Similar Datasets
Project description:The effect of NF90 on the abundance of miRNAs was measured using small RNA-seq.
2020-05-01 | GSE132339 | GEO
Project description:The effect of NF90 on transcript abundance was measured using RNA-seq.
2020-05-01 | GSE132332 | GEO
Project description:Two candidate small interfering RNAs (siRNAs) corresponding to severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike gene were designed and in vitro transcribed to explore the possibility of silencing SARS-CoV S gene. The plasmid pEGFP-optS, which contains the codon-optimized SARS-CoV S gene and expresses spike-EGFP fusion protein (S-EGFP) as silencing target and expressing reporter, was transfected with siRNAs into HEK 293T cells. At various time points of posttransfection, the levels of S-EGFP expression and amounts of spike mRNA transcript were detected by fluorescence microscopy, flow cytometry, Western blot, and real-time quantitative PCR, respectively. The results showed that the cells transfected with pEGFP-optS expressed S-EGFP fusion protein at a higher level compared with those transfected with pEGFP-S, which contains wildtype SARS-CoV spike gene sequence. The green fluorescence, mean fluorescence intensity, and SARS-CoV S RNA transcripts were found significantly reduced, and the expression of SARS-CoV S glycoprotein was strongly inhibited in those cells co-transfected with either EGFP- or S-specific siRNAs. Our findings demonstrated that the S-specific siRNAs used in this study were able to specifically and effectively inhibit SARS-CoV S glycoprotein expression in cultured cells through blocking the accumulation of S mRNA, which may provide an approach for studies on the functions of SARS-CoV S gene and development of novel prophylactic or therapeutic agents for SARS-CoV.
| S-EPMC7092946 | biostudies-literature
Project description:small RNA-seq in HEK-293t cells
| PRJNA547630 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below. MicroRNAs are predicted to regulate the expression of more than 60% of mammalian genes and play fundamental roles in most biological processes. Deregulation of miRNA expression is a hallmark of most cancers and further investigation of mechanisms controlling miRNA biogenesis is needed. The dsRNA-binding protein, NF90 has been shown to act as a competitor of Microprocessor for a limited number of pri-miRNAs. Here, we show that NF90 has a more widespread effect on pri-miRNA biogenesis than previously thought. Genome-wide approaches revealed that NF90 is associated with the stem region of 38 pri-miRNAs, in a manner that is largely exclusive of Microprocessor. Following loss of NF90, 25 NF90-bound pri-miRNAs showed increased abundance of mature miRNA products. NF90-targeted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. Mutations leading to less stable structures reduced NF90 binding while increasing pri-miRNA stability led to ac quisition of NF90 association, as determined by RNA EMSA. NF90-bound and modulated pri-miRNAs are embedded in introns of host genes and expression of several is concomitantly modulated, including an oncogene implicated in metastasis of hepatocellular carcinoma, TIAM2. These data suggest that NF90 controls the processing of a subset of highly stable, intronic miRNAs.
2020-05-01 | GSE132341 | GEO
Project description:To assess the efficacy of AdV-VP55 mediated degredation of host miRNAs. Small RNA profiles of HEK 293T cells treated with type 5 Adeno vectors expressing either GFP or GFP-VP55 for 24 hours
2016-08-03 | E-GEOD-74088 | biostudies-arrayexpress
Project description:BackgroundThe human orphan receptor TLX (NR2E1) is a key regulator of neurogenesis, adult stem cell maintenance, and tumorigenesis. However, little is known about the genetic and transcriptomic events that occur following TLX overexpression in human cell lines.AimsHere, we used cytogenetics and RNA sequencing to investigate the effect of TLX overexpression with an inducible vector system in the HEK 293T cell line.Methods and resultsConventional spectral karyotyping was used to identify chromosomal abnormalities, followed by fluorescence in situ hybridization (FISH) analysis on chromosome spreads to assess TLX DNA copy number. Illumina paired-end whole transcriptome sequencing was then performed to characterize recurrent genetic variants (single nucleotide polymorphisms (SNPs) and indels), expressed gene fusions, and gene expression profiles. Lastly, flow cytometry was used to analyze cell cycle distribution. Intriguingly, we show that upon transfection with a vector containing the human TLX gene (eGFP-hTLX), an isochromosome forms on the long arm of chromosome 6, thereby resulting in DNA gain of the TLX locus (6q21) and upregulation of TLX. Induction of the eGFP-hTLX vector further increased TLX expression levels, leading to G0-G1 cell cycle arrest, genetic aberrations, modulation of gene expression patterns, and crosstalk with other nuclear receptors (AR, ESR1, ESR2, NR1H4, and NR3C2). We identified a 49-gene signature associated with central nervous system (CNS) development and carcinogenesis, in addition to potentially cancer-driving gene fusions (LARP1-CNOT8 and NSL1-ZDBF2) and deleterious genetic variants (frameshift insertions in the CTSH, DBF4, POSTN, and WDR78 genes).ConclusionTaken together, these findings illustrate that TLX may play a pivotal role in tumorigenesis via genomic instability and perturbation of cancer-related processes.
| S-EPMC7941458 | biostudies-literature
Project description:DAWDLE (DDL) is a conserved forkhead-associated (FHA) domain-containing protein that plays essential roles in development and immunity. It was found to act in the biogenesis of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which regulate gene expression at transcriptional and/or post-transcriptional levels. However, its global effect on miRNA accumulation still is not known. To determine the global effect of DDL on the accumulation of miRNAs and siRNAs, we compared the small RNA profile in ddl-1 with that in WS (Wild-type, WT). Small RNA libraries prepared from inflorescences of ddl-1 and WS was subjected to Illumina deep sequencing analyses. The results show that many miRNAs and siRNAs were reduced in abundance in ddl relative to WS in two biological replicates
2018-03-01 | GSE104885 | GEO
Project description:In plants, DICER-LIKE1 is a critical enzyme in the biogenesis pathway of plant miRNAs. Zinc-finger nucleases were used to generate single and double-mutants of soybean DCL1 homologs. We created several small RNA libraries to investigate the effect on miRNA abundance in these various mutants. RNAseq transcript data was also generated in order to investigate targets of those impacted miRNAs.
2016-03-04 | GSE76036 | GEO
Project description:CDC5 is a conserved DNA-binding protein that is required for development and immunity. It promotes the accumulation of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which repress gene expression. In this project, we aim to determine its global effect of on the accumulation of miRNAs and siRNAs. We compared the small RNA profile in cdc5-1 with that in Col (Wild-type, WT). Small RNA libraries prepared from inflorescences of cdc5-1 and Col was subjected to Illumina deep sequencing analyses. The results show that many miRNAs and siRNAs were reduced in abundance in cdc5 relative to Col in two biological replicates.
2018-03-01 | GSE104677 | GEO