Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A genome-scale shRNA resource for transgenic RNAi in Drosophila

ABSTRACT: Existing transgenic RNAi resources in Drosophila utilize the expression of long double stranded hairpin RNAs and are powerful tools for the identification and characterization of genes involved in various processes. However, they are ineffective to knockdown genes during oogenesis, an important model system for the study of numerous fundamental questions in biology. Here, we show that short hairpin RNAs (shRNAs), modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress towards building a genome-wide shRNA resource.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE27039 | GEO | 2011/03/26

SECONDARY ACCESSION(S): PRJNA137667

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A genome-scale shRNA resource for transgenic RNAi in Drosophila

Project description:Existing transgenic RNAi resources in Drosophila utilize the expression of long double stranded hairpin RNAs and are powerful tools for the identification and characterization of genes involved in various processes. However, they are ineffective to knockdown genes during oogenesis, an important model system for the study of numerous fundamental questions in biology. Here, we show that short hairpin RNAs (shRNAs), modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress towards building a genome-wide shRNA resource. Total RNA was isolated using Trizol reagent (Invitrogen) and size-fractionated by PAGE. These were independently processed and sequenced using the Illumina GAII platform. In total, three libraries were analyzed.

2011-03-26 | E-GEOD-27039 | biostudies-arrayexpress

Large-scale tethered function assays identify factors that regulate mRNA stability and translation (HEK293T_RNA-seq)

Project description:we either depleted RBPs by lentiviral transduction of short-hairpin RNAs (shRNAs) or ectopically expressed the open reading frame of the protein. For each RBP, we performed two independent transductions of two different targeting shRNAs and two independent transductions of a non-targeting shRNA, or performed two independent transfections with a plasmid directing expression of the RBP as a V5-tagged fusion, with the FLAG construct as a control.

2020-08-18 | GSE117293 | GEO

Datasets Used in Evaluation Of RNAi And CRISPR Technologies By Large Scale Gene Expression Profiling In The Connectivity Map

Project description:This GEO Series contains datasets used in the paper "Evaluation Of RNAi And CRISPR Technologies By Large Scale Gene Expression Profiling In The Connectivity Map". The application of RNA interference (RNAi) to mammalian cells has provided the means to perform phenotypic screens to determine the functions of genes. Although RNAi has revolutionized loss of function genetic experiments, it has been difficult to systematically assess the prevalence and consequences of off-target effects. The Connectivity Map (CMAP) represents an unprecedented resource to study the gene expression consequences of expressing short hairpin RNAs (shRNAs). Analysis of signatures for over 13,000 shRNAs applied in 9 cell lines revealed that miRNA-like off-target effects of RNAi are far stronger and more pervasive than generally appreciated. We show that mitigating off-target effects is feasible in these datasets via computational methodologies to produce a Consensus Gene Signature (CGS). In addition, we compared RNAi technology to clustered regularly interspaced short palindromic repeat (CRISPR)-based knockout by analysis of 373 sgRNAs in 6 cells lines, and show that the on-target efficacies are comparable, but CRISPR technology is far less susceptible to systematic off-target effects. These results will help guide the proper use and analysis of loss-of-function reagents for the determination of gene function. Note: Related GEO projects include a large corpus of additional L1000 data, available at GSE92742. The Platform is GPL20573: Broad Institute Human L1000 epsilon https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20573 For questions or assistance with this dataset, please email the CMap support team at: clue@broadinstitute.org

2017-10-30 | GSE106127 | GEO

A genome-scale shRNA resource for transgenic RNAi in Drosophila.

Project description:Existing transgenic RNAi resources in Drosophila melanogaster based on long double-stranded hairpin RNAs are powerful tools for functional studies, but they are ineffective in gene knockdown during oogenesis, an important model system for the study of many biological questions. We show that shRNAs, modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress toward building a genome-wide shRNA resource.

| S-EPMC3489273 | biostudies-literature

Effect of VIRMA amplification on gene expression in breast cancer cells

Project description:To confirm the contribution of elevated VIRMA levels towards cell proliferation and colony formation, we depleted VIRMA in four breast cancer cell lines, SKBR3, HS578T, MCF7 and MDAMB453 using short-hairpin RNAs (shRNAs). We then performed gene expression profiling analysis using data obtained from RNA-seq data

2023-08-03 | GSE205855 | GEO

MicroRNA-seq of MDA-MB-231 cells transduced with anti-ELOVL5 and control shRNAs

Project description:MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at the 5’-end of a miRNA alter the seed region of the molecule, thus affecting the targetome of the miRNA. MDA-MB-231 cells were transduced with shRNAs against ELOVL5 and luciferase genes. Small RNA sequencing was used to study the cleavage profiles of shRNAs.

2021-05-03 | GSE173709 | GEO

THe role of CXCL8 in the mesenchymal state of glioblastoma stem cells

Project description:To determine the functional significance of the expression of CXCL8 in mesenchymal GSCs, we examined the effect of CXCL8 disruption with two non-overlapping small hairpin RNAs (shRNA) on the mesenchymal GSC maintenance. Silencing CXCL8 with two independent shRNAs significantly reduced CXCL8 expression on in mesenchymal GSCs (839 and 2907) .

2023-06-27 | GSE214248 | GEO

Lentiviral-mediated small hairpin RNAs (shRNAs)-based knockdown of OLFM2 or PKP2 in human adipocytes

Project description:Lentiviral-mediated small hairpin RNAs (shRNAs)-based knockdown of OLFM2 or PKP2 in human adipocytes

| PRJNA755335 | ENA

shRNA profiling of human breast carcinoma cells expressing over 300 shRNA constructs using barcode tiling arrays - screen 1

Project description:RNAi screens via pooled short hairpin RNAs (shRNAs) have recently become a powerful tool for the identification of essential genes in mammalian cells. We synthesized DNA microarrays with six overlapping 25 nt long tiling probes complementary to each unique 60 nt molecular barcode sequence associated with every shRNA expression construct.. In this part of the study pooled shRNAs were transduced into MDA-MB-231 breast carcinoma cell lines and their inhibitory effects four weeks post transduction were analyzed via microarray hybridization.

2009-12-08 | E-MEXP-2476 | biostudies-arrayexpress

shRNA profiling of human breast carcinoma cells expressing over 300 shRNA constructs using barcode tiling arrays - screens 2 and 3

2009-12-08 | E-MEXP-2477 | biostudies-arrayexpress