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
- 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 (FAX, 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 :______________________________________