array (1)
RIP-seq (1)
MicroRNA profiling by array (1)
RNA-seq of total RNA (1)

Release Date

2015 (88)
2014 (87)
2022 (84)
2020 (80)
2012 (70)
2016 (69)
2010 (69)
2013 (68)
2025 (65)
2023 (65)
2021 (65)
2017 (61)
2011 (58)
2019 (50)
2024 (49)
2018 (45)
2009 (44)
2008 (44)
2007 (36)
2006 (25)
2005 (23)
2026 (12)
2004 (9)
2003 (7)
2001 (7)
2000 (6)
2002 (4)
1999 (3)
1998 (2)
1997 (2)

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The Parkinson's disease protein alpha-synuclein is a direct modulator of Processing-bodies and mRNA stability

Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR,Carr SA, de Jager P, Myers CL, Lindquist S, Greenmyre TJ, Bartel DP, Feany MB, Sunyaev S, Chung CY and Khurana V. Alp...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2022-03-09 | MSV000089026 | MassIVE

Transcriptome reprogramming via Tob2-promoted global mRNA turnover

PRJNA564731 | ENA

Transcriptome reprogramming via Tob2-promoted global mRNA turnover

PRJNA629601 | ENA

Spt6 association with RNAPII directs mRNA turnover during transcription

PRJNA438236 | ENA

Contributions of transcription and mRNA turnover to gene expression dynamics of fission Yeast Extract mediumast in response to oxidative stress

The cooperation of transcriptional and post-transcriptional controls to shape gene regulation is poorly understood. Here we show that a combination of two simple and non-invasive genomic techniques, coupled with kinetic mathematical modelling, afford insight into the multi-layered regulation of gene...

ORGANISM(S): Schizosaccharomyces pombe

2013-07-01 | E-MTAB-504 | biostudies-arrayexpress

A dual-activity topoisomerase complex regulates mRNA translation and turnover

PRJNA779461 | ENA

Heat shock induces silent ribosomes and reorganizes mRNA turnover

PRJNA1223295 | ENA

Effects of m6A modification and YTHDF2 knockdown on global mRNA turnover

PRJNA902825 | ENA

Contributions of transcription and mRNA turnover to gene expression dynamics of fission yeast in response to oxidative stress

ORGANISM(S): Schizosaccharomyces pombe

2014-06-01 | E-MTAB-2579 | biostudies-arrayexpress

Differential effects of m6A modification and YTHDF2 knockdown on global mRNA turnover