GEO DataSets

(Submitter supplied) Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

14 Samples

Download data

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL9081 GPL10558

20 Samples

Download data: TXT

(Submitter supplied) This data set is part of a larger study: Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL9081

6 Samples

Download data: TXT

(Submitter supplied) We performed deep sequencing of small RNA from mouse insulinoma (MIN6) cells cultured in 25mM glucose. We then developed and implemented an in-house short-read mapping strategy to analyze isomiR diversity.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: BED

(Submitter supplied) MicroRNAs (miRNAs) are a class of small RNA molecules that regulate expression of specific mRNA targets. They can be released from cells, often encapsulated within extracellular vesicles (EVs), and therefore have the potential to mediate intercellular communication. It has been suggested that certain miRNAs may be selectively exported, although the mechanism has yet to be identified. Manipulation of the miRNA content of EVs will be important for future therapeutic applications. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9115

4 Samples

Download data: TXT

(Submitter supplied) Using miRDeep2 and a custom NGS data analysis workflow to annotate and quantify isomiRs in normal and neoplastic colorectal tissues.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

120 Samples

Download data: TXT

(Submitter supplied) Mouse Embryonic Stem (ES) cells express a unique set of microRNAs (miRNAs), the miR-290-295 cluster. To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets. The difficulty, however, arises from the limited complementarity of metazoan miRNAs to their targets, with the interaction requiring as few as six nucleotides of the miRNA seed sequence. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL10010

10 Samples

Download data: TXT

(Submitter supplied) Mouse Embryonic Stem (ES) cells express a unique set of microRNAs (miRNAs), the miR-290-295 cluster. To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets. The difficulty, however, arises from the limited complementarity of metazoan miRNAs to their targets, with the interaction requiring as few as six nucleotides of the miRNA seed sequence. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are single-stranded non-coding RNAs that negatively regulate target gene expression through mRNA cleavage or translational repression. There is mounting evidence that they play critical roles in heart disease. The expression of known miRNAs in the heart has been studied at length by microarray and quantitative PCR but it is becoming evident that microRNA isoforms (isomiRs) are potentially physiologically important. more...

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11282

9 Samples

Download data: TXT

(Submitter supplied) We performed extensive transcriptome analysis of the tiger pufferfish (Takifugu rubripes) using the next-generation sequencer SOLiD III, and profiled millions of small RNA sequences in somatic tissues and gonads, as well as identifying thousands of miRNAs. The number of miRNAs identified was the highest in fish species reported to date. We also report highly variable isomiR features.

Organism:

Takifugu rubripes

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19713

9 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL10558 GPL9442

14 Samples

Download data: BEDGRAPH

(Submitter supplied) Whole transcriptome identification of direct targets identify a new class of miRNA::mRNA interactions.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9442

1 Sample

Download data: BEDGRAPH

(Submitter supplied) Whole transcriptome Identification of direct targets identify a new class of miRNA::mRNA interactions.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

13 Samples

Download data: TXT

(Submitter supplied) Whole transcriptome Identification of direct targets of miR-199a-5p and miR-424-3p using biotinylated pull-downs found that both miRNAs are likely to have a role in the cell cycle.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

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

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by array; Expression profiling by array

6 related Platforms

90 Samples

Download data: PDF, TXT

(Submitter supplied) Pig mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a dedicated microarray platform to analyze mRNAs gene expression. Based on sequence similarity we rejected UniGene features that overlapped more than 40% with an Ensembl transcript. After this filter we obtained 40,267 UniGene clusters and 19,603 Ensembl transcripts (protein coding + pseudogenes + retrotransposed elements). more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL13411

1 Sample

Download data: TXT

(Submitter supplied) The short length of miRNAs results in a high dynamic range of melting temperatures and therefore impedes a proper selection of detection probes or optimized PCR primers. While miRNA microarrays allow for massive parallel and accurate relative measurement of all known miRNAs, they have so far been less useful as an assay for absolute quantification. Here we developed a new method based not only to the hybridization process that presents the limits before described, but integrating the hybridization to an enzymatic reaction. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by array

Platform:

GPL13322

28 Samples

Download data: TXT

(Submitter supplied) We applied a new computational approach to predict specie-specific and conserved miRNAs, than experimentally confirmed by a modified RNA-primed Array-based Klenow Extension (RAKE) method. We identified 489 conserved and 1,178 pig-specific novel miRNAs increasing our tally of confirmed miRNAs to 1,667 novel miRNAs. In addition, RAKE allowed the identification of miRNA isoforms (isomiRs) that we demonstrated to be differentially expressed across tissues suggesting that subtle variability in isomiR expression is regulated and biologically meaningful.

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by array

Platform:

GPL13321

9 Samples

Download data: TXT

(Submitter supplied) We applied a new computational approach to predict specie-specific and conserved miRNAs, than experimentally confirmed by a modified RNA-primed Array-based Klenow Extension (RAKE) method. We identified 489 conserved and 1,178 pig-specific novel miRNAs increasing our tally of confirmed miRNAs to 1,667 novel miRNAs. In addition, RAKE allowed the identification of miRNA isoforms (isomiRs) that we demonstrated to be differentially expressed across tissues suggesting that subtle variability in isomiR expression is regulated and biologically meaningful.

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by array

Platform:

GPL13320

12 Samples

Download data: TXT

(Submitter supplied) We applied a new computational approach to predict specie-specific and conserved miRNAs, than experimentally confirmed by a modified RNA-primed Array-based Klenow Extension (RAKE) method. We identified 489 conserved and 1,178 pig-specific novel miRNAs increasing our tally of confirmed miRNAs to 1,667 novel miRNAs. In addition, RAKE allowed the identification of miRNA isoforms (isomiRs) that we demonstrated to be differentially expressed across tissues suggesting that subtle variability in isomiR expression is regulated and biologically meaningful.

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by array

Platform:

GPL13319

12 Samples

Download data: TXT