ATAC-Seq/Fast-ATAC
Assay for Transposase-Accessible Chromatin Sequencing / ATAC-seq Optimized for Blood Cells
ATAC-Seq uses the Tn5 transposome to detect nucleosome-free regions of the genome (Buenrostro et al., 2013). The method is commonly used, and optimized protocols are available for tissues, such as blood (Fast-ATAC) (Corces et al., 2016), neurons (Milani et al., 2016), biobank specimens (Scharer et al., 2016), and single cells (scATAC-seq (Buenrostro et al., 2015) and single-cell ATAC-seq (Cusanovich et al., 2015) ).
In this method, gDNA is incubated with Tn5 transposomes, which fragments it and adds adapters simultaneously, in open chromatin regions. Deep sequencing of the purified regions provides base-pair resolution of nucleosome-free regions in the genome.
Advantages:
- Two-step protocol with no adapter ligation steps, gel purification, or crosslink reversal
- High signal-to-noise ratio compared to FAIRE-Seq
Disadvantages:
- During mechanical sample processing, bound chromatin regions might open and be tagged by the transposome
- Only half of the molecules contain the adapters in the orientation required for PCR amplification
- Distance between adapter sites may not be optimal for PCR amplification (Sos et al., 2016)
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Chaitankar V., Karakulah G., Ratnapriya R., Giuste F. O., Brooks M. J., et al. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res. 2016;55:1-31
Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109
References:
Bogdanovic O., Smits A. H., de la Calle Mustienes E., Tena J. J., Ford E., et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016;48:417-426
Corces M. R., Buenrostro J. D., Wu B., Greenside P. G., Chan S. M., et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016;48:1193-1203
Miller C. L., Pjanic M., Wang T., et al. Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci. Nat Commun. 2016;7:12092
Wu J., Huang B., Chen H., et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016;534:652-657
Ackermann A. M., Wang Z., Schug J., Naji A. and Kaestner K. H. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Mol Metab. 2016;5:233-244
Atianand M. K., Hu W., Satpathy A. T., et al. A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. Cell. 2016;165:1672-1685
Boukhaled G. M., Cordeiro B., Deblois G., et al. The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence. Cell Rep. 2016;16:1829-1837
de Dieuleveult M., Yen K., Hmitou I., Depaux A., Boussouar F., et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016;530:113-116
Flynn R. A., Do B. T., Rubin A. J., et al. 7SK-BAF axis controls pervasive transcription at enhancers. Nat Struct Mol Biol. 2016;23:231-238
George J., Uyar A., Young K., et al. Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells. Nat Commun. 2016;7:12166
Han D., Lu X., Shih A. H., et al. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations. Mol Cell. 2016;63:711-719
Hay D., Hughes J. R., Babbs C., Davies J. O., Graham B. J., et al. Genetic dissection of the alpha-globin super-enhancer in vivo. Nat Genet. 2016;48:895-903
Kaaij L. J., Mokry M., Zhou M., Musheev M., Geeven G., et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol. 2016;17:146
Kaufman C. K., Mosimann C., Fan Z. P., et al. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science. 2016;351:aad2197
Koues O. I., Collins P. L., Cella M., et al. Distinct Gene Regulatory Pathways for Human Innate versus Adaptive Lymphoid Cells. Cell. 2016;165:1134-1146
Lu F., Liu Y., Inoue A., Suzuki T., Zhao K., et al. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016;165:1375-1388
Proudhon C., Snetkova V., Raviram R., et al. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep. 2016;15:2159-2169
Rendeiro A. F., Schmidl C., Strefford J. C., et al. Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks. Nat Commun. 2016;7:11938
Sebe-Pedros A., Ballare C., Parra-Acero H., et al. The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity. Cell. 2016;165:1224-1237
Shih H. Y., Sciume G., Mikami Y., et al. Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality. Cell. 2016;165:1120-1133
Smith J. D., Suresh S., Schlecht U., et al. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol. 2016;17:45
Wang L., Siegenthaler J. A., Dowell R. D. and Yi R. Foxc1 reinforces quiescence in self-renewing hair follicle stem cells. Science. 2016;351:613-617
Wang W., Org T., Montel-Hagen A., et al. MEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesis. Nat Commun. 2016;7:12376
Related
History: ATAC-Seq/Fast-ATAC
Revision by sbrumpton on 2017-06-21 09:26:17 - Show/Hide
Assay for Transposase-Accessible Chromatin Sequencing / ATAC-seq Optimized for Blood Cells
ATAC-Seq uses the Tn5 transposome to detect nucleosome-free regions of the genome (Buenrostro et al., 2013). The method is commonly used, and optimized protocols are available for tissues, such as blood (Fast-ATAC) (Corces et al., 2016), neurons (Milani et al., 2016), biobank specimens (Scharer et al., 2016), and single cells (scATAC-seq (Buenrostro et al., 2015) and single-cell ATAC-seq (Cusanovich et al., 2015) ).
In this method, gDNA is incubated with Tn5 transposomes, which fragments it and adds adapters simultaneously, in open chromatin regions. Deep sequencing of the purified regions provides base-pair resolution of nucleosome-free regions in the genome.
Advantages:- Two-step protocol with no adapter ligation steps, gel purification, or crosslink reversal
- High signal-to-noise ratio compared to FAIRE-Seq
Disadvantages:- During mechanical sample processing, bound chromatin regions might open and be tagged by the transposome
- Only half of the molecules contain the adapters in the orientation required for PCR amplification
- Distance between adapter sites may not be optimal for PCR amplification (Sos et al., 2016)
Reagents:Illumina Library prep and Array Kit SelectorReviews:Chaitankar V., Karakulah G., Ratnapriya R., Giuste F. O., Brooks M. J., et al. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res. 2016;55:1-31Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109References:Bogdanovic O., Smits A. H., de la Calle Mustienes E., Tena J. J., Ford E., et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016;48:417-426Corces M. R., Buenrostro J. D., Wu B., Greenside P. G., Chan S. M., et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016;48:1193-1203Miller C. L., Pjanic M., Wang T., et al. Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci. Nat Commun. 2016;7:12092Wu J., Huang B., Chen H., et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016;534:652-657Ackermann A. M., Wang Z., Schug J., Naji A. and Kaestner K. H. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Mol Metab. 2016;5:233-244Atianand M. K., Hu W., Satpathy A. T., et al. A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. Cell. 2016;165:1672-1685Boukhaled G. M., Cordeiro B., Deblois G., et al. The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence. Cell Rep. 2016;16:1829-1837de Dieuleveult M., Yen K., Hmitou I., Depaux A., Boussouar F., et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016;530:113-116Flynn R. A., Do B. T., Rubin A. J., et al. 7SK-BAF axis controls pervasive transcription at enhancers. Nat Struct Mol Biol. 2016;23:231-238George J., Uyar A., Young K., et al. Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells. Nat Commun. 2016;7:12166Han D., Lu X., Shih A. H., et al. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations. Mol Cell. 2016;63:711-719Hay D., Hughes J. R., Babbs C., Davies J. O., Graham B. J., et al. Genetic dissection of the alpha-globin super-enhancer in vivo. Nat Genet. 2016;48:895-903Kaaij L. J., Mokry M., Zhou M., Musheev M., Geeven G., et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol. 2016;17:146Kaufman C. K., Mosimann C., Fan Z. P., et al. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science. 2016;351:aad2197Koues O. I., Collins P. L., Cella M., et al. Distinct Gene Regulatory Pathways for Human Innate versus Adaptive Lymphoid Cells. Cell. 2016;165:1134-1146Lu F., Liu Y., Inoue A., Suzuki T., Zhao K., et al. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016;165:1375-1388Proudhon C., Snetkova V., Raviram R., et al. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep. 2016;15:2159-2169Rendeiro A. F., Schmidl C., Strefford J. C., et al. Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks. Nat Commun. 2016;7:11938Sebe-Pedros A., Ballare C., Parra-Acero H., et al. The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity. Cell. 2016;165:1224-1237Shih H. Y., Sciume G., Mikami Y., et al. Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality. Cell. 2016;165:1120-1133Smith J. D., Suresh S., Schlecht U., et al. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol. 2016;17:45Wang L., Siegenthaler J. A., Dowell R. D. and Yi R. Foxc1 reinforces quiescence in self-renewing hair follicle stem cells. Science. 2016;351:613-617Wang W., Org T., Montel-Hagen A., et al. MEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesis. Nat Commun. 2016;7:12376Revision by sbrumpton on 2017-06-21 09:26:05 - Show/Hide
Assay for Transposase-Accessible Chromatin Sequencing / ATAC-seq Optimized for Blood Cells
ATAC-Seq uses the Tn5 transposome to detect nucleosome-free regions of the genome (Buenrostro et al., 2013). The method is commonly used, and optimized protocols are available for tissues, such as blood (Fast-ATAC) (Corces et al., 2016), neurons (Milani et al., 2016), biobank specimens (Scharer et al., 2016), and single cells (scATAC-seq (Buenrostro et al., 2015) and single-cell ATAC-seq (Cusanovich et al., 2015) ).
In this method, gDNA is incubated with Tn5 transposomes, which fragments it and adds adapters simultaneously, in open chromatin regions. Deep sequencing of the purified regions provides base-pair resolution of nucleosome-free regions in the genome.
Advantages:- Two-step protocol with no adapter ligation steps, gel purification, or crosslink reversal
- High signal-to-noise ratio compared to FAIRE-Seq
Disadvantages:- During mechanical sample processing, bound chromatin regions might open and be tagged by the transposome
- Only half of the molecules contain the adapters in the orientation required for PCR amplification
- Distance between adapter sites may not be optimal for PCR amplification (Sos et al., 2016)
Reagents:Illumina Library prep and Array Kit SelectorReviews:Chaitankar V., Karakulah G., Ratnapriya R., Giuste F. O., Brooks M. J., et al. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res. 2016;55:1-31Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109References:Bogdanovic O., Smits A. H., de la Calle Mustienes E., Tena J. J., Ford E., et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016;48:417-426Corces M. R., Buenrostro J. D., Wu B., Greenside P. G., Chan S. M., et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016;48:1193-1203Miller C. L., Pjanic M., Wang T., et al. Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci. Nat Commun. 2016;7:12092Wu J., Huang B., Chen H., et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016;534:652-657Ackermann A. M., Wang Z., Schug J., Naji A. and Kaestner K. H. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Mol Metab. 2016;5:233-244Atianand M. K., Hu W., Satpathy A. T., et al. A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. Cell. 2016;165:1672-1685Boukhaled G. M., Cordeiro B., Deblois G., et al. The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence. Cell Rep. 2016;16:1829-1837de Dieuleveult M., Yen K., Hmitou I., Depaux A., Boussouar F., et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016;530:113-116Flynn R. A., Do B. T., Rubin A. J., et al. 7SK-BAF axis controls pervasive transcription at enhancers. Nat Struct Mol Biol. 2016;23:231-238George J., Uyar A., Young K., et al. Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells. Nat Commun. 2016;7:12166Han D., Lu X., Shih A. H., et al. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations. Mol Cell. 2016;63:711-719Hay D., Hughes J. R., Babbs C., Davies J. O., Graham B. J., et al. Genetic dissection of the alpha-globin super-enhancer in vivo. Nat Genet. 2016;48:895-903Kaaij L. J., Mokry M., Zhou M., Musheev M., Geeven G., et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol. 2016;17:146Kaufman C. K., Mosimann C., Fan Z. P., et al. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science. 2016;351:aad2197Koues O. I., Collins P. L., Cella M., et al. Distinct Gene Regulatory Pathways for Human Innate versus Adaptive Lymphoid Cells. Cell. 2016;165:1134-1146Lu F., Liu Y., Inoue A., Suzuki T., Zhao K., et al. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016;165:1375-1388Proudhon C., Snetkova V., Raviram R., et al. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep. 2016;15:2159-2169Rendeiro A. F., Schmidl C., Strefford J. C., et al. Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks. Nat Commun. 2016;7:11938Sebe-Pedros A., Ballare C., Parra-Acero H., et al. The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity. Cell. 2016;165:1224-1237Shih H. Y., Sciume G., Mikami Y., et al. Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality. Cell. 2016;165:1120-1133Smith J. D., Suresh S., Schlecht U., et al. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol. 2016;17:45Wang L., Siegenthaler J. A., Dowell R. D. and Yi R. Foxc1 reinforces quiescence in self-renewing hair follicle stem cells. Science. 2016;351:613-617Wang W., Org T., Montel-Hagen A., et al. MEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesis. Nat Commun. 2016;7:12376