Time-courses sample description template

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