Published August 25, 2022 | Version 1.0
Dataset Open

Gene expression counts from induced Pluripotent Stem Cells

Authors/Creators

  • 1. Technical University of Munich
  • 2. European Molecular Biology Laboratory

Description

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 workflow DROP 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/

 

Title: induced Pluripotent Stem Cells
Number of samples: 330
Tissue: iPSCs
Organism: Homo sapiens
Genome assembly: hg19
Gene annotation: gencode34
Disease: None
Strand specific: True
Paired end: True
Dataset contact: Marc Bonder, marcj89 at gmail.com

Citation: Cite both the resource using Zenodo's citation and the publication under References

Files

Files (368.3 MB)

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md5:5d179ae7b32b4f09d7385157fd5df2ac
368.3 MB Download

Additional details

References

  • Bonder, M.J., Smail, C., Gloudemans, M.J. et al. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nat Genet 53, 313–321 (2021). https://doi.org/10.1038/s41588-021-00800-7