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| Status |
Public on Jan 31, 2019 |
| Title |
RNA seq analysis of the mouse pNC and Cornea transcriptome |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goal of this study is to provide a detailed transcriptome expression profile of the mouse cornea and evaluate changes in gene expression during mouse corneal development.
Methods: RNA-sequencing is used to profile the mouse transcriptome in the pNC isolated at E10.5 and corneas isolated at E14.5 and E16.5. Samples generated in triplicate for sequencing by Illumina Hiseq 4000. Clean reads are mapped to reference gene and GRCm38 by Bowtie2 and HISAT. Spatiotemporal expression patterns of select genes were validaed by in situ hybrdization.
Results: Analysis of the whole transcriptome profile between pNC and embryonic corneas identified 3815 unique differentially expressed genes. Pathway analysis revealed enrichment of differentially expressed genes involved in signal transduction (RA, TGFβ, and Wnt pathways) and transcriptional regulation.
Conclusions: Our study for the first time, identifies differential gene expression across progressive stages of mouse corneal development and provides a comprehensive transcriptomic profile of the developing cornea. This serves as a valuable resource for the identification of novel regulatory networks crucial for the advancement of studies in congential defects, stem cell therapy, bioengineering, and adult corneal diseases.
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| Overall design |
RNA sequencing of ocular tissues from a selection of three developmental stages: periocular neural crest (E10.5) and cornea (E14.5 and E16.5). Three biological replicates for each stage for a total of 9 samples. The E10.5 samples are considered the baseline but all samples are compared.
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| Contributor(s) |
Ma J, Lwigale PY |
| Citation(s) |
30786278 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R21 EY027048 |
Analysis of genes involved in neural crest cell fate decisions during corneal development. |
RICE UNIVERSITY |
PETER Y LWIGALE |
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| |
| Submission date |
Oct 09, 2018 |
| Last update date |
Mar 19, 2019 |
| Contact name |
Peter Y Lwigale |
| E-mail(s) |
lwigale@rice.edu
|
| Phone |
7133486785
|
| Organization name |
Rice University
|
| Department |
BioSciences
|
| Street address |
6100 Main street
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77005 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA495410 |
| SRA |
SRP164788 |
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