GEO DataSets

(Submitter supplied) The endoribonuclease Dicer is known for its central role in the biogenesis of eukaryotic small RNAs/microRNAs. Despite its importance, Dicer target transcripts have not been directly mapped. Here, we apply biochemical methods to human cells and C. elegans and identify thousands of Dicer binding sites. We find known and hundreds of novel miRNAs with high sensitivity and specificity. We also report structural RNAs, promoter RNAs, and mitochondrial transcripts as Dicer targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

5 Samples

Download data: TXT

(Submitter supplied) The endoribonuclease Dicer is known for its central role in the biogenesis of eukaryotic small RNAs/microRNAs. Despite its importance, Dicer target transcripts have not been directly mapped. Here, we apply biochemical methods to human cells and C. elegans and identify thousands of Dicer binding sites. We find known and hundreds of novel miRNAs with high sensitivity and specificity. We also report structural RNAs, promoter RNAs, and mitochondrial transcripts as Dicer targets. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

5 Samples

Download data: WIG

(Submitter supplied) The endoribonuclease Dicer is known for its central role in the biogenesis of eukaryotic small RNAs/microRNAs. Despite its importance, Dicer target transcripts have not been directly mapped. Here, we apply biochemical methods to human cells and C. elegans and identify thousands of Dicer binding sites. We find known and hundreds of novel miRNAs with high sensitivity and specificity. We also report structural RNAs, promoter RNAs, and mitochondrial transcripts as Dicer targets. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL11154

5 Samples

Download data: WIG

(Submitter supplied) The endoribonuclease Dicer is known for its central role in the biogenesis of eukaryotic small RNAs/microRNAs. Despite its importance, Dicer target transcripts have not been directly mapped. Here, we apply biochemical methods to human cells and C. elegans and identify thousands of Dicer binding sites. We find known and hundreds of novel miRNAs with high sensitivity and specificity. We also report structural RNAs, promoter RNAs, and mitochondrial transcripts as Dicer targets. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

3 Samples

Download data: TXT

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

Organism:

Caenorhabditis elegans; Homo sapiens

Type:

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

Platforms:

GPL11154 GPL13657

34 Samples

Download data: GFF, TSV, TXT, WIG

(Submitter supplied) Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivity. Small RNA production depended on structure of the binding site and is globally biased towards the 5' arm of hairpins. more...

Organism:

Caenorhabditis elegans

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13657

2 Samples

Download data: GFF, WIG

(Submitter supplied) Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivity. Small RNA production depended on structure of the binding site and is globally biased towards the 5' arm of hairpins. more...

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: GFF, TSV, WIG

(Submitter supplied) Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and C.elegans. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivity. Small RNA production depended on structure of the binding site and is globally biased towards the 5' arm of hairpins. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

3 Samples

Download data: FPKM_TRACKING, TXT, WIG

(Submitter supplied) Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivity. Small RNA production depended on structure of the binding site and is globally biased towards the 5' arm of hairpins. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: FPKM_TRACKING, TXT, WIG

(Submitter supplied) Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivity. Small RNA production depended on structure of the binding site and is globally biased towards the 5' arm of hairpins. more...

Organism:

Caenorhabditis elegans

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13657

3 Samples

Download data: GFF

(Submitter supplied) Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivity. Small RNA production depended on structure of the binding site and is globally biased towards the 5' arm of hairpins. more...

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: GFF

(Submitter supplied) Long noncoding RNAs (lncRNAs) are important regulators of cell fate, and their mis-expression has been implicated in many diseases. While distinct polymerases generate messenger vs. noncoding ribosomal or tRNAs3, little is known about distinct mechanisms controlling lncRNA expression. Here we show that transcription of lncRNAs is quantitatively different from that of messenger RNAs (mRNAs)--as revealed by deficiency of Dicer (Dcr), a key ribonuclease that generates microRNAs (miRNAs). more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL9250 GPL13112

11 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) C.elegans small RNAs from HA::ALG-1, HA::ALG-2 and HA::RDE-1 IP and rde-1 mutants

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9269 GPL9085

5 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of N2 vs. mir-243 worms, aiming to identify direct and indirect targets of the microRNA.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL8209

6 Samples

Download data: TXT

(Submitter supplied) A hallmark of RNA silencing is a class of ~22 nt RNAs which are processed from dsRNA precursor by Dicer. Accurate processing by Dicer is critical for the functionality of microRNAs (miRNAs). According to the current model, Dicer measures the length by anchoring the 3' overhang of the dsRNA terminus. Here we find that human Dicer binds to the 5' end of RNA and utilizes the 5' end as an additional reference point for cleavage site selection (5' counting rule). more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9250

5 Samples

Download data

(Submitter supplied) Effect of MCPIP1 knockdown on miRNA expression profile.

Organism:

Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Betapolyomavirus hominis; Murid gammaherpesvirus 4; Mus musculus; Rattus norvegicus; Murid betaherpesvirus 1; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; human gammaherpesvirus 4; Betapolyomavirus macacae

Type:

Non-coding RNA profiling by array

Platform:

GPL7723

2 Samples

Download data: TXT

(Submitter supplied) Biogenesis of canonical microRNAs (miRNAs) involves multiple steps: nuclear processing of primary miRNA (pri-miRNA) by DROSHA, nuclear export of precursor miRNA (pre-miRNA) by Exportin 5 (XPO5), and cytoplasmic processing of pre-miRNA by DICER. To gain a deeper understanding of the contribution of each of these maturation steps, we deleted DROSHA, XPO5, and DICER in the same human cell line, and analyzed their effects on miRNA biogenesis. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15520

9 Samples

Download data: TXT

(Submitter supplied) Drosophila Dicer-1 produces microRNAs (miRNAs) from pre-miRNA, whereas Dicer-2 generates small interfering RNAs (siRNAs) from long dsRNA. loquacious (loqs) encodes three Dicer partner proteins, Loqs-PA, Loqs-PB, and, Loqs-PD, generated by alternative splicing. To understand the function of each Loqs isoform, we constructed loqs isoform-specific rescue flies. Loqs-PD promotes siRNA production in vivo by Dicer-2. more...

Organism:

Drosophila melanogaster; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9061 GPL9250

24 Samples

Download data: TXT

(Submitter supplied) Alveolar macrophages from never smokers and active smokers were isolated by bronchoalveolar lavage and gene expression was measured. Chronic cigarette smoke exposure, as occurs in smoker's lungs, leads to significant changes in gene expression. Of note, RNA was isolated immediately following bronchoscopy. Alveolar macrophage levels were >95%.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

8 Samples

Download data: CEL

(Submitter supplied) MicroRNAs (miRNA) are short non-coding RNAs widely implicated in development, gene regulation, and disease progression. Most miRNAs utilize the RNase III enzymes Drosha and Dicer for biogenesis in animals. One notable exception is the RNA polymerase II transcription start sites (TSS) miRNAs whose biogenesis requires Dicer but not Drosha. The functional importance of the TSS-miRNA biogenesis pathway has remained uncertain due to their unelucidated targetomes. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL21290

43 Samples

Download data: TXT