GEO DataSets

(Submitter supplied) Measurements of cellular tRNA abundance are hampered by pervasive blocks to cDNA synthesis at modified nucleosides and the extensive similarity among tRNA genes. We overcome these limitations with modification-induced misincorporation tRNA sequencing (mim-tRNAseq), which combines a workflow for full-length cDNA library construction from mature tRNA with a simple-to-use computational analysis toolkit. more...

Organism:

Schizosaccharomyces pombe; Drosophila melanogaster; Homo sapiens; Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

29 Samples

Download data: CSV

(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) 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) 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) Eukaryotic transfer RNAs (tRNA) contain on average 13 modifications that perform a wide range of roles in translation and in the generation of tRNA fragments that regulate gene expression. Queuosine (Q) modification occurs in the wobble anticodon position of tRNAs for amino acids His, Asn, Tyr, and Asp. In eukaryotes, Q modification is fully dependent on diet or on gut microbiome in multi-cellular organisms. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15433

4 Samples

Download data: TXT, XLSX, ZIP

(Submitter supplied) Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced due to the abundant presence of post-transcriptional modifications and extensive structure that interfere with cDNA synthesis and adapter ligation. We achieve efficient and quantitative tRNA sequencing by removing base methylations using engineered demethylases and using a highly processive thermo-stable reverse transcriptase without the need for adapter ligation (DMTRT-tRNA-seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

8 Samples

Download data: TXT

(Submitter supplied) We report the identification and quantification of Watson-Crick modifications in tRNA and rRNA through the use of high throughput sequencing. We apply the recently published DM-tRNA-Seq method to generate demethylase treated and untreated 293T samples, and using computational methods we are able to flag sites using a modification index. This index allows us to generate site-resolved information about modification that we can use to identify and quantify Watson-Crick face modifications in tRNA and rRNA. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL15433

5 Samples

Download data: TXT

(Submitter supplied) Here we report a direct tRNA sequencing protocol and software to simultaneously examine the composition and biological activity of naturally occurring microbial communities. Our analysis of mouse gut microbiome with tRNA-seq and 16S ribosomal RNA gene amplicons revealed comparable microbial community structures, and additional physiological insights into the microbiome through tRNA abundance and modifications.

Organism:

Escherichia coli; Staphylococcus aureus; Bacillus subtilis; mouse gut metagenome; Barnesiella viscericola

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

28 Samples

Download data: TXT, XLSX

(Submitter supplied) Small RNAs include tRNA, snRNA, micro-RNA, tRNA fragments and others that constitute >90% of RNA copy numbers in a human cell and perform many essential functions. Popular small RNA-seq strategies limit the insights into coordinated small RNA response to cellular stress. Small RNA-seq also lacks multiplexing capabilities. Here, we report a multiplex small RNA-seq library preparation method (MSR-seq) to investigate cellular small RNA and mRNA response to heat shock, hydrogen peroxide, and arsenite stress. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL24676

64 Samples

Download data: TSV

(Submitter supplied) We report the application of high-throughput RNA sequencing to the human prefrontal cortex. The brain dataset was obtained by sequencing total RNAs extracted from the dorsolateral prefrontal cortex of five deceased human patients with no apparent pathology, followed by depletion of ribosomal RNA to obtain all non-rRNA coding and non-coding RNAs in the human brain transcriptome.

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

5 Samples

Download data: TXT

(Submitter supplied) The surprising observation that virtually the entire human genome is transcribed means we know very little about the function of many emerging classes of RNAs, except their astounding diversity. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their ability to classify classes of non-coding RNAs (ncRNAs). To address this, we developed CoRAL, a machine learning-based approach for classification of RNA molecules. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9115

4 Samples

Download data: TXT

(Submitter supplied) Current next-generation RNA sequencing methods do not provide accurate quantification of small RNAs within a sample due to sequence-dependent biases in capture, ligation, and amplification during library preparation. We present a method – AQRNA-seq – that minimizes biases and provides a direct, linear correlation between sequencing read count and copy number for small RNAs in a sample. The library preparation and data processing steps were optimized and validated using a 963-member microRNA reference library, oligonucleotide standards of varying lengths, and northern blots. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: XLSX

(Submitter supplied) We report the development of an RNA sequencing method – AQRNA-seq – that minimizes biases and enables absolute quantification of all small RNA species in a sample mixture. Validation of AQRNA-seq library preparation and data mining algorithms using a 963-member microRNA reference library, RNA oligonucleotide standards of varying lengths, and northern blots demonstrated a direct, linear correlation between sequencing read count and RNA abundance.

Organism:

synthetic construct

Type:

Other

Platform:

GPL19424

18 Samples

Download data: TXT

(Submitter supplied) Defects in tRNA biogenesis are associated with diverse neurological disorders, yet our understanding of these diseases has been hampered an inability to determine tRNA expression in individual cell types within a complex tissue. Here, we developed a mouse model in which RNA Polymerase III is conditionally epitope-tagged in a Cre-dependent manner, allowing us to accurately profile tRNA expression in any cell type in vivo. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

41 Samples

Download data: BIGWIG

(Submitter supplied) Defects in tRNA biogenesis are associated with multiple neurological disorders, yet our understanding of these diseases has been hampered an inability to determine tRNA expression in individual cell types within a complex tissue. Here, we developed a mouse model in which RNA Polymerase III is conditionally epitope-tagged in a Cre-dependent manner, allowing us to accurately profile tRNA expression in any cell type in vivo. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

22 Samples

Download data: TSV

(Submitter supplied) N7-methylguanosine (m7G) is a positively charged, essential modification at the 5′ cap of eukaryotic mRNA, regulating mRNA export, translation, and splicing. m7G also occurs internally within tRNA and rRNA, but its existence and distribution within eukaryotic mRNA remain to be investigated. Here, we show the presence of internal m7G sites within mammalian mRNA. We then performed transcriptome-wide profiling of internal m7G methylome using m7G-MeRIP sequencing (MeRIP-seq). more...

Organism:

Homo sapiens; Mus musculus

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL18573 GPL20301

104 Samples

Download data: BED, FPKM_TRACKING, TXT, XLSX

(Submitter supplied) We report RBS-Seq, a new RNA bisulfite sequencing method enabling the sensitive and simultaneous detection of m5C, pseudouridine, and m1A at single-base resolution transcriptome-wide. For each, we detect ‘signature’ base mismatches (for m5C and m1A), or 1-2 base deletions (for pseudouridine) structurally explained by ribose ring-opened pseudouridine-mono-bisulfite adducts.  Our profiles for pseudouridine reveal clear signatures at known sites in tRNAs and rRNAs, and provide hundreds of new targets in non-coding RNAs and mRNAs. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL15520 GPL16791

14 Samples

Download data: XLSX

(Submitter supplied) Covalent nucleotide modifications in noncoding RNAs such as tRNAs affect a plethora of biological processes, with new functions continuing to be discovered for even well-known tRNA modifications. To systematically compare the functions of a large set of ncRNA modifications in gene regulation, we carried out ribosome profiling and RNA-Seq in budding yeast for 57 nonessential genes involved in tRNA modification.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

232 Samples

Download data: TXT

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

Organism:

Homo sapiens; Escherichia coli; Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

60 Samples

Download data

(Submitter supplied) Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent Rhodamine labeling. Using Rho-seq, we report that the reduction of uridine to dihydrouridine by the Dus reductase family targets tRNAs in E. coli but expands to mRNAs is yeast. The modified mRNAs are enriched for cytoskeleton related encoded protein. We show that the a-tubulin encoding mRNA nda2 undergoes dihydrouridination, which affects its protein expression level. more...

Organism:

Schizosaccharomyces pombe; Homo sapiens; Escherichia coli

Type:

Other

4 related Platforms

44 Samples

Download data: XLSX