NGS in Large CAD Families: In-Depth Identification of Rare Risk Genomic Variants
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA671323 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Next generation rare variant discovery in multiplex AD families
| PRJNA517200 | ENA
Project description:Next generation rare variant discovery in multiplex AD families
| PRJNA517199 | ENA
Project description:Coronary artery disease (CAD) poses a worldwide health threat. Compelling evidence shows that pericardial adipose tissue (PAT), a brown-like adipose adjacent to the external surface of the pericardium, is associated with CAD. However, the specific molecular mechanisms of PAT in CAD are elusive. For characterizing human PAT and explore its association with CAD, the transcriptome characteristics were assessed in 5 CAD patients and 4 controls via RNA-sequencing.
2021-07-30 | GSE179397 | GEO
Project description:p53, a critical tumor suppressor, regulates the cell cycle in response to DNA damage and metabolic changes. While p53 stability and activity are predominantly governed by post-translational modifications, the role of deamidation in modulating p53 function remains unclear. This study demonstrates that 6-diazo-5-oxo-L-norleucine (DON) inhibits CAD, a glutamine amidotransferase, to block p53 deamidation, thereby activating the p53 signaling pathway and suppressing tumor cell proliferation. Metabolomic analyses confirmed that DON inhibits CAD-mediated pyrimidine biosynthesis, but this metabolic disruption is not the primary driver of p53 activation. CAD deamidates p53 at N235 and N239, impairing its transcriptional activity and promoting tumor growth. DON restores p53 function by inhibiting CAD’s deamidase activity. Clinical data revealed elevated CAD expression in tumors with wild-type TP53, correlating with poor patient survival. Our findings uncover a novel mechanism by which CAD suppresses p53 activity via deamidation and propose that DON treatment may benefit cancer patients with wild-type TP53 and high CAD expression.
2025-01-12 | GSE286372 | GEO
Project description:affy_rnai_cadpoplar - affy_rnai_cadpoplars - This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity). -RNAi-CAD transgenic poplars were produced using hairpin RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003). For this transcriptome anaylsis, 2 independent transgenic lines (named pHG8-CAD2 and pHG8-CAD19) from the same transformation procedure were used as biological repeats. Four-month-old poplar plants were inclined at 30° in the greenhouse and sampled after 26 days. Young differentiating xylem originating from the lower side of stems - opposite wood - (ODX) was sampled on each individual tree by scrapping slightly the debarked stem with a scalpel. Samples were immediately flash frozen in liquid nitrogen, ground with mortar and pestle, and total RNAs were extracted from fine ground powder using the QIAGEN miRNeasy kit according to the manufacturer. One Affymetrix slide corresponds to a pool of RNA samples from 2-4 individual trees (WT, RNAi-CAD transgenic lines 2 and 19). Total number of slides = 2 genotypes (WT/RNAi line) x 1 tissue x 2 biological replicates = 4 slides were done. 4 arrays - poplar; normal vs rnai mutant comparaison
2011-09-29 | E-GEOD-27063 | biostudies-arrayexpress
Project description:Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform
| PRJEB27504 | ENA
Project description:CAD cells were derived from Cath.a cells, a mouse central nervous system catecholaminergic cell line. Serum-starved CAD cells undergo morphological changes and resemble isolated neurons when observed by microscopy. We carried out an RNAseq transcriptomic analysis to examine differentiated CAD cells for expression signatures related to neuronal functions, identifying ~1900 transcripts whose expression changed with differentiation. Pathview analysis identified ~80 KEGG pathway gene sets that were differentially expressed, including upregulation of at least 13 neuron-related pathways. This dataset can be explored more deeply, allowing further investigation into expression changes relevant to studying neuronal functions in this easy-to-culture model system.
2025-03-12 | GSE291553 | GEO
Project description:affy_rnai_cadpoplar - affy_rnai_cadpoplars - This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity). -RNAi-CAD transgenic poplars were produced using hairpin RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003). For this transcriptome anaylsis, 2 independent transgenic lines (named pHG8-CAD2 and pHG8-CAD19) from the same transformation procedure were used as biological repeats. Four-month-old poplar plants were inclined at 30° in the greenhouse and sampled after 26 days. Young differentiating xylem originating from the lower side of stems - opposite wood - (ODX) was sampled on each individual tree by scrapping slightly the debarked stem with a scalpel. Samples were immediately flash frozen in liquid nitrogen, ground with mortar and pestle, and total RNAs were extracted from fine ground powder using the QIAGEN miRNeasy kit according to the manufacturer. One Affymetrix slide corresponds to a pool of RNA samples from 2-4 individual trees (WT, RNAi-CAD transgenic lines 2 and 19). Total number of slides = 2 genotypes (WT/RNAi line) x 1 tissue x 2 biological replicates = 4 slides were done.
2011-09-30 | GSE27063 | GEO
Project description:Targeting CAD enhances radiosensitivity by modulating cGAS-STING pathway activation, highlighting the significance of CAD as a potential therapeutic target for CRC.
2025-08-27 | GSE283230 | GEO