Resources

IMAGING MASS CYTOMETRY

We have created IMC panels to cover cytoarchitecture, pathology and disease mechanisms including those for glia, neurons, pathology, vascular, inflammatory and synapses markers.  

For the full list of optimised antibodies (including links to antibody manufacturers), please see here: 

 

For immunohistochemistry, immunofluorescence and IMC illustrative examples of the main ~20 markers, please see here:

 

For a detailed protocol of our IMC technique, please see here:

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'

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.  

Bioinformatics pipelines

 

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SCFLOW2

The scFlow R package provides the analytical back-end to the nf-core/scflow Nextflow pipeline for the orchestration of automated, scalable, and reproducible single-cell RNA sequencing analyses.

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github
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nfcore

 

 

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biorxiv

Khozoie et al., 2021 - scFlow: A Scalable and Reproducible Analysis Pipeline for Single-Cell RNA Sequencing Data

scFlow training workshop


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CoMarker

CoMarker is a standardised, reproducible image analysis pipeline to decrease the time taken to assess the colocalisation of tissue markers, whilst eliminating subjectivity and human bias.

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github

 

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.