Talk:ATAC-seq

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Edit Request: Page Rewrite

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.

@
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

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

ATAC-seq identifies accessible

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

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. ^
    PMC 3959825
    .
  2. ^
    doi:10.1002/0471142727.mb2129s109. {{cite journal}}: Cite journal requires |journal= (help
    )
  3. ISSN 1088-9051
    .
  4. ISSN 1559-6095
    .
  5. 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. ^
    ISSN 1088-9051
    .
  8. ISSN 1754-2189
    .
  9. ISSN 1088-9051
    .
  10. ISSN 1064-3745. {{cite journal}}: Cite journal requires |journal= (help
    )
  11. ^
    ISSN 0028-0836
    .
  12. ISSN 2041-1723
    .
  13. doi:10.1101/612713. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help
    )
  14. ISSN 2041-1723
    .

Request edit

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

  Section deleted  

  • The requested section was deleted.

plus 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

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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