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Depositordc.contributorWard, Paulineen
Funderdc.contributor.otherBBSRC - Biotechnology and Biological Sciences Research Council
Funderdc.contributor.otherMRC - Medical Research Council
Funderdc.contributor.otherNERC - Natural Environment Research Council
Spatial Coveragedc.coverage.spatialUK
Spatial Coveragedc.coverage.spatialUNITED KINGDOM
Data Creatordc.creatorFreem, Lucy
Data Creatordc.creatorSummers, Kim
Data Creatordc.creatorGheyas, Almas
Data Creatordc.creatorPsifidi, Androniki
Data Creatordc.creatorBoulton, Kay
Data Creatordc.creatorMacCallum, Amanda
Data Creatordc.creatorO’Dell, Jenny
Data Creatordc.creatorBush, Stephen
Data Creatordc.creatorHume, David
Date Accessioneddc.date.accessioned2019-09-05T16:23:28Z
Date Availabledc.date.available2019-09-06
Citationdc.identifier.citationFreem, Lucy; Summers, Kim; Gheyas, Almas; Psifidi, Androniki; Boulton, Kay; MacCallum, Amanda; O’Dell, Jenny; Bush, Stephen; Hume, David. (2019). Variant discovery from whole genome sequence data from a commercial broiler line and a CSFIR- mApple reporter transgenic layer line, [dataset]. University of Edinburgh. Roslin Institute. https://doi.org/10.7488/ds/2618en
Persistent Identifierdc.identifier.urihttp://hdl.handle.net/10283/3414
Persistent Identifierdc.identifier.urihttps://doi.org/10.7488/ds/2618
Dataset Description (abstract)dc.description.abstractThe data comprises variants calls from whole genome sequencing (WGS) data from a set of founder broilers (n=10) and transgenic layers (n=10). The broiler samples belong to commercial Ross 308 founder population and were sourced from PD Hook (Hatcheries) Ltd, Cote, Brampton, Oxfordshire, UK. The layer samples belong to founder population from a CSF1R-mApple reporter transgenic layer line on an ISA-Brown genetic background and were produced in The Roslin Institute. WGS was performed on Illumina HiSeqX platform in paired-end mode with read length of 150bp. After quality checking (using FASTQC v0.11.8) and trimming of poor quality data (using Trimmomatic software v3.5 and with trimming criteria: LEADING:20, SLIDINGWINDOW:10:20, MINLEN:50), sequence reads were mapped against chicken reference genome (Galgal5.0) using BWA_MEM algorithm (v0.7.8). Before proceeding to variant calling, the mapped reads in BAM files were further processed for marking duplicates (using Picard tools v2.1.1) and indel realignment (using GATK v 3.7.0). Variant calling was performed using samtools mpileup (v 1.1) in conjunction with bcftools with minimum base and mapping qualities set to 20. The variant data is present in the Variant Calling Format (VCF). ## Broiler samples: ## sample1662 (Male (M)), sample1674 (Female (F)), sample1678 (F), sample1679 (F), sample1684 (F), sample1686 (F), sample1687 (M), sample1696 (M), sample1697 (M), sample1698 (M). ## Transgenic layer samples: ## sample14 (F), sample16 (F), sample18 (M), sample24 (F), sample26 (M), sample29 (F), sample4937 (M), sample4946 (M), sample4 (F), sample6 (M).
Dataset Description (TOC)dc.description.tableofcontentsFile names and description: (1) broiler_transgenicLayer_variantCall.vcf.gz : Variant call data in VCF format from 20 chicken samples: 10 broilers and 10 transgenic layers (2) broiler_transgenicLayer_variantCall.vcf.gz.tbi : Index file of the VCF file above
Publisherdc.publisherUniversity of Edinburgh. Roslin Institute
Relation (Is Referenced By)dc.relation.isreferencedbyGheyas et al. "Analysis of the progeny of sibling matings reveals regulatory variation impacting the transcriptome of immune cells in commercial chickens" (In submission)
Subjectdc.subjectgenetic variant discovery
Subjectdc.subjectwhole genome sequencing
Subjectdc.subjectCSF1R-mApple reporter transgenic layer
Subjectdc.subjecttransgenic chicken
Subjectdc.subjectlayer
Subjectdc.subjectbroiler
Subject Classificationdc.subject.classificationVeterinary Sciences Agriculture and related subjects
Titledc.titleVariant discovery from whole genome sequence data from a commercial broiler line and a CSFIR- mApple reporter transgenic layer line
Typedc.typedataset

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