Agilent custom microarray data for Cyprinus carpio (common carp)

Agilent custom microarray data for common carp (Cyprinus carpio)================================================================ Dataset purpose---------------This dataset accompanies the manuscript *"Transcriptional profiling of common carp: a microarray-based framework for aquaculture research"* (Int. J. Mol. Sci., MDPI; in preparation).It provides raw Feature Extraction outputs, processed expression matrices, and platform annotation for a custom Agilent 8×60K array designed against the SPL01 reference genome. Contents--------- **Agilent custom microarray data for GEO_carp/** (zip root) - **Raw data files/** — Agilent Feature Extraction `.txt` files (two-color protocol GE2_1200_Jun14). - **Processed data file/** — normalized expression matrix for the healthy control set. - **Metadata spreadsheet/** — sample/experiment metadata aligned with MIAME (GEO/ArrayExpress-compatible). - **GEO_Agilent_custom_microarrray.xlsx** — platform and sample annotations (ProbeID/TargetID/GeneSymbol; study metadata). Recommended citation--------------------If you reuse the data, please cite:Pluta A., Paździor E., Fletcher D., Karwatowicz M. (2025). Agilent custom microarray data for *Cyprinus carpio* (common carp). Zenodo. https://doi.org/DOI_TBD Versioning----------Zenodo assigns a DOI to the dataset and a concept DOI for all versions. Please cite the specific version you used. Provenance & methods (short)----------------------------- Species: *Cyprinus carpio* (common carp); tissue: head kidney (pronephros), healthy controls.- RNA integrity: RIN ≥ 9.0; two independent RNA isolations pooled as A/B.- Labeling: Agilent Low Input Quick Amp, two-color workflow; spike-in A→Cy3, B→Cy5.- Hybridization: 65 °C, 17 h (8×60K), Gene Expression Wash Buffer kit.- Scanning: Agilent G2505C at 3 µm; Feature Extraction v12.0.3.1 (GE2_1200_Jun14).- Processing: FE background-corrected `gProcessedSignal`/`rProcessedSignal`; log2 transform; baseline-to-median centering; FE flags used to filter; technical replicates summarized to probe level. File integrity--------------A machine-readable checksum manifest (SHA256) is provided as `CHECKSUMS_SHA256.txt` for all files within the supplied zip archive. Licensing---------**CC BY 4.0**. You are free to share and adapt the material with attribution to the authors and the National Veterinary Research Institute (NVRI). Contact-------Corresponding: Aneta Pluta — [e-mail]: Ewa Paździor — [e-mail]