morrislab/rnahl-saluki-human

Overview

mRNA half-life is a measure of the degradation rate of mRNA molecules. This experiment reports the time that the expression level of a transcript takes to decrease by half. The original data source aggregates 39 human and 27 mouse transcriptome wide datasets -- this dataset contains the human datasets. Several data preprocessing steps are taken, reported in the original paper. Half-life measures per gene averaged across collected datasets, and PCA is performed on the gene x half-life matrix. To reduce experimental noise, this dataset reports the value of the first principle component.

This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench

Data Format

Description of data columns:

• target: First PCA component of half-life measurements across aggregated datasets.
• cds: Binary track which reports position of first nucleotide in each codon in CDS.
• splice: Binary track which reports position of the 3' end of each exon, indicating splice sites.

Data Source

This dataset is a Hugging Face redistribution of the mRNA half-life dataset originally collected in the Saluki paper (Agarwal and Kelley 2022), which itself is a collection of experimental datasets. See original paper for all data sources. The Saluki dataset is licensed under the Creative Commons Attribution 4.0 International License.

Original paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02811-x
Original dataset source: https://zenodo.org/records/6326409
Citation: Agarwal, V. & Kelley, D. R. The genetic and biochemical determinants of mRNA degradation rates in mammals. Genome Biol 23, 245 (2022).