Chicken gut-lung axis single-cell RNA-seq log-normalized expression matrices following oral cholera toxin administration
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Processed single-cell RNA-seq expression matrices supporting the manuscript: Single-Cell Transcriptomic Atlas of the Chicken Gut-Lung Axis Reveals Coordinated but Tissue-Divergent Immune Remodeling Following Oral Cholera Toxin Administration. Study design: Broiler chickens received oral cholera toxin at hatch (0.5 micrograms/g body weight) or saline control. Jejunum, cecal tonsil and lung were collected at three days of age. The manuscript reports 47,364 retained cells: 18,023 cecal tonsil, 15,547 jejunum and 13,794 lung; 22,261 control and 25,103 treated cells across 24 sequencing libraries. Methods: Illumina Single Cell 3' RNA Prep, T10 library preparation; Element Biosciences AVITI sequencing; Gallus gallus GRCg7b reference genome, Ensembl release 115; R 4.3.0, Seurat 5.0 and scDblFinder. Cells with fewer than 200 or more than 5,500 detected genes, or more than 7% mitochondrial transcripts, were excluded. Expression was log-normalized with scale factor 10,000. Files (gzip-compressed CSV):Lung.expression_matrix_logNormalized.lung.csv.gz - lung.expression_matrix_logNormalized.Jejunum.csv.gz - jejunum.Cecal.expression_matrix_logNormalized.Cecal.csv.gz - cecal tonsil.These are processed expression matrices, not raw sequencing reads. The matrices support analysis of cellular composition, differential expression, pathway enrichment, transcription-factor regulation and predicted cell-cell communication across the chicken gut-lung axis. Animal ethics: University of Saskatchewan Animal Research Ethics Board, protocol 201800085; Canadian Council on Animal Care guidelines. Funding: Chicken Farmers of Saskatchewan (CFS); Canadian Poultry Research Council (CPRC); Natural Sciences and Engineering Research Council of Canada (NSERC Alliance and NSERC Discovery); Mathematics of Information Technology and Complex Systems (MITACS); Results Driven Agriculture Research (RDAR). Corresponding authors: Susantha Gomis (susantha.gomis@usask.ca); Noor Ahmad Shaik (noor.shaik@usask.ca). Access: Data files are restricted. Please submit an access request stating your intended use. Requests are reviewed by the record owner; downloading requires approval.
