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The lack of functional annotation of the domestic pig genome prevents full exploitation of single nucleotide variant analysis for genetic improvement through traditional breeding, and limits efficiency of gene editing of specific genome components to understand function and accelerate genetic improvement. We will dramatically increase the depth and breadth of current porcine functional annotation and generate a community resource for scientists in both the public and private sectors. Across all objectives, we will use RNA assays (RNAseq, the 5' end mapping technique RAMPAGE, and PacBio Iso-seq) and epigenetics assays (histone ChIP-seq, ATAC-seq and DNA methylation) to annotate a tremendous breadth of biological states. In Objective 1, we will triple the number of adult tissues currently being annotated. In Objective 2, we will annotate four tissues at important stages of fetal development, and link allele-specific expression with allele-specific functional elements through analyzing divergent-breed reciprocal crosses. In Objective 3, we will annotate circulating white blood cell populations in healthy pigs, as well as macrophage responses to bacterial and viral mimics. We will also profile gene expression of single cells in complex cell populations to maximize annotation of critical immune tissues. In Objective 4, we will use all these data as well as public FAANG data to generate a first-generation chromatin state segmentation map. All data and associated metadata will be publically available. This is USDA-NIFA-AFRI project 2018-67015-27501 which addresses Program Area Priority A1202, Annotation of Agricultural Animal Genomes.

Related Publications


Related Datasets

Study name
Species
Archive
Assay type
PRJEB31481 Sus scrofa ENA transcription profiling by high throughput sequencing
PRJEB31482 Sus scrofa ENA ChIP-seq
PRJEB31483 Sus scrofa ENA ChIP-seq
PRJEB37103 Sus scrofa ENA ChIP-seq
PRJEB37735 Sus scrofa ENA ChIP-seq
PRJEB43826 Sus scrofa ENA transcription profiling by high throughput sequencing
PRJEB47517 Sus scrofa ENA methylation profiling by high throughput sequencing
PRJEB49412 Sus scrofa ENA whole genome sequencing assay
PRJEB51699 Sus scrofa ENA ChIP-seq
PRJEB57595 Sus scrofa ENA transcription profiling by high throughput sequencing
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Related Files

File name
Assay type
Experiment target
File size
Download
ERR10492608_1.fastq.gz transcription profiling by high throughput sequencing rna 1.79GB
ERR10492608_2.fastq.gz transcription profiling by high throughput sequencing rna 1.85GB
ERR10492609_1.fastq.gz transcription profiling by high throughput sequencing rna 1.93GB
ERR10492609_2.fastq.gz transcription profiling by high throughput sequencing rna 2.0GB
ERR12246838.fastq.gz RNA-seq of coding RNA open_chromatin_region 1.4GB
ERR12246839.fastq.gz RNA-seq of coding RNA open_chromatin_region 5.46GB
ERR12246840.fastq.gz RNA-seq of coding RNA open_chromatin_region 2.81GB
ERR12246841.fastq.gz RNA-seq of coding RNA open_chromatin_region 5.53GB
ERR12246842.fastq.gz RNA-seq of coding RNA open_chromatin_region 1.3GB
ERR12246843.fastq.gz RNA-seq of coding RNA open_chromatin_region 4.94GB
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Related Organisms

BioSamples ID
Species
Sex
Breed
SAMEA11506650 Sus scrofa female Pig crossbreed
SAMEA11506651 Sus scrofa female Pig crossbreed
SAMEA11506652 Sus scrofa female Pig crossbreed
SAMEA11506653 Sus scrofa female Pig crossbreed
SAMEA11506654 Sus scrofa female Pig crossbreed
SAMEA11506655 Sus scrofa female Pig crossbreed
SAMEA11506656 Sus scrofa female Pig crossbreed
SAMEA11506657 Sus scrofa female Pig crossbreed
SAMEA11506658 Sus scrofa male Meishan
SAMEA11506659 Sus scrofa female Meishan
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Related Specimens

BioSamples ID
Material
Organism part/Cell type
Sex
Species
Breed
SAMEA111352436 cell specimen mature neutrophil intact male Sus scrofa Pig crossbreed
SAMEA111352437 cell specimen mature neutrophil intact male Sus scrofa Pig crossbreed
SAMEA11506664 specimen from organism brain female Sus scrofa Pig crossbreed
SAMEA11506665 specimen from organism liver female Sus scrofa Pig crossbreed
SAMEA11506667 specimen from organism skeletal muscle tissue female Sus scrofa Pig crossbreed
SAMEA11506668 specimen from organism placenta female Sus scrofa Pig crossbreed
SAMEA11506669 specimen from organism brain female Sus scrofa Pig crossbreed
SAMEA11506670 specimen from organism liver female Sus scrofa Pig crossbreed
SAMEA11506671 specimen from organism skeletal muscle tissue female Sus scrofa Pig crossbreed
SAMEA11506672 specimen from organism placenta female Sus scrofa Pig crossbreed
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