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Transcriptomic analysis after transfection in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) of either a siRNA against SOX2 or a scramble siRNA

ABSTRACT: SOX2 is the main gene involved in anophthalmia. In order to identify genes regulated by SOX2 transcription factors (genes that could be good candidates to also be involved in ocular development), we studied transcriptomic profiles of murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) after transfection by a siRNA against SOX2 or a scramble siRNA.

ORGANISM(S): Mus musculus

PROVIDER: GSE74598 | GEO | 2015/11/04

SECONDARY ACCESSION(S): PRJNA300947

REPOSITORIES: GEO

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Transcriptomic analysis after transfection in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) of either a siRNA against SOX2 or a scramble siRNA

Project description:SOX2 is the main gene involved in anophthalmia. In order to identify genes regulated by SOX2 transcription factors (genes that could be good candidates to also be involved in ocular development), we studied transcriptomic profiles of murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) after transfection by a siRNA against SOX2 or a scramble siRNA. murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) after transfection by a siRNA against SOX2 or a scramble siRNA

2015-11-04 | E-GEOD-74598 | biostudies-arrayexpress

ChIP-seq after immunoprecipitation with either IgG or SOX2 antibodies in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells)

2015-11-04 | GSE74599 | GEO

ChIP-seq after immunoprecipitation with either IgG or SOX2 antibodies in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells)

Project description:In order to identify target genes of the SOX2 transcription factor, we tried to identify SOX2 binding site in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) by ChIP-seq. SOX2 gene mutations are involved in anophthalmia and our hypothesis was that target genes of SOX2 transcription factor may also be candidate to be involved in ocular development. High throughput sequencing after chromatin immunoprecipitation using either an antibody against our target transcription factor (SOX2) or using control antobodies (IgG). These experiments were performed on only one immunoprecipitation with each antibody.

2015-11-04 | E-GEOD-74599 | biostudies-arrayexpress

Mus musculus

Project description:Transcriptomic analysis after transfection in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) of either a siRNA against SOX2 or a scramble siRNA

| PRJNA300947 | ENA

The Rax homeoprotein in Müller glial cells is required for homeostasis maintenance of the postnatal mouse retina

Project description:To address the function of Rax in differentiated Müller glial cells, we generated Rax tamoxifen-induced conditional knock-out (Rax iCKO) mice, where Rax can be depleted in mTFP-labeled Müller glial cells upon tamoxifen treatment, by crossing Raxflox/flox mice with Rlbp1-CreERT2 mice and found histological characteristic of reactive gliosis and an enhanced gliosis of Müller glial cells in the Rax iCKO retina under normal and stress conditions, respectively. RNA sequencing using isolated Müller glial cells from the Rax iCKO retina by fluorescence-activated cell sorting demonstrated that reduced expression of suppressor of cytokine signaling-3 (Socs3), whose depletion leads to reactive gliosis in Müller glial cells. Reporter gene assays showed that Rax directly transactivates Socs3 and we observed decreased expression of Socs3 in Müller glial cells of the Rax iCKO retina by immunostaining. Taken together, these results suggest that the Rax homeoprotein suppresses reactive gliosis in Müller glial cells by transactivating Socs3 in vivo. Our results may shed light on the transcriptional regulatory mechanisms underlying Müller glial cell homeostasis.

2023-12-20 | GSE237650 | GEO

Mus musculus

Project description:ChIP-seq after immunoprecipitation with either IgG or SOX2 antibodies in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells)

| PRJNA300946 | ENA

XT mutant RNAseq

Project description:RNA was isolated from Xenopus tropicalis rax mutants and wild type siblings. We have identified by tilling a Xenopus tropicalis rax mutant in which the gene has a premature stop codon before the homeobox domain. The rax gene is essential for eye development and has been identified as a causative gene for human ocular malformations such as anophthalmia and microphthalmia. The phenotype of the X.tropicalis mutant replicates the human condition with complete loss or small eyes. By analysis of the full RNA complement of rax mutants compared to wild type siblings we hope to gain a better understanding of the role of rax during eye development and the genes that it regulates. This is part of an ongoing collaboration with Dr Robert Grainger, University of Virginia. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see www.sanger.ac.uk/datasharing/

2011-01-19 | E-ERAD-0 | biostudies-arrayexpress

Interaction between Lactiplantibacillus plantarum RX-8 and Wickerhamomyces anomalus Y-5 under co-culture by proteomics analysis

Project description:In present study, it was found that the co-culture of Wickerhamomyces anomalus Y-5 and L. plantarum RX-8 could enhance bacteriocin production. To analyze the interaction between W. anomalus Y-5 and L. plantarum RX-8, a quantitative proteomic approach was used to analyze and compare the proteome in L. plantarum RX-8 and W. anomalus Y-5 under mono-culture and co-culture. In total, 339 differently expressed proteins (DEPs) were screened in comparison of L. plantarum RX-8 under mono-culture and co-culture, 645 proteins of W. anomalus Y-5 changed in mono-culture and co-culture. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that DEPs participated in various metabolic pathways such as PTS system, glycolysis, galactose metabolism, glutamate, aspartate, arginine and cysteine metabolism etc. These pathways were related to inducing mechanism on improving bacteriocin production by co-culture. Quantitative proteomic analysis-based strategies can therefore provide further evidence for new regulated targets to improve the production of bacteriocins.

2022-12-04 | PXD038315 | Pride

RNA-seq of Xenopus tropicalis rax mutants and wild type siblings

Project description:RNA was isolated from Xenopus tropicalis rax mutants and wild type siblings. This was used to generate mutant and wild type RNA libraries for solexa sequencing. The sequencing data will be compared to isolate changes that may be caused by loss of rax activity. The RNA samples were extracted with Trizol, then were DNAse treated following the Invitrogen DNAse I protocol and re-precipitated with ethanol. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2013-01-08 | E-ERAD-130 | biostudies-arrayexpress

RNA-seq based transcriptome profiling of Carpesium cernuum extract (CCE) treated MDA-MB-231 cell lines

Project description:To understand the molecular mechanism of CCE, we performed the RNA-seq analysis. Cells were seeded at 5x10^5 cells/well in 6-well plates then treated with 1μg/mL CCE for 24 h. MDA-MB-231 cells were harvested, and RNA was isolated with TRIzol. The libraries were constructed by using the Quick cDNA Library Preparation Kit and sequenced on an XTEN sequencing system. RNA-seq data were mapped to the reference genome (hg19) by using HISAT2. The reads were counted, and StringTie was used to calculate the FPKM value of the genes. The differentially expressed genes (DEGs) were identified by comparing the experimental group with the control group.

2021-11-12 | GSE125356 | GEO

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