Resources
This lab generates high-throughput data on sensory neurons and myeloid cells. Here are some of our latest results:
Check out our plug & play website: http://rna-seq-browser.herokuapp.com/ - data from Liang & Hore et al, 2019: A transcriptional toolbox for exploring peripheral neuro-immune interactions.
Lopes et al, 2017: RNA-seq on MACS-sorted male and female nociceptors in naive and injury states: click here to download
Lopes et al, 2017(2): RNA-seq on pure trigeminal neurons compared to pure DRG neurons: click here to download
Denk et al, 2016: RNA-seq on spinal cord microglia (Percoll-isolated) after spinal nerve ligation: click here to download
Denk et al, 2016: ChIP-seq on spinal cord microglia (H3k4me1) after spinal nerve ligation: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=franziska.denk%40kcl.ac.uk&hgS_otherUserSessionName=ChIP_k4me1_spinal_microglia
Thakur et al, 2014: RNA-seq of nociceptive sensory neurons after magnetically activated cell sorting: click here to download
Check out other researchers' data
- an enormous amount of exciting, cell-type specific expression datasets have been generated over the past few years. There are many dedicated websites (see table) & ways to access data on GEO (see how-to-guide & video below).
If these resources end up being of help in your own work, make sure to quote the original research papers associated with them. It helps fund more of these projects for the community :)
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Name |
URL |
Summary |
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ARCHS4 |
A browser that allows you to visualize and extract sequencing data deposited via GEO and SRA. All data have been re-aligned with standard settings by the authors. |
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Astrocyte RNA-Seq Browser |
A browser to visualize astrocyte-specific RNA-seq in mice with or without spinal cord injury. No expression level cutoff is provided, so make sure to compare the FPKM level of your favourite gene to one that you know to be absent or lowly expressed |
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Allen Brain Atlas |
A large collection of brain atlases, initially based on in situ data in mouse, but now encompassing human data and data derived from a variety of techniques (e.g. virus injections, transgenic mice, calcium imaging) |
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Barres Brain RNA-seq |
A platform created by Ben Barres & his team at Stanford, where gene names can be used to search RNA-seq data on sorted human and mouse cortical cell types |
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BioGPS |
A gene expression portal collating microarray and annotation data |
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BioJupies |
A beautiful new tool based on ARCHS4 that allows you to re-analyse RNA-seq data deposited on GEO, as well as analyse your own experiments using a standardised pipeline |
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Blueprint |
A heroic initiative designed to decode the entire human haematopoietic epigenome and transcriptome using stringently purified cell types (http://www.blueprint-epigenome.eu/index.cfm?p=7BCEDA45-EC73-3496-2C823D929DD423DB) |
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BodyMap |
RNA-seq of 16 individual human tissues, accessible via a simple gene search function |
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CZ CELLxGENE |
The transcriptomic atlas funded by the Chan Zuckerberg Foundation. Contains data on lots of human cell types, including a very large post-mortem human brain dataset from 2023. |
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DRG TXome Database |
https://bbs.utdallas.edu/painneurosciencelab/sensoryomics/index.html |
Translational resources from the Ted Price lab, including easily searchable RNA-seq data of whole and dissociated sensory ganglia (DRG) from human & mouse |
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DropViz |
A mouse brain atlas generated using DropSeq by the McCarroll lab from the Broad Institute. Their great website allows you to visualize the differential expression of your favourite gene amongst the brain cell type clusters they identified. |
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ENCODE |
The Encyclopedia of DNA Elements. Set up in 2003, an initiative designed to map all regulatory and functional elements of the genome. It has generated vast amounts of data available on standard genome browsers and spawned many auxiliary projects, such as Blueprint & PsychENCODE |
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Gene Expression Omnibus |
The most commonly used data repository for sequencing data |
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New tools by bioinformaticians for biologists are regularly becoming available and can usually be found most quickly via Google |
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GTEx |
The website of the Gene-Tissue Expression project, which collects genotype and tissue specific RNA-seq data for the generation of expression quantitative trait loci (eQTLs) |
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Human Protein Atlas |
An atlas of human protein expression based on antibody staining and other evidence such as RNA-seq |
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ImmGen |
The Immunological Genome Project was originally designed to collate microarray datasets, but now also has a lot of cell-type specific RNA-seq. Check their 'Data Browsers' tab for many great tools |
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Microglial Atlas |
A wonderful website where you can browse gene expression in mouse microglia during development. Published by Beth Stevens, Steve McCarroll & their teams. |
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Mouse Single Cell Atlas |
An excellent resource provided by the Linnarsson Lab at Karolinska University which beautifully summarizes the scRNA-seq data they have generated over the years. Bear in mind these are whole cells, and the 'trinarization score', i.e. the blue dots, indicates probability of expression in a cluster, rather than expression level. |
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NeMO |
The data repository for projects funded through the BRAIN initiative. Right now, it has comprehensive transcriptional and epigenetic data on motor circuits across species. But keep checking back, as new amazing data are bound to be added over the next few years. |
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NOCICEPTRA |
A website where you can look up gene expression trajectories of stem-cell derived sensory neurons over the course of differentiation. |
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PanglaoDB |
A database which compiles single cell RNA-seq data from human and mouse for the community to explore, e.g. using a simple gene search function |
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PsychENCODE |
A new effort focused on generating cell-type specific maps of regulatory elements using post-mortem tissue from schizophrenic, bipolar and autistic patients. The first set of data were released in January 2016 (https://www.synapse.org/#!Synapse:syn4921369/wiki/235539), but currently still require slightly more advanced knowledge to access. |
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Spinal Cord Atlas |
An atlas combining various RNA-seq datasets of spinal cord neurons. The associated web-tool looks beautiful and very user-friendly. Please cite the associated pre-print (and eventual paper): https://doi.org/10.1101/2020.09.03.241760 |
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SNAT |
A lovely database containing both bulk & scRNA-seq data of mouse Schwann cell populations |
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Tabula Muris |
An exciting database with metadata from single cell transcriptomic data from 100,000 cells from 20 organs and tissues |
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Tabula Muris Senis |
A second version of tabula muris, now with data across the lifespan! |
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UCSC genome browser |
A great genome browser to visualise raw sequencing data. You can upload the bigwig files of other authors, your own sequencing files or display data provided by ENCODE |
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XSpecies DRG Atlas |
A lovely website comparing gene expression in DRG across species provided by a team at Genentech |