Suppressor trna

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Transcriptomics (951)
Unknown (198)
Genomics (105)
Proteomics (69)
Metabolomics (14)
Other (8)
Multiomics (1)

Organisms

Homo sapiens (326)
Mus musculus (166)
Saccharomyces cerevisiae (92)
Arabidopsis thaliana (37)
Drosophila melanogaster (33)
Caenorhabditis elegans (29)
Candida albicans (26)
Rattus norvegicus (17)
Danio rerio (17)
Oncorhynchus mykiss (16)
Gallus gallus (16)
Sus scrofa (16)
Escherichia coli (12)
Mycobacterium tuberculosis (11)
Zea mays (10)
Trypanosoma brucei (10)
Schizosaccharomyces pombe (9)
Chlorocebus sabaeus (8)
Apis mellifera (6)
Glycine max (6)
Francisella tularensis (5)
Mycobacterium tuberculosis H37Rv (5)
Escherichia coli K-12 (5)
Pseudomonas aeruginosa (5)
Tetrahymena thermophila (4)
Oryza sativa (4)
Staphylococcus aureus (4)
Salmonella enterica subsp. enterica serovar Typhimurium (4)
Escherichia coli str. K-12 substr. MG1655 (4)
Phytophthora infestans (3)

Organisms

Homo sapiens (15)
Mus musculus (8)
Saccharomyces cerevisiae (5)
Bacillus subtilis subsp. subtilis str. 168 (1)

Repository

biostudies-arrayexpress (996)
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geo (29)
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pride (20)
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Tissue

Cell culture (4)
Epithelial cell (1)
Stem cell (1)

Disease

Normal (10)
Breast cancer (3)
Neuroblastoma (2)
Hepatomegaly (1)
Unspecified peripheral T-cell lymphoma (1)
Perilobar nephrogenic rest (1)
Oropharynx squamous-cell carcinoma in DiseaseLocation oropharynx has DiseaseStaging lymph node negative (N0) (1)
Colon cancer Dukes C (1)
Unclassified carcinoid (1)
Invasive Ductal Carcinoma (1)
Hodgkin lymphoma, mixed cellularity, stage IV (1)
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Teratozoospermia and infertility (1)
Giant cell glioblastoma (1)
IRAK-4 Q293X mutation (1)
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Not infected (1)
Barrett's esophagus (1)
These mice have a relatively normal first wave of spermatogenesis but never become fertile. Older animals show increased apoptosis of germ cells, increasing in severity as germ cell stage advances. (1)
Chronic myeloid leukemia (1)
Diabetes mellitus (1)
S enteritidis (1)
Gastric cancer (1)
Glioblastoma (1)
Colorectal adenocarcinoma (1)

Technology Type

Mass Spectrometry (20)
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Mass spectrometry assay (7)
Mass spectrometry (6)
Bottom-up proteomics (5)
Data-dependent acquisition (5)
Gel-based experiment (2)
Illumina HiSeq 2000 (1)
NMR spectroscopy (1)
Affinity purification coupled with mass spectrometry proteomics (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
Data-independent acquisition (1)
RNA mass spectrometry (1)
SRM/MRM (1)
Top-down proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (25)
Illumina HiSeq 2500 (20)
NextSeq 500 (20)
Illumina HiSeq 2000 (12)
Axon GenePix 4000B scanning hardware (9)
Illumina HiSeq 4000 (8)
G2565BA DNA microarray scanner [Agilent] (6)
Illumina MiSeq (6)
Scanning hardware (5)
Vortex (5)
NextSeq 2000 (5)
Illumina Genome Analyzer IIx (4)
G2565AA DNA microarray scanner [Agilent] (3)
GenePix 4000B [Axon Instruments] (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)
MA900, Sony (2)
10x Chromium Controller (2)
10X Genomics Chromium (2)
Nanodrop N1000 spectrophotometer (2)
ScanArray [PerkinElmer] (2)
Other (2)
GenePix Personal 4100A [Axon Instruments] (2)
GenePix 4000A [Axon Instruments] (2)
DNA Microarray Scanner BA [Agilent Technologies] (2)
Axon- GenePix4000B (2)
Bellco roll-in incubator (2)
418 [Affymetrix] (2)
ScanArray Express HT [PerkinElmer] (2)
Illumina NovaSeq X (2)
NextSeq 550 (2)

Publication Date

2010 (162)
2014 (106)
2013 (86)
2015 (82)
2012 (75)
2011 (74)
2008 (65)
2016 (61)
2009 (55)
2007 (45)
2025 (41)
2006 (38)
2026 (35)
2021 (29)
2005 (27)
2024 (26)
2022 (19)
2023 (18)
2020 (18)
2004 (12)
2017 (11)
2019 (8)
2018 (6)
2003 (3)

UNIPROT ID/AC

14331_ORYSJ (1)
14331_SOLLC (1)
14334_ORYSJ (1)
14335_SOLLC (1)
14337_ORYSJ (1)
14337_SOLLC (1)
14338_SOLLC (1)
1433B_SOYBN (1)
2A5K_ORYSJ (1)
2ABA_ORYSJ (1)
3055.EDP00778 (1)
3055.EDP02272 (1)
3055.EDP03640 (1)
3055.EDP03813 (1)
3055.EDP04366 (1)
3847.GLYMA06G11530.1 (1)
3847.GLYMA07G36560.3 (1)
3847.GLYMA08G02375.1 (1)
3847.GLYMA08G11940.1 (1)
3847.GLYMA08G19320.1 (1)
3847.GLYMA09G19800.2 (1)
3847.GLYMA11G00590.2 (1)
3847.GLYMA11G15650.4 (1)
3847.GLYMA11G15700.1 (1)
3847.GLYMA11G15820.1 (1)
3847.GLYMA11G15850.4 (1)
3847.GLYMA11G15890.2 (1)
3847.GLYMA11G16040.1 (1)
3847.GLYMA11G16090.1 (1)
3847.GLYMA11G16190.1 (1)

CHEBI ID

CHEBI:16335 (4)
CHEBI:20597 (3)
CHEBI:20598 (3)
CHEBI:62005 (3)
CHEBI:20794 (3)
CHEBI:16750 (3)
CHEBI:16704 (3)
CHEBI:16020 (3)
CHEBI:17596 (3)
CHEBI:60193 (2)
CHEBI:19928 (2)
CHEBI:75654 (2)
CHEBI:229469 (2)
CHEBI:191041 (2)
CHEBI:19226 (2)
CHEBI:234279 (2)
CHEBI:19068 (2)
CHEBI:20129 (2)
CHEBI:19229 (2)
CHEBI:23774 (2)
CHEBI:19227 (2)
CHEBI:17822 (2)
CHEBI:26271 (2)
CHEBI:25094 (2)
CHEBI:18237 (2)
CHEBI:16040 (2)
CHEBI:22653 (2)
CHEBI:18186 (2)
CHEBI:28757 (2)
CHEBI:26986 (2)

Metabolite Name

3-Phosphoglyceric acid (3)
5-methoxycarbonylmethyluridine (3)
7-methylguanosine (3)
Adenylsuccinic acid (3)
Glycine (3)
Uridine (3)
Inosine (3)
Cytidine (3)
1-methyladenosine (3)
Valine (3)
Betaine (3)
Glucose 6-phosphate (3)
Citrulline (3)
Taurine (3)
Citric acid (3)
Myo-Inositol (3)
Glyceric acid (3)
Malic acid (3)
Adenosine (3)
Isoleucine (3)
Guanosine (3)
2-Methylguanosine (3)
Uridine (3)
Creatinine (3)
Creatine (3)
Hypoxanthine (3)
Phenol, 2-[4-[(3,5-dichlorophenyl)amino]-6-methyl-2-pyrimidinyl]- (2)
4-Amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid (2)
5-carbamoylmethyluridine (2)
Arachidonic sulfonic acid (2)

First Public Date

2025 (9)
2026 (8)
2021 (7)
2022 (5)
2024 (4)
2023 (4)
2020 (2)
2015 (2)
2018 (1)
2013 (1)

Study type

Transcription profiling by array (429)
RNA-seq of non coding RNA (124)
RNA-seq of coding RNA (116)
ChIP-chip by array (53)
ChIP-seq (45)
Comparative genomic hybridization by array (35)
Other (34)
Unknown experiment type (30)
Transcription profiling by tiling array (26)
ChIP-chip by tiling array (22)
RNA-seq of coding RNA from single cells (18)
Ribo-seq (16)
RNA-seq of total RNA (7)
Methylation profiling by high throughput sequencing (5)
Cell line - High-throughput sequencing (4)
DNA-seq (4)
Human - High-throughput sequencing (2)
MicroRNA profiling by high throughput sequencing (2)
Single nucleus RNA sequencing (2)
MicroRNA profiling by array (2)
Methylation profiling by array (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)
Translation profiling (1)
High-throughput sequencing (1)
Animal - High-throughput sequencing (1)
RNAi profiling by array (1)
Genotyping by array (1)

Release Date

2010 (167)
2014 (115)
2015 (97)
2013 (97)
2012 (79)
2011 (79)
2008 (69)
2016 (65)
2009 (57)
2007 (49)
2025 (42)
2006 (40)
2021 (30)
2024 (28)
2005 (28)
2022 (25)
2017 (22)
2020 (21)
2026 (18)
2004 (16)
2023 (15)
2019 (13)
2018 (13)
2003 (5)
2002 (1)
2000 (1)
1999 (1)
1998 (1)

Lab affiliation

Genomics Research Center, Academia Sinica, Taipei, Taiwan (2)
Ben-Gurion University of the Negev (1)
Chemistry Department, Boston College, USA (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 Biochemistry, The University of Western Ontario, London, Ontario, Canada. Department of Chemistry, The University of Western Ontario, London, Ontario, Canada. (1)
Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada. 2 Bioinformatic Solutions Inc., Waterloo, Ontario, Canada. Department of Chemistry, The University of Western Ontario, London, Ontario, Canada. (1)
Department of Chemistry University of Konstanz (1)
Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA (1)
IISER Kolkata Department of Biological Sciences Mohanpur, Dist. Nadia West Bengal, India (1)
Indiana University School of Medicine (1)
Jiangxi Provincial Key Laboratory of Cell Precision Therapy, School of Basic Medical Sciences, Jiujiang University (1)
Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA. (1)
Proteomics & Metabolomics Facility, University of Connecticut (1)
Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Sweden (1)
Qilu Hospital of Shandong University (1)
State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. (1)
Underwood-Prescott Professor, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 56-731 Cambridge, MA 02139-4307 (1)
University of Maryland, College Park (1)
VIB/KU LEUVEN Center for Microbiology (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

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

tRNA fragment profiling in CLP1 mutant (kinase-dead) mice

Loss of CLP1 activity results in the accumulation of novel sets of small RNA fragments derived from aberrant processing of tyrosine pre-tRNA. Such tRNA fragments sensitize cells to oxidative stress-induced p53 activation and p53-dependent cell death. 2 samples, Wt and Clp1(k/k), no replicates

ORGANISM(S): Mus musculus

2013-04-03 | E-GEOD-39275 | biostudies-arrayexpress

Identification of tRNA sequences in Lactococcus lactis

we report the identification and sequences of the tRNAome of industrially relevant microorganism Lactococcus lactis Three Next Generation sequencing runs annotated as S1, S2 and S3 were performed. Cells were harvested at exponential phase and tRNA was isolated. S1 and S2 were spiked with Phe-tRNAGAA...

ORGANISM(S): Lactococcus lactis subsp. cremoris MG1363

2014-07-29 | E-GEOD-55392 | 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

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

Suppressor mutant screening lacking growth-essential tRNA modification in bacteria

Post-transcriptional modifications are important for transfer RNAs (tRNAs) to be efficient and accurate in translation on the ribosome. The m1G37 modification on a subset of tRNAs in bacteria are generated by a conserved methyltransferase TrmD and is essential for bacterial growth. Previous studies ...

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

2022-09-24 | E-MTAB-12178 | 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

tRNA-Derived Small Non-Coding RNAs in Response to Ischemia Inhibit Angiogenesis

Ischemic injuries will lead to necrotic tissue damage, and post-ischemia angiogenesis plays critical roles in blood flow restoration and tissue recovery. Recently, several types of small RNAs have been reported to be involved in this process. In this study, we first generated a rat brain ischemic mo...

ORGANISM(S): Rattus norvegicus

2016-03-16 | E-GEOD-70473 | biostudies-arrayexpress

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern. TIP-seq recovery of transposon insertion junctio...

ORGANISM(S): Saccharomyces cerevisiae

2012-01-01 | E-GEOD-33986 | biostudies-arrayexpress

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