Resources

This lab generates high-throughput data on sensory neurons and spinal cord microglia. Here are some of our latest results:

RNA-seq on pure trigeminal neurons compared to pure DRG neurons: click here to download

RNA-seq on spinal cord microglia (Percoll-isolated) after spinal nerve ligation: click here to download

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

RNA-seq of nociceptive sensory neurons after magnetically activated cell sorting: click here to download


Also 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). 

Name

URL

Summary

Astrocyte RNA-Seq Browser

https://astrocyte.rnaseq.sofroniewlab.neurobio.ucla.edu/

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

Allen Brain Atlas

http://www.brain-map.org/

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)

Barres Brain RNA-seq

http://www.brainrnaseq.org/

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.

BioGPS

http://biogps.org/#goto=welcome

A gene expression portal collating microarray and annotation data

Blueprint

http://blueprint-data.bsc.es/#!/

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)

BodyMap

http://www.ebi.ac.uk/gxa/experiments/E-MTAB-513

RNA-seq of 16 individual human tissues, accessible via a simple gene search function

DRG TXome Database

https://www.utdallas.edu/bbs/painneurosciencelab/

Easily searchable RNA-seq data of whole sensory ganglia (DRG) from both human & mouse, integrated across several studies & allowing for comparison to other tissue types.

ENCODE

https://www.encodeproject.org/

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.

Gene Expression Omnibus

http://www.ncbi.nlm.nih.gov/geo/

The most commonly used data repository for sequencing data

Google

https://www.google.co.uk/

New tools by bioinformaticians for biologists are regularly becoming available and can usually be found most quickly via Google

GTEx

http://www.gtexportal.org/home/

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)

Human Protein Atlas

http://www.proteinatlas.org/

An atlas of human protein expression based on antibody staining and other evidence such as RNA-seq

PsychENCODE

http://psychencode.org/

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

UCSC genome browser

http://genome.ucsc.edu/index.html

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


Any published dataset should also be accessible on the Gene Expression Omnibus website. This how-to-guide and screenshot video will show you how to get the files - it takes 5 minutes tops!