How to prepare for your BioBox Onboarding
We are very excited to be supporting your scientific research journey. In order to best prepare for your onboarding session please have the following items prepared.
- An excel sheet of biological replicates and their metadata
- A excel sheet of the technical replicates and their metadata
- Raw or processed data accessible and ready for upload
- Google Chrome Browser
Models ( Biological Replicates)
A model is the overarching category that will connect all data within your Biobox organization. A model can be anything from a cell line, patient, mouse, organoid etc. Model Metadata would refer to any model information that you would like to keep track of e.g. a cell line mutation, a treatment applied to the cell line, a patient's date of birth etc.
If you are working with a cell line model, each time you create a new cell line record in your library, this is the information about the cell line you will have to provide. This information is completely customizable and can be updated at any time after the onboarding
Each record that you create within a model is a biological replicate. e.g. If you are working with a cell line model, each record within the cell line model would be a unique cell line that your lab works with. Please attend the onboarding with an excel sheet containing all of the model metadata as column headers and all of the biological replicates as rows.
In the example above, the model is a Cell Line. The metadata that will be added to the model include Mutation, Treatment, and Media. Each row corresponds to a biological replicate (model record) and they are the individual cell lines that DNA or RNA was extracted from for the sequencing experiment. Have this excel sheet ready so that this information and be copy and pasted into your library.
Experiments
Experiments refer to the specific sequencing technique that was applied to one of your biological replicates. Experiments are categorized according to Transcriptomic, Genomic, and Epigenomic sequencing techniques. The metadata associated with your experiment includes the type of experiment, run type (paired or single end) and the number of technical replicates.
Each biological replicate can have multiple experiments associated with it e.g. cell line CELL-001 could have been sent for total-RNA sequencing, whole genome sequencing, and single cell sequencing. The three different experiments could have a varying number of technical replicates and different files associated with them.
In the example above, seven experiments are listed. The "derived from" column refers to which biological replicate the experiment is associated with.
Why do I need to provide an experiment name and why do they have to be unique?
It is important that you provide unique names for all of your experiments because 1 biological replicate may be associated with multiple experiments. In the example above the biological replicate CELL-001 is associated with 2 different experiment
- 1 total RNAseq experiment -Single end with two technical replicates
- 1 Whole Genome Sequencing experiment- Paired end with 1 technical replicate
When you attend your onboarding, please have a list of your experiment names, their run type and the number of technical replicates associated with each experiment in an excel sheet.
Data and Files
We support raw as well as processed data uploads on the BioBox Platform. Please ensure that your data is in the following formats
- Differential Expression files or Gene Count files in .csv or .tsv formats
- VCF files in .vcf format Chromosome names must NOT have 'chr' in-front of them.
- FASTQ files in .gz or.gzipped formats