Talk:ATAC-seq

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.
 * 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 &#38; Evo)talk 08:38, 9 September 2019 (UTC)

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. 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. ATAC-seq is a faster and more sensitive analysis of the epigenome than DNase-seq or MNase-seq.
 * ✅ nothing controversial in these suggestions. T.Shafee(Evo &#38; Evo)talk 08:42, 9 September 2019 (UTC)

Description
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. 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 adaptors. The tagged DNA fragments are then purified, PCR-amplified, and sequenced using next-generation sequencing. 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. The number of reads for a region correlate with how open that chromatin is, at single nucleotide resolution. ATAC-seq requires no sonication or phenol-chloroform extraction like FAIRE-seq; no antibodies like ChIP-seq; and no sensitive enzymatic digestion like MNase-seq or DNase-seq. ATAC-seq preparation can be completed in under three hours.
 * ✅ Some repetitious material removed, and sensible wikilinks added. Reasonable additional references. T.Shafee(Evo &#38; Evo)talk 09:10, 9 September 2019 (UTC)

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. 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 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. But combinatorial cellular indexing requires additional, custom-engineered equipment or a large quantity of custom, modified Tn5.
 * ✅ 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 &#38; Evo)talk 10:08, 9 September 2019 (UTC)

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

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 12-SEP-2019

 * The requested section was deleted.

Regards, Spintendo  10:37, 12 September 2019 (UTC)
 * 1) Two instances where  was used were changed to, 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.

Wiki Education assignment: Bioinformatics
— Assignment last updated by Cornonthekaba (talk) 17:17, 5 October 2022 (UTC)