Your ChIP today and tomorrow

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Your ChIP assays today | Number of samples

1. How many ChIP are you doing / year?

  
  
  
  
  

 

2. Which kind of project / Which marks?
  
  
  
       
       

 

Your ChIP assays today | Starting Material

3. From which kind of material?

  
  
  
      

 

4. Cells or tissue?


  
  


  
  
  


  
  
  

 

5. How many cells are you using per IP?

  
  
  
  
  

 

6. How abundant is the protein you want to immunoprecipitate?

  
  
  
  
  

 

Your ChIP assays today | Method

7. What type of ChIP?

   Cross-linked ChIP
  
      

 

8. Which protocols?

  
  
  
      

 

9. How many ChIP in parallel?

  
  
  
  
  

 

10. How much time is needed for performing one entire ChIP experiment?

  
  
  
  

 

Your ChIP assays today | Experience

    

 

12. How many specific ChIP assays experiments are necessary for producing publishable results on average?

  
  
  
  

 

13. What is the most critical criteria for the success of your ChIP-seq experiments?

  
  
  
  
  
  
  

 

  1 2 3 4 5 6 7 8 9 10
 
Sample preparation
                     
Chromatin preparation
                     
Chromatin Shearing
                     
Immunoprecipitation
                     
DNA purification
                     
Analysis QPCR-Array-NGS
                     
Interpretation of results
                     
Other    

 


14. What is your ChIP assay cost repartition?

  1 2 3 4 5 6 7 8 9 10
 
Hands-on time
   
Sample preparation
   
Chromatin preparation
   
Antibody
   
Other reagents
   
Analysis PCR
   
Analysis QPCR
   
Analysis Array
   
Analysis NGS
   
Interpretation of results
   
Price

 

Your ChIP assays today | Antibody & beads

15. How do you choose the antibody you are going to use in ChIP?

  1 2 3 4 5 6 7 8 9 10
 
Number of publications
   
Information on technical sheet
   
Test on your model
   
Consortium validation
   
Feedback from colleague

 

16. Wich kind of beads are you using?

  
  
  
  
      

 

    

 

Your ChIP assays today | Chromatin preparation

17. Is a nuclei prep step necessary?

  
  

 


Formaldehyde    minutes  degree C°/F°

 

19. How do you achieve complete cell lysis?

  
  
  
      

 

20. How do you fragment your chromatin for ChIP experiments?


  
  
  
      

   Enzymatic digestion   

 


cells  ml 

 

    

 

23. Does the detergents composition of shearing buffers influences your ChIP experiments?

  
  
  

 

24. How do you analyse if the sonication was successful?

  


  
  
      

 

Your ChIP assays today | Immunoprecipitation

25. What compound in your IP buffer may be affecting the performance of the antibody?

  
  
  
      

 

    

 

27. What kind of antibody do you prefer to use for your ChIP experiments?

  
  
  
  
      

 

28. Why?

  
  
  
      

 

29. What kind of controls do you use for your Immunoprecipitation step?

  
  
  
  
  
      

 

Your ChIP assays today | Output DNA

       µg

 

       µg

 

32. Does the detergents composition of shearing buffers influences your ChIP experiments?

  
  
  

 

Your ChIP assays today | Analysis

33. Which Analysis techniques are you performing today?

  
  
  
  

 

34. Will you add another analysis method soon?

  
  
  
  
  

35. Which NGS platform are you running?

  
  
  
  
  
  
  
  
  

 


 


 

Your ChIP assays today | Quality control


 

39. Is your ChIP reproducible in your lab?

  
      
  

 


 

 

Your needs and whishes for tomorrow ChIP

41. Would you like to make the ChIP experiment shorter?

  
  
  

 

42. Would you like to optimize ChIP on small sample size?

  
  
  
  
  
  

 

43. How many such samples would you treat tomorrow per year?

  
  
  
  
  

 

44. Is ChIP assay a boring experiment?

  
  
  

 

45. If it would exist, would you use an easier way to explore Chromatin structure than ChIP?

  
  
  
  

 

46. Do you need 96-well ChIP format?

  
  
  

 

47. How much time do you need to train a new Chipper (student, colleague)?

  
  
  

 

48. Which approach is more reliable for performing consistent ChIP assays?

  
  
  
  

 

49. Which approach is more reliable for performing the optimisation of a ChIP assays?

  
  
  
  

 

50. Is automation the best solution for:

  
  
  
  

 

51. Would you subcontract your ChIP assay?

  

  

  
  
  
  
  
  

 

52. What would be the right price for such a service?
(Please precise the currency)

      

  
       
       
       
       
       
       

 

53. Why would you subcontract your ChIP assay?