GEO DataSets

(Submitter supplied) Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human Alu repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified new circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched compared to linear controls. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

12 Samples

Download data: TXT

(Submitter supplied) We profile gene expression upon circCDYL KD in HepG2 cells and in two bladder cancer cell lines J82 and UMUC3 as well as upon knockdown of the RNA binding proteins (RBP) GRWD1, IGF2BP1, and IGF2BP2 in J82 and UMUC3

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

36 Samples

Download data: TXT

(Submitter supplied) We profile the expression of circular RNAs (circRNAs) upon KHSRP KD in HepG2 and K562 cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: TXT

(Submitter supplied) Multidrug resistance-associated protein 4 (MRP4), a member of the C subfamily of ATP-binding cassette transporters, is highly expressed in the kidney of mammals and responsible for renal elimination of various drugs. Adenosine deaminase acting on RNA 1 (ADAR1) has been reported to regulate gene expression through catalyzing adenosine-to-inosine (A-to-I) RNA editing. In this study, we found that the down-regulation of ADAR1 increased the expression of MRP4 in human renal cells at post-transcriptional level. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL25134

2 Samples

Download data: TXT

(Submitter supplied) To investigate the role of ADAR1 in gastric carcinogenesis, RNA sequencing and small RNA sequencing were performed in AGS and MKN-45 cells with stable ADAR1 knock-down. Changed frequencies of editing and messenger RNA (mRNA) and microRNA (miRNA) expression were then identified by bioinformatic analyses.

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

8 Samples

Download data: TXT

(Submitter supplied) Circular RNAs (circRNAs) are single-stranded RNAs that are joined head to tail. Initially discovered as pathogen genomes such as hepatitis D virus (HDV) and plant viroids, circRNAs are recently recognized as a pervasive class of noncoding RNAs in eukaryotic cells, generated through back splicing. circRNAs have been postulated to function in cell-to-cell information transfer or memory due to their extraordinary stability. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: DOCX, TXT

(Submitter supplied) Transposable elements increase genetic diversity thus making them an important part of evolution and gene regulation in all organisms that carry these sequences. Bulk of our nascent transcriptome is comprised of transposable elements that have the propensity to form strong secondary structures. It is essential to resolve such strong secondary structures to maintain normal cellular function. Here, we show that the major nuclear RNA helicase DHX9/RHA interacts and remodels embedded Alu retrotransposable elements in the human transcriptome and B1 retrotransposable elements in the mouse transcriptome. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

4 Samples

Download data: BED, BIGWIG

(Submitter supplied) Transposable elements increase genetic diversity thus making them an important part of evolution and gene regulation in all organisms that carry these sequences. Bulk of our nascent transcriptome is comprised of transposable elements that have the propensity to form strong secondary structures. It is essential to resolve such strong secondary structures to maintain normal cellular function. Here, we show that the major nuclear RNA helicase DHX9/RHA interacts and remodels embedded Alu retrotransposable elements in the human transcriptome and B1 retrotransposable elements in the mouse transcriptome. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

4 Samples

Download data: BED, BIGWIG, GFF

(Submitter supplied) Transposable elements increase genetic diversity thus making them an important part of evolution and gene regulation in all organisms that carry these sequences. Bulk of our nascent transcriptome is comprised of transposable elements that have the propensity to form strong secondary structures. It is essential to resolve such strong secondary structures to maintain normal cellular function. Here, we show that the major nuclear RNA helicase DHX9/RHA interacts and remodels embedded Alu retrotransposable elements in the human transcriptome and B1 retrotransposable elements in the mouse transcriptome. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

4 Samples

Download data: BED, BIGWIG, GFF

(Submitter supplied) Transposable elements increase genetic diversity thus making them an important part of evolution and gene regulation in all organisms that carry these sequences. Bulk of our nascent transcriptome is comprised of transposable elements that have the propensity to form strong secondary structures. It is essential to resolve such strong secondary structures to maintain normal cellular function. Here, we show that the major nuclear RNA helicase DHX9/RHA interacts and remodels embedded Alu retrotransposable elements in the human transcriptome and B1 retrotransposable elements in the mouse transcriptome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: BED, BIGWIG, GFF

(Submitter supplied) Transposable elements are viewed as ‘selfish genetic elements’, yet they contribute to gene regulation and genome evolution in diverse ways. More than half of the human genome consists of transposable elements. With over 1 million insertions, Alu elements belong to the short interspersed nuclear element (SINE) family of repetitive elements, and with over 1 million insertions they make up more than 10% of the human genome. more...

Organism:

Homo sapiens; Drosophila melanogaster; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

6 related Platforms

90 Samples

Download data: BED, BIGWIG

(Submitter supplied) Transposable elements increase genetic diversity thus making them an important part of evolution and gene regulation in all organisms that carry these sequences. Bulk of our nascent transcriptome is comprised of transposable elements that have the propensity to form strong secondary structures. It is essential to resolve such strong secondary structures to maintain normal cellular function. Here, we show that the major nuclear RNA helicase DHX9/RHA interacts and remodels embedded Alu retrotransposable elements in the human transcriptome and B1 retrotransposable elements in the mouse transcriptome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: BIGWIG

(Submitter supplied) Transposable elements increase genetic diversity thus making them an important part of evolution and gene regulation in all organisms that carry these sequences. Bulk of our nascent transcriptome is comprised of transposable elements that have the propensity to form strong secondary structures. It is essential to resolve such strong secondary structures to maintain normal cellular function. Here, we show that the major nuclear RNA helicase DHX9/RHA interacts and remodels embedded Alu retrotransposable elements in the human transcriptome and B1 retrotransposable elements in the mouse transcriptome. more...

Organism:

Homo sapiens; Drosophila melanogaster; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

52 Samples

Download data: BED, BIGWIG, NARROWPEAK

(Submitter supplied) Circular RNAs (circRNAs) represent an abundant and conserved entity of non-coding RNAs, however the principles of biogenesis are currently not fully understood. To elucidate features important for circRNA production, we performed global analyses of RNA-binding proteins associating with the flanking introns of circRNAs, and we identified two factors, SFPQ and NONO, to be highly enriched with circRNAs. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL23227 GPL18573 GPL20301

36 Samples

Download data: TXT

(Submitter supplied) We generated RNA-seq libraries from three biological replicas of adbp-1 mutant worms at the embryo and L4 developmental stages. We wanted to identify editing sites globally in adbp-1 mutant worms and understand the preferable ADR-2 5’ and 3’ nearest neighbors of editing sites in wild-type worms in contrast to adbp-1 mutant worms. In addition, we wanted to test if the cytoplasmic localization of ADR-2 causes the downregulation of 3’UTR edited genes and lncRNAs, and test the effect of lacking ADBP-1 on global gene expression.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

6 Samples

Download data: XLSX

(Submitter supplied) We determined circRNA abundance in fly Heads and S2 cells by generating and analyzing high-throughput RNA-sequencing libraries prepared from rRNA-depleted RNA. In order to determine whether the observed sequencing reads are due to bona fide circRNAs, we pre-treated the RNA with RNAse-R before the rRNA-depletion procedure. Indeed, most of the identified circRNAs were more enriched in comparison to the canonical mRNA isoforms following the RNAse-R treatment. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

19 Samples

Download data: BED

(Submitter supplied) Circular RNAs (circRNAs) are an endogenous class of animal RNAs. Despite their abundance, their function and expression in the nervous system are unknown. Therefore, we sequenced RNA from different brain regions, primary neurons, isolated synapses, as well as during neuronal differentiation. Using these and other available data, we discovered and analyzed thousands of neuronal human and mouse circRNAs. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

25 Samples

Download data: BED

(Submitter supplied) Adenosine deaminases that act on RNA (ADARs) catalyze the conversion of adenosine to inosine in dsRNA. C. elegans ADARs, ADR-1 and ADR-2, promote the expression of genes containing dsRNA structures by preventing their processing into siRNAs and silencing by RNAi. The 26G endogenous siRNA (endo-siRNA) pathway generates a subset of siRNAs distinct from those made in adr-1;adr-2 mutants, but using many of the same factors. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

24 Samples

Download data: TXT

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

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13657 GPL18245

32 Samples

Download data

(Submitter supplied) Cellular RNAs containing double-stranded RNA (dsRNA) structures are subject to A-to-I RNA editing by the adenosine deaminases that act on RNA (ADARs). While A-to-I editing can alter mRNA coding potential, most editing is observed in non-coding sequences, the function of which remains poorly characterized. To correlate small RNA population with expression patterns of ADARs and hyperedited RNAs (editing-enriched regions: EERs) defined and characterized in a separate RNAseq analysis, we re-analyzed existing smallRNAseq datasets of a wildtype strain and a strain lacking ADARs (adr-1;adr-2). more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis

Download data: TXT, XLS