This page holds information about datasets and code used in our papers. Our intention is to make the data and code we have used accessible. If anything is unclear, please report it as an issue so I (and you) can track it. If you really don’t want to use github, as a last resort, email =cew54= at =cam.ac.uk=.
Need to be requested from the original study authors https://www.ncbi.nlm.nih.gov/pubmed/22922229
MS ImmunoChip data was accessed through application to the International Multiple Sclerosis Genetic Consortium (IMSGC). Primary analysis of these data is presented in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3882906/ and the dbGaP accession number for the US cohort is phs000357.v2.p2.
Primary analysis was by Eyre et al and data were accessed through a request to the authors.
is available from dbGaP
2000 T1D samples were genotyped as part of the WTCCC (and controls) - data access is described https://www.wtccc.org.uk/info/access_to_data_samples.html. An additional 4000 cases were genotyped by the T1DGC, available at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000180.v3.p2
Autoantibody data on T1D subjects is available by contacting study authors from http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002216.
ImmunoChip summary statistics
ImmunoBase: ImmunoChip summary GWAS statistics from multiple studies used to be nicely curated and available from ImmunoBase if you first register (free) then go to =Data..downloads= on the right, then click through to =data/immunochip/association_stats=. I’m not sure how to access it now.
Fairfax eQTL data
Ben Fairfax has published eQTL papers on sorted cells (monocytes, stimulated monocytes, B cells) from close to 300 samples. The expression data are freely available, but the genotype data require a data access agreement, available as detailed in either paper.
Fairfax et al. (2012) Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat. Genet. 44, 502-510
gene expression data: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-945; genotyping data: http://www.ebi.ac.uk/ega/EGAD00010000144.
Fairfax et al. (2014) Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 343, 1246949
gene expression data: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2232; genotyping data: http://www.ebi.ac.uk/ega/EGAD00010000144, http://www.ebi.ac.uk/ega/EGAD00010000520.
Cusanovich et al’s transcription factor knockdown
See http://europepmc.org/abstract/MED/24603674 for the paper. This dataset has a special place in my heart, as we requested it after Cusanovich posted a preprint and it was shared quickly and freely. As a result, I /think/ our paper using this data was actually preprinted and submitted before the Cusanovich paper was formally published in a journal. A true example of preprint publishing furthering research.
BABYDIET gene expression
PBMC gene expression from longitudinally sampled children at risk of type 1 diabetes, described by Ferreira et al.
http://www.ebi.ac.uk/arrayexpress, accession no. E-MTAB-1724
T1D gene expression
The T1D PBMCs were collected as part of the Genetic Resource Investigating Diabetes (GRID) cohort collection (http://www.childhood-diabetes.org.uk/grid.shtml). Expression data at http://www.ebi.ac.uk/arrayexpress, accession no. E-MTAB-1724
Asthma gene expression
Cardiogenics eQTL data
Garnier S et al. (2013) Genome-wide haplotype analysis of cis expression quantitative trait Loci in monocytes PLoS Genet. 9(1):e1003240
Monocytes eQTL study available from EGA: https://www.ebi.ac.uk/ega/studies/EGAS00001000411