Chromosome structural analysis : a practical approach /
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| Imprint: | Oxford ; New York : Oxford University Press, 1999. |
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| Description: | 1 online resource (xxiii, 209 pages) : illustrations (some color) |
| Language: | English |
| Series: | The practical approach series ; 200 Practical approach series ; 200. |
| Subject: | |
| Format: | E-Resource Book |
| URL for this record: | http://pi.lib.uchicago.edu/1001/cat/bib/11127774 |
Table of Contents:
- Intro; Contents; List of contributors; Abbreviations; 1. Mapping protein/DNA interactions in vivo using ligation-mediated polymerase chain reaction; 1. Introduction; Methods used in determining protein/DNA interactions in vitro; Determining protein/DNA interactions in vivo; 2. The ligation-mediated polymerase chain reaction (LMPCR); Applications of LMPCR; 3. Mapping protein factor binding sites in vivo with LMPCR and DMS; DNA modification by DMS in vitro; DMS modification of DNA in vivo; Amplification of DMS/piperidine-cleaved DNA by LMPCR; Analysis of LMPCR reactions
- 4. Mapping nucleosomes using micrococcal nuclease and LMPCRIsolation of nuclei from cultured cells; Preparation of DNA from nuclei treated with MNase; Cleavage of genomic DNA with MNase; Acknowledgements; References; 2. Mapping DNA target sites of chromatin-associated proteins by formaldehyde cross-linking in Drosophila embryos; 1. Introduction; 2. Outline of the method; 3. Formaldehyde cross-linking in staged Drosophila embryos; Preparation of fly cages and collection of staged embryos; Optimizing cross-linking conditions
- 4. Immunoprecipitation of cross-linked embryonic chromatin and PCR amplification of the immunoprecipitated DNA5. Analysing the enrichment of putative target sequences in the PCR-amplified DNA; Slot-blot analysis of the enrichment of putative PC target sequences; Mapping DNA target sites for Polycomb and GAGA factor in the Drosophila bithorax complex; 6. Concluding remarks; References; 3. Fission yeast chromosome analysis: fluorescence in situ hybridization (FISH) and chromatin immunoprecipitation (CHIP); 1. Introduction; 2. Fluorescence in situ hybridization (FISH) analysis of fission yeast
- Preparation of probesCell fixation and cell-wall digestion; 3. Chromatin immunoprecipitation from fission yeast; Fixation of yeast cells to maintain protein localization; Preparation of chromatin extract; Immunoprecipitation of chromatin; Analysis of immunoprecipitated DNA sequences; Acknowledgements; References; 4. Isolation of vertebrate metaphase chromosomes and their analysis by FISH; 1. Introduction; 2. General equipment required for FISH; 3. Production of metaphase chromosomes as substrates for FISH; Production of fixed metaphase chromosome spreads
- Production of long prometaphase chromosomesIsolation of suspensions of unfixed metaphase chromosomes; 4. Spreading fixed chromosomes; 5. Pretreatments of slides; Pretreatment of mitotic chromosome spreads; Salt extraction of isolated metaphase chromosomes; 6. Labelling DNA probes; Choice of label; Nick translation; Random priming; Labelling by PCR; Quantifying label incorporation; 7. Hybridization; Preparation of probes and slides; Hybridization; 8. Detecting hybridized probe; 9. Counterstaining and mounting; Simple counterstaining; Chromosome banding; Acknowledgements; References