168:
cells. scATAC-seq matrices can be extremely large (hundreds of thousands of regions) and is extremely sparse, i.e. less than 3% of entries are non-zero. Therefore, imputation of count matrix is another crucial step performed by using various methods such as non-negative matrix factorization. As with bulk ATAC-seq, scATAC-seq allows finding regulators like transcription factors controlling gene expression of cells. This can be achieved by looking at the number of reads around TF motifs or footprinting analysis.
112:
167:
Computational analysis of scATAC-seq is based on construction of a count matrix with number of reads per open chromatin regions. Open chromatin regions can be defined, for example, by standard peak calling of pseudo bulk ATAC-seq data. Further steps include data reduction with PCA and clustering of
158:
can be used to separate single nuclei and perform ATAC-seq reactions individually. With this approach, single cells are captured by either a microfluidic device or a liquid deposition system before tagmentation. An alternative technique that does not require single cell isolation is combinatorial
163:
to measure chromatin accessibility in thousands of individual cells; it can generate epigenomic profiles from 10,000-100,000 cells per experiment. But combinatorial cellular indexing requires additional, custom-engineered equipment or a large quantity of custom, modified Tn5. Recently, a pooled
78:
that inserts sequencing adapters into open regions of the genome. While naturally occurring transposases have a low level of activity, ATAC-seq employs the mutated hyperactive transposase. In a process called "tagmentation", Tn5 transposase cleaves and tags double-stranded DNA with sequencing
134:
The utility of high-resolution enhancer mapping ranges from studying the evolutionary divergence of enhancer usage (e.g. between chimps and humans) during development and uncovering a lineage-specific enhancer map used during blood cell differentiation.
1358:
Cao, Junyue; Cusanovich, Darren A.; Ramani, Vijay; Aghamirzaie, Delasa; Pliner, Hannah A.; Hill, Andrew J.; Daza, Riza M.; McFaline-Figueroa, Jose L.; Packer, Jonathan S.; Christiansen, Lena; Steemers, Frank J. (2018-09-28).
903:
Hendrickson DG, Soifer I, Wranik BJ, Botstein D, Scott McIsaac R (2018), "Simultaneous
Profiling of DNA Accessibility and Gene Expression Dynamics with ATAC-Seq and RNA-Seq",
138:
ATAC-Seq has also been applied to defining the genome-wide chromatin accessibility landscape in human cancers, and revealing an overall decrease in chromatin accessibility in
91:
binding sites and nucleosome positions. The number of reads for a region correlate with how open that chromatin is, at single nucleotide resolution. ATAC-seq requires no
1545:
142:. Computational footprinting methods can be performed on ATAC-seq to find cell specific binding sites and transcription factors with cell specific activity.
190:"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position"
164:
barcode method called sci-CAR was developed, allowing joint profiling of chromatin accessibility and gene expression of single cells.
689:
Hoeijmakers WA, Bártfai R (2018). "Characterization of the
Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq)".
103:; and no sensitive enzymatic digestion like MNase-seq or DNase-seq. ATAC-seq preparation can be completed in under three hours.
1565:
706:
411:
347:"DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells"
298:"Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions"
920:
124:
803:
Li, Zhijian; Schulz, Marcel H.; Look, Thomas; Begemann, Matthias; Zenke, Martin; Costa, Ivan G. (26 February 2019).
1100:"ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration"
119:
ATAC-Seq analysis is used to investigate a number of chromatin-accessibility signatures. The most common use is
394:
Bajic M, Maher KA, Deal RB (2018). "Identification of Open
Chromatin Regions in Plant Genomes Using ATAC-Seq".
490:"Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition"
87:. Sequencing reads can then be used to infer regions of increased accessibility as well as to map regions of
1272:
Lareau CA, Duarte FM, Chew JG, Kartha VK, Burkett ZD, Kohlway AS, Pokholok D, Aryee MJ, et al. (2019).
96:
943:
Prescott SL, Srinivasan R, Marchetto MC, Grishina I, Narvaiza I, Selleri L, et al. (September 2015).
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84:
593:"Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA"
992:
Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E, et al. (August 2014).
80:
1490:"chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data"
640:
Savic D, Partridge EC, Newberry KM, Smith SB, Meadows SK, Roberts BS, et al. (October 2015).
1217:"Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing"
743:
Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, et al. (July 2015).
1361:"Joint profiling of chromatin accessibility and gene expression in thousands of single cells"
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8:
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Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ (November 2015).
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Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, et al. (October 2018).
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Picelli S, Björklund AK, Reinius B, Sagasser S, Winberg G, Sandberg R (December 2014).
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945:"Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest"
544:"Tn5 transposase and tagmentation procedures for massively scaled sequencing projects"
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Mezger A, Klemm S, Mann I, Brower K, Mir A, Bostick M, et al. (September 2018).
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907:, Methods in Molecular Biology, vol. 1819, Springer New York, pp. 317–333,
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Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, et al. (April 2018).
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50:. In 2013, the technique was first described as an alternative advanced method for
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1274:"Droplet-based combinatorial indexing for massive scale single-cell epigenomics"
745:"Single-cell chromatin accessibility reveals principles of regulatory variation"
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1431:"Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen"
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506:
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HINT-ATAC: Identification of
Transcription Factor Binding Sites using ATAC-seq
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62:. ATAC-seq is a faster analysis of the epigenome than DNase-seq or MNase-seq.
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1394:
1303:"A rapid and robust method for single cell chromatin accessibility profiling"
1160:"High-throughput chromatin accessibility profiling at single-cell resolution"
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Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (December 2013).
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Li Z, Kuppe C, Cheng M, Menzel S, Zenke M, Kramann R, et al. (2021).
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120:
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805:"Identification of transcription factor binding sites using ATAC-seq"
246:"ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide"
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Modifications to the ATAC-seq protocol have been made to accommodate
59:
55:
51:
47:
642:"CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins"
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100:
856:"methyl-ATAC-seq measures DNA methylation at accessible chromatin"
398:. Methods in Molecular Biology. Vol. 1675. pp. 183–201.
1301:
Chen X, Miragaia RJ, Natarajan KN, Teichmann SA (December 2018).
994:"Immunogenetics. Chromatin state dynamics during blood formation"
693:. Methods in Molecular Biology. Vol. 1689. pp. 83–101.
1043:"The chromatin accessibility landscape of primary human cancers"
902:
541:
1357:
1300:
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Schep AN, Wu B, Buenrostro JD, Greenleaf WJ (October 2017).
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Buenrostro JD, Wu B, Chang HY, Greenleaf WJ (January 2015).
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Spektor R, Tippens ND, Mimoso CA, Soloway PD (June 2019).
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regions by probing open chromatin with hyperactive mutant
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Simon JM, Giresi PG, Davis IJ, Lieb JD (January 2012).
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mapping experiments, but it can be applied to mapping
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adaptors. The tagged DNA fragments are then purified,
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131:sites, or combined with sequencing techniques.
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1541:ATAC-seq probes open-chromatin state (figure)
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453:Reznikoff WS (2008). "Transposon Tn5".
159:cellular indexing. This technique uses
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467:10.1146/annurev.genet.42.110807.091656
250:Current Protocols in Molecular Biology
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345:Song L, Crawford GE (February 2010).
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99:like FAIRE-seq; no antibodies like
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125:transcription factor binding sites
14:
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83:-amplified, and sequenced using
42:uencing) is a technique used in
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1215:Cusanovich, Darren (May 2015).
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70:ATAC-seq identifies accessible
488:Adey, Andrew (December 2010).
481:
65:
1:
691:Chromatin Immunoprecipitation
262:10.1002/0471142727.mb2129s109
171:
1566:Molecular biology techniques
913:10.1007/978-1-4939-8618-7_15
404:10.1007/978-1-4939-7318-7_12
351:Cold Spring Harbor Protocols
97:phenol-chloroform extraction
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699:10.1007/978-1-4939-7380-4_8
16:Molecular biology technique
10:
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1456:10.1038/s41467-021-26530-2
1327:10.1038/s41467-018-07771-0
1184:10.1038/s41467-018-05887-x
1124:10.1038/s41467-018-03856-y
961:10.1016/j.cell.2015.08.036
905:Computational Cell Biology
507:10.1186/gb-2010-11-12-r119
85:next-generation sequencing
822:10.1186/s13059-019-1642-2
455:Annual Review of Genetics
396:Plant Chromatin Dynamics
115:Applications of ATAC-Seq
1386:10.1126/science.aau0730
1241:10.1126/science.aab1601
1067:10.1126/science.aav1898
1010:10.1126/science.1256271
48:chromatin accessibility
609:10.1038/nprot.2011.444
116:
46:to assess genome-wide
1435:Nature Communications
1307:Nature Communications
1164:Nature Communications
1104:Nature Communications
872:10.1101/gr.245399.118
658:10.1101/gr.193540.115
560:10.1101/gr.177881.114
314:10.1101/gr.192294.115
114:
363:10.1101/pdb.prot5384
152:single-cell analysis
146:Single-cell ATAC-seq
140:macular degeneration
89:transcription factor
1447:2021NatCo..12.6386L
1377:2018Sci...361.1380C
1371:(6409): 1380–1385.
1319:2018NatCo...9.5345C
1233:2015Sci...348..910C
1176:2018NatCo...9.3647M
1116:2018NatCo...9.1364W
1059:2018Sci...362.1898C
769:10.1038/nature14590
761:2015Natur.523..486B
357:(2): pdb.prot5384.
256:: 21.29.1–21.29.9.
1506:10.1038/nmeth.4401
1053:(6413): eaav1898.
206:10.1038/nmeth.2688
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413:978-1-4939-7317-0
127:, adapted to map
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66:Description
30:ransposase-
172:References
121:nucleosome
93:sonication
34:ccessible
1395:0036-8075
815:(1): 45.
717:1064-3745
422:1064-3745
161:barcoding
60:DNase-Seq
56:FAIRE-Seq
52:MNase-seq
26:ssay for
1560:Category
1524:28825706
1475:34737275
1413:30166440
1345:30559361
1259:25953818
1202:30194434
1142:29636475
1085:30361341
1028:25103404
979:26365491
931:30421411
890:31160376
841:30808370
787:26083756
725:29027167
676:26355004
627:22262007
578:25079858
526:21143862
475:18680433
440:29052193
381:20150147
332:26314830
280:25559105
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