Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a technique of choice for studying protein-DNA interactions. ChIP-seq has been used for mapping protein-DNA interactions and allocating histones modifications. The procedure is tedious and time consuming, and one of t...
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| Veröffentlicht in: | Journal of Visualized Experiments 2014-12 (94) |
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| creator | Berguet, Geoffrey Hendrickx, Jan Sabatel, Celine Laczik, Miklos Squazzo, Sharon Mazon Pelaez, Ignacio Saxena, Rini Pendeville, Helene Poncelet, Dominique |
| description | Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a technique of choice for studying protein-DNA interactions. ChIP-seq has been used for mapping protein-DNA interactions and allocating histones modifications. The procedure is tedious and time consuming, and one of the major limitations is the requirement for high amounts of starting material, usually millions of cells. Automation of chromatin immunoprecipitation assays is possible when the procedure is based on the use of magnetic beads. Successful automated protocols of chromatin immunoprecipitation and library preparation have been specifically designed on a commercially available robotic liquid handling system dedicated mainly to automate epigenetic assays. First, validation of automated ChIP-seq assays using antibodies directed against various histone modifications was shown, followed by optimization of the automated protocols to perform chromatin immunoprecipitation and library preparation starting with low cell numbers. The goal of these experiments is to provide a valuable tool for future epigenetic analysis of specific cell types, sub-populations, and biopsy samples. |
| doi_str_mv | 10.3791/52150 |
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ChIP-seq has been used for mapping protein-DNA interactions and allocating histones modifications. The procedure is tedious and time consuming, and one of the major limitations is the requirement for high amounts of starting material, usually millions of cells. Automation of chromatin immunoprecipitation assays is possible when the procedure is based on the use of magnetic beads. Successful automated protocols of chromatin immunoprecipitation and library preparation have been specifically designed on a commercially available robotic liquid handling system dedicated mainly to automate epigenetic assays. First, validation of automated ChIP-seq assays using antibodies directed against various histone modifications was shown, followed by optimization of the automated protocols to perform chromatin immunoprecipitation and library preparation starting with low cell numbers. The goal of these experiments is to provide a valuable tool for future epigenetic analysis of specific cell types, sub-populations, and biopsy samples.</description><identifier>ISSN: 1940-087X</identifier><identifier>EISSN: 1940-087X</identifier><identifier>DOI: 10.3791/52150</identifier><identifier>PMID: 25549003</identifier><language>eng</language><publisher>United States: MyJove Corporation</publisher><subject>Automation - methods ; Chromatin Immunoprecipitation - methods ; DNA - analysis ; DNA - genetics ; Epigenomics - methods ; Gene Library ; Genetics & genetic processes ; Génétique & processus génétiques ; HeLa Cells - physiology ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Life sciences ; Molecular Biology ; Oligonucleotide Array Sequence Analysis - methods ; Protein Interaction Mapping ; Sciences du vivant ; Sequence Analysis, DNA - methods</subject><ispartof>Journal of Visualized Experiments, 2014-12 (94)</ispartof><rights>Copyright © 2014, Journal of Visualized Experiments</rights><rights>Copyright © 2014, Journal of Visualized Experiments 2014</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c459t-cad2b2f7976ec3f6c96086857da6e10ef13c9b89b02bdbf3d215f090cedf3b603</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttps://www.jove.com/files/email_thumbs/52150.png</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4396938/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4396938/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,3830,27901,27902,53766,53768</link.rule.ids><linktorsrc>$$Uhttp://dx.doi.org/10.3791/52150$$EView_record_in_Journal_of_Visualized_Experiments$$FView_record_in_$$GJournal_of_Visualized_Experiments</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25549003$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Berguet, Geoffrey</creatorcontrib><creatorcontrib>Hendrickx, Jan</creatorcontrib><creatorcontrib>Sabatel, Celine</creatorcontrib><creatorcontrib>Laczik, Miklos</creatorcontrib><creatorcontrib>Squazzo, Sharon</creatorcontrib><creatorcontrib>Mazon Pelaez, Ignacio</creatorcontrib><creatorcontrib>Saxena, Rini</creatorcontrib><creatorcontrib>Pendeville, Helene</creatorcontrib><creatorcontrib>Poncelet, Dominique</creatorcontrib><title>Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells</title><title>Journal of Visualized Experiments</title><addtitle>J Vis Exp</addtitle><description>Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a technique of choice for studying protein-DNA interactions. 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The goal of these experiments is to provide a valuable tool for future epigenetic analysis of specific cell types, sub-populations, and biopsy samples.</description><subject>Automation - methods</subject><subject>Chromatin Immunoprecipitation - methods</subject><subject>DNA - analysis</subject><subject>DNA - genetics</subject><subject>Epigenomics - methods</subject><subject>Gene Library</subject><subject>Genetics & genetic processes</subject><subject>Génétique & processus génétiques</subject><subject>HeLa Cells - physiology</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humans</subject><subject>Life sciences</subject><subject>Molecular Biology</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Protein Interaction Mapping</subject><subject>Sciences du vivant</subject><subject>Sequence Analysis, DNA - methods</subject><issn>1940-087X</issn><issn>1940-087X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU9r3DAQxU1padI0X6CHokuhh7gdSZYsXQph2fyBheaQQm9ClseOFq-1keyl_fZVdrchvfWkB_rNm3m8ojin8IXXmn4VjAp4VZxSXUEJqv75-oU-Kd6ltAaQDIR6W5wwISoNwE-L-8t5Chs7-bEni4fbuzLhI1n-2mL0GxynRKZArnHEaCcky63vs568I3cxdH7ARMJIKFwAALnBlSULHIb0vnjT2SHh-fE9K35cLe8XN-Xq-_Xt4nJVukroqXS2ZQ3ral1LdLyTTktQUom6tRIpYEe5043SDbCmbTre5ogdaHDYdryRwM-Kbwff7dxssHX54GgHs8232_jbBOvNvz-jfzB92JmKa6m5ygb8YDB47NGE2HizY_vBvZ6H3lhnGjSMSWWoYqJ-Wvv5uDaGxxnTZDY-uRzcjhjmZKhUtaylUOo_0IpWTHIuMvrpgLoYUorYPeegYJ4qNvuKM_fxZehn6m-nGfhwANZhh2Yd5jjmEo7TfwAAY6gl</recordid><startdate>20141210</startdate><enddate>20141210</enddate><creator>Berguet, Geoffrey</creator><creator>Hendrickx, Jan</creator><creator>Sabatel, Celine</creator><creator>Laczik, Miklos</creator><creator>Squazzo, Sharon</creator><creator>Mazon Pelaez, Ignacio</creator><creator>Saxena, Rini</creator><creator>Pendeville, Helene</creator><creator>Poncelet, Dominique</creator><general>MyJove Corporation</general><general>MYJoVE Corporation</general><scope>ALOKQ</scope><scope>DRUMS</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7TM</scope><scope>Q33</scope><scope>5PM</scope></search><sort><creationdate>20141210</creationdate><title>Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells</title><author>Berguet, Geoffrey ; 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| subjects | Automation - methods Chromatin Immunoprecipitation - methods DNA - analysis DNA - genetics Epigenomics - methods Gene Library Genetics & genetic processes Génétique & processus génétiques HeLa Cells - physiology High-Throughput Nucleotide Sequencing - methods Humans Life sciences Molecular Biology Oligonucleotide Array Sequence Analysis - methods Protein Interaction Mapping Sciences du vivant Sequence Analysis, DNA - methods |
| title | Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells |
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