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Series GSE158416 Query DataSets for GSE158416
Status Public on Sep 24, 2020
Title Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (CTCF ChIP-Seq)
Organisms Gallus gallus; Sus scrofa; Bos taurus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.
 
Overall design CTCF ChIP-seq in 8 tissues from 3 livestock species (2 adult male replicates per species)
 
Contributor(s) Kern C, Zhou H, Ross P
Citation(s) 33758196, 34615879
Submission date Sep 23, 2020
Last update date Oct 14, 2021
Contact name Colin Kern
Organization name UC San Diego
Street address 9500 Gilman Dr
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (3)
GPL22475 Illumina HiSeq 4000 (Sus scrofa)
GPL23295 Illumina HiSeq 4000 (Bos taurus)
GPL23499 Illumina HiSeq 4000 (Gallus gallus)
Samples (48)
GSM4799655 CTCF from UC Davis FAANG chicken adipose rep A
GSM4799656 CTCF from UC Davis FAANG chicken adipose rep B
GSM4799657 CTCF from UC Davis FAANG cattle adipose rep M08
This SubSeries is part of SuperSeries:
GSE158430 Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility
Relations
BioProject PRJNA665197
SRA SRP285095

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE158416_RAW.tar 51.5 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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