RNA-seq analysis of Wild Type and Mll5-/- Retinal Transcriptomes
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE196935 | GEO | 2022/02/20
REPOSITORIES: GEO
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Project description:RNA-seq analysis of Wild Type and Mll5-/- Retinal Transcriptomes
| PRJNA807898 | ENA
Project description:Male mice but not female Mll5 -/- mice are infertile. This study showed that post-meiotic spermatogenic maturation is impaired in Mll5 -/- mice. In order to investigate the role of Mll5 in spermatogenesis, a transcriptome analysis of whole testes from Mll5 knock out and wildtype mice was performed. Affymetrix Mouse Exon chips were hybridized with testes material from three individual male mice from each wild-type or Mll5 -/- genotype, in order to identify gene regulation differences attributed to the loss of Mll5. One-way ANOVA: wildtype vs. Mll5-/-
2010-09-30 | E-GEOD-19648 | biostudies-arrayexpress
Project description:Male mice but not female Mll5 -/- mice are infertile. This study showed that post-meiotic spermatogenic maturation is impaired in Mll5 -/- mice. In order to investigate the role of Mll5 in spermatogenesis, a transcriptome analysis of whole testes from Mll5 knock out and wildtype mice was performed. Affymetrix Mouse Exon chips were hybridized with testes material from three individual male mice from each wild-type or Mll5 -/- genotype, in order to identify gene regulation differences attributed to the loss of Mll5.
2010-09-30 | GSE19648 | GEO
Project description:The human mixed lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle and survival, however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its PHD finger with the histone mark H3K4me3. The 1.48 Å resolution crystal structure of the MLL5 PHD finger in complex with the H3K4me3 peptide reveals a non-canonical binding mechanism, whereby K4me3 is recognized through a single aromatic residue and an aspartate. The binding induces a His-Asp swapping rearrangement mediated by a C-terminal α-helix. Phosphorylation of H3T3 and H3T6 abrogates the association with H3K4me3 in vitro and in vivo, releasing MLL5 from chromatin in mitosis. This regulatory switch is conserved in the Drosophila ortholog of MLL5, MLL5, and suggests the developmental control for targeting of H3K4me3. Together, our findings provide insight into the molecular basis for the recruitment, exclusion and regulation of MLL5 at chromatin.
2013-07-01 | GSE47100 | GEO
Project description:The human mixed lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle and survival, however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its PHD finger with the histone mark H3K4me3. The 1.48 Ã
resolution crystal structure of the MLL5 PHD finger in complex with the H3K4me3 peptide reveals a non-canonical binding mechanism, whereby K4me3 is recognized through a single aromatic residue and an aspartate. The binding induces a His-Asp swapping rearrangement mediated by a C-terminal α-helix. Phosphorylation of H3T3 and H3T6 abrogates the association with H3K4me3 in vitro and in vivo, releasing MLL5 from chromatin in mitosis. This regulatory switch is conserved in the Drosophila ortholog of MLL5, MLL5, and suggests the developmental control for targeting of H3K4me3. Together, our findings provide insight into the molecular basis for the recruitment, exclusion and regulation of MLL5 at chromatin. For determaning MLL5 chromatin profile, DamID-MLL5 chromatin profiling was determined in C2C12 cells . Three biological replicates were performed. Normalized data was averaged and HMM approach was applied to establish the bound regions (Straub, T., Grimaud, C., Gilfillan, G. D., Mitterweger, A., and Becker, P. B. (2008). PLoS Genet 4, e1000302)
2013-07-01 | E-GEOD-47100 | biostudies-arrayexpress
Project description:RNA-Seq Analysis of Wild Type and Elovl2C234W Mouse Retinal Transcriptomes
| PRJNA788542 | ENA
Project description:Purpose: The goal of this study is to compare the retinal transcriptomes of wild-type and CTGF-/- mice during postnatal development of the retinal vasculature. Results: The results from principal component analysis (PCA) showed a distinguishable gene expression profiling among the samples. The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM in group > 0.5. We have identified 24,818 transcripts for 12946 gene count in WT mouse retinas and 24708 transcripts for 12852 gene count in knockout mouse retinas. The significantly enriched GO terms of the differentially expressed genes include those involved in protein, lipid and DNA metabolism, neurogenesis and signal transduction and gene regulation.
2020-03-13 | GSE146900 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl-/-) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. 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 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. 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 retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Retinal mRNA profiles of 21-day old wild type (WT) and Nrl-/- mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.
2011-10-25 | E-GEOD-33141 | biostudies-arrayexpress
Project description:MLL5 is a novel trithorax group gene and a candidate tumor suppressor gene located within a 2.5 Mb interval of chromosome band 7q22 that is frequently deleted in human myeloid malignancy. Here we show that Mll5 is required for normal hematopoietic stem cell (HSC) homeostasis. Inactivation of the Mll5 gene in mice results in reduced cellularity of the long-term HSC compartment, which correlates with functional impairment of long-term repopulation potential under competitive conditions. Bone marrow cells from Mll5-deficient mice were defective in spleen colony-forming assays, and the mutant mice showed enhanced susceptibility to 5-Fluorouracil-induced myelosuppression. Heterozygous and homozygous Mll5 mutant mice did not spontaneously develop hematologic cancers, and loss of Mll5 did not alter the phenotype of a fatal myeloprolferative disorder induced by oncogenic Kras in vivo. Collectively, the data reveal an important role for Mll5 in HSC homeostasis, and provide a basis for further studies to explore its role in leukemogenesis. Keywords: Cell type comparision.
2008-05-22 | GSE10817 | GEO
Project description:Retinal transcriptomes of Plk3-deficient animals
| PRJNA304025 | ENA