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

View data repository wiki page.

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

UK DRI

Principal funder:

Medical Research Council