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Links from GEO DataSets

Items: 20

1.
Full record GDS3774

microRNA-124 guide strand segmentation effect on HCT-116 Dicer hypomorph cells

Analysis of HCT-116 dicer- cells transfected with miR-124 duplex containing a segmented guide strand. Following miRNA guide strand segmentation, seed-based (positions 2 through 8 at the 5' end of the guide strand) activity persisted. Results illustrate a structural flexibility in miRNA duplexes.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 3 protocol sets
Platform:
GPL10379
Series:
GSE25224
4 Samples
Download data: CEL
2.

Persistence of seed-based activity following microRNA segmentation

(Submitter supplied) microRNAs are ∼22 nucleotide regulatory RNAs that are processed into duplexes from hairpin structures and incorporated into Argonaute proteins. We find that a nick in the middle of the guide strand of an miRNA sequence allows for seed-based targeting characteristic of miRNA activity. Insertion of an inverted abasic, a dye, or a small gap between the two segments still permits target knockdown. While activity from the seed region of the segmented miRNA is apparent, activity from the 3' half of the guide strand is impaired, suggesting that an intact guide backbone is required for contribution from the 3' half. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS3774
Platform:
GPL10379
4 Samples
Download data: CEL
Series
Accession:
GSE25224
ID:
200025224
3.

miRNA-Targeted and siRNA-Mediated mRNA Degradation Regulated by Argonaute, Dicer and RdRP

(Submitter supplied) Microarray expression profiles of wild-type, ago1-10, ago1-11, and dcl1-9 Arabidopsis thaliana ec. Landsberg erecta seedling at 9, 21, and 35 days after germination. Keywords: mutant response
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL71
37 Samples
Download data
Series
Accession:
GSE4684
ID:
200004684
4.

DROSHA complementation experiments using small RNA sequencing

(Submitter supplied) DROSHA complementation experiments were performed to check whether dsRBD of DROSHA recognizes the lower stem of pri-miRNAs and affects miRNA biogenesis.
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL16791
17 Samples
Download data: TXT
Series
Accession:
GSE117603
ID:
200117603
5.

High-throughput in vitro DROSHA processing on 38,880 pri-miRNA variants

(Submitter supplied) To investigate the precise processing mechanism of pri-miRNA, we prepared 38,880 pri-miRNA variants which contain unique barcode sequences (Fang and Bartel, Mol Cell, 60: 131) and performed high-throughput processing experiments.
Organism:
synthetic construct
Type:
Other
Platform:
GPL19604
3 Samples
Download data: TXT
Series
Accession:
GSE117600
ID:
200117600
6.

Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer

(Submitter supplied) MicroRNAs (miRNAs) are small regulatory RNAs that are essential in all studied metazoans. Research has focused on the prediction and identification of novel miRNAs, while little has been done to validate, annotate, and characterize identified miRNAs. Using Illumina sequencing, ~20 million small RNA sequences were obtained from Caenorhabditis elegans. Of the 175 miRNAs listed on the miRBase database, 106 were validated as deriving from a stem–loop precursor with hallmark characteristics of miRNAs. more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9269
1 Sample
Download data: PDF, TXT
Series
Accession:
GSE24704
ID:
200024704
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.

The bulges control in pri-miRNA processing in the position and strand-dependent manner

(Submitter supplied) The microRNA (miRNA) biogenesis is responsible for the production of miRNAs that play critical roles in gene expression and numerous human diseases. The adequate biogenesis of miRNAs is largely determined by the efficiency and fidelity of primary microRNA (pri-miRNA) processing by Microprocessor. Here, we investigated the roles of a secondary RNA element, an RNA bulge, in pri-miRNA processing. We discovered that the 3p-strand bulges in positions 7-9 from the Microprocessor cleavage sites (midB_7-9) contributes to determining the cleavage sites of Microprocessor, the 5p- and 3p-strand bugles in positions 10-12 (midB_10-12) blocked the unproductive cleavage, and the 3p-strand bulges in positions 6-7 (seedB) inhibited the productive cleavage of Microprocessor. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL18573
15 Samples
Download data: FASTA, TXT
Series
Accession:
GSE158060
ID:
200158060
11.

Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway

(Submitter supplied) In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character—as is found in small interfering RNAs (siRNAs)—directs duplexes into Ago2, whereas central mismatches, like those found in miRNA/miRNA* duplexes, direct duplexes into Ago1. Central to this sorting decision is the affinity of the small RNA duplex for the Dcr-2/R2D2 heterodimer, which loads small RNAs into Ago2. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing; Other
Platform:
GPL9058
11 Samples
Download data: TAR, TXT
Series
Accession:
GSE18806
ID:
200018806
12.

miRNA* loading on Ago2

(Submitter supplied) In flies, microRNAs (miRNAs) are synthesized as a short imperfect duplex, where the miRNA is paired to another small RNA, dubbed the "miRNA*". Usually, miRNA*s are degraded in the last steps of miRNA maturation, but we found evidence that some of them can be loaded on the Ago2 protein.
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9058
7 Samples
Download data
Series
Accession:
GSE12462
ID:
200012462
13.

Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Expression profiling by high throughput sequencing
Platforms:
GPL8321 GPL11002
30 Samples
Download data: CEL
Series
Accession:
GSE41288
ID:
200041288
14.

Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [CLIP-seq data]

(Submitter supplied) microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3’ untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA—miR-155—in a genetically controlled manner. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11002
24 Samples
Download data: PDF, TXT
Series
Accession:
GSE41285
ID:
200041285
15.

Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [mRNA expression data]

(Submitter supplied) microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3’ untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA—miR-155—in a genetically controlled manner. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL8321
6 Samples
Download data: CEL
Series
Accession:
GSE41241
ID:
200041241
16.

DICER1 hotspot mutations cause defective miRNA processing

(Submitter supplied) Recurrent somatic hotspot mutations of DICER1 appear to be clustered around each of four critical metal binding residues in the RNase IIIB domain of DICER1. This domain is responsible for cleavage of the 3’ end of the 5p-miRNA strand of a pre-mRNA hairpin. To investigate the effects of these cancer-associated “hotspot” mutations we engineered mouse Dicer1-deficient ES cells to express wild-type and an allelic series of the mutant human DICER1 variants. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
28 Samples
Download data: CEL
Series
Accession:
GSE40965
ID:
200040965
17.

Regulation of miRNA biogenesis by MCPIP1

(Submitter supplied) Effect of MCPIP1 knockdown on miRNA expression profile.
Organism:
Mus musculus; Rattus norvegicus; Murid betaherpesvirus 1; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Murid gammaherpesvirus 4; human gammaherpesvirus 4; Betapolyomavirus macacae; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Betapolyomavirus hominis
Type:
Non-coding RNA profiling by array
Platform:
GPL7723
2 Samples
Download data: TXT
Series
Accession:
GSE31091
ID:
200031091
18.

Endogenous shRNAs, siRNAs, and Other Microprocessor-independent, Dicer-dependent Small RNAs in Mouse ES Cells

(Submitter supplied) Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by Dicer. dgcr8delta/delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1delta/delta mESCs, suggesting a physiological role for Microprocessor-independent, Dicer-dependent small RNAs. To identify these small RNAs with unusual biogenesis, we performed high-throughput sequencing from wild type, dgcr8delta/delta, and dicer1delta/delta mESCs. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL7196 GPL7195
5 Samples
Download data
Series
Accession:
GSE12521
ID:
200012521
19.

The HER2-encoded miR-4728-3p regulates ESR1 through a non-canonical internal seed interaction

(Submitter supplied) Since the early 1980s remarkable progress has been made in understanding the role of the HER2 locus in carcinogenesis, but many details of its regulatory network are still elusive. We recently reported the finding of 367 new human microRNA (miRNA) genes of which one, mir-4728, is encoded in an intron of the HER2 gene. Here, we confirm that the HER2 oncogene is a bi-functional locus encoding the membrane receptor and a functional miRNA gene. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platforms:
GPL10558 GPL6884
20 Samples
Download data: TXT
Series
Accession:
GSE55822
ID:
200055822
20.

MicroRNAs and their isomiRs function cooperatively to target common biological pathways

(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:
GPL10558 GPL9081
20 Samples
Download data: TXT
Series
Accession:
GSE29101
ID:
200029101
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