Resources

Training resources

 

We have a range of training resources written by our team, our collaborators or third parties. All of which are regularly used within the group to train our new recruits.  

Protocols

 

We have developed/modified/optimised a range of protocols in the group which we are happy to share with the field.  If you follow our protocols, please cite us in your manuscript. 

Users must follow their own local rules and health and safety procedures.

 

If you use our SOPs/protocols, please acknowledge us in your publications as follows: 'Protocols were adapted from those used in the UKDRI Multi-'omics Atlas Project'

Standard Operating Procedures

 

We have developed/modified/optimised a range of standard operating procedures in the group which we are happy to share with the field.  If you follow our protocols, please cite us in your manuscript. 

Users must follow their own local rules and health and safety procedures.

 

If you use our SOPs/protocols, please acknowledge us in your publications as follows: 'Protocols were adapted from those used in the UKDRI Multi-'omics Atlas Project'

Bioinformatics pipeline

 

The delivery of an analysis pipeline for single-cell/nuclei RNAseq has been a key aim for the project. Standardised analyses of millions of brain nuclei for case/control studies requires the efficient use of computational resources, the implementation of best practices for reproducible bioinformatics, and the flexibility to fine-tune complex parameters to address different biological questions.  The bioinformatics group have developed a new toolkit and associated analytical pipeline to meet these requirements.  Analytical steps from quality-control through to clustering, cell-type annotation, and differential gene expression are automated, without user intervention, and performed rapidly at scale in an HPC cluster or the cloud.  This pipeline has recently been finalised and is linked below as pre-release software with its associated documentation.

scflow-manual    scflow analysis pipeline

 

In addition, we have established a consortium, in partnership with the Broad Institute to develop a data management environment and analytical tools to catalyze both new scientific insights into these exciting datasets, and to foster a community spirit of free and open exchange of analytical ideas and data. Specifically, we propose to leverage the open infrastructure provided by Terra, an open, cloud-based environment for storing, sharing, and analyzing genomic and clinical data at scale built by the Broad Institute and its partners.

Explore public datasets

 

There are a range of publicly available tools to explore published datasets.  We have collated a few of interest.

MetExplore offers a free all-in-one online solution composed of interactive tools for metabolic network curation, network exploration and omics data analysis.

ARCHS4 provides access to gene counts from HiSeq 2000, HiSeq 2500 and NextSeq 500 platforms for human and mouse experiments.

AD Knowledge Portal to discover and download Alzheimer's Disease data, analyses, and tools from the National Institute on Aging's Alzheimer's Disease Translational Research Program.

The Aging, Dementia and Traumatic Brain Injury Study is a detailed neuropathologic, molecular and transcriptomic characterization of brains of control and TBI exposure cases from a unique aged population-based cohort.

The Neuroscience Multi-omic Archive (NeMO Archive) is a data repository specifically focused on the storage and dissemination of omic data generated from the BRAIN Initiative and related brain research projects.

AlzGPS for network-based multi-omics analysis informs Alzheimer's patient care and therapeutic development.