Project description:We performed single-cell RNA sequencing (scRNA-seq) on whole blood cells from a patient with biallelic BRF2 variants (c.782C>T and c.379C>T), exhibiting defective RNA polymerase III activity. The patient presented with recurrent infections, hypogammaglobulinemia, and was later diagnosed with low-grade B cell lymphoma. Our scRNA-seq analysis revealed alterations in gene expression related to BRF2-dependent Pol III transcription, particularly affecting redox genes, including GPX1 and GPX4.
Project description:To investigate the impact of TET2 loss on global transcription in HEL acute myeloid leukaemia (AML) cells. HEL AML cells, which have a monoallelic TET2 mutation, were targeted by CRISPR to inactivate the remaining TET2 allele, generating isogenic cell clones with either monoallelic or biallelic TET2 mutation.
Project description:To investigate the impact of TET2 loss on global genomic methylation in HEL acute myeloid leukaemia (AML) cells. HEL AML cells, which have a monoallelic TET2 mutation, were targeted by CRISPR to inactivate the remaining TET2 allele, generating isogenic cell clones with either monoallelic or biallelic TET2 mutation.
Project description:We performed DNA sequencing of potential biallelic SNPs in HD-B and DM1-A patient cell lines. These potential biallelic SNPs were identified in the 4C-seq interaction data. We selected a subset of these SNPs for confirmation by PCR, so we amplified the genomic regions that contained these potential SNPs and performed 2 x 150 bp paired-end sequencing on Illumina MiSeq nano.
Project description:Purpose: CEBPA mutations are found as either biallelic (biCEBPA) or monoallelic (moCEBPA). We set out to explore whether the kind of CEBPA mutation is of prognostic relevance in cytogenetically normal AML (CN-AML). Patients and Methods: 467 homogeneously treated CN-AML patients were subdivided into moCEBPA, biCEBPA and wildtype (wt) CEBPA patients. The subgroups were analyzed for clinical parameters and for additional mutations in the NPM1, FLT3 and MLL genes. Furthermore, we obtained gene expression profiles (GEP) for a subgroup of 61 patients using oligonucleotide microarrays. 61 bone-marrow samples from CN-AML patients were analyzed using Affymetrix HG-U133 oligonucleotide microarrays (Affymetrix, Santa Clara, CA). Sample preparation, hybridization and image acquisition were performed according to standard Affymetrix protocols. Custom chip definition files based on the GeneAnnot database were used for data analysis (Ferrari et al, BMC Bioinformatics 8:446). The twilight algorithm was used to comapre gene expression profiles of patients with wildtype CEBPA and mono- and biallelic CEBPA mutations.
Project description:This SuperSeries is composed of the following subset Series: GSE35551: Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression (1) GSE35552: Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression (2) GSE35553: Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression (3) Refer to individual Series
Project description:Analysis of long RNASeq (>200bp) of RNA obtained from Limphoblastoid cell lines derived from one heterozygous and one homozygous patient for TRMT1 frame-shift mutation