Comparison of wild-type and ctbp-1(lf) AIA neuron transcriptional profiles in L4 larval stage C. elegans
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ABSTRACT:
PROVIDER: PRJNA743925 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15044514.fastq.gz | Fastqsanger.gz | |||
| SRR15044515.fastq.gz | Fastqsanger.gz | |||
| SRR15044516.fastq.gz | Fastqsanger.gz | |||
| SRR15044517.fastq.gz | Fastqsanger.gz | |||
| SRR15044518.fastq.gz | Fastqsanger.gz |
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Project description:ctbp-1 mutant C. elegans display a number of late-onset defects in their AIA neurons including (so far only a few identified) changes in their transcriptional profile. We sought to better characterize the gene expression changes occuring in these neurons by conducting a single, exploratory single cell RNA-seq experiment comparing wild-type and ctbp-1(lf) mutant gene expression profiles. Our main focus was on changes occurring specifically in the AIA neurons, though we decided to sequence the whole of the C. elegans nervous system so as to have to possibility of analyzing data detailing changes in other cell types should we so choose
2022-01-10 | GSE179484 | GEO
Project description:To obtain AIA-related genes [the significant differentially expressed genes (DEGs) of AIA model group vs. Normal control group], the microarray analysis was carried out.
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Project description:CtBP is a global co-repressor by serving as transcriptional factor in multiple pathways. CtBP functioned as transcriptional factor by recruiting other cofactors such as G9a, HDAC1 and PcG proteins. CtBP is found to be over enriched in several type of tumor samples. To dipict the role of CtBP in globally regulating gene expression, we applied gene microarray technology to find out what subgroups of genes are mainly affected. 6 MCF-7 cell samples, 3 with CtBP knockdown and 3 with control knock down.
2013-03-20 | E-GEOD-36529 | biostudies-arrayexpress
Project description:CtBP is a global co-repressor by serving as transcriptional factor in multiple pathways. CtBP functioned as transcriptional factor by recruiting other cofactors such as G9a, HDAC1 and PcG proteins. CtBP is found to be over enriched in several type of tumor samples. To dipict the role of CtBP in globally regulating gene expression, we applied gene microarray technology to find out what subgroups of genes are mainly affected.
2013-03-20 | GSE36529 | GEO
Project description:CtBP is a global co-repressor by serving as transcriptional factor in multiple pathways. CtBP functioned as transcriptional factor by recruiting other cofactors such as G9a, HDAC1 and PcG proteins. CtBP is found to be over enriched in several type of tumor samples. To dipict the role of CtBP in globally regulating gene expression, we applied ChIP-seq technology to find out the binding profile of CtBP in breast cancer cell line MCF-7. Our data suggest CtBP plays a global regulatory role in DNA damage repair, tumor initiation, and EMT process. Examine CtBP binding in MCF-7 cells
2013-03-20 | E-GEOD-36546 | biostudies-arrayexpress
Project description:Identification of AIA-related genes
| PRJNA561625 | ENA
Project description:CtBP is a global co-repressor by serving as transcriptional factor in multiple pathways. CtBP functioned as transcriptional factor by recruiting other cofactors such as G9a, HDAC1 and PcG proteins. CtBP is found to be over enriched in several type of tumor samples. To dipict the role of CtBP in globally regulating gene expression, we applied ChIP-seq technology to find out the binding profile of CtBP in breast cancer cell line MCF-7. Our data suggest CtBP plays a global regulatory role in DNA damage repair, tumor initiation, and EMT process.
2013-03-20 | GSE36546 | GEO
Project description:Purpose: The goals of this study are to find out CtBP and PcG coregulated targets through transcriptome profiling (RNA-seq). Methods: Kc cell mRNA profiles of 7-day Ctrl and CtBP and ph-p+E(z) RNAi were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: hyper-geometric test and the Benjamini Hochberg FDR correction method and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the drosophila genome (build dm6) and identified 11,282 transcripts in the 9 samples, among which 381 PcG targets were selected for further analysis. Hierarchical clustering of differentially expressed genes divided these targets into three groups named CtBP co-activated genes,CtBP unaffected genes and CtBP co-repressed genes respectivly. RNA-seq data confirmed CtBP co-activated genes contain 22 known homeobox genes, and 4 of these were validated with qRT–PCR. These results suggest that CtBP is selectively required for the activation of PcG-repressed genes, especially the homeobox transcription factors including Hox genes.Conclusions: Our study represents the first detailed analysis of CtBP and PcG coregulated targets.
2022-05-17 | GSE88807 | GEO
Project description:Branching from conduits is a defining feature of the gas delivery systems of invertebrates (tracheae built from epithelial cells) and vertebrates (vasculature lined by endothelial cells). Here, we show that the vertebrate transcriptional repressor Tel plays an evolutionarily conserved role in angiogenesis: it is indispensable for sprouting of primary human endothelial cells and for the normal development of the Danio rerio embryo blood circulatory system. Tel controls endothelial sprouting via binding to the generic co-repressor C-terminal binding protein (CtBP). In endothelial cells, the Tel:CtBP complex temporally restricts a VEGF-mediated pulse of dll4 expression and consequently integrates VEGFR intracellular signaling and intercellular Notch-Dll4 signaling. It further refines branching by regulating expression of other factors that constrain angiogenesis such as sprouty family members and ve-cadherin. Thus, the Tel:CtBP complex moderates the balance between positive and antagonistic angiogenesis cues and thereby conditions endothelial cells for angiogenesis. Since the activity of CtBP is attuned to intracellular NADH levels, our results raise the possibility that Tel-mediated sprouting could be sensitized to the metabolic status of the tissue. Tel control of branching appears to be evolutionarily conserved since Yan, the invertebrate orthologue of Tel, is similarly required for branching morphogenesis of the invertebrate tracheae. Collectively, our work suggests that Tel is a central regulator of angiogenesis and highlights Tel and its associated networks as potential targets for the development of therapeutic strategies to inhibit pathological angiogenesis. 2 independent screens were performed testing effects of knockdown of Tel or CtBP (screen 1) or effects of VEGF-A (screen 2) on Human Umbilical Vein Endothelial Cells (HUVECs). For screen 1 we tested 3 different conditions. We established stable HUVEC cell lines which were either infected with control lentivirus (Mock), or lentivirus expressing short hairpin RNA constructs for the specific knockdown of Tel(Teli) or CtBP2 (CtBP2i). Expression in the Teli and CtBP2i cell lines was compared to expression in the Mock cell line for screen 1. For screen 2 we tested 2 conditions. We exposed HUVECs to VEGF (50ng/mL) for 30 minutes (samplename: VEGF30) and compared the transcriptome of these cells to untreated HUVECs (VEGF0). For each condition 2 independent repeats were analyzed and expression of genes was averaged for each repeat. HUVECs were grown under standard conditions (37degrees Celsius, 5% CO2) in EGM2 medium (Lonza).
2010-09-09 | E-GEOD-19335 | biostudies-arrayexpress