Research Use Cases

As a systems neuroscientist, I want to investigate how memories are encoded, consolidated and retrieved, so that I can identify the mechanisms by which they get disrupted in Alzheimer's disease.

As a computational researcher I would like to find genotype, functional genomics and cellular phenotype data from genetically diverse mice, so that I can study the influence of genetic variation on molecular traits and connect them to cellular phenotypes.

As a computational research scientist, I want to find genotype and phenotype data on male and female mice with variations in the NBPF1 gene and its regulatory elements, so that I can design experiments to assess whether the copy number of this gene impacts brain size.

Differential gene expression analysis

A user would like to conduct a differential gene expression (DGE) analysis of genes in specific neuronal regions to study the effect of a specific drug. The differentially expressed (DE) genes will be annotated according to cellular component, biological process, and molecular function. User will set up an RNA-Seq assay with the relevant biological samples and enter all the relevant metadata associated with the assay.

Creating a study in the BioConnect Data Curation System

At the completion of the experiment, user (and the authorized members in the study) will receive a unique ID via email and instructions to create a study in the JAX Omics Data Curation Tool to store the metadata and data associated with the assay. The unique ID will allow the user to associate additional data and metadata information to an existing study or to create a new study in the BioConnect data curation system in an automated fashion.

Data QC and preprocessing

The curation tool user interface (UI) will provide the fields to quality control and preprocess raw data from omics assays. In the above-mentioned use case, once the data and metadata files are in the curation tool user will kick off an RNA-Seq workflow. The workflow contains automated pipeline runs starting with the QC the raw reads from the FASTQ files to assess the quality of the sequence reads, followed by preprocessing of raw reads, Mapping RNA-Seq reads onto a reference genome, QC of mapped reads, and provide read coverage for genes.

Analysis

The above preprocessed RNA-Seq data could be used for multiple downstream analyses (differential expression between samples, detecting allele-specific expression, and identifying expression quantitative trait loci (eQTLs), etc.) using different tools in the BioConnect Tool App system.