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Genome Sequencing"],"omics_type":["Genomics"],"submitter":["SASTRA Deemed University"],"instrument_platform":["Illumina NovaSeq 6000"],"species":["Bos"],"full_dataset_link":["https://www.ebi.ac.uk/eva/?eva-study=PRJEB88461"],"repository":["EVA"],"name_synonyms":["Taurine, dairy cow, Biological Markers, Viral Marker, Beef Cows, Viral, Surrogate Endpoints, Surrogate Endpoint, cow, Clinical Markers, Laboratory, Taurus Cattles, Bos indicus Cattles, Clinical Marker, Holstein Cow, Serum Markers, Taurus Cattle, Biochemical, End Point, Endpoint, Cattle, Taurine Cattles, Biochemical Markers, Serum, Indicine, Bos indicus, Dairy Cows, Biologic Marker, Immune Marker, Domestic Cows., Surrogate End Points, Surrogate Markers, Laboratory Markers, Bos grunniens, cattle, Marker, Biological, Surrogate End Point, Bos taurus, Bos primigenius taurus, domestic cattle, Indicine Cattles, Yaks, Holstein, Cattles, Biologic Markers, Domestic Cows, Biomarker, Yak, Serum Marker, Clinical, Cows, End Points, Genomes, Surrogate, Domestic Cow, Biological Marker, Endpoints, Dairy Cow, Bos bovis, whole genome, Immunologic, Domestic, Dairy, Laboratory Marker, Taurine Cattle, Beef, Surrogate Marker, Bos Tauurus, Immunologic Markers, Immune, Beef Cow, oxen, Markers, ox, Biochemical Marker, Cow, Viral Markers, Taurus, Indicine Cattle, Zebu, domestic cow, Zebus, Bos indicus Cattle, bovine, Immunologic Marker, Biologic, Immune Markers"],"description_synonyms":["Taurine, dairy cow, Pooled, Testings, Data Pooling, Taurus Cattle, Nucleotide Polymorphisms, Dairy Cows, Pool, dacer, Sample Testings, Single Nucleotide Polymorphisms, cattle, animal breed, Screening, Indicine Cattles, Domestic Cows, study, Yak, ARS, CG13969, Complete, Whole Genome, Cows, Sample Testing, Genomes, Domestic Cow, Single Nucleotide, Dairy Cow, Bos bovis, Complete Genome Sequencing, DmelCG13969, Pooled Sample Screening, study., Domestic, Pooled Testings, Dairy, Taurine Cattle, Beef, Pooled Sample Testings, Sequencing, ArsB, Bos Tauurus, Beef Cow, oxen, 1110021N19Rik, Cow, Polymorphisms, Whole, Sample Screening, domestic cow, Zebus, Data Poolings, Pooled Samples, Beef Cows, Nucleotide Polymorphism, cow, DmelCG10120, Taurus Cattles, Bos indicus Cattles, Holstein Cow, Pooled Sample Screenings, MDH, Genome Sequencing, Cattle, Taurine Cattles, ANUP, MDM, ME, SNPs, Indicine, Bos indicus, Testing, AI415082, read, Bos grunniens, Screenings, Complete Genome, Pooled Sample, Bos taurus, Bos primigenius taurus, domestic cattle, Samples, Me, Yaks, Holstein, Cattles, LY6LS, Sample Screenings, Diagnostic Pool Testing, Pool Testings, mem, whole genome, men, Pooled Sample Testing, Single Nucleotide Polymorphism, Sample, Slurp-1, ox, Taurus, 38B.6, Indicine Cattle, anon-WO0118547.278, Zebu, Pool Testing, Single, Bos indicus Cattle, bovine, Mdh-NADP, CG10120"],"additional_accession":[]},"is_claimable":false,"name":"Genome-wide profiling to identify unique immune markers in Indigenous cattle (Kangayam, Gir, Tharparkar, Sahiwal) vs. exotic (Holstein Friesian), and crossbred cattle (Karan Fries)","description":"This study aims to identify immune signatures in Indigenous cattle breeds (Kangayam, Gir, Tharparkar, and Sahiwal) compared to exotic (Holstein Friesian) and crossbred (Karan Fries) cattle. A total of 6 samples were collected for three different location of each breed, resulting 108 samples (6 breeds x 6 samples x 3 locations) and these samples were pooled into 18 samples (6 breeds x 1 pooled sample x 3 locations) based on locations for whole genome sequencing. Sequencing was performed using an Illumina short-read platform NovoSeq 6000, with quality assessment and preprocessing conducted using FASTQC and Trimmomatic. Reads were mapped to the Bos taurus reference genome (ARS-UCD2.0) using BWA-Mem, and variants were identified using DELLY (structural variants) and FreeBayes (SNPs, MNPs, and indels). The study focuses on detecting common immune-related genomic variations across breeds.","dates":{"publication":"2025-04-14"},"accession":"PRJEB88461","cross_references":{"TAXONOMY":["9903"]}}