Time-courses sample description template: Difference between revisions

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The description of each of the time-course that is given by the time-course providers will be used to present the time-courses on the FANTOM website. Hence, it is important to present the time-courses in a comprehensive and consistent structure. During discussions at the FANTOM5 Time-courses meeting in October 2012 we decided to use the following structure with the key items listed below:
The description of each of the time-course that is given by the time-course providers will be used to present the time-courses on the FANTOM website. Hence, it is important to present the time-courses in a comprehensive and consistent structure. During discussions at the FANTOM5 Time-courses meeting in October 2012 we decided to use the following structure with the key items listed below:



⚫
*Provide detailed differentiation protocol to recognize e.g. serum changes etc.
*Description of the time course
⚫
**Developmental, differentiation, activation
**General background on the biology of this time-course
⚫
*Points of phenotypic change – tipping points
**Description of the samples: how many time-points, anything else relevant to share
⚫
*Lists of marker genes and when they come up
⚫
***Including detailed differentiation protocol to recognize for example serum changes etc. to observations during data analysis
⚫
*Negative list of marker genes
**Classify time-course into
⚫
*Efficiency of differentiation (how many cells differentiate)
⚫
***Developmental, differentiation, activation
*Literature reference, key reference
⚫
**Known points of phenotypic change – tipping points
⚫
*Sub-classification of cells
⚫
**Lists of marker genes and when they come up
⚫
**Negative list of marker genes
⚫
**Efficiency of differentiation (how many cells differentiate)
⚫
**Sub-classification of cells
**Cancer or not? Nearest expected target cell in phase 1?
**Cancer or not? Nearest expected target cell in phase 1?
**Literature reference inserted above, including key reference for the biology of the time-course
***with links to pubmed

*Paper plan
**either: link to the [[Time-courses_Satellite_papers]] page
**or write the plan here:
**outline
**key aspects
**figure descriptions
**link to manuscript drafts on the satellite paper page
**required validation experiments, can they be done in the collaborator's lab?

*Related samples
**already published data that can support for the analysis
**description of private (non-FANTOM) data that can be considered for the paper

*Quality control
**brief verbal summary of the key aspects of the QC report
**link to QC report

*Bioinformatics collaborators
**names of FANTOM collaborators who already work on the analysis of this time-course
**analysis X is taken care of by bioinformatics collaborator Y
**you can state here if you are looking for Bioinformatics collaborators for you satellite paper

*Links to available data
**expression table
**ZENBU configs
**motif activity table
**Enhancer expression and analysis
**TSS switching results

Latest revision as of 13:04, 4 November 2012

The description of each of the time-course that is given by the time-course providers will be used to present the time-courses on the FANTOM website. Hence, it is important to present the time-courses in a comprehensive and consistent structure. During discussions at the FANTOM5 Time-courses meeting in October 2012 we decided to use the following structure with the key items listed below:


  • Description of the time course
    • General background on the biology of this time-course
    • Description of the samples: how many time-points, anything else relevant to share
      • Including detailed differentiation protocol to recognize for example serum changes etc. to observations during data analysis
    • Classify time-course into
      • Developmental, differentiation, activation
    • Known points of phenotypic change – tipping points
    • Lists of marker genes and when they come up
    • Negative list of marker genes
    • Efficiency of differentiation (how many cells differentiate)
    • Sub-classification of cells
    • Cancer or not? Nearest expected target cell in phase 1?
    • Literature reference inserted above, including key reference for the biology of the time-course
      • with links to pubmed
  • Paper plan
    • either: link to the Time-courses_Satellite_papers page
    • or write the plan here:
    • outline
    • key aspects
    • figure descriptions
    • link to manuscript drafts on the satellite paper page
    • required validation experiments, can they be done in the collaborator's lab?
  • Related samples
    • already published data that can support for the analysis
    • description of private (non-FANTOM) data that can be considered for the paper
  • Quality control
    • brief verbal summary of the key aspects of the QC report
    • link to QC report
  • Bioinformatics collaborators
    • names of FANTOM collaborators who already work on the analysis of this time-course
    • analysis X is taken care of by bioinformatics collaborator Y
    • you can state here if you are looking for Bioinformatics collaborators for you satellite paper
  • Links to available data
    • expression table
    • ZENBU configs
    • motif activity table
    • Enhancer expression and analysis
    • TSS switching results
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