GEO DataSets

(Submitter supplied) While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). more...

Organism:

Leucoraja erinacea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30966

4 Samples

Download data: BW

(Submitter supplied) While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). more...

Organism:

Leucoraja erinacea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30966

26 Samples

Download data: TAB

(Submitter supplied) While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). more...

Organism:

Leucoraja erinacea

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30966

4 Samples

Download data: HIC

(Submitter supplied) Using MetylC-seq we investigated single-base resolution methylomes of embryonic and adult pelvic and pectoral fins of little skate.

Organism:

Leucoraja erinacea

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL31065 GPL31064

4 Samples

Download data: BEDGRAPH

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

Organism:

Leucoraja erinacea

Type:

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

Platform:

GPL30966

51 Samples

Download data: BW, HIC

(Submitter supplied) While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). more...

Organism:

Leucoraja erinacea

Type:

Other

Platform:

GPL30966

5 Samples

Download data: HIC

(Submitter supplied) While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). more...

Organism:

Leucoraja erinacea

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30966

4 Samples

Download data: HIC

(Submitter supplied) While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). more...

Organism:

Leucoraja erinacea

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30966

8 Samples

Download data: BW

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

Organism:

Gallus gallus; Mus musculus; Leucoraja erinacea

Type:

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

Platforms:

GPL17021 GPL22922 GPL26853

18 Samples

Download data

(Submitter supplied) The little skate, a cartilaginous fish evolutionarily distal from tetrapods, displays walking-like behavior and has conserved genetic programs and neuronal substrates for land-walking. Studies on little skate have been limited due to lack of high-quality genome assembly. Here, we generated an improved genome assembly of little skate reflecting precise gene annotation and structures and performed integrated analysis of gene expression and chromatin accessibility to investigate molecular mechanisms of fin motor neuron development. more...

Organism:

Gallus gallus; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26853 GPL17021

11 Samples

Download data: TXT

(Submitter supplied) The little skate, a cartilaginous fish evolutionarily distal from tetrapods, displays walking-like behavior and has conserved genetic programs and neuronal substrates for land-walking. Studies on little skate have been limited due to lack of high-quality genome assembly. Here, we generated an improved genome assembly of little skate reflecting precise gene annotation and structures and performed integrated analysis of gene expression and chromatin accessibility to investigate molecular mechanisms of fin motor neuron development. more...

Organism:

Leucoraja erinacea

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22922

7 Samples

Download data: BED, BW

(Submitter supplied) Polycomb repressive complexes (PRCs) 1 and 2 maintain stable cellular memories of early developmental patterning programs by establishing heritable patterns of gene repression. PRCs repress transcription through histone modifications and chromatin compaction, but their roles in neuronal subtype diversification are poorly defined. We unexpectedly found that PRC2 is dispensable to preserve the Hox transcription factor-dependent positional identity of spinal motor neurons (MNs), while PRC1 is essential for the specification of segmentally-restricted subtypes. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21103 GPL19057 GPL24247

38 Samples

Download data: BW, TXT

(Submitter supplied) The goal of this study is to find skate pectoral fin motor neuron markers. Total RNA was extracted from manually sorted pectoral fin MNs, which were retrogradely labeled and tail spinal cord cells. By comparing RNA expression profiles of pectoral fin MNs and tail spinal cord neurons, we could identity general MN, MN columnar, and subset MN pool markers for fin MNs.

Organism:

Leucoraja erinacea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24146

6 Samples

Download data: FASTA, XLSX

(Submitter supplied) Gene expression profiling of pooled late stage embryos from Leucoraja erinacea, Scyliorhinus canicula and Callorhinchus milii show that HOXC cluster genes are not expressed in the two elasmobranch fishes, L. erinacea and S. canicula. This finding supports the observations that these genes are not found in whole genome shotgun sequencing of L. erinacea or genomic clones from S. canicula.

Organism:

Scyliorhinus canicula; Leucoraja erinacea; Callorhinchus milii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11347 GPL11348 GPL11349

3 Samples

Download data: CSV, FA

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

Organism:

Mus musculus; Chiloscyllium punctatum

Type:

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

Platforms:

GPL21273 GPL27153 GPL18480

43 Samples

Download data: BW

(Submitter supplied) We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.

Organism:

Chiloscyllium punctatum; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27153 GPL18480

30 Samples

Download data: TXT

(Submitter supplied) We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

13 Samples

Download data: BW

(Submitter supplied) Despite their evolutionary, developmental, and functional importance the origin of vertebrate paired appendages remains a mystery. Classical ideas center on three hypotheses: that paired fins relate to gill arches, are derived from a fin fold, or that median fins evolved first and paired fins arose by co-option of ancient genetic patterning modules. Importantly, the third hypothesis makes specific predictions about the function and phylogenetic history of cis-regulatory elements (CREs) involved in appendage patterning. more...

Organism:

Oryzias latipes; Mus musculus

Type:

Other

Platforms:

GPL17021 GPL23308

4 Samples

Download data: BEDGRAPH