Abstract:

The dataset contains sample collection information for liver samples collected in August 2011 that were used in a transcriptomic analysis of the response of seaside sparrows (Ammospiza maritima) to Deepwater Horizon oil. The dataset also contains a complete list of genes with their associated statistics of expression. The transcriptomic data were obtained using a microarray cross-species hybridization approach.

Suggested Citation:

Bonisoli Alquati, A.. 2020. A microarray analysis of transcriptomic response of seaside sparrows (Ammospiza maritima) to Deepwater Horizon oil in southeastern Louisiana, 2011-08-28. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/BJ32YQ5A

Publications:

Bonisoli-Alquati, A., Xu, W., Stouffer, P. C., & Taylor, S. S. (2020). Transcriptome analysis indicates a broad range of toxic effects of Deepwater Horizon oil on Seaside Sparrows. Science of The Total Environment, 720, 137583. doi:10.1016/j.scitotenv.2020.137583

Purpose:

The purpose of the transcriptomic analysis was for identifying the genes differentially expressed between birds exposed to oil and control birds, after verifying differential expression of cytochrome P4501A gene in exposed birds (Perez-Umphrey et al., 2018).

Data Parameters and Units:

Worksheet: Sample Information Date of Field Collection: DD-Mon-YY; Site: Descriptive name for field collection site; Latitude: Decimal degrees; Longitude: Decimal degrees; Treatment: Site condition based on SCAT map criteria (in parentheses): oiled (heavily oiled), unoiled (very light or no oil observed); Sex: The sex of each bird (M=male, F=female); Age: Denotes whether the bird was an adult (After Hatch Year=AHY) or juvenile (Hatch-Year=HY); Sample ID: User-defined identifier for each sample. Worksheet: Microarray data ID: ID of the probe in the array; Oiled_Avg_log2: log2 value of the average signal intensity for the specific gene in the oil-exposed birds; Control_Avg_log2: log2 value of the average signal intensity for the specific gene in the control birds; Oiled_SD: Standard deviation of the signal intensity (i.e., Oiled_Avg_log2) among the oil-exposed birds; Control_SD: Standard deviation of the signal intensity (i.e., Control_Avg_log2) among the control birds; Fold_Change: Fold change in expression in exposed birds compared to the control birds; P-val: p value of the difference in expression between the two groups (oil-exposed and control); FDR_P-val: q value, or false discovery rate (FDR)-corrected p value of the difference in expression: Public_Gene_IDs: ID of the gene in the Ensembl database (i.e., stable gene identifiers); Gene_Symbol: Gene symbol, according to conventional gene nomenclature; Description: Homologous gene of each probe.

Methods:

The microarray analysis was performed using total RNA from liver samples on the Affymetrix microarray platform at the Interdisciplinary Center for Biotechnology Research (ICBR) Microarray Core, University of Florida. Total RNA was extracted using a Qiagen RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). The total RNA concentration was determined on a Qubit 2.0 Fluorometer (ThermoFisher Scientific), and sample quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). All microarray sample preparation reactions used the GeneChip® WT PLUS Reagent Kit (Affymetrix, Inc), and reactions were done following the manufacturer’s protocols. Briefly, double-stranded cDNA was synthesized from 200 ng of total RNA. Thereafter, the antisense RNA was synthesized and amplified by in vitro transcription (IVT) of the second-stranded cDNA template using T7 RNA polymerase. Purified cRNA (15µg) was used for sense-strand DNA synthesis by reverse transcription using 2nd cycle primers followed by RNAase H to hydrolyze the cRNA template, leaving single-stranded cDNA. After hydrolysis, the 2nd-cycle single-stranded (ss) cDNA was purified to remove enzymes, salts, and unincorporated dNTPs, then the purified ss cDNA was fragmented, biotin-labeled, and hybridized with rotation at 45°C for 16 hours to the Affymetrix GeneChip® Zebra Finch Transcriptome Array 2.0 developed for the Zebra Finch. The arrays were washed and stained with the reagents supplied in the GeneChip® Hybridization Wash and Stain kit (Affymetrix, Inc) on an Affymetrix Fluidics Station 450, and scanned with a GeneChip® 7G Scanner (Affymetrix, Inc). Quality control was performed for each of IVT, ssDNA, fragment, and biotin labeled products to ensure high quality of data.

Instruments:

Affymetrix microarray platform and a GeneChip® Zebra Finch Transcriptome Array 2.0 developed for the Zebra Finch (Taenyopygia guttata).

Provenance and Historical References:

Perez-Umphrey, A. A., Bergeon Burns, C. M., Stouffer, P. C., Woltmann, S., & Taylor, S. S. (2018). Polycyclic aromatic hydrocarbon exposure in seaside sparrows (Ammodramus maritimus ) following the 2010 Deepwater Horizon oil spill. Science of The Total Environment, 630, 1086–1094. doi:10.1016/j.scitotenv.2018.02.281

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