GEO DataSets

(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) 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:

Talpa occidentalis

Type:

Other

Platform:

GPL25619

1 Sample

Download data: TXT

(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

Type:

Expression profiling by array

Platforms:

GPL10787 GPL11202 GPL7202

14 Samples

Download data: TXT

(Submitter supplied) We have employed whole genome microarray expression profiling to identify genes regulated by Sall1 in the kidney.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

6 Samples

Download data: TXT

(Submitter supplied) We have employed whole genome microarray expression profiling to identify genes regulated by Sall1 in the kidney.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

4 Samples

Download data: TXT

(Submitter supplied) We have employed whole genome microarray expression profiling to identify genes regulated by Sall1 in the kidney.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

4 Samples

Download data: TXT

(Submitter supplied) Sall1 is a multi-zinc finger transcription factor that regulates kidney organogenesis. It is considered to be a transcriptional repressor, preferentially localized on heterochromatin. Mutations or deletions of the human SALL1 gene are associated with the Townes-Brocks syndrome. Despite its high expression, no function was yet assigned for Sall1 in embryonic stem (ES) cells. In the present study we show that Sall1 is expressed in a differentiation-dependent manner and physically interacts with Nanog and Sox2, two components of the core pluripotency network. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

3 Samples

Download data: BAR, CEL

(Submitter supplied) The goal of this study is to identify genes differentially expressed between microglia and infiltrating macrophages in the injured retina Methods: mRNA profiles of microglia (Cont) and infiltrating macrophages (GFP) at day 7 post-injry, quadruplicated, were generated by deep-sequencing using Illumina HiSeq 2500 sequencer. Results: RNA-seq tags were mapped to the mouse mm9 reference genome assembly using Tophat2 ver. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach towards understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL18573

29 Samples

Download data: TXT

(Submitter supplied) To delineate the epigenomic profile of the Six2+ mouse nephron progenitor cells, we mapped open chromatin using ATAC-Seq in Six2+ cells from E16.5 mouse kidneys.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: BW, TXT

(Submitter supplied) The Six2 distal enhancer regulates expression of the 60 kb-downstream gene Six2, but does not regulate the Six3 gene which is 70 kb further downstream. CTCF ChIP-Seq and Hi-C data points to a chromatin domain boundary between Six2 and Six3 which may intervene interaction between Six2-DE and Six3. The irradiation-induced Brachyrrhine (Br) mutant allele was found to carry a 320 kb genomic inversion that includes Six2 and Six3, but not Six2DE. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

2 Samples

Download data: BEDGRAPH

(Submitter supplied) In developing mammalian kidney, nephron progenitor cells (NPC) give rise to all cells in mature nephrons. Several transcription factors, including Six2, Hoxd11, Osr1 and Wt1, are expressed in NPC and are essential for its maintenance and/or specification. In order to understand the regulatory functions of these factors, we mapped binding sites of Six2, Hoxd11 and Osr1 in NPC using a novel transgenic strategy, and of Wt1 in wild-type developing kidney.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

23 Samples

Download data: BW, TXT