Collaboration form
Transcriptome platform
Genomics service of the École Normale Supérieure
Collaboration Form
for microarray hybridization and analysis
Project holder:
Name (function):
Title of the project:
Financial support:
Number of man x month dedicated to the project:
Laboratory:
Address:
Associated publications:
Brief description of the experiment’s goals:
Experimental design:
Describe the experiments you plan, the different conditions to compare or to analyze and the
biological model studied. Example: wild-type mouse versus knock-out, at different developmental
stages, in particular cells (heterogenous samples).
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Collaboration form
Transcriptome platform
Genomics service of the École Normale Supérieure
How many replicates have you planned for each experiment?
experimental design (loops, unique references, …)?
Have you already defined an
Is there any specific limitations considering the maximum amount of RNA that can be obtained?
Which are the gene validation ways you plan for the DNA microarray experiments result genes?
What is the context of these experiments in your research project? What do you expect from this
result?
□ Screening
□ New gene targets isolation
□ Diagnosis
□ Complete analysis / Networks regulation
□ Other ; please describe it in a few words:
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Collaboration form
Transcriptome platform
Genomics service of the École Normale Supérieure
DNA microarrays :
Which microarray type do you want to use?
What is the approximate number of desired arrays? BECARFUL! Arrays must be used by a
multiple of two.
What is your background in the DNA microarray field (already used protocols, followed
formations, analysis method knowledge, …)?
For information the average cost of one DNA microarray experiment is evaluated by hybridization
(array of 2 conditions):
- Sample quality control:
22,00 €HT
- Indirect labelling:
65,00 €HT
- DNA amplification:
120,00 €HT
- Cost for hybridization and washing:
24,50 €HT
- Image scanning:
69 €HT
- Array prices depend on the slide format:
o 8x15k custom
96,00 € HT
o 8x60k custom
116,00 € HT
o 4x44k catalogue
200,00 € HT
o 4x180k custom
203,00 € HT
o 2x105k custom
292,00 € HT
o 2x400k custom
347,00 € HT
o 1x240k custom
435,00 € HT
o 1x1000k custom
542,00 € HT
These prices include all the required products for the RNA labelling and quality control, for the
hybridization and for the chips treatment. The RNA are extracted by the interested person following
the platform recommendations.
Technical recommendations:
RNA must be treated with DNase and concentrated at 200 ng/µl. You must provide at least 1.5 µg
total RNA by hybridization. We can perform from 200 ng of total RNA. If you have to send us your
sample you must provide enough dry ice in a polystyrene box so that the sample stay frozen for at
least 3 days.
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Collaboration form
Transcriptome platform
Genomics service of the École Normale Supérieure
Project follow-up:
Fill the table for each person who will be involved in the project. The project leader has to be
indicated in first rank. Describe also at which step of the project each of these person will be
involved (samples preparation, hybridization, data analysis, results validation, …).
Name
First name
Position
% of time for the
project
Stage of
involvement
Describe the provisional program of the experiments.
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Collaboration form
Transcriptome platform
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Platform implication:
At which level do you wish help from the transcriptome platform?
 Labelling and hybridization?
 Image analysis?
 Normalisation and search for significant differential activated genes?
 Deep analysis (clustering, search in promoters, …)?
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Collaboration form
Transcriptome platform
Genomics service of the École Normale Supérieure
General collaboration conditions about help for DNA microarray hybridization
and analysis help
The transcriptome platform can perform DNA microarray experiments and/or result analyses. The
operative mode is based on the principle of collaboration between the interested laboratory and the
platform. The collaboration conditions are listed below: please read them carefully and sign this
form, if you agree with the different points.
1 – RNA should be sent to the platform in a dry ice parcel.
The platform assistants will perform the quality control of the RNA (BioAnalyzer Agilent) before
launching the experiments. Any sample not complying with quality criteria (peak profile) will not
be included in the experiments.
An “hybridization-analysis” team of two persons will be selected to be in charge of the project.
They will establish with the interested laboratory a provisional schedule for hybridization and
analyses.
Any modification of this schedule by the platform, in case of unexpected events, is possible but will
be announced and justified.
2- A preliminary hybridization/analysis will be performed to anticipate any possible difficulties.
The experimental design can be modified accordingly. For experiments with complex designs,
meetings during the ongoing process can be planned.
3- Labelling and hybridization data, until image and results files obtention (JPEG, GPS, TIFF and
GPR), will be stored by the platform.
The platform can not be held responsible in case of experiment failure if the protocol routinely used
on the platform (see http://transcriptome.ens.fr) has been followed, for example in case of power cut
or for any other event independent of its will.
4- Microarray analyses can be carried out by the platform team even if the hybridization step has
been carried outside the platform. In this case, however, the platform team will estimate if the
microarray quality can lead to reliable analyses. If not, appropriate solution will be proposed.
5- An anlysis report (CD) indicating all the methods, tests and parameters used, and exposing the
results will be provided.
The whole data will also be stored by the plaform.
6- Access to the data produced by the platform and concerning the project will be restricted to the
platform project leader, the hybridization/analysis team and yourself. No results propagation, under
any forms, will be possible without your explicit and written agreement.
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Collaboration form
Transcriptome platform
Genomics service of the École Normale Supérieure
7- The hybridization/analysis team (2 persons) will be part of the author list of the paper reporting
the results of the experiments carried out in the frame of this project.
7- The price list included in this document is available for one year from the date indicated on the
signed form and will be update by a new collaboration after one year.
For agreement, done at
, the
Project leader signature (for the ENS)
Name:
Function:
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PI project signature and stamp
Name :
Function :
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