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Links from GEO DataSets

Items: 20

1.

Regulation of miRNA biogenesis by MCPIP1

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

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
4.

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
5.

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
6.

Novel microRNA-like viral small regulatory RNAs arising during human hepatitis A virus infection

(Submitter supplied) MicroRNAs (miRNAs), including host miRNAs and viral miRNAs, play vital roles in regulating host-virus interactions. DNA viruses encode miRNAs that regulate the viral life cycle. However, it is generally believed that cytoplasmic RNA viruses do not encode miRNAs, owing to inaccessible cellular miRNA processing machinery. Here, we provide a comprehensive genome-wide analysis and identification of miRNAs that were derived from hepatitis A virus (HAV; Hu/China/H2/1982), which is a typical cytoplasmic RNA virus. more...
Organism:
Homo sapiens; Hepatovirus A
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL18215 GPL11154
2 Samples
Download data: FA
Series
Accession:
GSE54368
ID:
200054368
7.

The Lupus autoantigen La prevents mis-channeling of tRNA fragments into the human microRNA pathway

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL11154 GPL15520
8 Samples
Download data: TXT
Series
Accession:
GSE77898
ID:
200077898
8.

The Lupus autoantigen La prevents mis-channeling of tRNA fragments into the human microRNA pathway [PAR-CLIP]

(Submitter supplied) The Lupus autoantigen (La) is a single-stranded RNA-binding protein that stabilizes RNA polymerase III (pol III) transcripts and supports RNA folding. In addition, La has been implicated in different steps of the mammalian small RNA pathway. Here, we have analyzed effects of La depletion on the Argonaute (Ago)-bound small RNAs in human cells. We find that in the absence of La, distinct tRNA fragments are loaded into Ago protein complexes and our data suggests that La prevents the production and loading of such tRNA fragments. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL11154
4 Samples
Download data: TXT
Series
Accession:
GSE77897
ID:
200077897
9.

The Lupus autoantigen La prevents mis-channeling of tRNA fragments into the human microRNA pathway [miRNA-seq]

(Submitter supplied) The Lupus autoantigen (La) is a single-stranded RNA-binding protein that stabilizes RNA polymerase III (pol III) transcripts and supports RNA folding. In addition, La has been implicated in different steps of the mammalian small RNA pathway. Here, we have analyzed effects of La depletion on the Argonaute (Ago)-bound small RNAs in human cells. We find that in the absence of La, distinct tRNA fragments are loaded into Ago protein complexes and our data suggests that La prevents the production and loading of such tRNA fragments. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL15520
4 Samples
Download data: TXT
Series
Accession:
GSE76676
ID:
200076676
10.

ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus; Homo sapiens
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL9115 GPL9250
8 Samples
Download data: BED, SAM, TXT, WIG
Series
Accession:
GSE43192
ID:
200043192
11.

Small RNA analysis of ADAR1-knock down HeLa cells by RNAi

(Submitter supplied) Small RNA expression was analysed in total RNA of HeLa cells treated with siRNA toward Luciferase (negative cotrol) or ADAR1.
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9115
2 Samples
Download data: TXT
Series
Accession:
GSE43167
ID:
200043167
12.

Small RNA analysis of wildtype Mouse embryo and Adar1 null mouse embryo at E11.0 and E11.5 together with mRNA-seq results of E11.5

(Submitter supplied) Adar1 is an essential gene for mouse embryonic development. Adar1 null mouse embryos dies around E11.5 because of massive apoptosis.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9250
6 Samples
Download data: BED, SAM, TXT, WIG
Series
Accession:
GSE33473
ID:
200033473
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.

Gene expression profiling of mouse bone marrow-derived macrophages (RNA-Seq)

(Submitter supplied) Bone marrow (BM) cells were obtained by flushing the long bones of 8-week old C57BL/6 mice. BM cells were then were plated in macrophage SFM medium (Life Technologies) supplemented with penicillin-streptomycin and CSF-1 (Peprotech, 100 ng/ml) and cultured for one week to allow macrophage differentiation. BMDMs were polarized by adding IL-4 to the medium (40 ng/ml, Peprotech) for 72h or left untreated.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17021
8 Samples
Download data: GTF, TXT
Series
Accession:
GSE58283
ID:
200058283
15.

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
16.

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
17.

The menu of features that define primary microRNAs and enable de novo design of microRNA genes

(Submitter supplied) MicroRNAs (miRNAs) are small regulatory RNAs processed from stem-loop regions of primary transcripts (pri-miRNAs), with the choice of stem-loops for initial processing largely determining what becomes a miRNA. To identify sequence and structural features influencing this choice, we determined cleavage efficiencies of >50,000 variants of three human pri-miRNAs, focusing on the regions intractable to previous high-throughput analyses. more...
Organism:
Homo sapiens; synthetic construct
Type:
Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL11154 GPL15228
22 Samples
Download data: FASTA, TXT, XLSX
18.

Intertwined pathways for Argonaute-mediated microRNA biogenesis in Drosophila

(Submitter supplied) Ago1-IP small RNA sequencing from S2R+ cells, with dsRNA knockdown of Dicer1 (and GFP control)
Organism:
Drosophila melanogaster
Type:
Other; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13304
2 Samples
Download data: TXT
19.

Expression data from Dicer and Ago2-knockdown HeLa cells

(Submitter supplied) Dicer and Argonaute2 (Ago2) gene is involving in microRNA (miRNA) maturation. Knockdown of these genes has great impact on miRNA expression profiles. We used microarrays to detail the miRNA expression profiles in Dicer- and Ago2-knockdown HeLa cells and demonstarted that the significant difference between Ago2-knockdown and Dicer- and Ago2-co-knockdown HeLa cells were not found.
Organism:
synthetic construct; Homo sapiens
Type:
Non-coding RNA profiling by array
Platform:
GPL19117
5 Samples
Download data: CEL
Series
Accession:
GSE67992
ID:
200067992
20.

H3K27me3 ChIP-seq profiling in MCF7 cell lines under hypoxia

(Submitter supplied) Purpose: Study hypoxia induced changes in genome-wide H3K27me3 occupancy Methods: Using the MCF7 breast epithelial adenocarcinoma cell line as a model, we studied epigenomic reprogramming as a function of fluctuating oxygen tension. To this end, we combined chromatin-immunoprecipitation and deep-sequencing analysis to identify H3K27me3-marks in MCF7 cells subjected to changes in oxygenation (i.e. acute hypoxia, chronic hypoxia). more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL10999
3 Samples
Download data: WIG
Series
Accession:
GSE61740
ID:
200061740
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