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| Status |
Public on Aug 31, 2017 |
| Title |
Next generation sequencing based analysis of the embryonic (E15.5) transcriptome of wild type and β1-integrin-cKO lenses |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
β1-integrin is the major β-integrin subunit expressed in both lens epithelial and fiber cells. Our previous research indicated that β1-integrin is essential for the maintenance of lens epithelial integrity and survival in late embryonic lens development (Simirskii et al, 2009). Lack of β1-integrin in the lens will lead to severe micropthalmia and lack of lens in adult mice. In order to study the mechanisms involved, high throughput RNA sequencing (RNAseq) was performed to determine the genes that are differentially expressed between E15.5 wild type (WT) lenses and lenses that lack β1-integrin expression due to the action of MLR10 CRE (β1-cKO). The methodology used here is similar to the other RNAseq experiments that were previously performed in our lab (Manthey et al., 2014a and Audette et al, 2015) (Geo accession: GSE 49949 and GSE69940) . Meanwhile, the filtering criteria and processing procedures were also published (Manthey et al., 2014b). Compared to WT, 120 genes were found to be differentially expressed in β1-cKO lenses. Moreover, bioinformatics tools (DAVID (the database for Annotation, Visulization and Integrated Discovery), and PANTHER (Protein Analysis through Evolutionary Relationship) classification system) as well as manual literature searching was applied for further data analysis. It showed that genes involved in EMT and stress-responses were differentially expressed in β1-cKO compared to that of WT. Description of filtering criteria: To identify the differentially expressed genes, pair-wise qCML method exact tests with a Benjamini Hochberg false discovery rate correction greater than the threshold of P<0.05 was applied, which identified 5120 genes. As previously described (Manthey et al., 2014b), most of the genes differentially expressed between inbred C57Bl/6 <har> and mice with a mixed background were below a threshold of 2.5 fold change. Therefore, all differentially expressed genes with a less than 2.5 fold change were filtered out. Further, genes whose expression level were not high enough to be biologically significant were also filtered out, based on the RPMK (Reads per Kilobase per million reads) value. Any gene in the final list has RPKM greater that 2 in either WT or β1-cKO samples, a value that corresponds to approximately 1 mRNA molecule per cell. By applying a combination of these filtering criteria, 120 differentially expressed genes were found, which could potentially elucidate the molecular connections between conditional deletion of β1-intergrin from the lens and the observed phenotypic abnormalities. Manthey, A. L., Lachke, S. A., FitzGerald, P. G., Mason, R. W., Scheiblin, D. A., McDonald, J. H. and Duncan, M. K. (2014a) 'Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development', Mech Dev 131: 86-110. Manthey, A. L., Terrell, A. M., Lachke, S. A., Polson, S. W. and Duncan, M. K. (2014b) 'Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis', Genom Data 2: 369-374.
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| Overall design |
RNA-Seq comparison of C57Bl/6 <har> wild type controls and β1-integrin conditional knockout lenses at E15.5, three biological replicates were used in each group
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| Contributor(s) |
Terrell AM, Wang Y, Duncan MK |
| Citation(s) |
28763805 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 EY015279 |
The influence of capsule composition on lens biology: The Influence of Capsule Composition on Lens Biology: The Influence of Capsule Composition on Lens Biology: The Influence of Capsule Composition on Lens Biology: The Influence of Capsule Composition on Lens Biology: The influence of capsule composition on lens biology: The influence of capsule composition on lens biology: The influence of capsule composition on lens biology: The Influence of Capsule Composition on Lens Biology: The Influence of Capsule Composition on Lens Biology: The Influence of Capsule Composition on Lens Biology: The influence of capsule composition on lens biology |
UNIVERSITY OF DELAWARE |
MELINDA K. DUNCAN |
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| Submission date |
Jan 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Melinda K. Duncan |
| E-mail(s) |
duncanm@udel.edu
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| Phone |
3028310533
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| Organization name |
University of Delaware
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| Department |
Biological Sciences
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| Lab |
Vertebrate Development
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| Street address |
327 Wolf Hall
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19716 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA309677 |
| SRA |
SRP068845 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77188_RAW.tar |
6.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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