Gene expression counts from the Kremer et al study

File description:

1. Gene-level counts using the gtf file from the release 34 of GENCODE https://www.gencodegenes.org/human/release_34

2. Split counts spanning from one exon to another using an annotation-free algorithm, therefore capturing new splice sites

3. Non-split counts covering exon-intron boundaries

4. Sample annotation describing each sample from the dataset

5. Description file with global information from the dataset

Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired end specifications match. Afterwards, the DROP pipeline can be used to compute expression and splicing outliers (https://github.com/gagneurlab/drop).

Maintainer: Vicente A. Yépez, yepez@in.tum.de

URL: https://github.com/gagneurlab/drop/

Number of samples: 119
Tissue: Fibroblast
Organism: Homo sapiens
Genome assembly: hg19
Gene annotation: gencode34
Disease (ICD-10: N): E75: 1, E79: 13, E88: 84, G31: 9, K72: 3, NONE: 9
Strand specific: FALSE
Paired end: TRUE
Cite as: RNA-Seq count tables were obtained from Zenodo (DOI: 10.5281/zenodo.3887451) based on the study of Kremer et al. [1]
1. Kremer, L., Bader, D., Mertes, C. et al. Genetic diagnosis of Mendelian disorders via RNA sequencing. Nat Commun 8, 15824 (2017). https://doi.org/10.1038/ncomms15824

Dataset contact: Vicente Yepez, yepez@in.tum.de