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Bioruptor® in Action Video

Expertise

IP Automation
Sonication
- More about
- Bioruptor specifications
DNA Methylation
Antibodies
- Antibody production
Chromatin Function
Protocol Optimization

Your ChIP today and tomorrow

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Your ChIP assays today | Number of samples

1. How many ChIP are you doing / year?

  1-50
  50-100
  100-500
  500-1000
  More

2. Which kind of project / Which marks?
  Large number of samples
  Same target
  Different targets
   Histone
   Transcription Factor

Your ChIP assays today | Starting Material

3. From which kind of material?

  Mammalian (human - mouse - rat - ...)
  Plants
  Yeast
  Other

4. Cells or tissue?

Cultured cells
  Fresh
  Frozen

Tissues
  Fresh tissues
  Frozen tissues
  Embedded tissues

Biopsies
  Fresh biopsies
  Frozen biopsies
  Embedded biopsies

5. How many cells are you using per IP?

  Less than 10,000 cells
  Less than 100,000 cells
  Less than 1,000,000 cells
  Less than 10,000,000 cells
  More

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

  Very low
  Low
  Average
  High
  Very High

Your ChIP assays today | Method

7. What type of ChIP?

   Cross-linked ChIP (xChIP)
  Native ChIP
  Other

8. Which protocols?

   In-house
  Kits
  Consortium standard
  Mix of

9. How many ChIP in parallel?

  1-5
  5-10
  10-50
  50-100
  More

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

  1 day
  2 days
  3 days
  More

Your ChIP assays today | Experience

11. How long have you been performing ChIP?

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

  1-5
  5-10
  10-20
  More

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

   Cell - Tissue preparation
  Chromatin Preparation
  Chromatin Shearing
  Immunoprecipitation
   DNA recovery and purification
  QPCR-Array-NGS
  Bioinformatics

	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?

  Magnetic
  Agarose
  Protein A
  Protein G
  Other

Beads main criteria of choice?

Your ChIP assays today | Chromatin preparation

17. Is a nuclei prep step necessary?

Yes
No

18. How do you cross-link my protein of interest to the DNA?
Formaldehyde % minutes degree C°/F°

19. How do you achieve complete cell lysis?

  Sonication
  Douncing
  Enzymatic digestion
  Other

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

   Sonicator type:
  Tip
  Bath
  Cuphorn
  Other

   Enzymatic digestion

21. What concentration of cells for shearing?
cells ml

22. What are your standard shearing conditions?

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

  Yes
  No
  I do not know

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

  No control

   Control size on:
  Agarose Gel
  Bioanalyser
  Other

Your ChIP assays today | Immunoprecipitation

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

  Salts
  Detergents
  PH value
  Other

26. What are your criteria to select antibodies for ChIP experiments?

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

   Mouse monoclonal
   Rabbit monoclonal
   Rabbit polyclonal
   Goat polyclonal
  Other

28. Why?

  Better specificity
  Better epitope recognition
  Lower background
  Other

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

   Input DNA
  No Ab
  IgG
  Pre immunized serum
  Invariant H3 forms
  Other

Your ChIP assays today | Output DNA

30. What amount of output DNA do you need? µg

31. What amount of output DNA do you recover on average? µg

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

  Yes
  No
  I do not know

Your ChIP assays today | Analysis

33. Which Analysis techniques are you performing today?

  PCR
  QPCR
  Chip on chip
  ChIP-Seq

34. Will you add another analysis method soon?

  No
  ChIP-Seq
  Chip on chip
  QPCR
  PCR

35. Which NGS platform are you running?

  Sanger 1st gen
  MySeq
  HiSeq
  PGM
  SOLiD
  454
  Pac Bioscience
  Helicos
  Oxford Nanopore

36. What kind of controls do you use for your analysis step?

37. How do you determine the abundance of a target DNA sequence?

Your ChIP assays today | Quality control

38. How do you reduce background in your experiments?

39. Is your ChIP reproducible in your lab?

  Totally
  Depends on:
  It's an issue

40. How do you ensure reproducibility between your experiments?

Your needs and whishes for tomorrow ChIP

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

  2 days
  1 day
  Less

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

  1 Cell
  100 cells
   1,000 cells
   10,000 cells
   100,000 cells
  More

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

  10
  100
  500
   1,000
  More

44. Is ChIP assay a boring experiment?

  No
  Moderatly
  Totally

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

  Immediately
  No
  Maybe
  Never

46. Do you need 96-well ChIP format?

  No
  Today
  Tomorrow

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

  Days
  Weeks
  Months

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

  A robot
  A student
  An experienced technician
  An experienced researcher

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

  Using a robot
  A student
  An experienced technician
  An experienced researcher

50. Is automation the best solution for:

  Better Consistency
  Higher throughput
  Long term Savings
  Shorter Optimization phase

51. Would you subcontract your ChIP assay?

  All process

  One or multiple steps:

  Cell-Tissue preparation
  Long term Savings
  Chromatin Preparation
  IP
   Analysis QPCR-Array-NGS
  Bioinformatics

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

  All process

  one or multiple steps:
  Cell-Tissue preparation
  Chromatin Preparation
  Chromatin Shearing
  IP
   Analysis QPCR-Array-NGS
  Bioinformatics

53. Why would you subcontract your ChIP assay?

  Urgent project to achieve
  Difficult sample
  Garantee on consistency
  Ponctual project, no expertise in-house
  Other

Institute / Company :

Last name:

First name:

City:

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