Transfer rna (trna)

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Transcriptomics (1782)
Unknown (1637)
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Organisms

Homo sapiens (81)
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Saccharomyces cerevisiae BY4741 (1)
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Caenorhabditis elegans (1)
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Disease

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Instrument Platform

Illumina NovaSeq 6000 (23)
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ScanArray [PerkinElmer] (3)
GenePix Personal 4100A [Axon Instruments] (3)
Other (3)
NextSeq 2000 (3)
MinION (3)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
Nanodrop N1000 spectrophotometer (2)
Other (2)

Publication Date

2010 (352)
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2019 (14)
2003 (7)

UNIPROT ID/AC

P02994 (1)
P04147 (1)
P05453 (1)
P06103 (1)
P06634 (1)
P07260 (1)
P09032 (1)
P09064 (1)
P10081 (1)
P12385 (1)
P12754 (1)
P14741 (1)
P16521 (1)
P20459 (1)
P29547 (1)
P32324 (1)
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P34167 (1)
P36008 (1)
P38249 (1)
P38431 (1)
P38912 (1)
P39730 (1)
P39935 (1)
P39936 (1)

CHEBI ID

CHEBI:17596 (7)
CHEBI:16335 (6)
CHEBI:16704 (6)
CHEBI:16020 (5)
CHEBI:16750 (5)
CHEBI:17562 (5)
CHEBI:20794 (5)
CHEBI:17802 (4)
CHEBI:19068 (4)
CHEBI:19227 (4)
CHEBI:19229 (4)
CHEBI:20129 (4)
CHEBI:20607 (4)
CHEBI:45996 (4)
CHEBI:16040 (3)
CHEBI:16467 (3)
CHEBI:16708 (3)
CHEBI:17191 (3)
CHEBI:17295 (3)
CHEBI:17509 (3)
CHEBI:178091 (3)
CHEBI:178092 (3)
CHEBI:18050 (3)
CHEBI:19062 (3)
CHEBI:15996 (1)
CHEBI:17552 (1)
CHEBI:17843 (1)
CHEBI:2651 (1)
CHEBI:29173 (1)
CHEBI:33699 (1)

Metabolite Name

Adenosine (7)
Guanosine (6)
1-methyladenosine (5)
7-methylguanosine (5)
Betaine (5)
Citrulline (5)
Creatinine (5)
Cytidine (5)
Hypoxanthine (5)
L-Phenylalanine (5)
Uridine (5)
Xanthine (5)
1-methylinosine (4)
1-methylpseudouridine (4)
2'-O-methylcytidine (4)
2'-O-methylguanosine (4)
2'-O-methyluridine (4)
3-Phosphoglyceric acid (4)
3-methylcytidine (4)
5-methylcytidine (4)
Adenylsuccinic acid (4)
Caprylic acid (4)
Choline (4)
Creatine (4)
D-Glucose (4)
Guanine (4)
Inosine (4)
L-Glutamine (4)
L-Isoleucine (4)
L-Methionine (4)

First Public Date

2024 (42)
2026 (36)
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2023 (28)
2022 (16)
2016 (15)
2021 (12)
2020 (11)
2019 (7)
2018 (7)
2015 (6)
2013 (6)
2017 (5)
2014 (4)

Modelling Approach

Ordinary differential equation model (1)

Lab affiliation

UPR 9002 CNRS-ARN Université De Strasbourg IBMC (2)
Aging $ Metabolism, Gene Translation Laboratory, Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain. (1)
Associate Professor of Biochemistry Schulich School of Medicine and Dentistry Scientist, Children’s Health Research Institute (CHRI) Medical Sciences Building 358 Western University London, Ontario N6A 5C1, Canada (1)
Daegu Catholic University School of Medicine (1)
Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1 (1)
Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada. Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada (1)
Department of Cell Biology and Molecular Genetics University of Maryland (1)
Department of Genome Sciences, University of Washington, Seattle, WA, USA (1)
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States (1)
Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center (1)
Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway (1)
Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. (1)
Dept of Biochemistry, Medical Sciences Building, Schulich School of Medicince and Dentistry, University of Western Ontario, London, ON, Canada (1)
Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden (1)
Dr Peter C Dedon, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore (lab head) (1)
Head Proteomics Platform, MDC Berlin (1)
Institut Pasteur, Université de Paris, UMR3691 CNRS, Unité de Biologie cellulaire de l'infection microbienne, F-75015, Paris, France. (1)
Kaiser Isotope Lab, Department of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438 (1)
MIT (1)
Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland (1)
Massachusetts Institute of Technology (1)
Medical University of Vienna,Vienna, Austria (1)
Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (1)
Proteomics Platform CIC bioGUNE, Bizkaia Tec. Park Build. 800, derio 48160 Bizkaia (Spain) (1)
Schulich School of Medicine and Dentistry, Biochemistry Department, Western University, Ontario, Canada (1)
UCSF (1)
Underwood-Prescott Professor, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 56-731 Cambridge, MA 02139-4307 (1)
University of North Carolina, Department of Biology and Genetics, Lineberger Comprehensive Cancer Center, USA (1)
University of Utah (1)
University of Western Ontario, Canada, Department of Biochemistry (1)

IsPrivate

False (1)

Classification

bacteria (6)
protozoa (1)
fungi (1)

Study type

Transcription profiling by array (953)
RNA-seq of non coding RNA (186)
RNA-seq of coding RNA (166)
Comparative genomic hybridization by array (87)
ChIP-seq (67)
Unknown experiment type (66)
ChIP-chip by array (65)
Other (55)
ChIP-chip by tiling array (54)
Transcription profiling by tiling array (22)
Methylation profiling by array (12)
RNA-seq of coding RNA from single cells (10)
Methylation profiling by high throughput sequencing (10)
Ribo-seq (7)
DNA-seq (6)
RNA-seq of total RNA (6)
High-throughput sequencing (4)
Cell line - High-throughput sequencing (4)
MicroRNA profiling by array (4)
MicroRNA profiling by high throughput sequencing (3)
RNAi profiling by array (2)
Genotyping by array (2)
Single nucleus RNA sequencing (2)
Genotyping by high throughput sequencing (2)
RNA-seq of non coding RNA from single cells (1)
Two-color microarray (1)
Cell line - Two-color microarray (1)
Animal - One-color microarray (1)
Human - High-throughput sequencing (1)
Plant - High-throughput sequencing (1)

Release Date

2010 (366)
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2004 (32)
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2003 (12)
2000 (3)
2002 (1)
2001 (1)
1998 (1)
1971 (1)

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Neuronal tRNA modifications in Aplysia californica are repatterned during behavioral habituation

Transfer RNA (tRNA) modifications have been increasingly implicated as post-transcriptional regulators of basic neuronal functions. However, characterizing tRNA modification profiles in specific neural circuits that control well-defined behaviors is notoriously difficult due to the complexity of con...

2026-09-01 | MTBLS15420 | MetaboLights

Virus-induced codon-specific reprogramming to favor viral RNA translation

Recent evidence indicates that codon usage bias regulates gene expression. How viruses, such as the emerging mosquito-borne Chikungunya virus (CHIKV), express their genomes at high levels despite an enrichment in rare codons remains a puzzling question. Using ribosome footprinting, here we analysed ...

2025-06-16 | MTBLS2443 | MetaboLights

Translational repression of viral RNA mediates arbovirus persistence in mosquitoes

Persistent infection of mosquito vectors is essential for the transmission of arboviruses, yet how these viruses produce sufficient progeny without compromising host cell fitness remains unclear. Arbovirus genomes exhibit suboptimal codon usage for both human and mosquito hosts, raising questions...

2026-02-12 | MTBLS12760 | MetaboLights

RNA modification dynamics during Enterococcus faecalis OG1RF growth

Quantitative analysis of relative levels of RNA modifications in small (primarily tRNA) and large (primarily 16S/23S rRNA) RNAs isolated from Enterococcus faecalis OG1RF across a growth time course in BHI media.

2026-08-20 | MTBLS14602 | MetaboLights

A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo

Argonaute/Piwi proteins associate with small RNAs that typically provide sequence specificity for RNP function in gene and genome regulation. Here we show that Twi12, a Tetrahymena Piwi protein essential for growth, is loaded with mature tRNA fragments. The tightly bound ~18-22 nt tRNA 3M-bM-^@M-^Y ...

ORGANISM(S): Tetrahymena thermophila

2010-10-26 | E-GEOD-24916 | biostudies-arrayexpress

tRNA Over-Expression in Breast Cancer

Increased proliferation and elevated levels of protein synthesis are characteristic of transformed and tumor cells. Though components of the translation machinery are often misregulated in cancers, how tRNA plays a role in cancer cells has not been explored. We compare genome-wide tRNA expression in...

ORGANISM(S): Homo sapiens

2010-05-22 | E-GEOD-17945 | biostudies-arrayexpress

The Translin-TRAX complex/C3PO is a ribonuclease in tRNA processing

The endogenous RNA substrates of Translin-TRAX complexes (also known as C3POs) and how they regulate diverse biological processes remain unknown. Here we show that Translin and TRAX do not play a significant role in RNAi in the filamentous fungus Neurospora crassa. Instead, the Neurospora C3PO compl...

ORGANISM(S): Neurospora crassa

2012-07-30 | E-GEOD-38334 | biostudies-arrayexpress

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

Parental dietary conditions can influence the metabolic traits of offspring. In mice, paternal consumption of low protein diet alters cholesterol and lipid metabolism of progeny. Here, we examine RNA species expressed in male reproductive tissues of mice. Protein restriction leads to altered levels ...

ORGANISM(S): Mus musculus

2016-01-04 | E-GEOD-74537 | biostudies-arrayexpress

Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling

Transfer RNA (tRNA) modifications enhance the efficiency, specificity and fidelity of translation in all organisms. The anticodon modification mcm5s2U34 is required for normal growth and stress resistance in yeast; mutants lacking this modification have numerous phenotypes. Mutations in the homologo...

ORGANISM(S): Saccharomyces cerevisiae

2013-08-01 | E-GEOD-45366 | biostudies-arrayexpress

Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection [life cycle]

Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key ...

ORGANISM(S): Phytophthora infestans

2014-12-12 | E-GEOD-62674 | biostudies-arrayexpress

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