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Links from GEO DataSets

Items: 20

1.

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
2.

small RNAs produced in the wild-type and mutant Dicer-2 transgenic flies

(Submitter supplied) Examine the abundance and length of siRNAs produced by mutant Dicer-2 in vivo and in vitro in order to understand the mechanism by which Dicer-2 produces highly precise 21 nt siRNAs.
Organism:
Drosophila melanogaster; synthetic construct
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL21306 GPL21616
12 Samples
Download data: TXT
Series
Accession:
GSE84532
ID:
200084532
3.

Regulation of miRNA biogenesis by MCPIP1

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

small RNAs produced in the mutant Dicer-2 transgenic flies

(Submitter supplied) Examine the abundance and length of siRNAs produced by mutant Dicer-2 in vivo and in vitro in order to understand the mechanism by which Dicer-2 produces highly precise 21 nt siRNAs.
Organism:
synthetic construct; Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL21616 GPL21306
4 Samples
Download data: TXT
Series
Accession:
GSE94803
ID:
200094803
5.

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
6.

Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis

(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
Series
Accession:
GSE77989
ID:
200077989
7.

In vivo structure-function analysis of human Dicer reveals directional processing of precursor miRNAs

(Submitter supplied) Dicer is an RNase III-family endoribonuclease and haploinsufficient tumor suppressor that is required for the biogenesis of miRNAs, yet in vivo structure-function characterization of its RNase IIIA and IIIB domains have not been reported. In murine Dicer knockout fibroblasts, we expressed human Dicer with point mutations in the RNase III, helicase, and PAZ domains and characterized miRNA expression by Northern blot and massively parallel sequencing of small RNAs. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13112
16 Samples
Download data: TXT
Series
Accession:
GSE36978
ID:
200036978
8.

Derivation and characterization of Dicer and microRNA deficient human cells

(Submitter supplied) We have used genome editing to generate inactivating deletion mutations in all three copies of the dicer (hdcr) gene present in the human cell line 293T. As previously shown in murine ES cells lacking Dicer function, hDcr-deficient 293T cells are severely impaired for the production of mature microRNAs (miRNAs). Nevertheless, RNA-induced silencing complexes (RISCs) present in these hDcr-deficient cells are readily programmed by transfected, synthetic miRNA duplexes to repress mRNAs bearing either fully or partially complementary targets, including targets bearing incomplete seed homology to the introduced miRNA. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL11154
14 Samples
Download data: CSV, TSV
Series
Accession:
GSE56836
ID:
200056836
9.

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
10.

Dicer deficiency reveals microRNAs predicted to control gene expression in developing adrenal cortex

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Expression profiling by RT-PCR
Platforms:
GPL1261 GPL16971
32 Samples
Download data: CEL
Series
Accession:
GSE45812
ID:
200045812
11.

Dicer deficiency reveals microRNAs predicted to control gene expression in developing adrenal cortex [RT-PCR]

(Submitter supplied) MicroRNAs (miRNAs) are small, endogenous, non-protein coding RNAs that are an important means of post-transcriptional gene regulation. Deletion of Dicer, a key miRNA processing enzyme, is embryonic lethal in mice, and tissue-specific Dicer deletion results in developmental defects. Using a conditional knockout model, we generated mice lacking Dicer in the adrenal cortex. These Dicer knockout (KO) mice exhibited perinatal mortality and failure of the adrenal cortex during late gestation between embryonic day 16.5 (E16.5) and E18.5. more...
Organism:
Mus musculus
Type:
Expression profiling by RT-PCR
Platform:
GPL16971
16 Samples
Download data: TXT
Series
Accession:
GSE45810
ID:
200045810
12.

Dicer deficiency reveals microRNAs predicted to control gene expression in developing adrenal cortex [array]

(Submitter supplied) MicroRNAs (miRNAs) are small, endogenous, non-protein coding RNAs that are an important means of post-transcriptional gene regulation. Deletion of Dicer, a key miRNA processing enzyme, is embryonic lethal in mice, and tissue-specific Dicer deletion results in developmental defects. Using a conditional knockout model, we generated mice lacking Dicer in the adrenal cortex. These Dicer knockout (KO) mice exhibited perinatal mortality and failure of the adrenal cortex during late gestation between embryonic day 16.5 (E16.5) and E18.5. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
16 Samples
Download data: CEL
Series
Accession:
GSE45592
ID:
200045592
13.

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
14.

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
15.

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
16.

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
17.

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:
Homo sapiens; Caenorhabditis elegans
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
18.

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
19.

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
20.

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
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