RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs

Use of RNA interference (RNAi) in forward genetic screens is proliferating. Currently, short-interfering RNAs (siRNAs) and short-hairpin RNAs (shRNAs) are being used to silence genes to tease out functional information. It is becoming easier to harness RNAi to silence specific genes, owing to the development of libraries of readymade shRNA and siRNA gene-silencing constructs by using a variety of sources. RNAi Codex, which consists of a database of shRNA related information and an associated website, has been developed as a portal for publicly available shRNA resources and is accessible at . RNAi Codex currently holds data from the Hannon–Elledge shRNA library and allows the use of biologist-friendly gene names to access information on shRNA constructs that can silence the gene of interest. It is designed to hold user-contributed annotations and publications for each construct, as and when such data become available. We will describe features of RNAi Codex and explain the use of the tool.

• Publication year

  2005

• Venue

  Nucleic Acids Res.

• Publication date

  2005-12-28

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/nar/gkj051PMID 16381835PMCID 1347414
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy

  2005cited by this paper
• GeneSeer: A sage for gene names and genomic resources

  2005cited by this paper
• RNAi as a bioinformatics consumer

  2005cited by this paper
• Synthetic shRNAs as potent RNAi triggers

  2005cited by this paper
• Mechanisms of gene silencing by double-stranded RNA

  2004cited by this paper
• Intensified Cloning Efforts Have Revealed Numer

  2004cited by this paper
• A large-scale RNAi screen in human cells identifies new components of the p53 pathway

  2004cited by this paper
• The role of RNA interference in heterochromatic silencing

  2004cited by this paper
• A resource for large-scale RNA-interference-based screens in mammals

  2004cited by this paper
• Cloning of short hairpin RNAs for gene knockdown in mammalian cells

  2004cited by this paper
• Epigenetics: Imprinting in Plants and Mammals – the Same but Different?

  2004cited by this paper
• Noise amidst the silence: off-target effects of siRNAs?

  2004cited by this paper
• Genew: the Human Gene Nomenclature Database, 2004 updates

  2004cited by this paper
• Drosophila RNase Z processes mitochondrial and nuclear pre-tRNA 3' ends in vivo.

  2004cited by this paper
• Functional siRNAs and miRNAs exhibit strand bias.

  2003cited by this paper
• The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

  2003cited by this paper
• Expression profiling reveals off-target gene regulation by RNAi

  2003cited by this paper
• Asymmetry in the assembly of the RNAi enzyme complex.

  2003cited by this paper
• Asymmetry in the Assembly of the RNAi Enzyme Complex

  2003cited by this paper
• Genew: the Human Gene Nomenclature Database

  2002cited by this paper
• Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells.

  2002cited by this paper
• Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells

  2001cited by this paper
• Self-assembly of mesoscopically ordered chromatic polydiacetylene/silica nanocomposites

  2001cited by this paper
• The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans

  2000cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• Induction of apoptosis by the dsRNA-dependent protein kinase (PKR): Mechanism of action

  2000cited by this paper
• Induction of the

  1996cited by this paper
• Interactions between double-stranded RNA regulators and the protein kinase DAI

  1992cited by this paper

• Circuit-selective cell-autonomous regulation of inhibition in pyramidal neurons by Ste20-like kinase

  2022cites this paper
• A Synthetic, Closed-Looped Gene Circuit for the Autonomous Regulation of RUNX2 Activity during Chondrogenesis

  2021cites this paper
• Ste20-like Kinase Is Critical for Inhibitory Synapse Maintenance and Its Deficiency Confers a Developmental Dendritopathy

  2020cites this paper
• Computational Biology of Non-Coding RNA

  2019cites this paper
• Systems-level Analysis Reveals Multiple Modulators of Epithelial-mesenchymal Transition and Identifies DNAJB4 and CD81 as Novel Metastasis Inducers in Breast Cancer*

  2019cites this paper
• Noncoding RNAs Databases: Current Status and Trends.

  2019cites this paper
• Identification of SERPINE1 as a Regulator of Glioblastoma Cell Dispersal with Transcriptome Profiling

  2019cites this paper
• The pro-apoptotic Bcl-2 family member Harakiri (HRK) induces cell death in glioblastoma multiforme

  2019cites this paper
• Protein tyrosine phosphatase receptor type R (PTPRR) antagonizes the Wnt signaling pathway in ovarian cancer by dephosphorylating and inactivating β-catenin

  2019cites this paper
• The fungal metabolite chaetocin is a sensitizer for pro-apoptotic therapies in glioblastoma

  2019cites this paper
• The E3 ubiquitin ligase UBR5 regulates centriolar satellite stability and primary cilia

  2018cites this paper
• Doxycycline modulates VEGF-A expression: Failure of doxycycline-inducible lentivirus shRNA vector to knockdown VEGF-A expression in transgenic mice

  2018cites this paper
• Cellular / Molecular Interdependent Roles for Accessory KChIP 2 , KChIP 3 , and KChIP 4 Subunits in the Generation of Kv 4-Encoded I A Channels in Cortical Pyramidal Neurons

  2018cites this paper
• Bioinformatics Challenges and Advances in RNA interference

  2017cites this paper
• The Generation of Mouse and Human Huntington Disease iPS Cells Suitable for In vitro Studies on Huntingtin Function

  2017cites this paper
• SJMLS-2 ( 1 )-2017-016 The Use of Antibody as Drug Carrier in Cancer Chemotherapy

  2017cites this paper
• The Heat Shock Transcription Factor HSF1 Induces Ovarian Cancer Epithelial-Mesenchymal Transition in a 3D Spheroid Growth Model

  2016cites this paper
• The E3 ubiquitin ligase UBR5 regulates centriolar satellite stability and primary cilia formation via ubiquitylation of CSPP-L

  2016cites this paper
• Experimental design for stable genetic manipulation in mammalian cell lines: lentivirus and alternatives

  2015cites this paper
• Impaired Reelin-Dab1 Signaling Contributes to Neuronal Migration Deficits of Tuberous Sclerosis Complex.

  2015cites this paper
• Function of bromodomain and extra-terminal motif proteins (BETs) in GATA1-mediated transcription

  2015cites this paper
• Widespread FRA1-Dependent Control of Mesenchymal Transdifferentiation Programs in Colorectal Cancer Cells

  2014cites this paper
• Antagonizing c-Cbl enhances EGFR-dependent corneal epithelial homeostasis.

  2014cites this paper
• Multiplex in vitro and in vivo RNAi screening to identify treatment response modifiers of targeted therapies in HCC

  2014cites this paper
• Identification and analysis of cellular factors involved in v-Abl transformation of B lineage cells By

  2013cites this paper
• DNA-damaging agents in cancer chemotherapy: serendipity and chemical biology.

  2013cites this paper
• Production and application of long dsRNA in mammalian cells.

  2013cites this paper
• Chromatin-modifying enzymes as modulators of reprogramming

  2013cites this paper
• Development and Application of High-throughput Chemical Genomic Screens for Functional Studies of Cancer Therapeutics

  2013cites this paper
• Creation of a Retroviral RNAi Knockdown System to Investigate Gene Variants in SLE

  2013cites this paper
• Down-regulation of viral replication by lentiviral-mediated expression of short-hairpin RNAs against vesicular stomatitis virus ribonuclear complex genes.

  2012cites this paper
• Molecular Dissection of IA Channels in Cortical Pyramidal Neurons

  2012cites this paper
• Chromatin modifying enzymes as modulators of reprogramming

  2012cites this paper
• Programmed Cell Death 4 ( PDCD 4 ) Enhances the Sensitivity of Gastric Cancer Cells to TRAIL-Induced Apoptosis by Inhibiting the PI 3 K / Akt Signaling Pathway

  2012cites this paper
• Resource A Rapid and Scalable System for Studying Gene Function in Mice Using Conditional RNA Interference

  2011cites this paper
• COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines

  2011cites this paper
• Programmed Cell Death 4 (PDCD4) Enhances the Sensitivity of Gastric Cancer Cells to TRAIL-Induced Apoptosis by Inhibiting the PI3K/Akt Signaling Pathway

  2010cites this paper
• Shortcomings of short hairpin RNA-based transgenic RNA interference in mouse oocytes

  2010cites this paper
• Interdependent Roles for Accessory KChIP2, KChIP3, and KChIP4 Subunits in the Generation of Kv4-Encoded IA Channels in Cortical Pyramidal Neurons

  2010cites this paper
• Mutant p53-induced Up-regulation of Mitogen-activated Protein Kinase Kinase 3 Contributes to Gain of Function*

  2010cites this paper
• Resources for Small Regulatory RNAs

  2009cites this paper
• Resources for Small Regulatory RNAs

  2009cites this paper
• CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus.

  2009cites this paper
• Long-term BRCA1 down-regulation by small hairpin RNAs targeting the 3' untranslated region.

  2008cites this paper
• Chapter 13. Identifying substrates of mRNA decay factors by a combined RNA interference and DNA microarray approach.

  2008cites this paper
• Gene knockdown by ecdysone-based inducible RNAi in stable mammalian cell lines

  2008cites this paper
• Porphyrin Homeostasis Maintained by ABCG2 Regulates Self-Renewal of Embryonic Stem Cells

  2008cites this paper
• Telomere stability in cancer cells and the role of DNA mismatch repair.

  2007cites this paper
• Gene Suppression Technologies in High-Throughput Analysis: Front- and Back-side Applications

  2007cites this paper
• Site-directed, virus-free, and inducible RNAi in embryonic stem cells

  2007cites this paper
• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

  2007cites this paper
• Epigenetic regulation of hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors CoREST and LSD1.

  2007cites this paper
• Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer

  2007cites this paper
• Knockdown of human Oxa1l impairs the biogenesis of F1Fo-ATP synthase and NADH:ubiquinone oxidoreductase.

  2007cites this paper
• A protein interaction network for pluripotency of embryonic stem cells

  2006cites this paper
• Specific and nontoxic silencing in mammalian cells with expressed long dsRNAs

  2006cites this paper