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. 


Transcription Factor mapping and prediction

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Modified: 4 April 2019, 3:14 PM   User: Samar El Sherbiny  → 

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List of subjects:

1. TF binding site mapping genome-wide

2. TF sequence element prediction

3. biochemical determination of binding sequence (e.g. SELEX)

4. Activity assays for TFs

(Samar El Sherbiny)

TF binding site mapping genome-wide

The identification of transcription factor binding sites (TFBS) is an important initial step in determining the DNA signals that regulate transcription of the genome. We have different techniques able to identify this TFBS: 

a. ChIP-seq

ChIP-seq is a technique that combines two aspects: chromatine immunoprecipitation with sequencing. It's a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins. Following ChIP protocols, DNA-bound protein is immunoprecipitated using a specific antibody. The bound DNA is then coprecipitated, purified, and sequenced. 

Advantages:

  • We can analyze the entire genome;
  • It reveals gene regulatory networks in combination with RNA sequencing and methylation analysis;
  • It offers compatibility with various input DNA samples.

ChIP-seq workflow:

ChIP-seq workflow