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Series GSE27176

Query DataSets for GSE27176

Status

Public on Mar 01, 2011

Title

Analysis of Gene Expression in the Chicken Otocyst

Organism

Gallus gallus

Experiment type

Expression profiling by SAGE

Summary

The inner ear arises from multipotent placodal precursors that are gradually committed to the otic fate and further differentiate into all inner ear cell types, with the exception of a few neural crest-derived cells. The otocyst has a pivotal role during inner ear development: otic progenitor cells sub-compartmentalize into non-sensory regions and regions giving rise to prosensory domains where subsequently also hair cells differentiate. The genes and pathways underlying this progressive subdivision and differentiation process are not entirely known. The goal of this study was to identify a comprehensive set of genes expressed in the chicken otocyst using the serial analysis of gene expression (SAGE) method. Our analysis revealed several hundred transcriptional regulators, potential signaling proteins, and receptors. We identified a substantial collection of genes that were previously known in the context of inner ear development, but we also found many new candidate genes, such as Sox4, Sox5, Sox7, Sox8, Sox11, and Sox18, which previously were not known to be expressed in the developing inner ear. Despite its obvious limitation of not being all-inclusive, the generated otocyst SAGE library is a practical bioinformatics tool to study otocyst gene expression and to identify candidate genes for developmental studies.

Overall design

Otocysts were dissected from HH stage 18-19 chicken embryos, total RNA was extracted, and subjected to a commercial long-SAGE protocol, resulting in a library of concatemerized tags. 3,512 individual clones of SAGE concatemers were sequenced resulting in 39,326 17-bp tags with tag counts up to 718 for the most abundant tag; 3,292 tags that were represented between two and five times, whereas the majority of tags (11,717) were only found once. Overall, we identified 16,008 unique sequence tags.

Contributor(s)

Sinkkonen ST, Starlinger V, Galaiya DJ, Laske RD, Myllykangas S, Oshima K, Heller S

Citation(s)

21853378

Submission date

Feb 09, 2011

Last update date

Mar 09, 2020

Contact name

Samuel Myllykangas

E-mail(s)

smyllyka@stanford.edu