GEO DataSets

(Submitter supplied) The inner ear continues to grow and develop until the auditory and vestibular systems reach full maturity and all of the genes involved in this process have yet to be identified. Previous gene based analysis have primarily focused on the early developmental stages following induction and initial formation of the inner ear. The aim of this study is to identify new candidate genes for inner ear development. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL10756

3 Samples

Download data: CEL

(Submitter supplied) The inner ear continues to grow and develop until the auditory and vestibular systems reach full maturity and all of the genes involved in this process have yet to be identified. Previous gene based analysis have primarily focused on the early developmental stages following induction and initial formation of the inner ear. The aim of this study is to identify new candidate genes for inner ear development. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL10756

3 Samples

Download data: CEL

(Submitter supplied) Purpose: To identify orthologous genes in Xenopus that are implicated in deafness and vestibular disorders in humans and to compare RNA-Seq and microarray to determine the advantages of each technology for Xenopus transcriptomic analysis. Methods: Inner ear RNA from X. laevis stages 56-58 was isolated with the Qiagen® RNeasy® Mini Kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer. The RNA was sent to the National Center for Genome Resources, for Illumina-Solexa sequencing using the genome analyzer II and to MIT for microarray processing usign the Affymetrix GeneChip® X. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14834

1 Sample

Download data: TXT

(Submitter supplied) The genes involved in inner ear development have yet to be fully characterized. Previous gene-based analyses have primarily focused on the early developmental stages following induction and initial formation of the inner ear. The inner ear continues to grow and develop until the auditory and vestibular systems reach full maturity; all of the genes involved in this process have yet to be identified. The aim of this study is to identify additional candidate genes for inner ear development. Microarrays were used to produce expression profiles from the post-metamorphic juvenile stage of the Xenopus laevis inner ear.

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL10756

3 Samples

Download data: CEL

(Submitter supplied) We implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis. Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear.

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL1318

3 Samples

Download data: CEL

(Submitter supplied) We report a gene expression changes during development and maturation of the murine utricle

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: TXT

(Submitter supplied) Xenopus laevis tadpoles are capable of limb regeneration following amputation, in a process which initially involves the formation of a blastema. However, Xenopus has full regenerative capacity only through premetamorphic stages. We have used the Affymetrix Xenopus laevis Genome Genechip® microarray to perform a large-scale screen of gene expression in the regeneration-complete, stage 53 (st53), and regeneration-incomplete, stage 57 (st57), hindlimbs at 1 and 5 days post-amputation. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL1318

16 Samples

Download data

(Submitter supplied) RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the discovery of a group of novel animally enriched RNAs, this study revealed a surprisingly low conservation of vegetal RNA localization between the two frog species.

Organism:

Xenopus tropicalis; Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15472 GPL17682

12 Samples

Download data: CSV, TXT

(Submitter supplied) We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. In total, we obtained over 900 million reads and the deep coverage allowed us to examine the transcriptome in detail. First, we found that ~150 genes are transcribed before embryonic genome activation when transcription is generally thought to be repressed. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15472

40 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL9250

14 Samples

Download data: TXT

(Submitter supplied) An immortalized multipotent otic progenitor (iMOP) cell was generated by transient expression of c-Myc in Sox2-expressing otic progenitor cells. The procedure activated endogenous c-Myc expression in the cells and amplified existing Sox2-dependent transcripts to promote self-renewal. Downregulation of c-Myc expression following growth factor withdrawal resulted in a molecular switch from self-renewal to otic differentiation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

7 Samples

Download data: TXT

(Submitter supplied) An immortalized multipotent otic progenitor (iMOP) cell was generated by transient expression of c-Myc in Sox2-expressing otic progenitor cells. The procedure activated endogenous c-Myc expression in the cells and amplified existing Sox2-dependent transcripts to promote self-renewal. Downregulation of c-Myc expression following growth factor withdrawal resulted in a molecular switch from self-renewal to otic differentiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

7 Samples

Download data: TXT

(Submitter supplied) Hair cells of the inner ear are essential for hearing and balance. As a consequence, pathogenic variants in genes specifically expressed in hair cells often cause hereditary deafness. Hair cells are few in number and not easily isolated from the adjacent supporting cells, so the biochemistry and molecular biology of hair cells can be difficult to study. To study gene expression in hair cells, we developed a protocol for hair cell isolation by FACS sorting. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

18 Samples

Download data: TXT

(Submitter supplied) Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. Here, we use this wealth of knowledge as leverage in the design and analysis of a genomic visualization of organizer-related gene transcription. Using ectopic expression of the two major activities of the organizer, BMP and Wnt inhibition, as well as endogenous tissues, we generate a focused set of samples that represent different aspects of organizer signaling. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Dataset:

GDS2301

Platform:

GPL1318

20 Samples

Download data: CEL

Analysis of stage 10 early and stage 11.5 late gastrula embryos ectopically expressing Noggin, Dkk-1, or both to induce different aspects of organizer activity. The organizer patterns vertebrate embryos during gastrulation. Results provide insight into organizer function during gastrulation.

Organism:

Xenopus laevis

Type:

Expression profiling by array, count, 4 agent, 2 development stage, 4 other, 2 tissue sets

Platform:

GPL1318

Series:

GSE3368

20 Samples

Download data: CEL

(Submitter supplied) To understand the basic biological properties of inner ear hair cells (HCs) from non-mammalian vertebrates, we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP-labeled HCs were isolated from inner-ear sensory epithelia of a pou4f3 promoter-driven GAP-GFP line of transgenic zebrafish. One thousand HCs and 1,000 non-sensory surrounding cells (nsSCs) were separately collected for each biological replicate, using the suction pipette technique. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

6 Samples

Download data: XLSX

(Submitter supplied) To understand the basic biological property of hair cells (HCs) from lower vertebrates, we examined transcriptomes of adult zebrafish HCs. GFP-labeled HCs were isolated from the utricle, saccule, and lagena, the three inner-ear sensory epithelia of a pou4f3 promoter-driven GAP-GFP line of transgenic zebrafish. 2,000 HCs and 2,000 non-sensory cells from the inner ear were individually collected by suction pipet technique. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

6 Samples

Download data: XLSX

(Submitter supplied) We characterize the genetic diversity of Xenopus laevis strains using allele-specific RNA-seq data analysis and provide a catalogue of coding variation which can be used for improving the genomic sequence, as well as for better sequence alignment, probe design, and proteomic analysis. In addition, we paint a broad picture of the genetic landscape of the species by functionally annotating different classes of mutations with a well-established prediction tool (PolyPhen-2). more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

3 Samples

Download data: TSV, TXT, VCF

(Submitter supplied) Here, we show lists of 10 up- and 87 down-regulated genes obtained by a cDNA microarray analysis that compared developing Myf5-/-:Myod-/- (and Mrf4-/-) petrous part of the temporal bone, containing middle and inner ear, to the control, at embryonic day 18.5. Myf5-/-:Myod-/- fetuses entirely lack skeletal myoblasts and muscles. They are unable to move their head, which interferes with the perception of angular acceleration. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

2 Samples

Download data: CEL, CHP

(Submitter supplied) A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non-mammalian vertebrates such as zebrafish, regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability, the degree to which the inner ears of fish and mammals share common hair and supporting cell types remains unresolved. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

2 Samples

Download data: CSV, RDS