Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene Expression from hair cells and supporting cells in chick utricle

ABSTRACT: In adult mammals, hair cell loss is irreversible and may result in hearing and balance deficits. In contrast, birds can regenerate hair cells through differentiation of supporting cells and restore inner ear function, suggesting that hair cell progenitors are present in the population of supporting cells. We used microarrays to identify novel genes related to the regeneration in the chicken utricle. Supporting cell and hair cell populations of chicken utricle obtained by laser capture microdissection, following to do RNA extraction and hybridization on Affymetrix microarrays.

ORGANISM(S): Gallus gallus

SUBMITTER: Takahiro Wakasaki

PROVIDER: E-GEOD-81461 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene Expression from hair cells and supporting cells in chick utricle

Project description:In adult mammals, hair cell loss is irreversible and may result in hearing and balance deficits. In contrast, birds can regenerate hair cells through differentiation of supporting cells and restore inner ear function, suggesting that hair cell progenitors are present in the population of supporting cells. We used microarrays to identify novel genes related to the regeneration in the chicken utricle.

2016-05-17 | GSE81461 | GEO

Embryonic day 15 chick utricle single cell analysis

Project description:Single-cell proteomics can reveal the changing protein composition of differentiating cells. We used shotgun mass spectrometry to determine the abundant proteins present in single or small pools of subpicoliter-sized cells from the embryonic day 15 (E15) utricle of the chicken inner ear, when many hair cells are differentiating from progenitor (supporting) cells. The actin monomer binding protein thymosin β4 (TMSB4X) was present in E15 progenitor cells at nearly equimolar levels relative to actin, but dropped to one-tenth that value in hair cells, with little change in total actin. Single-cell RNA-seq analysis of E15 utricle cells showed that TMSB4X transcripts fell in abundance once hair-cell differentiation initiated. These results suggest that most actin is sequestered in progenitor cells, but upon differentiation to hair cells, actin is released, permitting assembly of the sensory hair bundle.

2019-11-12 | PXD014256 | Pride

Cell-type identity of the avian utricle

Project description:The avian utricle, a vestibular organ of the inner ear, displays turnover of sensory hair cells throughout life. This is in sharp contrast to the mammalian utricle, which shows limited regenerative capacity. Here, we use single-cell RNA-sequencing to identify distinct marker genes for the different sensory hair cell subtypes of the chicken utricle, which we validated in situ . We provide markers for spatially distinct supporting cell populations, and identified two transitional cell populations of dedifferentiating supporting cells and developing hair cells. Trajectory reconstruction resulted in an inventory of gene expression dynamics of natural hair cell generation in the avian utricle.

2022-09-07 | GSE212831 | GEO

The Transcriptome of Utricle Hair Cell Regeneration in the Avian Inner Ear

Project description:A comprehensive transcriptome profile of chicken utricle hair cell across a 7 days regenerative time course.

2014-04-29 | GSE57134 | GEO

The Transcriptome of Utricle Hair Cell Regeneration in the Avian Inner Ear

Project description:A comprehensive transcriptome profile of chicken utricle hair cell across a 7 days regenerative time course. Compare gene expression changes in chicken utricle treated with streptomycin to the control. A total of 60 samples were collected from 11 different time points. Each time point contains at least 2 biological samples.

2014-04-29 | E-GEOD-57134 | biostudies-arrayexpress

Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1

Project description:The mammalian cochlea loses its ability to regenerate new hair cells prior to the onset of hearing. In contrast, the adult vestibular system can produce new hair cells in response to damage, or by reprogramming of supporting cells with the hair cell transcription factor Atoh1. We used RNA-seq and ATAC-seq to probe the transcriptional and epigenetic responses of utricle supporting cells to damage and Atoh1 transduction. We show that the improved regenerative response of the utricle correlates with a more accessible chromatin structure in utricle supporting cells compared to their cochlear counterparts. We also provide evidence that Atoh1 transduction of supporting cells is able to promote increased transcriptional accessibility of some hair cell genes. Our study offers a possible explanation for regenerative differences between sensory organs of the inner ear, but shows that additional factors to Atoh1 may be required for optimal reprogramming of hair cell fate.

2019-04-30 | GSE121610 | GEO

Expression data from chick cochlea and utricle

Project description:Inner ear auditory and vestibular tissues differ in their responses to mechanical stimuli. Chick cochlea and utricle sensory epithelia were microdissected at E20-E21. RNA was extracted and cRNA hybridized to Affymetrix microarrays.

2012-01-01 | E-GEOD-32272 | biostudies-arrayexpress

Utricle Neomycin Timecourse

Project description:Much of human hearing loss is caused by loss of auditory hair cell (HC) function. Mammals cannot regenerate these essential mechanoelectrical transducers of sound. However, birds have retained the ability to regenerate HCs from surrounding supporting cells. To better understand hair cell regeneration, we have expression profiled the sensory epithelia from chicken cochleae and utricles. Pure sensory epithelia, consisting of HCs plus supporting cells, were damaged with either neomycin or laser treatment. Changes in gene expression at various points during regeneration were compared to undamaged control cultures on a custom microarray that interrogates the vast majority of transcription factor (TF) genes. These experiments involved multiple biological samples and hundreds of microarray comparisons. Keywords: timecourse

2007-02-01 | GSE5991 | GEO

Utricle Laser Timecourse

2007-02-01 | GSE6052 | GEO

GATA3 siRNA in utricle sensory epithelia

Project description:The inner ear utilizes sensory hair cells as mechano-electric transducers for sensing sound and balance. In mammals, these hair cells lack the capacity for regeneration. Unlike mammals, hair cells from non-mammalian vertebrates, such as birds, can be regenerated throughout the life of the organism making them a useful model for studying inner ear genetics pathways. The zinc finger transcription factor GATA3 is required for inner ear development and mutations cause sensory neural deafness in humans. In the avian cochlea GATA3 is expressed throughout the sensory epithelia; however, expression is limited to the striola of the utricle. The striola corresponds to an abrupt change in morphologically distinct hair cell types and a 180Â° shift in hair cell orientation. We used 3 complimentary approaches to identify potential downstream targets of GATA3 in the avian utricle. Specifically we used microarray expression profiling of GATA3 knockdown by siRNA and GATA3 over-expression treatments as well as direct comparisons of GATA3 expressing cells from the striola and non GATA3 expressing cells from the extra-striola. Whole utricle specimens were treated with streptomycin for 24 hrs, rinsed and allowed to recover for an additional 24 hrs. Whole utricles were transfected with either GATA3 or GFP 21mer synthetic siRNAs for an additional 48 hrs and pure sensory epithelia were isolated. There are 2 biological samples and experiments include technical replicates as well as dye-switches for a total of 8 microarrays.

2010-06-24 | E-GEOD-14785 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data