GEO DataSets

(Submitter supplied) Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. more...

Organism:

Talpa occidentalis

Type:

Other

Platforms:

GPL25619 GPL25620

3 Samples

Download data: HIC

(Submitter supplied) Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. more...

Organism:

Mus musculus; Talpa occidentalis

Type:

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

Platforms:

GPL25619 GPL17021 GPL25620

70 Samples

Download data: BEDGRAPH, BW, HIC

(Submitter supplied) Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. more...

Organism:

Talpa occidentalis

Type:

Other

Platforms:

GPL25619 GPL25620

2 Samples

Download data: BEDGRAPH, FA, GFF

(Submitter supplied) Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. more...

Organism:

Talpa occidentalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25619

6 Samples

Download data: BED, BW, FA, GFF

(Submitter supplied) Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. more...

Organism:

Talpa occidentalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25619

24 Samples

Download data: BED, BW, FA, GFF

(Submitter supplied) Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. more...

Organism:

Talpa occidentalis; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25619 GPL17021

35 Samples

Download data: BW, FA, GFF

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

Organism:

Mus musculus; Talpa occidentalis

Type:

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

Platforms:

GPL25619 GPL17021

37 Samples

Download data: TXT

(Submitter supplied) Changes in gene expression represent an important source for phenotypical innovation. Yet, how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing comparative analyses of epigenetic and transcriptional data in mole and mouse, we identified SALL1 as a co-opted gene for the formation of testicular tissue in mole ovotestes. more...

Organism:

Talpa occidentalis; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL25619

32 Samples

Download data: BW

(Submitter supplied) Changes in gene expression represent an important source for phenotypical innovation. Yet, how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing comparative analyses of epigenetic and transcriptional data in mole and mouse, we identified SALL1 as a co-opted gene for the formation of testicular tissue in mole ovotestes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TXT

(Submitter supplied) Changes in gene expression represent an important source for phenotypical innovation. Yet, how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing comparative analyses of epigenetic and transcriptional data in mole and mouse, we identified SALL1 as a co-opted gene for the formation of testicular tissue in mole ovotestes. more...

Organism:

Talpa occidentalis

Type:

Other

Platform:

GPL25619

1 Sample

Download data: TXT

(Submitter supplied) We sequenced polyA-selected RNA from bone marrow derived cells from 47 bone samples collected from 16 captive, adult female Damaraland mole-rats (Fukomys damarensis). The 16 females were experimentally manipulated to either remain as nonbreeders (either as helpers or solitaires) or become breeders, and breeding status was maintained for over 1 year prior to tissue collection and cell culture. A subset of cultured cells were treated for 24 hours with 10 nM estradiol prior to sample collection.

Organism:

Fukomys damarensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28700

47 Samples

Download data: TXT

(Submitter supplied) Changes in gene regulation have long been though to underlie most phenotypic differences between species. Subterranean rodents, and in particular the naked mole-rat (NMR), have attracted substantial attention due to their proposed phenotypic adaptations, which include hypoxia tolerance, metabolic changes and cancer resistance. However, it is largely unknown what regulatory changes may associate with these phenotypic traits, and whether these are unique to the NMR, the mole-rat clade or also present in other mammals. more...

Organism:

Mus musculus; Fukomys damarensis; Heterocephalus glaber; Cavia porcellus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

13 related Platforms

160 Samples

Download data: NARROWPEAK, WIG

(Submitter supplied) Deep sequencing of mRNA from naked mole rat

Organism:

Heterocephalus glaber

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13793

13 Samples

Download data: BEDGRAPH

(Submitter supplied) The overall goal of this project is to investigate the role of TGF-beta signaling in palate development in order to discover candidate therapeutics for preventing and treating congenital birth defects. Here, we conducted gene expression profiling of embryonic palatal tissue from wild type mice as well as those with a neural crest specific conditional inactivation of the Tgfbr2 gene. The latter mice provide a model of cleft palate formation.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4483

Platform:

GPL1261

10 Samples

Download data: CEL

Analysis of palatal tissues from E14.5 animals depleted for f TGF-beta receptor type II in cranial neural crest cells. Palatal fusion takes place at E14.5. Results provide insight into the role of TGF-beta signaling in palate development.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE22989

10 Samples

Download data: CEL

(Submitter supplied) Placenta transcriptome from two species of Spalax. Associated with the article "Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax."

Organism:

Spalax carmeli; Nannospalax galili

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17526 GPL20184

2 Samples

Download data: FASTA, TXT

(Submitter supplied) Deep sequencing of mRNA from Spalax galili and Rattus norvegicus

Organism:

Nannospalax galili; Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17526 GPL14844

12 Samples

Download data: BEDGRAPH

(Submitter supplied) Bread wheat is allohexaploid with 16 Gb genome, which has large intergenic region with abundant TEs and regulatory sequences . Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide the first systematic epigenomic map for functional annotation of the allohexaploid wheat genome.

Organism:

Triticum aestivum

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24354

18 Samples

Download data: BED, BW, TXT

(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

(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