GEO DataSets

(Submitter supplied) The human genome encodes hundreds of tRNA genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and post-transcriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: XLS

(Submitter supplied) Here, we apply tRNA-seq and YAMAT-seq to profile the expressions of tRFs and tRNAs in plants. We provide a high-quality expression atlas of tRFs and tRNAs in Arabidopsis and rice, and uncover complex tRF population and the dynamic expressions of tRNA genes in plants.

Organism:

Setaria italica; Zea mays; Arabidopsis thaliana; Glycine max; Hordeum vulgare; Triticum aestivum; Sorghum bicolor

Type:

Non-coding RNA profiling by high throughput sequencing

7 related Platforms

13 Samples

Download data: TXT, XLSX

(Submitter supplied) Here, we adopt a method that combines tRNA-seq and cp-RNA-seq to identify and quantify tRFs and tRNAs in plants. We provide a high-quality expression atlas of tRFs and tRNAs in Arabidopsis and rice, and uncovers complex tRFs repertoire and the dynamic expressions of tRNA genes in plants.

Organism:

Arabidopsis thaliana; Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21785 GPL23013

24 Samples

Download data: XLSX

(Submitter supplied) Transfer RNAs (tRNA) are quintessential in deciphering the genetic code; disseminating nucleic acid triplets into correct amino acid identity. While this decoding function is clear, an emerging theme is that tRNA abundance and functionality can powerfully impact protein production rate, folding, activity, and messenger RNA stability. Importantly, however, the expression pattern of tRNAs (in even simple systems) is obliquely known. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21626 GPL21697

29 Samples

Download data: CSV

(Submitter supplied) We applied a tRNA-specific sequencing pipeline to analyze tRNA expression during infection of MC57G fibroblasts with the gammaherpesvirus MHV68. We find that expression of 14% of tRNA genes is significantly upregulated during infection. By mapping reads to either premature tRNA (pre-tRNA) or mature tRNA sequences, we find that increased expression of tRNA genes is manifested at the level of the pre-tRNA only, indicating a homeostatic mechanism to maintain the size and composition of mature tRNA pools.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: TXT

(Submitter supplied) Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas the substrate for Q-modification in tRNA in mammals is queuine, the catabolic product of the Q-base of gut bacteria. more...

Organism:

Escherichia coli; Homo sapiens

Type:

Other

Platforms:

GPL21433 GPL24676

29 Samples

Download data: TSV

(Submitter supplied) We have performed RNA sequencing after tRNA/tRF overexpression

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) Embryos generated with the use of assisted reproductive technologies (ART) can develop overgrowth syndromes. In ruminants, the condition is referred to as large offspring syndrome (LOS) and exhibits variable phenotypic abnormalities including overgrowth, enlarged tongue, and abdominal wall defects. These characteristics recapitulate those observed in the human loss-of-imprinting (LOI) overgrowth syndrome Beckwith-Wiedemann (BWS). more...

Organism:

Bos indicus x Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21383

32 Samples

Download data: TXT

(Submitter supplied) We sequenced the small RNA transcriptome of prostate cancer at different stages and generated a quantified catalogue of 3927 small non-coding RNAs (sncRNAs) detected in normal and malignant prostate tissue. From these sncRNAs less than half are microRNAs. The remaining sncRNAs represent stable sncRNAs species that originate from snoRNA, tRNA and other sncRNAs.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9052

11 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19872

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL18573

97 Samples

Download data: BEDGRAPH, BROADPEAK, NARROWPEAK

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: CSV

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

5 Samples

Download data: CSV

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: CSV, TXT

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

68 Samples

Download data: BEDGRAPH, BROADPEAK, NARROWPEAK

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: CSV, NARROWPEAK

(Submitter supplied) The participation of transfer RNAs (tRNAs) in fundamental aspects of biology and disease necessitates an accurate, experimentally confirmed annotation of tRNA genes, and curation of precursor and mature tRNA sequences. This has been challenging, mainly because RNA secondary structure and nucleotide modifications, together with tRNA gene multiplicity, complicate sequencing and sequencing read mapping efforts. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) In this study, we performed deep sequencing and bioinformatics analyses of short RNAs from three strains of Trichomonas vaginalisto identify and characterize novel type of small RNAs. We detected a new type of small RNA from tranfer RNA known as tRFs and tRNA-halves.

Organism:

Trichomonas vaginalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22655

3 Samples

Download data: FA, TXT

(Submitter supplied) Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the stable structures of these molecules and their numerous base modifications. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

58 Samples

Download data: CSV

(Submitter supplied) Here we develop a high throughput sequencing method that enables accurate determination of charged tRNA fractions at single base resolution (Charged tRNA-seq). Our method takes advantage of the recently developed DM-tRNA-seq method, but includes additional chemical steps that specifically remove the 3'A residue in the uncharged tRNA. Charging fraction is obtained by counting the fraction of A-ending reads versus A+C-ending reads for each tRNA species. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT, XLSX