We have collated a selection of standard operating procedures (SOPs), protocols and datasets that we have developed/modified/optimised over the course of this project, and we are happy to share those as an open source library for researchers in the field. If you use our guidance, we would ask that you please cite us in your manuscript as follows: "Protocols were adapted from those used in the UK DRI Multi-'omics Atlas Project". Please note that users must follow their own local rules and health and safety procedures.
Imaging Mass Cytometry (IMC) Resources
We have created IMC panels to cover cytoarchitecture, pathology and disease mechanisms including those for glia, neurons, pathology, vascular, inflammatory and synapses markers. Feel free to use these resources, but make sure to cite us in your manuscript!
IMC Protocols
Illustrative examples of antibodies optimised for IMC by IHC and IF
Click the link below for immunohistochemistry, immunofluorescence and IMC illustrative examples of the main ~20 markers.
IMC IF IHC Validations
IMC Markers
Please click the link below to download a full list of optimised antibodies (including links to antibody manufacturers).
IMC Markers Full List
Detailed IMC Methodology
Click the link below to download a detailed protocol of our Imaging Mass Cytometry technique.
IMC Methodology
Data
Diverse human astrocyte and microglial transcriptional responses to Alzheimer's pathology
To better define roles that astrocytes and microglia play in Alzheimer's disease (AD), we used single-nuclei RNA-sequencing to comprehensively characterise transcriptomes in astrocyte and microglia nuclei selectively enriched during isolation post-mortem from neuropathologically defined AD and control brains with a range of amyloid-beta and phospho-tau (pTau) pathology.
Smith et al., 2022 - Diverse human astrocyte and microglial transcriptional responses to Alzheimer’s pathology
View and download raw data
Two brain regions were studied: entorhinal cortex (EC) and somatosensory cortex (SSC) and enriched for astrocytes ('astro'), microglia ('micro') and perivascular macrophages ('PerivascMacrophages').
Analysis Pipelines
- scFlow - Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
- Omix - A Transcriptomics-Proteomics Integration Pipeline
- CoMarker - a standardised, reproducible image analysis pipeline which was built to vastly decrease the time taken to assess the colocalisation of tissue markers, whilst eliminating subjectivity and human bias.
Data Repository
Protocols List
Below are links to several Standard Operating Procedures (SOPs) and Risk Assessments (RAs). These are free to download and use with acknowledgement.
SOP and RA List
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How temperature and circadian rhythms intersect to regulate a protein shown to protect against neurodegeneration
A new study led by Dr Marco Brancaccio (UK DRI at Imperial) and Dr Marieke Hoekstra (former UK DRI at Imperial, now VIB-KU Leuven Center for Brain & Disease Research) offers a deeper insight into how a neuroprotective pathway is regulated both by temperature and the body clock. This research, published in the journal PNAS, could open up new therapeutic avenues for neurodegenerative disease. Read more on the UK DRI website
Introducing Cynthia Sandor: Pioneering earlier detection of Parkinson’s
Dr Cynthia Sandor, former Emerging Leader at the UK DRI at Cardiff, joins the UK DRI at Imperial as a Group Leader, where she will be tackling early diagnosis of Parkinson’s.
With a background in genetics, Dr Sandor uses computational methods to bring greater understanding to the underlying molecular mechanisms of Parkinson’s. Read more about Cynthia's work on the UK DRI website.
