PCR Protocol--Multiplex PCR

Multiplex PCR

PCR and multiplex PCR guideOctavian Henegariu,Yale University
Multiplex PCR
A step by step protocol
Troubleshooting for PCR and Multiplex PCR
Octavian Henegariu,Yale University
Multiplex PCR Handbook
Qiagen
Multiplex PCR System Protocol
GenScript
MultiPlex PCR-based Sequencing
Bruce Roe
Efficient Multiplex PCR Optimization - Online
Bioscience Tech
Multiplex PCR-based reverse line blot hybridization assay.
Nature protocols
Multiplex PCR with TaqMan VIC Probes
http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_041019.pdf
AB Applied Biosystems
Multiplex PCR (Chamberlain and Beggs)
Leiden Muscular Dystrophy pages

PCR Protocol--Regenerate PCR

Degenerate PCR

Degenerate PCR
The identification of novel members of gene families by PCR using degenerate primers is described and protocols given. Article by Michael Koelle 1996 on the ...www.dartmouth.edu/~ambros/protocols/other/koelle/degenerate_PCR.html
Degenerate PCR.html (Michael Koelle)
by Michael Koelle. The identification of novel members of gene families by PCR using degenerate primers has been considered more of an art than a science, ...www.med.yale.edu/mbb/koelle/protocols/protocol_degenerate_PCR.html
PCR Primer Design
However, I have used primers with as high as 256- and 1024-fold degeneracy for the successful amplification and subsequent direct sequencing of a wide range ...www.mcb.uct.ac.za/pcroptim.htm
Degenerate PCR (NTNU Cell and Molecular Biology Group)
X - Services · Open Positions, Degenerate PCR Degenerate PCR is in most respects identical to ordinary PCR, but with one major difference. ...http://boneslab.bio.ntnu.no/degpcrshortguide.htm
Designing degenerate PCR primers
The purpose of CODEHOP is to help in the design of degenerate PCR primers from protein sequence. Given a multiple alignment of a series of target proteins, ...genomebiology.com/2000/1/1/reports/240
Nature Protocols: Quantitative multiplex degenerate PCR for human endogenous retrovirus expression profiling.
Last, the protocol below provides general rules for the design of MD-PCR applications. Once primers have been designed and optimized, the procedure can be ...www.natureprotocols.com/2007/01/25/quantitative_multiplex_degener.php

PCR Protocol--Inverse PCR

Inverse PCR

Inverse PCR & Cycle Sequencing of P Element Insertions for STS GenerationJay Rehm
Inverse PCR for PAC-end sequencingBrad Barbazuk
Inverse PCR:For use with Snyder mTn-lacZ/LEU2 based mutagenesisFred Hutchinson Cancer Research Center
Cloning flanking DNA from pD991 enhancer trap T-DNA insertsDepartment of Biological Sciences Dartmouth College

Inverse PCR protocol
Maddock Lab.

Inverse PCR and Sequencing Protocol
E. Jay Rehm

Inverse PCR
Trevor Epp

Springer Protocols: Inverse PCR (IPCR) for Obtaining Promoter Sequence.
Springer Protocols

PCR Protocol--PCR Elisa

What is PCR Elisa?
PCR products are labeled (e.g., by digoxigenin) during amplification. A capture probe specific to the PCR amplicon is used to immobilize the amplicon to well plate. ELISA against the label (e.g., anti-digoxigenin) is then used to quantitate PCR products.

PCR-ELISA, an alternative to real time PCR for detecting.
PCR-ELISA is an alternative to real time PCR used to detect sequences within the polymerase chain reaction products.www.btc-bti.com/pcrelisa.htm

Mycoplasma Detection by the Mycoplasma PCR ELISAMycoplasma Detection by the. Mycoplasma PCR ELISA. Introduction. The most frequent contaminants of animal ...www.roche-applied-science.com/PROD_INF/BIOCHEMI/jlp33-35.pdf B

Telomerase PCR ELISATelomerase PCR ELISA. For fast and sensitive detection of ... The indicated number of cells were analyzed in the Telomerase PCR ELISA.Assays were ...www.roche-applied-science.com/PROD_INF/BIOCHEMI/No.4_96/p7-8.pdf

Optimisation of one-tube PCR Elisa to detect femtogram amounts of genomic DNA.
A simple, high-throughput, low-cost polymerase chain reaction-enzyme linked immunosorbent assay (PCR-ELISA) protocol that detects the presence of 4 fg of ...linkinghub.elsevier.com/retrieve/pii/S0167701202000556

Qualitative PCR-ELISA protocol for the detection and typing of viral genomes.
Nature Protocols is an interactive online resource for all laboratory protocols relevant to biological and biomedical research. Nature Protocols includes a ...npg.nature.com/nprot/journal/v2/n10/abs/nprot.2007.311.html

PCR Protocol--Nested PCR

Nested PCR

What is nested PCR? Nested PCR is a variation of the polymerase chain reaction (PCR), in that two pairs (instead of one pair) of PCR primers are used to amplify a fragment.

The first pair of PCR primers amplify a fragment similar to a standard PCR. However, a second pair of primers called nested primers (as they lie / are nested within the first fragment) bind inside the first PCR product fragment to allow amplification of a second PCR product which is shorter than the first one.
The advantage of nested PCR is that if the wrong PCR fragment was amplified, the probability is quite low that the region would be amplified a second time by the second set of primers. Thus, Nested PCR is a very specific PCR amplification.

PCR amplification of cDNA segments by 2 stage nested PCRprotocolNCBI
Standard Nested PCR ProtocolC. elegans Gene Knockout Project, Vancouver Lab
Poison Primer Nested PCR Protocol
Moerman Lab.
Nested PCR and Sequencing of T-DNA Junctions in Arabidopsis
http://signal.salk.edu/T-DNArecovery.pdf
ECKER LAB
Protocol for nested PCR amplification.

PCR Protocol--In Situ PCR

In Situ PCR

The In Situ PCR:
(Amplification and Detection in a Cellular Context)

Ernest F. Retzel, Katherine A. Staskus, Janet E. Embretson and Ashley T. Haase
Department of Microbiology, University of Minnesota, Minneapolis, MN 55455

Table of Contents
Introduction Technical Aspects/Philosophy Primer Design Reaction Conditions "Mechanics" of the Reaction Methodology
A. Cell and Tissues.
1. Cultured Cells: Infection and Preparation. 2. Tissues: Pulmonary infection and preparation.
B. In Situ Amplification
1. Cultured Cells in Suspension. 2. Tissues on Slides.
C. Detection of Amplified DNA by in situ Hybridization
1. Solution amplification. 2. Tissue Sections.
References

In Situ PCR on Plant Material (Bo Johansen)Required materialsRequired solutionsTissue preparationPectinase treatmentProtease treatmentAcetylationDNase treatmentReverse transcriptionThermal cyclingDetectionMountingAcrobat version of PosterReferencesOther ISPCR linksBotanical Institute

RT IN SITU PCR
Gerard J. Nuovo
TABLE OF CONTENTS
1. Abstract
2. Introductory statement
3. The key preparatory steps
3.1. Fixative
3.1.1. Protease digestion
3.1.2. Definition of optimal protease digestion
3.1.3. Definitions of suboptimal and over-digestion
3.1.4. DNase digestion
3.1.5. Direct incorporation of the reporter nucleotide
4. A one step protocol for RT in situ PCR
5. Applications of RT in situ PCR Matrix metalloprotease expression in cancer as a model for RT in situ PCR
5.1. MMP and TIMP expression in cervical cancer
6. Concluding remarks
7. References
8. Entire manuscript

In situ PCR: protocols and applications.
groups have published protocols and data using in situ PCR techniques. (5). This article will discuss some of the basic concepts of in situ PCR, the proto- ...www.genome.org/cgi/reprint/4/4/S151.pdf
Co-labeling Using In Situ PCR: A Review
Figure 2 Background vs signal with RT in situ PCR. This renal biopsy was analyzed for mRNA by RT in situ PCR. After digestion for 10 min in ...www.jhc.org/cgi/reprint/49/11/1329.pdf
Protocols for the : in situ: PCR-amplification and detection of mRNA and DNA sequencing.
In this protocol we describe the in situ PCR method for the amplification of both DNA and mRNA targets [in situ reverse transcriptase-PCR (RT-PCR)], ...www.nature.com/nprot/journal/v2/n11/abs/nprot.2007.395.html
96-well RNA In Situ Hybridization Protocol
1. Materials. 1.1. Probe Preparation. 1.1.1. Cell Inoculation. 1. 96-well, deep square-well round bottom plate (E&K Scientific Ritter Riplate). ...www.fruitfly.org/about/methods/RNAinsitu.html
A protocol for PCR in situ hybridization of hyphomycetesIntroduction. Within the last years the focus of mycological studies has shifted. emphasis from mere taxonomic studies to more ecological. questions. ...www.im.microbios.org/03setember98/08%20Sterflinger.pdf

PCR Protocol--Tail PCR

TAIL PCR

An introduction of TAIL PCR
Many product bands from the primary TAIL-PCR reaction disappeared after the secondary TAIL-PCR, indicating that these were non-specific type II products ...ihome.cuhk.edu.hk/~z045478/TAIL-PCR%5Bfinal%5D.ppt
TAIL-PCR to clone flanking sequence from Feldmann's linesChun-Ming Liu's HomepageTAIL PCR ANALYSIS
TAIL PCR ANALYSIS. For this service Investigators have three purification options. Our standard purification protocol from the Jackson laboratory, ...www.lajollaneuroscience.org/sr/homepage/dna/tailpcranalysis.html
TAIL PCR ProtocolThe Preuss LabDivision of Biological Sciences, University of Chicago
TAIL PCR
Below is a summary of the responses: I've been using TAIL PCR to isolate the ends of BACs during my chromosome walk. I obtained the sequences of my ...net.bio.net/bionet/mm/arab-gen/1998-September/006602.html
Tail PCR Protocol
Purpose: Mu TAIL PCR produces a population of fragments with one end anchored in Robertson's Mutator (Mu) TIR's and the other in the Mu flanking DNA. ...currant.hos.ufl.edu/mutail/tail.htm
Springer Protocols:High-Throughput TAIL-PCR as a tool to identify DNA flanking insertions.
Springer Protocols is the largest subscription-based electronic database of reproducible laboratory protocols in the Life and Biomedical Sciences.www.springerprotocols.com/Abstract/doi/10.1385/1-59259-413-1:241
TAIL-PCR to clone flanking sequence from Feldmann's lines
The first thing you need to do before starting your TAIL-PCR is to figure out which border of the T-DNA is flanking the plant genome, especially with Ken ...http://www.plant.wageningen-ur.nl/projects/hybtech/Liu/tail_PCR.htm
Isolation of genomic fragment by TAIL-PCR
More than 50bp must be remained downstream of a third gene specific primer to check if a gained TAIL PCR fragment is correctly extended from an original ...www.nibb.ac.jp/evodevo/PHYSCOmanual/4.3.htm