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Links from GEO DataSets

Items: 20

1.

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
2.

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
3.

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; 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.

Cigarette smoking alters mRNA expression in human alveolar macrophages

(Submitter supplied) Alveolar macrophages from never smokers and active smokers were isolated by bronchoalveolar lavage and gene expression was measured. Chronic cigarette smoke exposure, as occurs in smoker's lungs, leads to significant changes in gene expression. Of note, RNA was isolated immediately following bronchoscopy. Alveolar macrophage levels were >95%.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL5175
8 Samples
Download data: CEL
Series
Accession:
GSE34517
ID:
200034517
5.

Mouse embryonic fibroblast (MEF) cells after 2, 3 or 4 days of inducible genetic deletion of Dicer1

(Submitter supplied) To investigate the suitable normalization for miRNA arrays from samples with global miRNA decrease. Our comparisons of five preprocess steps performed at the probe level demonstrated that the use of cyclic loess relying on non-miRNA small RNAs present on the Affymetrix platform significantly improved specificity and sensitivity of detection of decreased miRNAs.
Organism:
synthetic construct; Mus musculus
Type:
Non-coding RNA profiling by array
Platform:
GPL8786
9 Samples
Download data: CEL
Series
Accession:
GSE45886
ID:
200045886
6.

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
7.

Real-time quantitative PCR analysis of miRNA expression in human melanoma MMRU cell line after Sox4 knockdown

(Submitter supplied) We used Applied Biological Materials (ABM)’s miRNA profiling platform to quantitate expression of miRNAs in a human melanoma cell line (MMRU) in Sox4 siRNA treated cells (siSox4) compared with the control siRNA treated cells (siCTR) or after overexpression of Flag-Dicer in Sox4 knockdown cells (siSox4=F-Dicer) compared with control cells.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL15373
4 Samples
Download data: TXT
Series
Accession:
GSE36715
ID:
200036715
8.

Gene expression profiles of DKO172 cells expressing DICER1 wildtype or hotspot mutants

(Submitter supplied) DICER1 plays a critical role in microRNA (miRNA) biogenesis. Recurrent somatic “hotspot” mutations at four mental binding sites within the RNase IIIb domain of DICER1, were identified in ovarian sex cord-stromal tumors and have since been described in other pediatric tumors. In this study, we identified and characterized DICER1 hotspot mutations in endometrial cancers derived from The Cancer Genome Atlas (TCGA) and our local tumor bank. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL10787
12 Samples
Download data: TXT
Series
Accession:
GSE65092
ID:
200065092
9.

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
10.

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
11.

MiRNA expression profile in the aortas of Apoe-/- mice with an specific knock-out of Dicer in endothelial cells compared to control mice after 4 weeks of a high-fat diet

(Submitter supplied) Increased monocyte adhesion to dysfunctional endothelial cells (ECs) orchestrated by chemokines plays an important role in arterial inflammation during atherosclerosis. Endothelial microRNAs (miRNAs) processed by the RNase Dicer1 determine the phenotype of ECs by posttranscriptional regulation of gene expression. However, the impact of endothelial miRNAs on endothelial inflammation and atherosclerosis is currently unclear. more...
Organism:
Mus musculus
Type:
Expression profiling by RT-PCR
Platform:
GPL18082
6 Samples
Download data: TXT
Series
Accession:
GSE53435
ID:
200053435
12.

MiRNA profiling in aortas of Apoe-/- mice with an specific knock-out of Dicer in endothelial cells compared to control mice after 12 weeks of a high-fat diet

(Submitter supplied) Increased monocyte adhesion to dysfunctional endothelial cells (ECs) orchestrated by chemokines plays an important role in arterial inflammation during atherosclerosis. Endothelial microRNAs (miRNAs) processed by the RNase Dicer1 determine the phenotype of ECs by posttranscriptional regulation of gene expression. However, the impact of endothelial miRNAs on endothelial inflammation and atherosclerosis is currently unclear. more...
Organism:
Mus musculus
Type:
Expression profiling by RT-PCR
Platform:
GPL18082
6 Samples
Download data: TXT
Series
Accession:
GSE53433
ID:
200053433
13.

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
14.

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
15.

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
16.

Gene expression profiles of ovarian Sertoli-Leydig cell tumors

(Submitter supplied) Analysis of the global gene expression in ovarian Sertoli-Leydig cell tumor samples with or without DICER1 RNase IIIb domain mutation
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL14951
8 Samples
Download data: TXT
Series
Accession:
GSE71160
ID:
200071160
17.

Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box RNA helicase CGH-1

(Submitter supplied) In this study we show that global levels of mature miRNAs are unaffected in C. elegans after knockdown of either subunit of CK2 (encoded by kin-3 and kin-10) by RNAi.
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13657
4 Samples
Download data: TXT
Series
Accession:
GSE66764
ID:
200066764
18.

secondary structure based on icSHAPE of pre-let-7 and hDicer-TRBP bound pre-let-7

(Submitter supplied) we resolved precusor let7 (pre-let-7) and human Dicer-TRBP complex bound precusor let7 (hDicer-TRBP-pre-let-7) secondary structure based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We found the free pre-let-7 RNA is more flexible comparing with hDicer-TRBP-pre-7 in the double strand region [10-20nt and 50- 60 nt].
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20795
4 Samples
Download data: TXT
Series
Accession:
GSE110516
ID:
200110516
19.

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
20.

MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Agilent miRNA array)

(Submitter supplied) This data set is part of a larger study: Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by array
Platform:
GPL9081
6 Samples
Download data: TXT
Series
Accession:
GSE29100
ID:
200029100
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