Ontology highlight
ABSTRACT:
PROVIDER: PRJEB32072 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We used the nanopore Cas9 targeted sequencing (nCATS) strategy to specifically sequence 125 L1HS-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. The genome-wide profile of L1 methylation was also assessed by bs-ATLAS-seq in the same cell lines (E-MTAB-10895).
2023-09-22 | E-MTAB-12247 | biostudies-arrayexpress
Project description:An autosomal recessive disease is caused by biallelic loss-of-function mutations. However, when more than two disease-causing variants are found in a patient’s gene, it has been challenging to determine which two of the variants are responsible for the disease phenotype. To decipher the pathogenic variants by precise haplotyping, we applied nanopore Cas9-targeted sequencing (nCATS) to three truncation COL7A1 variants detected in a patient with recessive dystrophic epidermolysis bullosa (EB). The distance between the most 5’ and 3’ variants was around 19 kb at the level of genomic DNA. nCATS successfully delineated that the most 5’ and 3’ variants were located in one allele while the variant in between was in the other allele. Intriguingly, the proband’s mother, who was phenotypically intact, was heterozygous for the allele that harbored the two truncation variants, which could otherwise be misinterpreted as those of typical recessive dystrophic EB. Our study illuminates nCATS as a useful tool to determine haplotypes of complicated genetic cases. Haplotyping of multiple variants in a gene can tell which variant should be therapeutically targeted when nucleotide-specific gene therapy is applied.
2022-05-02 | GSE196673 | GEO
Project description:To compare the impact of CRISPR-egineered R175 TP53 mutant variants in HCT116 and H460 cells, mutations at the amino acid position 175 were generated systematically by CRISP/Cas9 editing. Here, genomic amplicon regions covering the TP53 Exons 5 were sequenced via targeted sequencing.
2024-10-16 | E-MTAB-14322 | biostudies-arrayexpress
Project description:Revertant mosaicism (RM) is a phenomenon in which inherited mutations are spontaneously corrected in somatic cells. RM occurs in some congenital skin diseases, although genetic validation of RM in clinically revertant skin has been challenging, especially when homologous recombination (HR) is responsible for RM. We introduced Nanopore Cas9-targeted sequencing (nCATS) for identifying HR in clinically revertant skin.
2022-01-13 | GSE186002 | GEO
Project description:We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of human full-length LINE-1 elements (L1) in the genome of 2102Ep cells (E-MTAB-10895). We also achieved targeted nanopore sequencing to assay DNA methylation over a subset of loci (E-MTAB-12247). To further study the link between L1 DNA methylation and expression, we performed, in the same cell line, RNA-seq (E-MTAB-12246), as well as YY1 and H3K4me3 ChIP-seq (this dataset).
2023-09-23 | E-MTAB-12249 | biostudies-arrayexpress
Project description:Identity and plasticity of CD4 T helper (Th) cells are regulated in part by epigenetic mechanisms. Cytosine methylation in CpG context (5mCpG) and cytosine hydroxymethylation (5hmCpG) are DNA modifications that identify stable cell phenotypes. To assess transition states in Th cells, we developed a method based on Cas9-targeted single molecule nanopore sequencing and found that 5mCpG can be used as markers of cellular identity. Targeting as few as 10 mouse selected genomic loci, we were able to distinguish major differentiated T cell subtypes as well as intermediate phenotypes by their native DNA 5mCpG patterns. Moreover, by using off-target sequences we were able to infer transcription factor activities relevant to each cell subtype. Our data highlight the potential to exploit native DNA methylation profiling to study physiological and pathological Th transition states.
2024-01-08 | GSE248540 | GEO