Extended Mouse Genome Annotation for Gastruloid Models

A gene annotation file (GTF) generated by Lucille Lopez‐Delisle at École Polytechnique Fédérale de Lausanne. It extends the 3' ends of genes using RefSeq and bulk RNA-seq data from three public studies (GSE106225, GSE113885, GSE205781). All command lines for its generation are available in a public GitHub repository.

Use Cases

• Improving transcript quantification accuracy based on extended 3' gene boundaries.
• Analyzing gene expression in gastruloid time-course experiments based on the referenced RNA-seq data.
• Validating custom genome annotations for mouse developmental studies based on the provided RefSeq and experimental data.

Strengths

• Builds upon the established Ensembl version 102 mm10 genome annotation.
• Integrates data from three specific public RNA-seq studies (GSE106225, GSE113885, GSE205781).
• Provides fully reproducible methods with command lines available on GitHub.

Limitations

• Row count and file size are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

Generated from a customized Ensembl GTF and public RNA-seq data.

Collection Method

Computational extension of gene 3' ends using RefSeq and bulk RNA-seq data.