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Links from GEO DataSets

Items: 20

1.

Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL small RNA)

(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
Series
Accession:
GSE55332
ID:
200055332
2.

A variety of Dicer substrates in human and C. elegans (HEK RNA-seq)

(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
Series
Accession:
GSE63475
ID:
200063475
3.

A variety of Dicer substrates in human and C. elegans (HEK small RNA)

(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
Series
Accession:
GSE63458
ID:
200063458
4.

A variety of Dicer substrates in human and C. elegans (HEK PAR-CLIP)

(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
Series
Accession:
GSE63437
ID:
200063437
5.

A variety of Dicer substrates in human and C. elegans (CEL RNA-seq)

(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
Series
Accession:
GSE63435
ID:
200063435
6.

Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates

(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
Series
Accession:
GSE55333
ID:
200055333
7.

Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (small RNA AGO-IP)

(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
Series
Accession:
GSE55331
ID:
200055331
8.

Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL RNA-Seq)

(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
Series
Accession:
GSE55329
ID:
200055329
9.

Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK RNA-Seq)

(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
Series
Accession:
GSE55326
ID:
200055326
10.

Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL PAR-CLIP)

(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
Series
Accession:
GSE55325
ID:
200055325
11.

Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK PAR-CLIP)

(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
Series
Accession:
GSE55324
ID:
200055324
12.

MicroRNA-Directed siRNA Biogenesis in Caenorhabditis elegans

(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
Series
Accession:
GSE20649
ID:
200020649
13.

Adult Caenorhabditis elegans: wild-type (N2) and mir-243 mutant worms

(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
Series
Accession:
GSE20558
ID:
200020558
14.

Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs

(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
Series
Accession:
GSE55338
ID:
200055338
15.

The effects of the 5' pocket motif of Dicer on miRNA biogenesis

(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
Series
Accession:
GSE27903
ID:
200027903
16.

Microarray profiling reveals broad and differential effects of RBM3 on miRNA expression.

(Submitter supplied) MicroRNAs (miRNAs) are a family of short, noncoding RNAs that regulate translation of mRNAs by mechanisms involving the binding of complementary sequences. The influence of miRNAs on the proteome and cellular events is extensive as they regulate an estimated 60% of the transcriptome and play key roles in differentiation, plasticity, circadian rhythm, immunity, and disease. The post-transcriptional biogenesis of most miRNAs involves a sequential cleavage process mediated by RNase III family enzymes. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by array
Platform:
GPL8824
4 Samples
Download data: TXT
Series
Accession:
GSE33519
ID:
200033519
17.

The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans

(Submitter supplied) RNA interference (RNAi) is a potent mechanism for down-regulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary siRNAs. Exogenous double stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13657
8 Samples
Download data: TXT
Series
Accession:
GSE53830
ID:
200053830
18.

Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals

(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:
Mus musculus; Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL9061 GPL9250
24 Samples
Download data: TXT
Series
Accession:
GSE37443
ID:
200037443
19.

Small RNA profiling of RNase III enzyme deficient DN3 thymocytes, Tregs, activated CD4+ T cells, and embryonic fibroblasts

(Submitter supplied) Here we analyze the small RNA species in the following: 1. DN3 thymocytes following inactivation of LoxP flanked Drosha and Dicer alleles with Lck-cre 2. Tregs following inactivation of LoxP flanked Drosha and Dicer alleles with CD4-cre 3. activated CD4+ T cells following inactivation of LoxP flanked Drosha and Dicer alleles with CD4-cre 4. MEFs following inactivation of LoxP flanked Drosha and Dicer alleles with Rosa26-CreER and 4-OH tamoxifen treatment
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9250
12 Samples
Download data: TXT
Series
Accession:
GSE22760
ID:
200022760
20.

Regulation of miRNA biogenesis by MCPIP1

(Submitter supplied) Effect of MCPIP1 knockdown on miRNA expression profile.
Organism:
Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Macaca mulatta polyomavirus 1; Mus musculus; Rattus norvegicus; Murid betaherpesvirus 1; Human gammaherpesvirus 4; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Human polyomavirus 1; Murid gammaherpesvirus 4
Type:
Non-coding RNA profiling by array
Platform:
GPL7723
2 Samples
Download data: TXT
Series
Accession:
GSE31091
ID:
200031091
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