RNA sequencing of T cells from individuals with variants in CD101
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA639140 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12004872_1.fastq.gz | Fastqsanger.gz | |||
| SRR12004872_2.fastq.gz | Fastqsanger.gz | |||
| SRR12004873_1.fastq.gz | Fastqsanger.gz | |||
| SRR12004873_2.fastq.gz | Fastqsanger.gz | |||
| SRR12004874_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
Project description:In this study, we sought to determine if there are transcriptional differences in CD4 and CD8 T cells in individuals with different types of variants in the gene CD101.
2021-06-30 | GSE152381 | GEO
Project description:The project will use exome sequencing to search for genetic predispositions for familial colorectal cancer (CRC). Except for certain syndromes there is today no good method for identifying individuals with a hereditary high risk for CRC (about 25% of the cases). There is currently no routine screening of the population in Norway for CRC today. Coloscopy, which is the most reliable method, is demanding with respect to resources, it can be painful, and may have complications. This project will attempt to find genetic determinants for identification of individuals with increased risk for familial CRC. Such methods will reduce unnecessary medical examination of unaffected family members, and will make it easier to focus health services on individuals with increased risk. This will represent a significant contribution towards improved health reduced death rate caused by CRC. The project includes research on the ethical aspects, in particular challenges related to how feedback to donors is handled.
| 2148709 | ecrin-mdr-crc
Project description:Neurodevelopmental disorders (NDDs) result from highly penetrant variation in hundreds of different genes, some of which have not yet been identified. Using the MatchMaker Exchange, we assembled a cohort of 27 individuals with rare, protein-altering variation in the transcriptional coregulator gene ZMYM3, located on the X chromosome. Most (n=24) individuals were males, 17 of which have a maternally inherited variant and four of which have de novo variants. Overlapping features included developmental delay, intellectual disability, behavioral abnormalities, and a specific facial gestalt in a subset of males. Variants in almost all individuals (n=26) are missense, including six with variants that have arisen independently at the same codon at least two times. Four unrelated probands were identified with inherited variation at Arg441 (Arg441Trp or Arg441Gln), a site at which variation has been previously seen in NDD-affected siblings, and two individuals have de novo variation at Arg1294 (Arg1294Cys). All variants affect evolutionarily conserved sites, and most are predicted to damage protein structure or function. ZMYM3 is relatively intolerant to variation in the general population, is widely expressed across human tissues, and encodes a component of the KDM1A-RCOR1 chromatin-modifying complex. ChIP-seq experiments on one mutant, Arg1274Trp, indicate dramatically reduced genomic occupancy, supporting a hypomorphic effect. Similarly, RNA-seq comparing mutant cells to reference revealed numerous expression changes. Such changes were not seen in edited cells harboring a likely benign variant, Arg688His. While we are unable to perform statistical evaluations to support a conclusive causative role for variation in ZMYM3 in disease, the totality of the evidence, including 27 affected individuals, recurrent variation affecting at least two codons, overlapping phenotypic features, protein-modeling data, evolutionary constraint, and experimentally-confirmed functional effects strongly support ZMYM3 as a novel NDD gene.
2024-03-02 | GSE259222 | GEO
Project description:This study explores the interaction between various SARS-CoV-2 variants and host cells by using RNA sequencing (RNA-seq) of human airway epithelial cells. The primary objective was to elucidate the host cellular responses, including metabolic and immune pathways, to different SARS-CoV-2 variants. Human airway epithelial cells were infected with SARS-CoV-2 variants (IC19, Alpha, Beta, Delta, Omicron BA.1, and BA.5) and compared with mock samples at time 0. Samples were collected at 24 and 72 hours post-infection for RNA isolation and subsequent bulk RNA-sequencing. The RNA-seq data processing involved quality checks, mapping reads to a reference genome, and identifying differentially expressed genes to determine changes in gene expression in response to viral infection. This analysis aims to provide a deeper understanding of the molecular interactions between SARS-CoV-2 variants and host cells, contributing to the broader knowledge of viral pathogenicity and host-pathogen interactions.
2025-07-01 | GSE271378 | GEO
Project description:Sequencing of genes, such as BRCA1 and BRCA2, is recommended for individuals with a personal or family history of early onset and/or bilateral breast and/or ovarian cancer, or a history of male breast cancer. Such sequencing efforts have resulted in the identification of more than 6000 BRCA2 variants. The functional significance of most variants remains unknown; consequently, they are called variants of uncertain clinical significance (VUS). We have previously developed mouse embryonic stem cell (mESC)-based assays for functional classification of BRCA2 variants. While the assays are reliable, the experimental process is time-consuming. This has impeded the number of variants that can be examined at a time. To overcome this, we have now developed a next-generation sequencing (NGS)-based approach for functional evaluation of BRCA2 variants. In this approach, instead of using clonogenic or XTT-based cell survival assays, pools of mESC expressing 25-30 BRCA2 variants from a given exon are analyzed by NGS. We have also developed a statistical model that utilizes the NGS data to determine the probability of impact on function (PIF) for these variants. While CRISPR/Cas9-based high throughput methods have resulted in the functional characterization of thousands of variants, only a fraction of the variants are included in ClinVar. In contrast, our targeted approach, which involves generating specific variants, resulted in the functional evaluation of 223 variants that are all listed in ClinVar. Our functional classification of BRCA2 variants is concordant with the classification reported in ClinVar or reported by other well-established assays.
2023-11-20 | GSE244578 | GEO
Project description:Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [RNA-seq]
| PRJNA449340 | ENA
Project description:KAT5 encodes an essential lysine acetyltransferase previously called TIP60 involved in gene expression, DNA repair, chromatin remodeling, apoptosis and cell proliferation; but it remains unclear whether variants in this gene causes a genetic disease. Here, we study three individuals with heterozygous de novo missense variants in KAT5 that affect normally invariant residues, with one at the chromodomain (p.Arg53His) and two at or near the acetyl-CoA binding site (p.Cys369Ser and p.Ser413Ala). All three individuals have cerebral malformations, seizures, global developmental delay or intellectual disability, and severe sleep disturbance. Progressive cerebellar atrophy was also noted. Histone acetylation assays with purified mutant KAT5 demonstrated that the variants decrease or abolish the ability of the resulting NuA4/TIP60 multi-subunit complexes to acetylate the histone H4 tail in chromatin. Transcriptomic analysis in patient-derived fibroblasts showed deregulation of multiple genes controlling development. Moreover, there was also upregulated expression of PER1 (a key gene involved in circadian control), in agreement with sleep anomalies in all the patients. In conclusion, dominant missense KAT5 variants cause histone acetylation deficiency with transcriptional dysregulation of multiples genes, thereby leading to a neurodevelopmental syndrome with sleep disturbance, cerebellar atrophy and facial dysmorphisms suggesting a recognizable syndrome.
2020-07-11 | GSE154199 | GEO
Project description:An RNA sequencing analysis of fibroblasts derived from affected individuals with neuropathy, who carry biallelic variants in MCMC3AP gene. The expression levels are compared with healthy controls.
2020-04-07 | GSE135098 | GEO
Project description:Aortic single-cell RNA sequencing in ACTA2 R179 variants
| PRJNA828323 | ENA
Project description:Patients suspected of adenomatous polyposis were included. The criteria used were more than 10 polyps observed under colonoscopy, and pathological confirmation of adenoma. Clinical data and pedigree information were collected. The variants of 139 genes associated with different hereditary cancers and polyposis were screened by NGS, which was performed by Genetron Health on the HiSeqX-ten sequencing platform.
| 2383243 | ecrin-mdr-crc