Setting up your Library and Uploading Data

How to create records, experiments and upload data to your library

Creating Records 

Each record that you create is a biological replicate. e.g. If you are working with a cohort of patients, each record corresponds to one patient. 

Record Properties pertain to any information associated with the record that you would like to keep track of e.g. mutational status, a treatment applied to the cell line, a patient's date of birth etc. The properties that are associated with a record are unique to your research needs and are fully customizable.

Step 1. Select the "Create" button on the records tab of the library. 

Step 2. Provide Record Metadata.

Multiple record create GIPH"Create Multiple" will open a data table where you can copy and paste in all of the record properties and their values. The first row of the table corresponds to the Name of the property you are keeping track of, and the subsequent rows correspond to their values. Use the drop down to select the appropriate proerpty or create a new one if it does not currently exist in your record dictionary. 

Single Record Create

"Create Single" will enable you to create one record at a time where you can add as many properties as you would like. 

Unnamed Records creation

"Create Blank Records" will enable you to create as many records as you would like using UUIDs (Universally Unique Identifiers). This will enable you to create records without having to specify a name at the time of creation. A name and other record properties can be added later on. 

Step 3. Select "Submit" and your records will be created

The properties that you would like to keep track of can be customized in the Record Dictionary. Within the Dictionary you can update/ delete existing properties or create new ones. There are 7 types of properties you can create, Text, Number, Date, Boolean, Link, Dropdown and Count. Learn more about dictionary properties here. 

Once you have created your records you can move on to create experiments. 

Optional - Models 

Models allow for the optional grouping and categorization of records. Within a model, you can define the specific record properties and their values that must be captured for the record to be included in the model.

Example: Let's say you wanted to group all patients with the following properties 

Disease:  Includes "Glioblastoma"

Treatment: Includes "CART-X "

Clinical Trial: Is "A"

Antibiotics: Is "False"

A model called GBM patients could be created to group all patients with the aforementioned properties into a model. Any new records created that also have the same properties will be added to the model. Note: Properties can be defined by a specific value or condition e.g. "Is Known", "Includes", "Does Not Include".

To create a model 

Step 1. Select the "Create Model" button located in the left hand panel of the Records tab

Step 2. Provide a Name, Description and Conditions 

Model conditions refer to the properties and the their values that must be satisfied for records to be included in the model. Following the creation of a model, all records that satisfy the model conditions will be associated with the mode. Using the menu icon next to the model name you can edit the conditions associated with your model

Creating 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. 

Create Experiments 2Step 1:  Go to the "Experiments" tab and select the type of experiment you would like to create. e.g. If you would like to create a total RNAseq experiment, select the "Total RNAseq" experiment type under the subsection "Transcriptomics".  Select the "Create" button, you will have the option to create 1 or more experiments. Selecting " Create Multiple" will allow you to create multiple experiments at once by copy and pasting your metadata from excel or typing it into the table. 

Step 2: Fill out the table to create your experiments. You will be required to provide 

  • Experiment Name 
  • Species 
  • Derived from (Which model record the experiment corresponds to)
  • Run Type (Paired or Single end)
  • Number of technical replicates

Optional- Creating Series

Series allow for the optional grouping of experiments to be used in tertiary analyses. Select the experiments you would like to include  and create your series.

Create series 2


Uploading Raw Data

Step 1:  Go to the "Data" tab within your library.  Select "FASTQ"  and "Upload", you will be able to drag multiple FASTQ files in to be uploaded simultaneously.

Step  2: Once all of files have been selected, you will specify which Experiment and technical replicate they correspond to. 

Step 3: Wait for your FASTQ files to upload. Do not close or refresh the browser during this time or it will cancel the upload. Feel free to continue to work on the platform as the files are in the process of uploading. 

Uploading Processed Data

Step 1:  Go to the "Data" tab within your library.  Select the tab corresponding to the type of processed data you would like to upload (Differential Expression, Gene Counts, VCF, BED, BigWig) 

Step 2: Once you are on the tab corresponding to the file type that you would like to upload, select the upload button. Select the file from your computer and fill in the information required in the file uploader 

  • Gene counts: Specify which column in your file correspond to the "Gene ID Column", your Gene ID format ( Gene Symbol or Ensemble), the units of your counts, and which Experiments your file corresponds to. 
  • Differential Expression:  Specify which columns correspond to Gene ID, Fold Change,  and P-Value. Specify which Experiments your file corresponds to.
  • VCF: Specify the VCF type (SNV or SV) and which experiment the file corresponds to. 
  • BED: Specify the type of BED file you are uploading (Standard BED or BED6+4) and which experiment the file corresponds to.
  • BigWig: Specify the experiment the file corresponds to. 

Once a processed data file has been uploaded, it undergoes a data cleaning check to ensure no errors such as NAs or invalid cells are detected in the file. If errors have been detected in the file an X will appear in the status column. Select the X and "Repair File" to begin the data cleaning process. Once the data has been cleaned and is ready for visualization within a project, a green check mark will appear in the status column. Learn more about the data cleaning process here.