GEO DataSets

(Submitter supplied) Little is known about how miRNAs are turned over, in particular in mammalian cells. A target-dependent miRNA degradation mechanism (TDMD) has been recently suggested, in which RNA targets may induce miRNA degradation. However, endogenous RNA targets involved in TDMD have not been yet identified. During serum stimulation of quiescent fibroblasts, a deep change of miRNA expression occurs in few hours. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: XLS

(Submitter supplied) Little is known about how miRNAs are turned over, in particular in mammalian cells. A target-dependent miRNA degradation mechanism (TDMD) has been recently suggested, in which RNA targets may induce miRNA degradation. However, endogenous RNA targets involved in TDMD have not been yet identified. During serum stimulation of quiescent fibroblasts, a deep change of miRNA expression occurs in few hours. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: XLS

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL13112

28 Samples

Download data

(Submitter supplied) Little is known about how miRNAs are turned over, in particular in mammalian cells. A target-dependent miRNA degradation mechanism (TDMD) has been recently suggested, in which RNA targets may induce miRNA degradation. However, endogenous RNA targets involved in TDMD have not been yet identified. During serum stimulation of quiescent fibroblasts, a deep change of miRNA expression occurs in few hours. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

10 Samples

Download data: XLS

(Submitter supplied) How many RNA transcripts can induce degradation of microRNAs (miRNA) via the mechanism known as target-directed miRNA degradation (TDMD) is currently unknown. We developed TDMDfinder, a bioinformatics pipeline and webtool, which is based on combined sequence alignment and feature selection approaches to identify ‘high confidence’ TDMD interactions either in Human or Mouse transcriptomes. Predictions suggest that TDMD is widespread, and every miRNA is possibly under the control of endogenous targets. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

68 Samples

Download data: XLSX

(Submitter supplied) We show that target mRNAs trigger the non-templated addition of nucleotides (mainly adenosines and uridines) and shortening of their cognate miRNAs in primary hippocampal neurons. The induced effect is observable both in total RNA and in Ago2-associated RNA, demonstrating that the process is initiated in Ago2 bound miRNAs.

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL14844 GPL18694

54 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19057

48 Samples

Download data: CSV

(Submitter supplied) MicroRNAs (miRNAs) play an important role in the regulation of gene expression and are often dysregulated in disease. The recent development of the CRISPR-Cas9 gene-editing system, composed of the Cas9 nuclease in complex with a single guide RNA (sgRNA), allows researchers to direct DNA cleavage at a predetermined site and to conduct genome-scale knockout screens. To determine the functional role of miRNAs in cancer, we designed and constructed a library of 7,382 sgRNAs to target 85% of the 1,881 annotated human miRNA stem-loops. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

5 Samples

Download data: CSV

(Submitter supplied) We used HSUR1 – a small non-coding RNA from Herpesvirus saimiri that induces degradation of host miR-27 – to validate structural insights into target-directed miRNA degradation (TDMD). While performing systematic mutagenesis of HSUR1 we noticed that HSUR1 mutants exhibiting complementarity to the extreme 3' end of miR-27, lead to generation of extended miR-27 isoforms (isomiRs). These isomiRs likely represent failed products of TDMD and could mean that features of the pairing between the TDMD target and miRNA dictate which enzymes are recruited to modify the miRNA 3′ end. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: XLSX

(Submitter supplied) MicroRNAs (miRNAs) typically direct degradation of their mRNA targets. However, five miRNA targets in vertebrate animals are reported to have unusual miRNA-binding sites that direct degradation of cognate miRNAs. Here, we identify six sites, five in mRNAs and one in a non-coding RNA named Marge, that serve this purpose in Drosophila cells or embryos, which shows that target-directed miRNA degradation (TDMD) shapes endogenous miRNA levels in some invertebrate animals. more...

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL17275 GPL25244

136 Samples

Download data: CSV

(Submitter supplied) Twenty-four triple-negative breast cancer and 14 adjacent normal tissues were collected from breast cancer patients during surgeries at National Taiwan University Hospital (NTUH, Taipei, Taiwan). All triple-negative breast cancer samples were invasive ductal carcinomas (IDC) and were negative in immunohistochemical statuses of ER, PR, and HER2 receptors, as confirmed by professional pathologists. Treatment procedure of all patients followed the National Comprehensive Cancer Network (NCCN) guideline. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13393

38 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are noncoding RNAs of approximately 22 nucleotides in length that usually suppress the translation of target messenger RNAs (mRNAs) through partial complementarity to the 3¡¦ untranslated region (3¡¦ UTR) of protein-coding mRNAs in animals. However, there is increasing evidence that miRNAs can also reduce the steady-state levels of their target mRNAs in animals. In this investigation, both miRNA and mRNA profiles from the undifferentiated human embryonic stem cell line hES-T3 (T3ES), hES-T3 derived embryoid bodies (T3EB) and hES-T3 differentiated fibroblast-like cells (T3DF) were quantitatively determined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) MicroRNAs are small, non-coding RNAs that post-transcriptionally regulate gene expression by binding to 3’UTRs of target mRNAs. Kaposi’s sarcoma-associated herpesvirus (KSHV), a virus linked to malignancies including primary effusion lymphoma (PEL), encodes 12 miRNA genes, but only a few regulatory targets are known. We found that KSHV-miR-K12-11 shares 100% seed-sequence homology with hsa-miR-155, a miRNA frequently found up-regulated in lymphomas and critically important for B cell development. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3007

Platform:

GPL570

12 Samples

Download data: CEL, EXP

Analysis of cells expressing microRNA (miR) K12-11 from Kaposi's sarcoma-associated herpesvirus. miR-K12-11 shares sequence homology with hsa-miR-155, a miRNA up-regulated in lymphomas and important in B cell development. Results provide insight into the biological activity of miR-K12-11.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 protocol sets

Platform:

GPL570

Series:

GSE9264

12 Samples

Download data: CEL, EXP

(Submitter supplied) To study the effect of miRNA depletion in the embryonic forebrain, we isolated RNA from E13.5 dorsal telencephalon of mice homozygous for a floxed Dicer allele and hemizygous for the forebrain expressed Emx1Cre (Dicer KO mice). These samples were compared to littermates heterozygous for the floxed allele and hemizygous for Emx1Cre.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7635

9 Samples

Download data: CEL

(Submitter supplied) To explore HER2 3’-UTR-dependent transcriptional programs, we analyzed gene-expression profiles of T47D cells transfected with HER2 3’-UTR.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

2 Samples

Download data: TXT

(Submitter supplied) KS lesions consist of endothelial cells latently infected with KSHV which express the KSHV miRNAs. Identifying the targets of the KSHV miRNAs will help us understand their role in viral oncogenesis. Cross-Linking and Sequencing of Hybrids (CLASH) is a method for unambiguously identifying miRNA targetomes. We developed a streamlined version of CLASH, called quick CLASH (qCLASH). qCLASH requires a lower initial input of cells than its parent protocol. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

9 Samples

Download data: TXT

(Submitter supplied) In this study, we employed massively parallel sequencing technology to identify miRNAs expressed in Zmpste24 WT MEF and Zmpste24-/- MEF. With data from 19.5 ×106 reads from WT MEFs and 16.5 × 106 reads from Zmpste24-/- MEFs, we discovered a total of 306 known miRNAs expressed in MEFs with a wide dynamic range of read counts ranging from 10 to over 1 million. A total of 8 miRNAs were found to be significantly down-regulated, with only 2 miRNAs upregulated, in Zmpste24-/- MEFs as compared to WT MEFs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: TXT

(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:

GPL11532 GPL15829

44 Samples

Download data: CEL, TXT

(Submitter supplied) The purpose of this study was to determine the miRNA expression profile of in vitro differentiation of human skeletal muscle cells and to couple changes in individual miRNA expression to transcriptional output of target genes. miRNA expression profiling at six different time points during the in vitro differentiation process of human skeletal muscle cells from six subjects. RNA was harvested from myoblasts before induction of differentiation and at every other day for 10 following days.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL15829

35 Samples

Download data: TXT