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Links from GEO DataSets

Items: 20

1.

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
2.

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
3.

Regulation of miRNA biogenesis by MCPIP1

(Submitter supplied) Effect of MCPIP1 knockdown on miRNA expression profile.
Organism:
Human polyomavirus 1; 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; Murid gammaherpesvirus 4
Type:
Non-coding RNA profiling by array
Platform:
GPL7723
2 Samples
Download data: TXT
Series
Accession:
GSE31091
ID:
200031091
4.

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
5.

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
6.

MiRNAs expression data from GM0637 treated with and without ATM inhibitor after DNA damage

(Submitter supplied) GM0637 cell were pretreated with ATM inhibitor before adding DNA damaging agent neocarzinostatin (NCS), and cells were harvested after 4 hours for the microarray analyses of whole-genome miRNAs.
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by array
Platform:
GPL15517
4 Samples
Download data: GPR
Series
Accession:
GSE42248
ID:
200042248
7.

Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and novel substrates

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL16791
13 Samples
Download data
Series
Accession:
GSE93653
ID:
200093653
8.

Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and novel substrates [fCLIP-seq]

(Submitter supplied) MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gate-keeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated on a genomic scale, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL16791
4 Samples
Download data: TSV
Series
Accession:
GSE93651
ID:
200093651
9.

Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and novel substrates [RNA-seq]

(Submitter supplied) MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gate-keeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated on a genomic scale, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
9 Samples
Download data: TSV
Series
Accession:
GSE93650
ID:
200093650
10.

XPO5 is required for miRNA biogenesis and promotes primary miRNA processing independent of RanGTP

(Submitter supplied) XPO5 mediates nuclear export of miRNA hairpin precursors in a RanGTP-dependent manner. However, the requirement of XPO5 for global miRNA biogenesis and mammalian development and XPO5-associated RNA species are not determined. Here we show that XPO5 is required for mouse embryonic development and morphogenesis of skin and brain. Loss of XPO5 compromises the biogenesis of most miRNAs and that leads to severe developmental defects. more...
Organism:
Mus musculus; Homo sapiens
Type:
Other; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL11154 GPL13112
13 Samples
Download data: BED, TSV, TXT
11.

Precursor and mature microRNA expression in MCF7 cells in hypoxia

(Submitter supplied) Background: Cancers are commonly characterised by hypoxia and also by global reductions in the levels of mature microRNAs. We have examined the hypothesis that hypoxia might mediate this reduction through repressive effects on microRNA biogenesis proteins. Methods: Breast cancer cell lines were exposed to hypoxia and manipulations of hypoxia inducible factor (HIF) and HIF hydroxylase activity. The effects of hypoxia on the mRNA and protein levels of enzymes involved in microRNA biogenesis (Dicer, Drosha, TARPB2, DCGR8, XPO5) was determined by RT PCR and immunoblotting. more...
Organism:
synthetic construct; Homo sapiens
Type:
Non-coding RNA profiling by array
Platform:
GPL16384
9 Samples
Download data: CEL
Series
Accession:
GSE49999
ID:
200049999
12.

Circadian analysis of miRNAs and their targets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila melanogaster
Type:
Expression profiling by array; Expression profiling by genome tiling array
Platforms:
GPL5919 GPL1322
28 Samples
Download data: BAR, CEL, TXT
Series
Accession:
GSE17629
ID:
200017629
13.

Tiling arrays from control and flies without Drosha or Pasha

(Submitter supplied) Little is known about the contribution of translational control to circadian rhythms. To address this issue and in particular translational control by microRNAs (miRNAs), we knocked down the miRNA biogenesis pathway in Drosophila circadian tissues. In combination with an increase in circadian-mediated transcription, this severely affected Drosophila behavioral rhythms, indicating that miRNAs function in circadian timekeeping. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by genome tiling array
Platform:
GPL5919
1 Sample
Download data: BAR, CEL, TXT
Series
Accession:
GSE17628
ID:
200017628
14.

Genome wide identification of targets of the drosha-pasha/DGCR8 complex

(Submitter supplied) Drosha is a type III RNAse, which plays a critical role in miRNA biogenesis. Drosha and its double-stranded RNA-binding partner protein Pasha/DGCR8 likely recognize and cleave miRNA precursor RNAs or pri-miRNA hairpins co-transcriptionally. To identify RNAs processed by Drosha, we used tiling microarrays to examine transcripts after depletion of drosha mRNA with dsRNA in Drosophila Schneider S2 cells. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL6629 GPL5919
7 Samples
Download data: BAR, CEL
Series
Accession:
GSE14215
ID:
200014215
15.

Expression profile of control, Drosha or Dicer deleted LSKs

(Submitter supplied) To determine genes regulated independently of microRNAs in early haematopoietic progenitors (LSKs) we compared the expression profiles of Drosha or Dicer deficient LSKs and control. Those genes differentially expressed between Drosha or Dicer deficient LSKs are likely regulated indepedently of microRNAs as either Drosha or Dicer deletion will lead to a complete and equivalent loss of microRNAs.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL13912
9 Samples
Download data: TXT
Series
Accession:
GSE61305
ID:
200061305
16.

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
17.

DGCR8 is required for microRNA maturation

(Submitter supplied) To determine whether DGCR8 is required for maturation of all miRNAs, we performed miRNA microarray analysis. Using RNA from wild-type ES cells as our reference sample, we observed a global loss of miRNAs in DGCR8 knockout cells, but normal levels of expression in DGCR8 heterozygous cells. The similarity in expression levels between wild-type and heterozygous cells suggests that DGCR8 is not limiting in the maintenance of steady-state levels of miRNAs in ES cells. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by array
Platform:
GPL4690
9 Samples
Download data: GPR
Series
Accession:
GSE6586
ID:
200006586
18.

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
19.

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

(Submitter supplied) Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. more...
Organism:
Dictyostelium discoideum AX2
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL24705 GPL24706
16 Samples
Download data: TXT
Series
Accession:
GSE111592
ID:
200111592
20.

Gene expression profiling of mouse uterine tissue from progesterone receptor-Cre knockout of Dicer

(Submitter supplied) Epithelial-stromal interactions in the uterus are required for normal uterine functions such as pregnancy, and multiple signaling pathways are essential for this process. Although Dicer and microRNAs (miRNA) have been implicated in several reproductive processes, the specific role of Dicer and miRNA in uterine development is not known. To address the roles of miRNA in the regulation of these key uterine pathways, we generated a conditional knockout (cKO) of Dicer in the postnatal uterine epithelium and stroma using progesterone receptor (PR)-Cre. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6887
5 Samples
Download data: TXT
Series
Accession:
GSE39181
ID:
200039181
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