GEO DataSets

(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) 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:

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:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30966

8 Samples

Download data: BW

(Submitter supplied) Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally-distinct subtypes of motor neurons (MNs). MNs are essential to movement and differentially susceptible in disease, but little is known about how MNs acquire functional subtype-specific features during development. Using single-cell RNA profiling in embryonic and larval zebrafish, we identify novel and conserved molecular signatures for MN functional subtypes, and identify genes expressed in both early post-mitotic and mature MNs. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

7 Samples

Download data: H5

(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) The goal of this study was to identify potential Hox5 target genes in cervical motor neurons (C3-C6) using unbiased genomic screens (RNA-seq). We examined expression changes independently of motor neuron cell death by deleting the pro-apoptotic gene Bax in both control and experimental mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: XLSX

(Submitter supplied) Comparison of the transcriptome of embryonic day 12 motor neurons and postnatal day 8 motor neurons. Comparison of the transcriptome of motor neurons without Hoxc8 protein and control littermates. Comparison of the transcriptome of postnatal day 8 motor neurons from the brachial, thoracic and lumbar regions of the spinal cord.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

18 Samples

Download data: TAB

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL16158

20 Samples

Download data: BIGWIG, GFF, PAIR, TXT

(Submitter supplied) The nucleoprotein Geminin (Gmnn) promotes neural cell fate acquisition of embryonic stem cells, while knockdown reduces the efficiency of neural gene activation. This occurs, at least in part, through Geminin’s ability to promote histone hyperacetylation at neural genes, to activate their expression. In mouse models in vivo, Geminin deficiency in the embryonic neural tube between embryonic days 8.5-10.5 also reduces the expression of genes controlling neural specification and/or differentiation, contributing to neural tube defects. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL16158

12 Samples

Download data: GFF, PAIR, TXT

(Submitter supplied) Cell intrinsic factors that control neuroectoderm specification of early embryonic cells include the nucleoprotein Geminin (Gmnn) and the Zic family of zinc finger transcription factors. Gmnn modulates chromatin state to activate neural gene expression during neural cell fate acquisition, while Gmnn deficiency in the forming neural plate disrupts transcriptional programs that control neural cell specification, neural plate patterning and neurogenesis, resulting in neural tube defects. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: BIGWIG