Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni [version 2; peer review: 2 approved, 1 approved with reservations]
In living cells, the genetic information stored in the DNA sequence is always associated with chromosomal and extra-chromosomal epigenetic information. Chromatin is formed by the DNA and associated proteins, in particular histones. Covalent histone modifications are important bearers of epigenetic i...
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| Format: | Article |
| Language: | English |
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Wellcome
2024-02-01
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| Series: | Wellcome Open Research |
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| Online Access: | https://wellcomeopenresearch.org/articles/7-133/v2 |
| _version_ | 1797307103733350400 |
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| author | Ronaldo de Carvalho Augusto Christoph Grunau Chrystelle Lasica Cristian Chaparro Anne-Clémence Veillard Hélène Moné Agnieszka Zelisko-Schmidt Gabriel Mouahid |
| author_facet | Ronaldo de Carvalho Augusto Christoph Grunau Chrystelle Lasica Cristian Chaparro Anne-Clémence Veillard Hélène Moné Agnieszka Zelisko-Schmidt Gabriel Mouahid |
| author_sort | Ronaldo de Carvalho Augusto |
| collection | DOAJ |
| description | In living cells, the genetic information stored in the DNA sequence is always associated with chromosomal and extra-chromosomal epigenetic information. Chromatin is formed by the DNA and associated proteins, in particular histones. Covalent histone modifications are important bearers of epigenetic information and as such have been increasingly studied since about the year 2000. One of the principal techniques to gather information about the association between DNA and modified histones is chromatin immunoprecipitation (ChIP), also combined with massive sequencing (ChIP-Seq). Automated ChIPmentation procedure is a convenient alternative to native chromatin immunoprecipitation (N-ChIP). It is now routinely used for ChIP-Seq in many model species, using in general roughly 106 cells per experiment. Such high cell numbers are sometimes difficult to produce. Using the human parasite Schistosoma mansoni, whose production requires sacrificing animals and should therefore be kept to a minimum, we show here that automated ChIPmentation is suitable for limited biological material. We define the operational limit as ≥20,000 Schistosoma cells with 30,000-300,000 cells as optimum. We also present a streamlined protocol for the preparation of ChIP input libraries. |
| first_indexed | 2024-03-08T00:52:28Z |
| format | Article |
| id | doaj.art-f854b9ddf585464b800df4d52855b48c |
| institution | Directory Open Access Journal |
| issn | 2398-502X |
| language | English |
| last_indexed | 2024-03-08T00:52:28Z |
| publishDate | 2024-02-01 |
| publisher | Wellcome |
| record_format | Article |
| series | Wellcome Open Research |
| spelling | doaj.art-f854b9ddf585464b800df4d52855b48c2024-02-15T01:00:00ZengWellcomeWellcome Open Research2398-502X2024-02-01723255Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni [version 2; peer review: 2 approved, 1 approved with reservations]Ronaldo de Carvalho Augusto0https://orcid.org/0000-0003-1147-0043Christoph Grunau1https://orcid.org/0000-0003-3180-344XChrystelle Lasica2Cristian Chaparro3https://orcid.org/0000-0002-5162-349XAnne-Clémence Veillard4Hélène Moné5https://orcid.org/0000-0003-3180-344XAgnieszka Zelisko-Schmidt6Gabriel Mouahid7IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, FranceIHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, FranceIHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, FranceIHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, FranceDiagenode, Seraing, 4100, BelgiumIHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, FranceDiagenode, Seraing, 4100, BelgiumIHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, FranceIn living cells, the genetic information stored in the DNA sequence is always associated with chromosomal and extra-chromosomal epigenetic information. Chromatin is formed by the DNA and associated proteins, in particular histones. Covalent histone modifications are important bearers of epigenetic information and as such have been increasingly studied since about the year 2000. One of the principal techniques to gather information about the association between DNA and modified histones is chromatin immunoprecipitation (ChIP), also combined with massive sequencing (ChIP-Seq). Automated ChIPmentation procedure is a convenient alternative to native chromatin immunoprecipitation (N-ChIP). It is now routinely used for ChIP-Seq in many model species, using in general roughly 106 cells per experiment. Such high cell numbers are sometimes difficult to produce. Using the human parasite Schistosoma mansoni, whose production requires sacrificing animals and should therefore be kept to a minimum, we show here that automated ChIPmentation is suitable for limited biological material. We define the operational limit as ≥20,000 Schistosoma cells with 30,000-300,000 cells as optimum. We also present a streamlined protocol for the preparation of ChIP input libraries.https://wellcomeopenresearch.org/articles/7-133/v2ChIPmentation ChIP-seq N-ChIP limited biological material Epigenetics Schistosoma mansonieng |
| spellingShingle | Ronaldo de Carvalho Augusto Christoph Grunau Chrystelle Lasica Cristian Chaparro Anne-Clémence Veillard Hélène Moné Agnieszka Zelisko-Schmidt Gabriel Mouahid Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni [version 2; peer review: 2 approved, 1 approved with reservations] Wellcome Open Research ChIPmentation ChIP-seq N-ChIP limited biological material Epigenetics Schistosoma mansoni eng |
| title | Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_full | Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_fullStr | Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_full_unstemmed | Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_short | Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_sort | automated chipmentation procedure on limited biological material of the human blood fluke schistosoma mansoni version 2 peer review 2 approved 1 approved with reservations |
| topic | ChIPmentation ChIP-seq N-ChIP limited biological material Epigenetics Schistosoma mansoni eng |
| url | https://wellcomeopenresearch.org/articles/7-133/v2 |
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