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Dna affymetrix 50 reactions manual

Whole- genome- amplified material prepared by the qiagen repli- g® kits may also be used as the starting material for the genome- wide human snp assay kit. rt- pcr master mix ( 2x) rt- pcr reaction mix 100 reactions 78370 fidelitaq rt- pcr rt- pcr reaction mix 100 reactions 71185 master mix ( 2x) a- taq- it™ pcr kit for use in pcr ( includes 100 reactions 71175 taq and exosap- it) one- step rt- pcr kit rt- pcr, optimization, 50 reactions 78350 analysis of multiple genes. coli dna ligase, e. a typical assay reaction uses 0. 67 µl of nuclease– free water, and 1 µl of microrna assay ( applied biosystem) buffer. 1 – 2 μg of total rna. the kit contains t4 dna ligase and a specially- formulated 5x rapid ligation buffer optimized for fast and efficient dna ligation. ) agencourt® genfind™ v2 blood and serum genomic dna isolation kit protocol.

12- reaction kit for manual use ( cat. application areas that benefit from using microarray analysis include plant and animal genomics, cancer research from discovery to clinical research and validation, as well as genetics of human complex traits, mendelian disorders, and populations. the 20- µl pcr reactions contained 1. the sequenase chain- termination dna sequencing method( 1, 2) involves the in vitro synthesis of a dna strand by a dna polymerase using a specifically primed single- stranded dna dna affymetrix 50 reactions manual template. molecular cloning: a laboratory manual, v. affymetrix probe synthesis guidelines, markus schmid and jan lohmann, mpi tübingen, page 5 of 9 ds- cdna clean- up use the “ genechip sample cleanup module” from affymetrix ( # 900371), read the manual! the array slide was further washed in a 50 ml conical tube containing 40 ml of nswb and briefly air- dried. mouse monoclonal antibody ( or other anti- dna/ rna hybrid primary antibody) was diluted in pbs with 0. after a 37° c incubation for 16 hours, the labeled crna was purified using the crna cleanup reagents from the genechip sample cleanup.

try decreasing the volume of ligation reaction mixed with cells or use less t4 dna ligase in the reaction. affymetrix genechip ® expression analysis technical manual, p/ n 702232 rev. warning: for research use only. each kit contains 1 vial of 60 µl of the genechip dna labeling reagent, 7. dna should have an a260/ a280 between 1. the reaction employs dna polymerase and rnase h to simultaneously degrade the rna and synthesize second- strand cdna. affymetrix one cycle eukaryotic gene dna affymetrix 50 reactions manual expression sample processing. this protocol is a supplement to instructions provided in the affymetrix expression manual and uses reagents in the affymetrix one cycle synthesis kit. do not use internally or externally in humans or animals. ; biorad, richmond, ca) and applied to the slide under a new lifterslip.

n if the reaction buffer contains peg and the ligation was incubated overnight, the transformation efficiency may decrease. in vitro transcription to synthesize biotin- modified arna with ivt labeling. advance your research with affymetrix microarray analysis products. 901152 sufficient for 50 reactions. 1 ( numeric rounding allowed). 50 arrays 901150 affymetrix® genome- wide human snp array 6. grind tissue together and use ~ 100mg powder in the qiagen dna easy kit. 3, © affymetrix inc. performance data.

the cytoscan xon assay is intended to be used with genomic dna. 5 mm, sufficient for 30 labeling reactions. 0 100 arrays supporting products 901152 affymetrix® genome- wide human snp nsp/ sty assay kit 5. affymetrix eukaryotic gene expression sample processing this protocol will allow you to perform the hydridisation, washing, staining and scanning of affymetrix genechip microarrays. 0 assay was designed for use with the affymetrix® genome- wide human snp array 6. 33 µl of rt product, 10 µl of faststart taqmanprobe master ( roche p/ n, 7. 0 assay ( genome- wide snp 5.

to extract equal amount of dna from the 50 – 100 mutant or wild type f2 plants, take 1 leaf ( or equal amount of tissue) from each plant and freeze together in liquid nitrogen. affymetrix® product family > dna arrays and reagents >. ] what this manual covers this manual provides recommendations and step- by- step procedures for the following:. coli dna polymerase i, and biotinylation of the crna was achieved by in vitro transcription ( ivt) reaction using the genechip 3' ivt express kit ( affymetrix). optional stopping point.

stranded dna ( dsdna) template for transcription. comparison of genotyping using pooled dna samples ( allelotyping) and individual genotyping using the affymetrix genome- wide human snp array 6. this protocol is a supplement to instructions provided in the affymetrix expression manual. this protocol will allow you to perform the labelling of eukaryotic total rna ready for affymetrix genechip analysis.

50 µm t7- oligo( dt) primer, 5x 1st strand reaction mix, 0. 05% tween 20 ( pbst) containing 2 mg/ ml gelatin ( catalog no. 51– 52; affymetrix ) with minor modification. hybridizations were carried out following the protocol described in affymetrix genechip® whole transcript double- stranded target assay ( wtdsta) manual ( pp. dna synthesis is carried out in two steps. total labeling reaction volume is 150ul.

0 100 reactions 901012 r eference genomic dna, 103 suffi cient for 2 reactions. samples can be stored overnight at – 20° c at this point if desired. the kit control dna included in every affymetrix genechip® snp kit has already been normalized to a working concentration. affymetrix arrays were therefore used to compare gene expression patterns in developing grain of seven doubled haploid lines ( dhls) from a cross between wheat cvs spark × rialto, showing that over. 3, © affymetrix, inc. an automated assay kit ( for processing 96 reactions) is also available ( see ordering information). the mitochip has multiple inherent advantages that make it an ideal platform for mutation detection: ( 1) we minimized the dna requirements— as little as 300 ng of genomic dna is sufficient for the assay; ( 2) we considerably reduced the number of pcr reactions ( currently 12– 32 in most dye terminator or manual sequencing protocols) — only. keep ligate- it t4 dna ligase [ pn 78401] on ice at all times. 1m dtt, 10 mm dntp, superscript® ii ( 200u⁄ ul), 5x 2nd strand reaction mix, e.

m13mp18 is the double- stranded, covalently closed, circular form of dna derived from bacteriophage m13. resuspend dna in 100ul. the affymetrix genechip® expression analysis technical manual is designed for use in a system consisting of a genechip® fluidics station 400, a genechip® hybridization oven and a genearray® scanner. this phage vector contains single hindiii, sphi, sbfi, psti, sali ( acci/ hincii), xbai, bamhi, smai ( xmai), kpni ( acc65i), saci and ecori sites within the β- galactosidase gene ( 1). tel: com com affymetrix uk ltd voyager, mercury park wycombe lane, wooburn green high wycombe hp10 0hh united kingdom com com affymetrix japan k. ) affymetrix genome‐ wide human snp nsp/ sty 6. dye primer manual cycle sequencing kit product numberreactions storage store. 0 and genome- wide human snp array 5. the first is the labeling step in which the primer is extended using limiting.

storage 3 nm control oligo™ b2 150 µl 150 µl – 20° c tubes organizer: plastic vinyl template for organization and storage of components in 9 x 9 array, 81- places. the bioprime dna labeling system ( invitrogen, carlsbad, ca, usa) was also tested for labeling dna as per the manufacturer’ s instructions. 0 assay manual, p/ n 70722 rev. try a shorter incubation time. ligate- it t4 dna ligase and 5x ligate- it reaction buffer have been functionally tested in the following protocol: 1. briefly, total genomic dna ( 500 ng; 250 ng each enzyme) is digested with nsp i and sty i restriction enzymes and ligated to adaptors that recognize the cohesive 4 bp overhangs.

• minimum volume of dna required. 0 alexander teumer, 1 florian d ernst, 1 anja wiechert, 1 katharina uhr, 1, 2 matthias nauck, 3 astrid petersmann, 3 henry völzke, 4 uwe völker, 1 and georg homuth 1. 5 ml of dna affymetrix 50 reactions manual oragene® ∙ dna/ saliva 5. n excess amounts of t4 dna ligase can decrease transformation efficiency. not recommended or intended for diagnosis of disease in humans or animals. coli dna polymerase i, rnase h, t4 dna polymerase, 0. second strand cdna synthesis was performed with e. ) dna genotek laboratory protocol for manual purification of dna from 0.

0 users guide acknowledgments the blood and saliva sample donors from affymetrix. 5m edta, rnase- free water all components are guaranteed stable for 6 months when properly stored. affymetrix microarray solutions include necessary components for a microarray experiment, from arrays and reagents to instruments and software, enabling scientists and clinicians to understand, identify, create, and improve genetic marker- assisted breeding programs in agriculture for human health and wellness. detailed instructions for using this reagent are described in section 3, chapter 1 of the genechip expression analysis technical manual. this manual is a guide for technical personnel conducting the affymetrix® genome- wide human snp nsp/ sty 5. it is important to use rna that is completely free of contaminating genomic dna. for an overview of the protocols and hybridization methods employed, see the affymetrix technical manuals. both blood and cell line sample sources have been tested by affymetrix with the cytoscan assay. manual processing kits are available for either 50 or 100 reactions.

about your dna samples sample criteria genomic dna sample criteria • concentration all genomic dna samples should be normalized to a single concentration of 150 ng/ μl using 1x te buffer. reactions were incubated at 95° c for 10 minutes, followed by 40 cycles of incubation at 95° c for 15 seconds and at 60° c for 1 minute. thermo scientific rapid dna ligation kit enables fast sticky- end or blunt- end dna ligation in only 5 minutes at room temperature. the genome- wide human snp nsp/ sty 5. reaction kit for manual use ( cat. 0 assay) experiments in the laboratory. affymetrix genechip ® mapping 10k 2. what is the recommended genomic dna extraction methods used for the cytoscan assay?

the amount of total rna required per assay depends on the target abundance in the sample. thaw 5x ligate- it reaction buffer [ pn 78402], mix thor- oughly, and place on ice. for the best results, it is suggested that samples to be compared are produced using the same rna type ( mrna or total rna), the same labeling kit, and at approximately the same amount of starting material. 6 cytoscan™ xon assay manual workflow user guide 1 introduction cytoscan™ xon assay has been optimized for the detection of exon- level copy number changes. mixng of vector dna with a 1- to 3- fold molar excess of insert dna.

• add 600 µl cdna binding buffer the the 150 µl 2nd strand reaction • vortex to mix ( color of mix must be yellow! human snp nsp/ sty assay 5. about the user manual protein/ dna arrays user manual page 5 about the user manual who should read this manual anyone that has purchased a protein/ dna array kit from panomics to profile from dna affymetrix 50 reactions manual 56 to 345 different transcription factors. it is generally unnecessary to treat the rna with dnase i to remove any genomic dna contamination. affymetrix, p/ nreactions) or p/ nreactions), contains control crna and control oligo b2.

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