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Talk:ATAC-seq

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Latest comment: 3 years ago by Cornonthekaba in topic Wiki Education assignment: Bioinformatics

Edit Request: Page Rewrite

[edit]
Latest comment: 6 years ago1 comment1 person in discussion

Hello,

I've made numerous minor edits to this page to make it conform with Wikipedia's style, and I also added a "cleanup" template message at the top to encourage others to continue improving the page. But since this a low priority page according to WikiProject Molecular and Cellular Biology and WikiProject Computational Biology and therefore doesn't receive much attention, I took it upon myself to rewrite the page to remove promotional and overly technical language. However, I have a conflict of interest and cannot ethically make edits myself. Therefore, I kindly request that another replace the content on the page with the content below. You'll notice that besides removing inappropriate language, I did not add any new information, except citations and crosslinks where they were lacking.

@Cglife.bmarcus: Thank you for your handling of this and your note on the WP:MOLBIO talkpages. I'll go through your suggestions section-by section. T.Shafee(Evo&Evo)talk 08:38, 9 September 2019 (UTC)Reply

Here is my full rewrite:

ATAC-seq

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ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility.[1] In 2013, the technique was first described as an alternative advanced method for MNase-seq (sequencing of micrococcal nuclease sensitive sites), FAIRE-Seq and DNase-Seq.[1] ATAC-seq is a faster and more sensitive analysis of the epigenome than DNase-seq or MNase-seq.[2][3][4]

 Done nothing controversial in these suggestions. T.Shafee(Evo&Evo)talk 08:42, 9 September 2019 (UTC)Reply

Description

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Latest comment: 6 years ago1 comment1 person in discussion

ATAC-seq identifies accessible DNA regions by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. [2][5] While naturally occurring transposases have a low level of activity, ATAC-seq employs the mutated hyperactive transposase.[6] In a process called "tagmentation,"Tn5 transposase cleaves and tags double-stranded DNA with sequencing adaptors.[7] The tagged DNA fragments are then purified, PCR-amplified, and sequenced using next-generation sequencing.[7] Sequencing reads can then be used to infer regions of increased accessibility as well as to map regions of transcription factor binding sites and nucleosome positions.[2] The number of reads for a region correlate with how open that chromatin is, at single nucleotide resolution.[2] ATAC-seq requires no sonication or phenol-chloroform extraction like FAIRE-seq;[8] no antibodies like ChIP-seq;[9] and no sensitive enzymatic digestion like MNase-seq or DNase-seq.[10] ATAC-seq preparation can be completed in under three hours.[11]

 Done Some repetitious material removed, and sensible wikilinks added. Reasonable additional references. T.Shafee(Evo&Evo)talk 09:10, 9 September 2019 (UTC)Reply

Single-cell ATAC-seq

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Latest comment: 6 years ago1 comment1 person in discussion

Modifications to the ATAC-seq protocol have been made to accommodate single-cell analysis. Microfluidics can be used to separate single nuclei and perform ATAC-seq reactions individually.[11] With this approach, single cells are captured by either a microfluidic device or a liquid deposition system before tagmentation.[11] [12] An alternative technique that does not require single cell isolation is combinatorial cellular indexing. This technique uses barcoding to measure chromatin accessibility in thousands of individual cells; it can generate epigenomic profiles from 10,000-100,000 cells per experiment.[13] But combinatorial cellular indexing requires additional, custom-engineered equipment or a large quantity of custom, modified Tn5. [14]

 Done I agree with the suggestions. The above suggestion also replaces a lot of the promotional language with a far more neutral summary of the info and the cells-per-experiment range is clearer. T.Shafee(Evo&Evo)talk 10:08, 9 September 2019 (UTC)Reply

Thank you, cglife.bmarcus (talk) 1:06, 5 September 2019 (UTC)

References

  1. 1 2 Buenrostro, Jason D; Giresi, Paul G; Zaba, Lisa C; Chang, Howard Y; Greenleaf, William J (2013). "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position". Nature Methods. 10 (12): 1213–1218. doi:10.1038/nmeth.2688. ISSN 1548-7091. PMC 3959825.
  2. 1 2 3 4 Buenrostro, Jason D.; Wu, Beijing; Chang, Howard Y.; Greenleaf, William J. (2015). "ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide": 21.29.1–21.29.9. doi:10.1002/0471142727.mb2129s109. {{cite journal}}: Cite journal requires |journal= (help)
  3. ↑ Schep, Alicia N.; Buenrostro, Jason D.; Denny, Sarah K.; Schwartz, Katja; Sherlock, Gavin; Greenleaf, William J. (2015). "Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions". Genome Research. 25 (11): 1757–1770. doi:10.1101/gr.192294.115. ISSN 1088-9051.
  4. ↑ Song, L.; Crawford, G. E. (2010). "DNase-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells". Cold Spring Harbor Protocols. 2010 (2): pdb.prot5384–pdb.prot5384. doi:10.1101/pdb.prot5384. ISSN 1559-6095.
  5. ↑ Bajic, Marko; Maher, Kelsey A.; Deal, Roger B. (2018). "Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq". 1675: 183–201. doi:10.1007/978-1-4939-7318-7_12. ISSN 1064-3745. {{cite journal}}: Cite journal requires |journal= (help)
  6. ↑ Cite error: The named reference Reznikoff2008 was invoked but never defined (see the help page).
  7. 1 2 Picelli, Simone; Björklund, Åsa K.; Reinius, Björn; Sagasser, Sven; Winberg, Gösta; Sandberg, Rickard (2014). "Tn5 transposase and tagmentation procedures for massively scaled sequencing projects". Genome Research. 24 (12): 2033–2040. doi:10.1101/gr.177881.114. ISSN 1088-9051.
  8. ↑ Simon, Jeremy M; Giresi, Paul G; Davis, Ian J; Lieb, Jason D (2012). "Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA". Nature Protocols. 7 (2): 256–267. doi:10.1038/nprot.2011.444. ISSN 1754-2189.
  9. ↑ Savic, Daniel; Partridge, E. Christopher; Newberry, Kimberly M.; Smith, Sophia B.; Meadows, Sarah K.; Roberts, BrianS.; Mackiewicz, Mark; Mendenhall, Eric M.; Myers, Richard M. (2015). "CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins". Genome Research. 25 (10): 1581–1589. doi:10.1101/gr.193540.115. ISSN 1088-9051.
  10. ↑ Hoeijmakers, Wieteke Anna Maria; Bártfai, Richárd (2018). "Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq)". 1689: 83–101. doi:10.1007/978-1-4939-7380-4_8. ISSN 1064-3745. {{cite journal}}: Cite journal requires |journal= (help)
  11. 1 2 3 Buenrostro, Jason D.; Wu, Beijing; Litzenburger, Ulrike M.; Ruff, Dave; Gonzales, Michael L.; Snyder, Michael P.; Chang, Howard Y.; Greenleaf, William J. (2015). "Single-cell chromatin accessibility reveals principles of regulatory variation". Nature. 523 (7561): 486–490. doi:10.1038/nature14590. ISSN 0028-0836.
  12. ↑ Mezger, Anja; Klemm, Sandy; Mann, Ishminder; Brower, Kara; Mir, Alain; Bostick, Magnolia; Farmer, Andrew; Fordyce, Polly; Linnarsson, Sten; Greenleaf, William (2018). "High-throughput chromatin accessibility profiling at single-cell resolution". Nature Communications. 9 (1). doi:10.1038/s41467-018-05887-x. ISSN 2041-1723.
  13. ↑ Lareau, Caleb A.; Duarte, Fabiana M.; Chew, Jennifer G.; Kartha, Vinay K.; Burkett, Zach D.; Kohlway, Andrew S.; Pokholok, Dmitry; Aryee, Martin J.; Steemers, Frank J.; Lebofsky, Ronald; Buenrostro, Jason D. (2019). doi:10.1101/612713. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  14. ↑ Chen, Xi; Miragaia, Ricardo J.; Natarajan, Kedar Nath; Teichmann, Sarah A. (2018). "A rapid and robust method for single cell chromatin accessibility profiling". Nature Communications. 9 (1). doi:10.1038/s41467-018-07771-0. ISSN 2041-1723.

Request edit

[edit]
Latest comment: 6 years ago2 comments2 people in discussion
User:Evolution and evolvability, thank you for your timely and considerate addition of my edits to the page. I also intended to delete the Efficiency and Specifications section. You'll notice I pulled some of the language from that section up to the Applications section, so there is now some repetition. The rest of the section, I believe, is promotional and does not not conform with Wikipedia's guidelines. Therefore, I request that you delete the Efficiency and Specifications section. Thank you, Cglife.bmarcus (talk) 14:53, 9 September 2019 (UTC)Reply

Reply 12-SEP-2019

[edit]

  Section deleted  

  • The requested section was deleted.

Additional changes made:

  1. Two instances where {{cite journal}} was used were changed to {{cite book}}, as the references listed were their own publications covering a specialized area of information and published in editions (as are textbooks), rather than typical journals which publish on a regular schedule and which usually cover discordant topics (linked by a category) under sequential volumes and issues.

Regards,  Spintendo  10:37, 12 September 2019 (UTC)Reply

Wiki Education assignment: Bioinformatics

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Latest comment: 3 years ago1 comment1 person in discussion

This article was the subject of a Wiki Education Foundation-supported course assignment, between 29 August 2022 and 15 December 2022. Further details are available on the course page. Student editor(s): Cornonthekaba (article contribs).

— Assignment last updated by Cornonthekaba (talk) 17:17, 5 October 2022 (UTC)Reply

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