# 🐜 A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees

**William Cameron Jasper, Timothy A. Linksvayer, Joel Atallah, Daniel Friedman, Joanna C. Chiu, Brian R. Johnson** (2023) · *Zenodo*

[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.10400744-blue)](https://doi.org/10.5281/zenodo.10400744)

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## Abstract

> The honey bee (*Apis mellifera*) is a key model organism for complex social behavior and physiology, where tissue-specific gene expression (TSGE) is difficult to analyze given large bioinformatics datasets and manual tissue processing. We present a meta-analytic approach to TSGE in *A. mellifera* using open-source bioinformatics packages: from an initial pool of 4,349 samples and 12,398 loci, rigorous analysis yields a publicly available snapshot of 731 samples and 177 loci representing high-quality TSGE estimates, intended as a reusable resource for honey bee and comparative gene-expression research.

## Keywords

`honey bees` · `Apis mellifera` · `tissue-specific gene expression` · `meta-analysis` · `RNA-seq` · `bioinformatics pipeline` · `open-source`

## Key Contributions

- Presents a reproducible meta-analytic pipeline for tissue-specific gene expression (TSGE) in honey bees built on open-source bioinformatics tools.
- Curates a high-quality public snapshot of 731 samples and 177 loci from an initial pool of 4,349 samples and 12,398 loci.
- Provides a reusable community resource for comparative gene-expression analysis in *Apis mellifera* and beyond.

## Methods

- Aggregated and standardized publicly available honey bee RNA-seq datasets across tissues.
- Applied open-source bioinformatics packages to filter samples and loci for quality.
- Reduced 4,349 samples and 12,398 loci to a curated snapshot of 731 samples and 177 loci representing high-quality TSGE estimates.

## 🎯 Consulting & Tutoring

**Available for AI Research Consulting and Tutoring.** [Contact Daniel Ari Friedman, PhD](https://danielarifriedman.com/) for collaboration on Active Inference, Bayesian modeling, and computational biology.

## Citation

```bibtex
@article{2023_HoneyBeeGeneExpression,
  author = {William Cameron Jasper, Timothy A. Linksvayer, Joel Atallah, Daniel Friedman, Joanna C. Chiu, Brian R. Johnson},
  title = {{A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees}},
  journal = {Zenodo},
  year = {2023},
  doi = {10.5281/zenodo.10400744},
}
```

## File Inventory

- `AGENTS.md` (2,037 bytes)
- `2023_HoneyBeeGeneExpression.pdf` (537,373 bytes)
- `README.md` (1,910 bytes)
- `SKILL.md` (1,956 bytes)