Kickoff Template

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):

_____________________________________________________________________

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
- Visium HD
- 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____________________________________________________________________

___________________________________________________________________________

Tissue description____________________________________________________________

_____________________________________________________________________________

Cell types____________________________________________________________________

_____________________________________________________________________________

Genetic Manipulation____________________________________________________________

_____________________________________________________________________________

Lab manipulation (FACS, nuclei)_____________________________________________________

_____________________________________________________________________________

Other information_______________________________________________________________

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.

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

______________________________________________________________________________

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 :______________________________________