MiRNAseq analysis of Chrnb4-cre driven Dicer conditional knockout (Dicer CKO) whole retinas
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ABSTRACT:
PROVIDER: PRJEB30775 | ENA |
REPOSITORIES: ENA
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Project description:We have shown that Chrnb4-cre; Dicerflox/flox retinas (Dicer CKO) display a cone dystrophy by postnatal day P21, independent of rod degeneration. To elucidate which gene pathways were affected by Dicer loss, RNA sequencing was performed in whole neural retinas of P21 control and Dicer CKO mice. This experiment aims to identify which genes were differentially expressed between Dicer conditional knockout and control mice.
2019-01-14 | E-MTAB-6133 | biostudies-arrayexpress
Project description:We have shown that Chrnb4-cre; Dicerflox/flox retinas (Dicer CKO) display a cone dystrophy by postnatal day P21, independent of rod degeneration. To elucidate which miRNAs were involved in such phenotype, miRNA sequencing was performed in whole retinas of P21 and 3.5 month old control and Dicer CKO mice. This experiment aims to identify which miRNAs were differentially expressed in Dicer conditional knockout mice when compared to control mice.
2019-01-14 | E-MTAB-6132 | biostudies-arrayexpress
Project description:RNAseq analysis of Chrnb4-cre driven Dicer conditional knockout (Dicer CKO) whole retinas
| PRJEB30776 | ENA
Project description:Epithelial-stromal interactions in the uterus are required for normal uterine functions such as pregnancy, and multiple signaling pathways are essential for this process. Although Dicer and microRNAs (miRNA) have been implicated in several reproductive processes, the specific role of Dicer and miRNA in uterine development is not known. To address the roles of miRNA in the regulation of these key uterine pathways, we generated a conditional knockout (cKO) of Dicer in the postnatal uterine epithelium and stroma using progesterone receptor (PR)-Cre. These Dicer cKO are sterile with small uteri, which demonstrate significant defects including absence of glandular epithelium and enhanced stromal apoptosis, beginning at postnatal day 15 with expression of Cre and deletion of Dicer. Although these mice had normal serum steroid hormone levels, critical uterine signaling pathways, including progesterone-responsive genes, Indian hedgehog signaling, and the Wnt/Beta-catenin canonical pathway, were dysregulated at the mRNA level. Gene expression profiling data from pools of Dicer cKO and control uteri groups, at 15 days. two group comparison
2012-08-14 | E-GEOD-39181 | biostudies-arrayexpress
Project description:Epithelial-stromal interactions in the uterus are required for normal uterine functions such as pregnancy, and multiple signaling pathways are essential for this process. Although Dicer and microRNAs (miRNA) have been implicated in several reproductive processes, the specific role of Dicer and miRNA in uterine development is not known. To address the roles of miRNA in the regulation of these key uterine pathways, we generated a conditional knockout (cKO) of Dicer in the postnatal uterine epithelium and stroma using progesterone receptor (PR)-Cre. These Dicer cKO are sterile with small uteri, which demonstrate significant defects including absence of glandular epithelium and enhanced stromal apoptosis, beginning at postnatal day 15 with expression of Cre and deletion of Dicer. Although these mice had normal serum steroid hormone levels, critical uterine signaling pathways, including progesterone-responsive genes, Indian hedgehog signaling, and the Wnt/Beta-catenin canonical pathway, were dysregulated at the mRNA level.
2012-08-15 | GSE39181 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare small non-coding RNA profiling (snRNA-seq) in WT oocyte, sperm and 2PN stage embryos to those sperm and 2PN stage embryos derived from WT, Dicer cKO and Drosha cKO. We further study the roles of sperm-borne small RNA on fertilization and pre-implantation embryonic development. Methods: Small RNA profiles of adult wild-type (WT) oocytes, adult WT sperm, 2PN stage embryos, adult Dicer cKO/Drosha cKO sperm, 2PN stage embryos were generated by deep sequencing in duplicate, using Ion Torrent Proton. The sequence reads that passed quality filters were analyzed at the small RNA level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 small RNA (miRNA and endo-siRNA) in the oocyte, sperm and 2PN stage of WT and Dicer cKO/Drosha cKO mice with BWA workflow and 34,115 transcripts with TopHat workflow. Approximately 47% of the miRNAs showed differential expression between the WT and Dicer cKO sperm, ~52% of miRNAs were shown dysregulated in Drosha cKO sperm compared to those in WT sperm with a fold change ≥2.0 and p value <0.05. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of small non-coding RNAs (miRNAs) in sperm and demonstrated that sperm-borne small RNAs are important for fertilization and early embrynic develoment, with biologic duplicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of small RNAs profiles in mouse sperm, oocytes and 2PN stage of embryos. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of small RNA contents within sperm or oocytes/embryos. We conclude that RNA-seq based small RNAs characterization in gametes would expedite genetic network analyses and permit the dissection of complex biologic functions during fertilization and embryonic development.
2015-10-08 | GSE73824 | GEO
Project description:RNAseq analysis of Chrnb4-cre driven Dicer conditional knockout (Dicer CKO) whole retinas
2019-01-21 | E-MTAB-6133 | ExpressionAtlas
Project description:We used microarray gene profiling to study the transcriptome of retinas lacking CRB2 during late retinal development. Unexpectedly, the retinas of newborn mice lacking CRB2 showed no changes in the transcriptome during retinal development. Comparison between Control and CRB2 null retinas at different time points (P0, P3, P6 and P10)
2013-12-31 | E-GEOD-50845 | biostudies-arrayexpress
Project description:We used microarray gene profiling to study the transcriptome of retinas lacking CRB2 during late retinal development. Unexpectedly, the retinas of newborn mice lacking CRB2 showed no changes in the transcriptome during retinal development.
2013-12-31 | GSE50845 | GEO
Project description:Control and EMC3 CKO retinas (n = 3 each group) at E17.5 and P7 were used for tandem mass spectrometry (LC-MS/MS)–based label-free proteomics
2021-01-04 | PXD023349 | iProX