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): 

_____________________________________________________________________

_____________________________________________________________________

_____________________________________________________________________

_____________________________________________________________________

_____________________________________________________________________

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BioInfo Analysis Type

• RNA-seq analysis
• DNA-seq analysis
• Genetic variation
• ChiP-seq analysis
• ATAC-seq analysis
• Single cell Analysis
  • Single cell GEX
  • Single cell ATAC-Seq
  • Single cell GEX + Hashing
  • CITE-Seq
  • Multiome (GEX + ATAC-Seq)
  • Single cell GEX + BCR/TCR
  • Other -__________
• Small-RNA analysis
• Functional/pathway analysis
• Methylation analysis
• Proteomics
• Integration
• Other: (comments) -__________

Sample Features

Sample Cells/tissue description (gender, type of cells, genetic manipulation, FAX, treatment..) 

Species ___________________________________________________________________

Gender____________________________________________________________________

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Tissue description____________________________________________________________

_____________________________________________________________________________

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Cell types____________________________________________________________________

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Genetic Manipulation____________________________________________________________

_____________________________________________________________________________

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Lab manipulation (FACS, nuclei)_____________________________________________________

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Other information_______________________________________________________________

Estimating replicates needed

• Sample Purity (% of cells which are of interest, reproducibility of this percentage)

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• Genetic purity  cell line (at least 3 replicates)
   whole organism inbreed (at least  3 replicates)  other (even 10 replicates)

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• Pooling – avoid if possible. At least 5 samples. Need to have 3 replicates.

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• 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.

For single cell analysis estimation of abundancy of cell population of interest (in percent)

______________________________________________________________________________

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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  for initial analysis :_____________________________________________

Expected date when the sequences will be ready :______________________________________