Dataset Open Access

Population-scale single-cell RNA-sequencing of iPS cells differentiating towards dopaminergic neurons

Cuomo Anna SE

This upload contains data objects associated with our paper "Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation" (https://www.nature.com/articles/s41588-021-00801-6).

In particular, available here are:

1) four objects containing scRNA-seq counts and associated metadata for:

- three compressed files for all cells from each of day 11, day 30 and day 52, respectively (i.e. day.h5, day30.h5 and day52.h5) - these contain both normalised and raw count matrices,

- a subsample of 20% cells across all time points (all_timepoints_subsampled.h5) - normalised counts only;

2) one compressed folder containing eQTL summary statistics for each of the 14 contexts (cell type + condition) analysed in the paper.

3) two compressed files containing summary statistics for colocalisation analyses between 25 neurological traits and our 14 eQTL maps (neuroseq) and 49 eQTL maps from GTEx (gtex), as well as a text file describing the GWAS trait ids used. 

The corresponding raw scRNA-seq data are accessible in the EGA for managed access lines (study number: EGAS00001002885, dataset: EGAD00001006157) and ENA for open access ones (ERP121676). The file files_to_samples.txt provides a map between the files on EGA/ENA and the sample IDs in the h5 objects.

Files (27.9 GB)
Name Size
all_timepoints_subsampled.h5
md5:4695a336a12fcafb7152cd6a2e8a770f
4.9 GB Download
coloc_gtex_25_traits.tsv.gz
md5:b38e10d699488a5d69c890a32022bb41
62.8 MB Download
coloc_neuroseq_25_traits.tsv.gz
md5:dc5afdb84ccb5759f8e40628e97234a8
9.9 MB Download
day11.h5.zip
md5:17ed66493ef5f50be904161949c562c7
3.1 GB Download
day30.h5.zip
md5:af62e81202dca0384a946d5ac0ef550b
3.1 GB Download
day52.h5.zip
md5:b90a155be40a0fa561456417b0cb24f2
7.1 GB Download
eqtl_summary_stats.tar.gz
md5:5165124ce3b6a3de15295f613b436f66
9.7 GB Download
files_to_samples.txt
md5:b10289c0076490501ed53251c77c394e
28.8 kB Download
gwas_trait25.txt
md5:95c585834de6653eb17aba223b7e763a
999 Bytes Download
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