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Links from GEO DataSets

Items: 20

1.

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
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.

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
4.

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
5.

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
6.

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
7.

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
8.

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
9.

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
10.

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; Human polyomavirus 1; Murid gammaherpesvirus 4
Type:
Non-coding RNA profiling by array
Platform:
GPL7723
2 Samples
Download data: TXT
Series
Accession:
GSE31091
ID:
200031091
11.

MicroRNA function is globally suppressed in mouse oocytes and early embryos

(Submitter supplied) Dicer, which is required for the processing of both microRNAs (miRNAs) and small interfering RNAs (siRNAs), is essential for oocyte maturation. Oocytes express both miRNAs and endogenous siRNAs (endo-siRNAs). To determine whether the abnormalities in Dicer knockout oocytes during meiotic maturation are secondary to the loss of endo-siRNAs and/or miRNAs, we deleted Dgcr8, which encodes a RNA binding protein specifically required for miRNA processing. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
9 Samples
Download data: CEL
Series
Accession:
GSE19894
ID:
200019894
12.

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
13.

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
14.

Mature thymic NKT and T cells

(Submitter supplied) Invariant Natural killer T (iNKT) cells are a separate lineage of T lymphocytes with innate effector functions. They express an invariant TCR specific for lipids presented by CD1d and their development and effector differentiation rely on a unique gene expression program. We asked whether this program includes microRNAs, small non-coding RNAs that regulate gene expression posttranscriptionally and play key role in the control of cellular differentiation programs. more...
Organism:
Rattus norvegicus; Murid gammaherpesvirus 4; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Macaca mulatta polyomavirus 1; Mus musculus; Murid betaherpesvirus 1; Human gammaherpesvirus 4; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Human polyomavirus 1
Type:
Non-coding RNA profiling by array
Platform:
GPL7723
6 Samples
Download data: PDF, TXT
Series
Accession:
GSE15925
ID:
200015925
15.

Transcriptome analyses of miRNA pathway mutants and injury response in developing and adult sciatic nerves

(Submitter supplied) We addressed the requirement of DGCR8, DROSHA and DICER functions in developing and adult Schwann cells (SCs) using mouse mutants. We found that the microprocessor components DGCR8 and DROSHA are crucial for axonal radial sorting and to establish correct SC numbers upon myelination. Transcriptome analysis revealed that the microprocessor is essential to prevent aberrant accumulation and de novo expression of injury-response genes. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL17021 GPL13112
38 Samples
Download data: TXT
Series
Accession:
GSE109075
ID:
200109075
16.

Gene expression in adult sciatic nerves upon miRNA ablation and crush injury

(Submitter supplied) We report RNA sequencing data from induced Schwann cell specific knockouts for DICER and DGCR8 as well as crush injured wild type animals. Induced deletion of DICER and DGCR8 results in expression of numerous injury response genes suggesting a requirement of those proteins in maintaining the myelinated Schwann cell fate.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
23 Samples
Download data: TXT
Series
Accession:
GSE109074
ID:
200109074
17.

RNA expression in mutants of the miRNA pathway during myelination

(Submitter supplied) RNA sequencing was performed comparing sciatic nerves of Schwann cell specific DICER mutants with SC-specific DGCR8 and DROSHA mutants.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
15 Samples
Download data: TXT
Series
Accession:
GSE64880
ID:
200064880
18.

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
19.

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
20.

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
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