NGS - "Kickoff" meeting Protocol

Please download the file, save and then fill. 

Project Title: ____________________________________________________________

Project Aim:  ____________________________________________________________

_______________________________________________________________________

_______________________________________________________________________

Date of meeting:  ______________________________________________________

Participants:  _________________________________________________________

Student_______________________  PI ______________________________ 

Institute:  ____________________________________________________________

Phone:  ______________________________________________________________

Previous Biological Knowledge

Previous evidence (perhaps known gene markers): 

_____________________________________________________________________

_____________________________________________________________________

__________________________________________________________________________________________________________________________________________

Sampling time after treatment

_____________________________________________________________________

_____________________________________________________________________

BioInfo Analysis Type

• RNA-seq analysis
• DNA-seq analysis
• Genetic variation
• ChiP-seq analysis
• ATAC-seq analysis
• Single cell RNA-Seq
• Small-RNA analysis
• Functional/pathway analysis
• Methylation analysis
• Proteomics
• Integration
• Other: (comments)

Sample Features

Estimating replicates needed

• Sample Purity (% of cells which are of interest, reproducibility of this percentage) __________________________________________________________________________________________________________________________________
• Genetic purity  cell line (at least 3 replicates)
   whole organism inbreed (at least  3 replicates)  other (even 10 replicates) ____________________________________________________________________________________________________________________________________
• Pooling – avoid if possible. At least 5 samples. Need to have 3 replicates.
  __________________________________________________________________
• If there is small variance between treatments more replicates needed  yes  no

Batch Effect:

Collect samples at the same time (otherwise batch effect)  yes    no

If not – perform each replicate of the experiment at the same time.

Summary:

Platform name:                ILLUMINA     PACBIO    NANOPORE     MS

Number of groups:         __________                Number of replicates:  __________

Total number of samples: __________

Type of Illumina design:  PE                                    SR   

                                          Length of the read _________                 

Number of reads _____

Protocol type _______                                        

Duration for first analysis:

Evaluation of project size for bioinformatics analysis: Low/Medium/Large

Duration (Relative to data received date):_________