license: unknown
tags:
- biology
- rna
- genomics
configs:
- config_name: GV
data_files:
- split: train
path: pal-tail-length-xiang-gv.parquet
- config_name: GVtoMII
data_files:
- split: train
path: pal-tail-length-xiang-gvtomii.parquet
Overview
This dataset contains measured poly(A)-tail length changes during oocyte maturation from germinal vesicle (GV) to metaphase II (MII) stages in human oocytes. This dataset is collected from Xiang and Bartel 2025, where the PAL measurements for human oocytes (in vivo) were deposited. 3' UTRs were inferred based on PAL-seq tag peaks, and then assigned to the nearest transcript isoform (from the original paper where the dataset was generated - Xiang, Ly, and Bartel 2024. Developmental Cell). In this uploaded data, 5' UTR sequences were prepended to the CDS and 3' UTR based on the annotated transcript isoform's 5' UTR from Gencode to provide a full mRNA transcript sequence.
This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench
Data Format
Description of data columns:
target: GV poly (A) tail-length, if GV data specified, else GV-to-MII poly(A) tail-length change.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 generated using the data collected in Xiang and Bartel 2025.
Original paper: https://www.biorxiv.org/content/10.1101/2024.10.29.620940v2
Original dataset source: https://github.com/coffeebond/PAL-AI/tree/main/Data
Citation: Xiang, K. & Bartel, D. P. PAL-AI reveals genetic determinants that
control poly(A)-tail length during oocyte maturation, with relevance to human
fertility. bioRxiv (2025).