Similar studies for GEO DataSets (Select 200206511) - GEO DataSets

Select item 2002065111.

Comparative analyses of DNA methylomes in the liver among three ruminants

(Submitter supplied) This study is the first to report a genome-wide comparative DNA methylation map of liver in three ruminants using WGBS technology.

Organism:: Bos taurus; Capra hircus; Ovis aries

Type:: Methylation profiling by high throughput sequencing

Platforms:: GPL23810 GPL24230 GPL25639
9 Samples

Download data: TXT

Series

Accession:: GSE206511

ID:: 200206511

PubMed Full text in PMC Similar studies

Select item 2002067362.

Dynamics of regulatory elements in the liver during ruminant evolution

(Submitter supplied) To investigate the evolutionary changes of regulatory elements in ruminants, we then performed regulatory elements profiling analysis using ChIP-seq datasets (H3K27ac and H3K4me3) of liver from three ruminants.

Organism:: Bos taurus; Capra hircus; Ovis aries

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL19778 GPL19172 GPL19149
26 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE206736

ID:: 200206736

PubMed Full text in PMC Similar studies

Select item 2002061843.

Dynamic changes of gene expression in the liver during ruminant evolution

(Submitter supplied) To investigate the evolutionary changes of gene expression in ruminants, we performed gene expression profiling analysis using RNA-seq data of liver from three ruminants.

Organism:: Capra hircus; Ovis aries; Bos taurus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24230 GPL25639 GPL23810
9 Samples

Download data: TXT

Series

Accession:: GSE206184

ID:: 200206184

PubMed Full text in PMC Similar studies

Select item 2002133174.

Comparative gene expressions profiling of brain and muscle across ruminants

(Submitter supplied) To describe the gene expression profile of brain and muscle across ruminants, we performed gene expression analysis of brain and muscle using RNA-seq data for three ruminants.

Organism:: Ovis aries; Bos taurus; Capra hircus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24230 GPL23810 GPL25639
18 Samples

Download data: TXT

Series

Accession:: GSE213317

ID:: 200213317

PubMed Full text in PMC Similar studies

Select item 2002113535.

Comparative epigenomic analyses of DNA methylomes and gene expression during ruminant evolution

(Submitter supplied) This study is the first to report a genome-wide comparative DNA methylation map in three ruminants using WGBS technology.

Organism:: Bos taurus; Capra hircus; Ovis aries

Type:: Methylation profiling by high throughput sequencing

Platforms:: GPL23810 GPL24230 GPL25639
24 Samples

Download data: TXT

Series

Accession:: GSE211353

ID:: 200211353

PubMed Full text in PMC Similar studies

Select item 2001471846.

Analyses of methylomes of Bones in cattle

(Submitter supplied) In this study, we generated whole genome bisulfite sequencing data of 2 samples for Bones in Holstein cattle. We analyzed the variations of DNA methylation among tissues compared to other tissues we generated before.

Organism:: Bos taurus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL19172
2 Samples

Download data: TXT

Series

Accession:: GSE147184

ID:: 200147184

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Select item 2001470877.

Analyses of methylomes of multiple tissues in cattle

(Submitter supplied) In this study, we generated whole genome bisulfite sequencing data of 19 samples for 13 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues. In this study, we generated whole genome bisulfite sequencing data of 6 samples for 5 tissues in Hereford cattle. We analyzed the variations of DNA methylation among tissues.

Organism:: Bos taurus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL24230
25 Samples

Download data: TXT

Series

Accession:: GSE147087

ID:: 200147087

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001584308.

Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Bos taurus; Gallus gallus; Sus scrofa

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

9 related Platforms
334 Samples

Download data: BED, TXT

Series

Accession:: GSE158430

ID:: 200158430

PubMed Full text in PMC Similar studies

Select item 2001584299.

Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (H3K4me3 ChIP-Seq)

(Submitter supplied) 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. more...

Organism:: Gallus gallus; Bos taurus; Sus scrofa

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL23499 GPL23295 GPL22475
48 Samples

Download data: BED

Series

Accession:: GSE158429

ID:: 200158429

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015842710.

Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (H3K4me1 ChIP-Seq)

(Submitter supplied) 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. more...

Organism:: Gallus gallus; Sus scrofa; Bos taurus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL23499 GPL22475 GPL23295
48 Samples

Download data: BED

Series

Accession:: GSE158427

ID:: 200158427

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015841911.

Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (H3K27me3 ChIP-Seq)

(Submitter supplied) 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. more...

Organism:: Sus scrofa; Gallus gallus; Bos taurus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL23499 GPL23295 GPL22475
48 Samples

Download data: BED

Series

Accession:: GSE158419

ID:: 200158419

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015841812.

Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (H3K27ac ChIP-Seq)

(Submitter supplied) 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. more...

Organism:: Gallus gallus; Sus scrofa; Bos taurus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL23499 GPL22475 GPL23295
48 Samples

Download data: BED

Series

Accession:: GSE158418

ID:: 200158418

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015841713.

Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (DNase-Hypersensitivity)

(Submitter supplied) 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. more...

Organism:: Gallus gallus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL19005
15 Samples

Download data: BED

Series

Accession:: GSE158417

ID:: 200158417

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015841614.

Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (CTCF ChIP-Seq)

(Submitter supplied) 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. more...

Organism:: Sus scrofa; Gallus gallus; Bos taurus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL23295 GPL22475 GPL23499
48 Samples

Download data: BED

Series

Accession:: GSE158416

ID:: 200158416

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015841415.

Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (ATAC-Seq)

(Submitter supplied) 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. more...

Organism:: Bos taurus; Sus scrofa

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL27907 GPL29175
31 Samples

Download data: BED

Series

Accession:: GSE158414

ID:: 200158414

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015841216.

Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (RNA-Seq)

(Submitter supplied) 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. more...

Organism:: Bos taurus; Gallus gallus; Sus scrofa

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL22626 GPL21659 GPL24486
48 Samples

Download data: TXT

Series

Accession:: GSE158412

ID:: 200158412

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20011926317.

Comparative sperm methylome analysis provide insights into complex phenotypes and epigenome evolution

(Submitter supplied) Using whole-genome bisulfite sequencing (WGBS), we profiled 18 DNA methylomes of cattle sperms that were collected from 18 representative age-matched Holstein bulls with high reliable phenotypes on many complex traits, including sire-conception rate (SCR), gestation length (GL), sire calving ease (SCE), cow conception rate (CCR) and body depth (BDE). Through comparison with human sperm methylome, we observed that genomic regions with differetial DNA methylation levels were enriched for GWAS signals and had important evolutionary impact. more...

Organism:: Bos taurus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL24230
18 Samples

Download data: BED

Series

Accession:: GSE119263

ID:: 200119263

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20010653818.

Genome-wide sequencing and comparative profiling of cattle sperm DNA methylome

(Submitter supplied) Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperms through comparison with three bovine somatic tissues (mammary grand, brain and blood). Large differences between cattle sperms and somatic tissues were observed in the methylation patterns.

Organism:: Bos taurus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL24230
10 Samples

Download data: BED

Series

Accession:: GSE106538

ID:: 200106538

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20018939719.

H3K27ac BL HiChIP and GRID-seq data of LW and MS

(Submitter supplied) For Large White (LW) and Meishan (MS) skeletal muscle, we performed H3K27ac BL HiCHIP to establish enhancer-promoter interaction maps. We also performed GRID-seq which uses a bivalent linker to ligate RNA to DNA in situ.

Organism:: Sus scrofa

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:: GPL19176
12 Samples

Download data: BEDPE, MCOOL, TXT

Series

Accession:: GSE189397

ID:: 200189397

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014328820.

A compendium map of Cis-Regulatory Elements in the Pig Genome and epigenetic comparison with the human Genome

(Submitter supplied) Although major advances in genomics have initiated an exciting new era of research, the lack of information about cis-regulatory elements has limited the genetic improvement or manipulation of pig as meat source and biomedical model. Here, we systematically characterize the cis-regulatory elements and their functions in the pig genome in 12 diverse tissues from 4 pig breeds through RNA-Seq, ATAC-Seq, and ChIP-Seq analyses. more...

Organism:: Sus scrofa

Type:: Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL22918
200 Samples

Download data: BED, BEDGRAPH, BIGWIG, NARROWPEAK

Series

Accession:: GSE143288

ID:: 200143288

PubMed Full text in PMC Similar studies SRA Run Selector

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