Student Wiki on methodology

This Wiki is intended to collectively make the point on methodologies employed in research papers we analyze during the course. "Writers" are students who wish to contribute to a specific subject. Before contributing, please add your name in the "Writers group choice". When initiating a contribution, please indicate your name in brackets.


PLEASE:  DO NOT change the INDEX page !!!
This page contains the links to the nine official subjects, which are the same in the Choice.

To contribute, go to the correct page by clicking on the description here in the index, then click EDIT and contribute. At the end, please save.

 IMPORTANT !!!

Please do not make extensive cut-and-paste: it s useless, anybody can go to the source you use and read it.  Read the texts, digest, and make a short résumé. If you wih you can include link(s) to the source(s).

Other contributors can revise, add, erase, modify...   Please do not repeat the same text as well. 


Epigenomics: ChIP-Seq, DNase-Seq, FAIRE, ATAC-Seq, Nucleosome positioning

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Modified: 26 March 2020, 12:21 PM   User: Emilia Petrachi  → 

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Epigenomics:

ChIP-Seq



DNase-Seq

DNase-Seq is one of the several approaches in molecular biology useful to identify DNA response elements, or regulatory regions in general, through genome-wide sequencing of regions sensitive to cleavage by DNase I.
A brief outline of the technique is the following:

  1. DNA-protein complexes are treated with DNase I;
  2. DNA extraction and sequencing are perfomed;
  3. Sequences bound by regulatory proteins are protected  from DNase I digestion;
  4. Deep sequencing is performed to provide accurate representation of location of regulatory proteins in the genome.

Pros

  • Can detect open chromatin
  • No prior knowledge of the sequence or binding protein is required
  • Compared to formaldehyde-assisted isolation of regulatory elements and sequencing (FAIRE-seq), has greater sensitivity at promoters

Cons

  • DNase l is sequence-specific and hypersensitive sites might not account for the entire genome
  • DNA loss through the multiple purification steps limits sensitivity
  • Integration of DNase I with ChIP data is necessary to identify and differentiate similar protein-binding sites

More information can be found at the website:
https://emea.illumina.com/science/sequencing-method-explorer/kits-and-arrays/dnase-seq-dnasel-seq.html
And this is a video made by a Biology Professor at Davidson College, it explains the protocol in really easy terms:

Brief outline of the DNase-Seq protocol

Another outline of the protocol

(Emilia Petrachi)


FAIRE



ATAC-Seq




Nucleosome positioning