refimprove date July 2008 Immunoprecipitation IP is the technique of Precipitation chemistry precipitating ... many thousands of different proteins. Immunoprecipitation requires that the antibody be coupled to a solid Substrate materials science substrate at some point in the procedure. Types of immunoprecipitation Individual protein Immunoprecipitation IP Involves using an antibody that is specific ... sample types could be bodily fluids or other samples of biological origin. Protein complex immunoprecipitation Co IP Immunoprecipitation of intact protein complex es i.e. antigen along with any proteins or ligands that are bound to it is known as co immunoprecipitation Co IP . Co IP works by selecting ... target one of the newly identified proteins and repeat the entire immunoprecipitation experiment ... the immunoprecipitation in this way, the researcher verifies that each identified member ... s status as a member of the complex may be subject to question. Chromatin immunoprecipitation ChIP Chromatin immunoprecipitation ChIP is a method used to determine the location of DNA binding sites ... is broken into pieces 0.2 1 kb in length by sonication . At this point the immunoprecipitation is performed ... that can localize protein binding sites in a high throughput, cost effective fashion. RNA immunoprecipitation RIP Similar to chromatin immunoprecipitation ChIP outlined above, but rather than targeting DNA binding proteins as in ChIP, RNA immunoprecipitation targets RNA binding proteins. RIP is also ... RNA and RNA binding proteins. Cells are then lysed and the immunoprecipitation is performed with an antibody ... proteins One of the major technical hurdles with immunoprecipitation is the great difficulty in generating ... are so great that this technique has become commonplace for all types of immunoprecipitation including ... general methods for immunoprecipitation are the direct capture method and the indirect capture method ... the solid phase support for immunoprecipitation used by the majority of scientists has been highly ... more details
File ChIP procedure.jpg thumb right 300px The procedure of chromatin immunoprecipitation ChIP assay and methods of analysis Chromatin Immunoprecipitation ChIP is a type of immunoprecipitation experimental technique used to investigate the interaction between protein s and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factor s on promoter biology promoter s or other DNA binding site s, and possibly defining cistrome ... journal author Collas, Philippe. title The Current State of Chromatin Immunoprecipitation journal ... crosslinked chromatin immunoprecipitation journal Trends in Biochemical Sciences volume ... cite journal author O Neill, Laura P Turner, Bryan M title Immunoprecipitation of native chromatin ... embryo with a chromatin immunoprecipitation protocol applicable to small cell populations journal ... to target proteins and thereby reduces immunoprecipitation time ii a resin based Chelex 100 DNA ... chromatin immunoprecipitation assay journal Nucleic Acids Research volume 34 issue 1 pages e2 year 2006 ... chromatin immunoprecipitation ChIP method journal Nature Protocols volume 1 issue 1 pages 179 85 ... name pmid19588084 cite journal author Nelson J, Denisenko O, Bomsztyk K title The fast chromatin immunoprecipitation ... immunoprecipitation assay, unravels epigenetic dynamics of developmentally regulated genes in human ... journal author Dahl, John Arne Collas, Philippe title A rapid micro chromatin immunoprecipitation ... Dahl, John Arne Collas, Philippe title MicroChIP chromatin immunoprecipitation for small cell numbers ... Microplate based chromatin immunoprecipitation method, Matrix ChIP a platform to study signaling of complex ... ref tags which will then appear here automatically Reflist External links MeshName Chromatin immunoprecipitation ... content full 2006 23 pdb.prot4560 Chromatin Immunoprecipitation ChIP of Protein Complexes Mapping of Genomic ... Immunoprecipitation Category Protein methods Category Molecular biology techniques Category Protein ... more details
Methylated DNA immunoprecipitation MeDIP or mDIP is a large scale chromosome or genome wide technique that is used to enrich for DNA methylation methylated DNA sequences . It consists of isolating methylated DNA fragments via an antibody raised against 5 methylcytosine 5mC . This technique was first described by Weber M. et al. ref name weber2005 cite journal author Weber M, Davies JJ, Wittig D, et al. title Chromosome wide and promoter specific analyses identify sites of differential DNA methylation in normal and transformed human cells journal Nat. Genet. volume 37 issue 8 pages 853 62 year 2005 month August pmid 16007088 doi 10.1038 ng1598 ref and has helped pave the way for viable methylome level assessment efforts, as the purified fraction of methylated DNA can be input to high throughput DNA detection methods such as high resolution DNA microarray s Tiling array MeDIP chip MeDIP chip or DNA sequencing New sequencing methods next generation sequencing MeDIP seq . Nonetheless, understanding of the methylome remains rudimentary its study is complicated by the fact that, like other ... A or high throughput next generation sequencing B Methylated DNA immunoprecipitation MeDIP Genomic ... author Jacinto FV, Ballestar E, Esteller M title Methyl DNA immunoprecipitation MeDIP hunting down ... step in immunoprecipitation, and reducing fragment length effects or biases. Also, the size of the fragment ... 5mC antibodies. The classical immunoprecipitation technique is then applied magnetic beads ... 5 Cy5 red deoxy cytosine triphosphate while the methylated DNA, enriched after the immunoprecipitation ... Down TA, Rakyan VK, Turner DJ, et al. title A Bayesian deconvolution strategy for immunoprecipitation ... issue is its effect on the efficiency of immunoprecipitation. In their study, Down et ... the inactivation of the HOXA gene cluster See also Epigenetics Immunoprecipitation Methylome ... Dna Immunoprecipitation Category Molecular biology Category Epigenetics Category Genomics Category ... more details
Summary An outline of one of the fundamental methods of phosphoproteomics, the purification of phosphoproteins by immunoprecipitation with anti phosphotyrosine antibodies. Phosphoproteins are depicted in blue, with yellow phosphate groups. Anti phosphotyrosine antibodies are pink. br Licensing PD self date February 2007 ... more details
see also Chip disambiguation CHIP can mean several things State Children s Health Insurance Program As CHiP for the California Highway Patrol One of various Child Identification Programs around the world Masonic Child Identification Programs CHIP Masonic Child Identification Programs in many states in the United States of America. CHIP programming language , based on Prolog CHIP 8 , a programming language used for video game programming in the 1970s Chromatin immunoprecipitation CHIP CHromatin ImmunoPrecipitation CHIP magazine CHIP magazine , a German computer magazine Chip India CHIP India magazine , Indian edition of German magazine CHIPSat CHIP, a character in Sonic Unleashed a human gene, also known as STUB1 disambig ... more details
Summary Information Description Schematic outline of MeDIP. Genomic DNA is sheared into 400 700bp using sonication and subsequently denatured. Incubation in 5mC antibodies, along with standard immunoprecipitation, enriches for fragments that are methylated IP fraction . This IP fraction can become the input sample to one of two DNA detection methods array hybridization using high density microarrays A or high throughput sequencing using the latest in sequencing technology B . Output from these methods are then analyzed for methylation patterns to answer the biological question. Source self drawn Date February 27, 2009 Author Gavinha Permission other versions Licensing PD author ... more details
Cistrome This term http cistrome.pbwiki.com was coined by investigators at the Dana Farber Cancer Institute and Harvard Medical School to define the set of cis acting cis acting targets DNA binding site s of a trans acting factor transcription factor , pioneer factor, restriction enzyme , etc on a genome scale. Technologies such as chromatin immunoprecipitation combined with microarray ChIP on chip or with massively parallel DNA sequencing ChIP Seq have greatly facilitated the definition of the cistrome of transcription factors and other chromatin associated proteins. References http www.dana farber.org abo news press 2006 molecular atlas provides new tool for understanding estrogen fueled breast cancer.html http www.cell.com content article abstract?uid PIIS0092867408001189 http erc.endocrinology journals.org cgi content full 16 2 381 genetics stub Category Molecular genetics fr Cistrome zh ... more details
V snoRNA1 is a box CD snoRNA identified in B lymphocytes infected with Epstein Barr virus . ref name pmid19680535 Cite pmid 19680535 ref This snoRNA is the first known example of a snoRNA expressed from a viral genome. It is homologous to eukaryotic snoRNAs as it contains the C and D boxes sequence motifs but lacks a terminal stem loop structure. The nucleolar localization of v snoRNA1 was determined by in situ hybridization . V snoRNA1 can form into a ribonucleoprotein complex snoRNP as co immunoprecipitation CoIP assays showed that this snoRNA interacts with the snoRNA core proteins, fibrillarin , Nop56, Nop58. It has also been proposed that this snoRNA may act as a miRNA like precursor that is processed into 24 nucleotide sized RNA fragments that target the 3 untranslated region UTR of viral DNA polymerase mRNA. ref name pmid19680535 References reflist Category RNA Category Molecular genetics Category Non coding RNA ... more details
Small RNA s sRNAs have been identified within the Caenorhabditis elegans C. elegans genome and comparative genomics has shown that they are conserved across several nematode species. These sRNAs contain a characteristic 2,2,7 trimethylguanosine TMG cap structure that identifies them as non coding RNA s that have a functional role within the cell but at present the exact function of these sRNAs is unknown. Immunoprecipitation using antibodies against TMG and RNA microarrays were used to identify these sRNA. ref name pmid17903271 Cite pmid 17903271 ref Examples of C. elegans sRNA sbRNA SmY RNA See also Mycobacterium tuberculosis sRNA Bacillus subtilis BSR sRNAs Escherichia coli sRNA References reflist Category Caenorhabditis elegans Category RNA Category Non coding RNA ... more details
PAR CLIP ref name pmid20371350 cite journal author Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. title Transcriptome wide identification of RNA binding protein and microRNA target sites by PAR CLIP. journal Cell volume 141 issue 1 pages 129 141 year 2010 pmid 20371350 doi 10.1016 j.cell.2010.03.009 pmc 2861495 ref Photoactivatable Ribonucleoside Enhanced Crosslinking and Immunoprecipitation is a novel method, used for identifying the binding sites of cellular RNA binding proteins RBPs and microRNA containing ribonucleoprotein complexes miRNPs . The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4 thiouridine 4 SU and 6 thioguanosine 6 SG into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next generation sequencing technology ref name pmid20371350 ref Cite pmid 20644507 ref . Recently, PAR CLIP have been applied to determine the transcriptome wide binding sites of several known RBPs and microRNA containing ribonucleoprotein complexes at high resolution ref name pmid20371350 ref name pmid21037263 cite journal author Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. title starBase a database for exploring microRNA mRNA interaction maps from Argonaute CLIP Seq and Degradome Seq data. journal Nucl. Acids Res. volume issue Database issue pages 1 8 year 2010 pmid 21037263 doi 10.1093 nar gkq1056 ref . References Reflist External links http starbase.sysu.edu.cn starBase database a database for exploring Ago mRNA interactions from PAR CLIP data. DEFAULTSORT Clip Seq Category Pro ... more details
Rfam box acc RF00563 description Small nucleolar RNA SNORA53 abbreviation SNORA53 avg length 216.20 avg identity 62.00 type Gene snRNA snoRNA HACA box se Marantidis E, INFERNAL ss Predicted RNAalifold release 10.0 The snoRNA ACA53 belongs to the snoRNA H ACA family of pseudouridylation guide snoRNAs . This H ACA box RNA was cloned by Kiss et al. 2004 ref cite journal last Kiss first AM coauthors Jady BE, Bertrand E, Kiss T year 2004 title Human box H ACA pseudouridylation guide RNA machinery journal Mol Cell Biol. volume 24 pages 5797&ndash 5807 pmid 15199136 doi 10.1128 MCB.24.13.5797 5807.2004 issue 13 pmc 480876 ref from a HeLa cell extract immunoprecipitation immunoprecipitated with an anti GAR1 antibody. It has no identified target RNA. RNA residues targeted for Pseudouridine pseudouridylation by this molecule have not been identified. References reflist 1 External links Rfam id RF00563 name Small nucleolar RNA SNORA53 http www snorna.biotoul.fr plus.php?id ACA53 snoRNAbase entry snoRA53 Category Small nuclear RNA molecular cell biology stub Small nucleolar RNA SNORA ... more details
infobox biodatabase title CLIPZ logo File Database.png description Experimentally determined binding sites of RNA binding protein s. scope organism center Swiss Institute of Bioinformatics laboratory author pmid PMID 21087992 released 2010 standard format url http www.clipz.unibas.ch download webservice sql sparql webapp standalone license versioning frequency curation bookmark version CLIPZ is a database of post transcriptional regulatory elements RNA binding protein s built from cross linking and immunoprecipitation data. ref cite journal quotes yes last Khorshid first Mohsen authorlink coauthors Rodak Christoph, Zavolan Mihaela year 2011 month Jan title CLIPZ a database and analysis environment for experimentally determined binding sites of RNA binding proteins journal Nucleic Acids Res. volume 39 issue Database issue pages D245 52 publisher location England issn pmid 21087992 doi 10.1093 nar gkq940 bibcode oclc id url language eng format accessdate laysummary laysource laydate quote ref References references See also RNA binding protein External links http www.clipz.unibas.ch Biodatabase stub Category Gene expression Category RNA Category Protein protein interaction assays Category Biological databases ... more details
File Lambda repressor 1LMB.png thumb The lambda repressor protein interacting with the lambda operator DNA. 250px Protein DNA interactions are when a protein binds a molecule of DNA , often to regulate the function biology biological function of DNA, usually the gene expression expression of a gene . Among the proteins that bind to DNA are transcription factors that activate or repress gene expression by binding to DNA motifs and histones that form part of the structure of DNA and bind to it less specifically. In general, proteins bind to DNA in the major groove , however there are exceptions. ref name pmid9646864 cite journal author Bewley CA, Gronenborn AM, Clore GM title Minor groove binding architectural proteins structure, function, and DNA recognition journal Annu Rev Biophys Biomol Struct volume 27 issue pages 105 31 year 1998 pmid 9646864 doi 10.1146 annurev.biophys.27.1.105 url ref See also Chromatin immunoprecipitation DNA binding protein Protein protein interaction References Reflist Category Systems biology Category Bioinformatics Category Biochemistry methods Category Biotechnology ... more details
Protein methods are the techniques used to study protein s. There are genetic methods for studying proteins, methods for detecting proteins, methods for isolating and purifying proteins and other methods for characterizing the structure and function of proteins, often requiring that the protein first be purified. Genetic methods conceptual translation many proteins are never directly sequenced, but their sequence of amino acids is known by conceptual translation of a known mRNA sequence. See genetic code . site directed mutagenesis allows new variants of proteins to be produced and tested for how structural changes alter protein function. insertion of protein tags such as the His tag . See also green fluorescent protein . evolutionary analysis of sequence changes in different species using software such as BLAST . Proteins that are involved in human diseases can be identified by matching allele s to disease and other phenotypes using methods such as Genetic linkage calculation of LOD scores . Detecting proteins microscopy, Immunostaining protein immunostaining Immunoprecipitation Protein immunoprecipitation Immunoelectrophoresis Immunoblotting Bicinchoninic acid assay BCA Protein Assay Western blot Spectrophotometry Enzyme assay Protein purification Protein Isolation chromatography methods Protein Extraction and Solubilization Protein Concentration Determination Methods, Bradford protein assay Concentrating Protein Solutions Gel electrophoresis Gel Electrophoresis Under denaturing conditions Gel Electrophoresis Under non denaturing conditions 2D Gel Electrophoresis Electrofocusing Protein structures X ray crystallography Protein NMR Protein DNA interactions ChIP on chip Chip Sequencing DamID Microscale Thermophoresis Other methods Hydrogen deuterium exchange Mass spectrometry Molecular dynamics Protein structure prediction Protein sequencing Protein structural alignment Protein ontology Protein synthesis Proteomics Peptide mass fingerprinting Ligand binding assay Ea ... more details
functions via Protein protein interactions Protein protein interactions . Immunoprecipitation Pull ... hybrid screening Yeast two Hybrid , Immunoprecipitation Pull down assay , X ray Crystallography Structure ... Hybrid , Immunoprecipitation Pull down assay Actin PET? ref name Garvalov 2003 Immunoprecipitation Pull down assay Actinin PET? ref name Garvalov 2003 Immunoprecipitation Pull down assay Paxillin PET? ref name Garvalov 2003 Immunoprecipitation Pull down assay Garvalov et al. showed that the interaction ... more details
See also Chips disambiguation CHIP disambiguation wiktionarypar chip TOCright Chip may refer to Food Potato chip s Canada and USA usage , a snack food made from potatoes, also known as crisps in the UK and some other English speaking countries Chips, the UK term for large cuts of potato that are deep fried or baked in an oven, known as french fries in Canada and the U.S. Corn chip , a snack food made from corn Tortilla chip , a snack food made from corn tortillas Chocolate chip , small chunks of chocolate, used for making chocolate chip cookies, among other things Banana chips , deep fried or dried slices of banana Sports Chip timing Transponder timing is sporting events. A Chip stroke or Chip In A Golf Stroke mechanics Golf term, a type of Golf stroke mechanics golf shot A type of association football football soccer shot Technology Chip CDMA , the fundamental unit of transmission in CDMA Smart card Chip card , credit card, payment card or identification card containing an embedded integrated circuit Chipseal , a pavement surface treatment Chiptune , music synthesized by a computer sound chip ChiP ChucK for iOS Apple iPhone iPad , a programming language used for Synthesizer music synthesis Chromatin immunoprecipitation ChIP Chromatin ImmunoPrecipitation , a molecular biology method to map DNA sites of specific protein DNA interaction, such as promoters Chip, another name for an integrated circuit . Chip, another name for a microprocessor . Modchip , hardware modification to circumvent DRM systems in game consoles Chip s Challenge a game designed by chuck sommerville and Tony Krueger. People Chip Arndt , winner of The Amazing Race 4 Charles Eustis Bohlen Charles Eustis Chip Bohlen , American diplomat Chip Kidd , American author Chip Esten , American actor Chip Carter, son of Jimmy Carter Chip Flagston, son of Hi and Lois Other Buffalo chip or cow dung , dried bovine feces Casino token or poker chip, a token of currency in gambling Chip, one of the Chip n Dale animat ... more details
Human Proteinpedia is a portal for sharing and integration of human proteomic data,. ref Kandasamy et al. Human Proteinpedia a unified discovery resource for proteomics research. Nucleic Acids Research. Advance Access published on October 23, 2008, DOI 10.1093 nar gkn701. ref ref Mathivanan et al. Human Proteinpedia enables sharing of human protein data. Nat Biotechnology. 2008 Feb 26 164 7 ref It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database, ref Mishra et al. Human protein reference database 2006 update. Nucleic Acids Res. 2006 Jan 34 Database issue D411 4 ref ref Peri et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003 Oct 13 2363 71. ref HPRD integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information at the context of an individual protein. In essence, researchers can add new data to HPRD by registering to Human Proteinpedia. The data deposited in Human Proteinpedia is freely available for download. Emphasizing the importance of proteomics data disposition to public repositories, Nature Methods recommends Human Proteinpedia in their editorial. ref Editorial. Thou shalt share your data. Nat Mehods. 2008 Mar 5 209 ref More than 70 labs participate in this effort. What data can be shared? Data pertaining to post translational modifications , protein protein interactions , tissue expression, expression in cell lines , subcellular localization and enzyme substrate relationships can be submitted to Human Proteinpedia Proteomics portal Experimental platforms Protein annotations present in Human Proteinpedia are derived from a number of platforms such as Co immunoprecipitation and mass spectrometry based protein protein interaction Co immunoprecipitation and Western blotting based protein protein interaction Fluorescence based experiments Immunohistochemistry Mass Spectr ... more details
unreferenced date October 2009 Regulome refers to the whole set of regulation components in a cell biology cell . Those components can be gene s, mRNA s, protein s, and metabolite s. The description includes the interplay of regulatory effects between these components, and their dependence on variables such as subcellular localization , Biological tissue tissue , developmental stage, and pathological state. Components One of the major players in cellular regulation are transcription factor s, proteins that regulate the expression of genes. Other proteins that bind to transcription factors to form transcriptional complex es might modify the activity of transcription factors, for example blocking their capacity to bind to a promotor biology promoter . Signaling pathway s are groups of proteins that produce an effect in a chain that transmit a signal from one part of the cell to another part, for example, linking the presence of substance at the exterior of the cell to the activation of the expression of a gene. Measuring High throughput technologies for the analysis of biological samples for example, DNA microarray s, proteomics analysis allow the measurement of thousands of biological components such as mRNAs, proteins, or metabolites. Chromatin immunoprecipitation of transcription factors can be used to map transcription factor binding sites in the genome. Such techniques allow researchers to study the effects of particular substances and or situations on a cellular sample at a genomic level for example, by addition of a drug, or by placing cells in a situation of stress . The information obtained allows parts of the regulome to be inferred. Modeling One of the objectives of systems biology is the modelization of biological processes using mathematics and computer simulation . The production of data from techniques of genomic analysis is not always amenable to interpretation mainly due to the complexity of the data and the large amount of data points. Modelization c ... more details
protein Name nebulette caption image width HGNCid 16932 Symbol NEBL AltSymbols EntrezGene 10529 OMIM 605491 RefSeq NM 006393 UniProt O76041 PDB ECnumber Chromosome 10 Arm p Band 12 LocusSupplementaryData Nebulette is an protein isoform isoform of the protein nebulin . While nebulin 600 900 kDa is expressed preferentially in skeletal muscle , nebulette 107 kDa is expressed in cardiac muscle . Nebulette was identified in 1995 by Moncman and Wang using primary cultures of chicken embryonic cardiomyocyte s by immunoprecipitation s with certain anti nebulin monoclonal antibodies . ref name moncman cite journal author Moncman & Wang title Nebulette a 107 kD nebulin like protein in cardiac muscle journal Cell Motil Cytoskeleton volume 32 issue 3 pages 205 25 year 1995 pmid 8581976 doi 10.1002 cm.970320305 last2 Wang first2 K ref Normal expression of nebulette is essential for the assembly and muscle contraction contractile function of myofibril s. ref name moncman2 cite journal author Moncman & Wang title Targeted disruption of nebulette protein expression alters cardiac myofibril assembly and function journal Exp Cell Res volume 273 issue 2 pages 204 18 year 2002 pmid 11822876 doi 10.1006 excr.2001.5423 last2 Wang first2 K ref References Reflist External links MeshName nebulette Category Proteins gene 10 stub Cell biology stub Muscle tissue ... more details
Orphan date February 2009 Rfam box acc RF00615 description Listeria Hfq binding LhrA abbreviation LhrA avg length 265.20 avg identity 97.00 type Gene sRNA se Daub J ss Published PMID 16682563 release 10.0 Listeria Hfq binding LhrA is a ncRNA that was identified by screening for RNA molecules which Immunoprecipitation co immunoprecipitated with the Hfq protein RNA chaperone Hfq . ref cite journal author Christiansen JK, Nielsen JS, Ebersbach T, Valentin Hansen P, S gaard Andersen L, Kallipolitis BH title Identification of small Hfq binding RNAs in Listeria monocytogenes journal RNA volume 12 issue 7 pages 1383 96 year 2006 pmid 16682563 doi 10.1261 rna.49706 pmc 1484441 ref This RNA is transcribed from a region overlapping with a predicted protein of unknown function Lmo2257 and is located between a putative intracellular protease and a putative protein of the Epimerase and racemase ribulose phosphate 3 epimerase family. It is highly expressed in the Bacterial growth stationary growth phase but the function is unknown. It is proposed to be a regulatory RNA which controls gene expression at the Transcription genetics post transcriptional level by binding the target mRNA in an Hfq dependent fashion. This RNA molecule appears to be conserved amongst Listeria species but has not been identified in other bacteria l species. References reflist 1 External links Rfam id RF00615 name Listeria Hfq binding LhrA Category Non coding RNA molecular cell biology stub ... more details
Orphan date February 2009 Rfam box acc RF00616 description Listeria Hfq binding LhrC abbreviation LhrC avg length 106.00 avg identity 90.00 type Gene sRNA se Daub J ss Published PMID 16682563 release 10.0 Listeria Hfq binding LhrC this ncRNA was identified by screening for RNA molecules which Immunoprecipitation co immunoprecipitated with the Hfq protein RNA chaperone Hfq ref cite journal author Christiansen JK, Nielsen JS, Ebersbach T, Valentin Hansen P, S gaard Andersen L, Kallipolitis BH title Identification of small Hfq binding RNAs in Listeria monocytogenes journal RNA volume 12 issue 7 pages 1383 96 year 2006 pmid 16682563 doi 10.1261 rna.49706 pmc 1484441 ref . This RNA is transcribed from an intergenic region between the protein coding genes cysK, a putative cysteine synthase and sul, a putative dihydropteroate synthase . In Listeria monocytogenes four additional copies of lhrC have been identified in the genome, three of which are located in tandem repeat upstream of the originally characterised lhrC. The function of LhrC is not known. This RNA molecule appears to be conserved amongst Listeria species but has not been identified in other bacterial species. References reflist 1 External links Rfam id RF00616 name Listeria Hfq binding LhrC Category Non coding RNA molecular cell biology stub ... more details
RIP Chip is immunoprecipitation of an RNA binding protein coupled to reverse transcription and a DNA microarray microarray . It has been used to find interactions between RNA and protein one protein but many RNA species per analysis . ref cite journal author Townley Tilson WH, Pendergrass SA, Marzluff WF, Whitfield ML title Genome wide analysis of mRNAs bound to the histone stem loop binding protein journal RNA volume 12 issue 10 pages 1853 67 year 2006 month October pmid 16931877 pmc 1581977 doi 10.1261 rna.76006 ref ref cite journal author Khalil AM, Guttman M, Huarte M, et al. title Many human large intergenic noncoding RNAs associate with chromatin modifying complexes and affect gene expression journal Proc. Natl. Acad. Sci. U.S.A. year 2009 month July pmid 19571010 pmc 2704857 doi 10.1073 pnas.0904715106 volume 106 issue 28 pages 11667 72 ref ref cite journal author Hendrickson DG, Hogan DH, Herschlag D, Ferrell JEF, Brown PB title Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance journal PLoS One year 2008 ref A similar technique is ChIP on chip , which detects the binding of proteins to genomic DNA rather than RNA. A competing technique is CLIP Seq also called RIP Seq , where high throughput sequencing replaces the microarray. References Reflist Category RNA Category Protein methods Category Microarrays Molecular biology stub ... more details
Orphan date February 2009 Radioimmunoprecipitation assay buffer is a lysis buffer used to Lysis lyse cells and tissue, for radio immunoprecipitation assay RIPA . ref name pmid2094444 cite journal author Alcaraz C, De Diego M, Pastor MJ, Escribano JM title Comparison of a radioimmunoprecipitation assay to immunoblotting and ELISA for detection of antibody to African swine fever virus journal J. Vet. Diagn. Invest. volume 2 issue 3 pages 191 6 year 1990 month July pmid 2094444 doi url http www.jvdi.org cgi pmidlookup?view long&pmid 2094444 ref ref name pmid18950484 cite journal author Ngoka LC title Sample prep for proteomics of breast cancer proteomics and gene ontology reveal dramatic differences in protein solubilization preferences of radioimmunoprecipitation assay and urea lysis buffers journal Proteome Sci volume 6 issue 1 pages 30 year 2008 month October pmid 18950484 doi 10.1186 1477 5956 6 30 url pmc 2600628 ref This buffer is more denaturing than NP 40 or Triton X 100 lysis buffer because it contains the ionic detergents SDS and sodium deoxycholate as active constituents and is particularly useful for nuclear membrane disruption for nuclear extracts. The RIPA buffer gives low background but can denature kinases. Recipe RIPA buffer recipe for total protein extract is as follows Tris 50mM NaCl 150 mM SDS 0.1 Na.Deoxycholate 0.5 Triton X 100 or NP40 1 Protease inhibitors such as PMSF or cocktail protease inhibitors which are commercially available use according to the manufacturer s guide References Reflist External links http carmen.salk.edu sefton Hyper protocols immunoprecip.html anchor1446740 1X RIPA Buffer Category Laboratory techniques biology stub ... more details
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