Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1122202 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We present HiChew (High efficient chromatin conformation capture with post-enrichment), a novel method for analyzing three-dimensional chromatin organization in single cells and low-input samples. HiChew combines efficient sticky-end ligation with post-PCR enrichment using methylation-based selection, addressing key limitations of existing chromatin conformation capture methods. The method achieves significantly higher valid pair ratios (approximately 50%) compared to unenriched methods (8%) while maintaining high capture sensitivity. For single-cell applications, snHiChew demonstrates superior performance with 45-50% valid pair ratios and the ability to generate up to 7.3 million unique valid contacts per cell. This enhanced efficiency enables high-resolution mapping of chromatin interactions at 5-10 kb resolution with 70-80% bin coverage. We validate HiChew's accuracy through comparative analyses with conventional Hi-C data, showing high correlations in compartment scores, topologically associating domains (TADs), and loop detection. The method's scalability and cost-effectiveness make it particularly suitable for large-scale single-cell chromatin conformation studies. HiChew represents a significant advancement in chromatin architecture analysis, offering improved efficiency without compromising data quality or sensitivity.
2024-12-23 | GSE284602 | GEO
Project description:Igk locus capture-based target enrichment sequencing
| PRJNA574914 | ENA
Project description:We used the technology of MNase-seq and capture-based target enrichment to analyze nucleosome positioning on the HIV DNA.
2020-03-02 | GSE135551 | GEO
Project description:We used the technology of MNase-seq and capture-based target enrichment to analyze nucleosome positioning on the HIV DNA.
2020-03-02 | GSE139556 | GEO
Project description:<p>Next generation sequencing has aided characterization of genomic variation. While whole genome sequencing may capture all possible mutations, whole exome sequencing is more cost-effective and captures most phenotype-altering mutations. Initial strategies for exome enrichment utilized a hybridization-based capture approach. Recently, amplicon-based methods were designed to simplify preparation and utilize smaller DNA inputs. We appraised two hybridization capture-based and two amplicon-based whole exome sequencing methods, utilizing both Illumina and Ion Torrent sequencers, comparing on-target alignment, uniformity, and variant calling. While the amplicon methods had higher on-target rates, the hybridization capture-based approaches showed better uniformity. All methods identified many of the same single nucleotide variants, but each amplicon-based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform-specific variant calling algorithms. All methods demonstrated effective copy number variant calling when compared against a single nucleotide polymorphism array. This study illustrates some differences between various whole exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach.</p>
| phs000938 | dbGaP
Project description:Here, we report an enrichment-based ultra-low input cfDNA methylation profiling method using methyl-CpG binding proteins capture, termed cfMBD-seq. We optimized the conditions of cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data showed that cfMBD-seq performs equally to the standard MBD-seq (>1000 ng input) even when using 1 ng DNA as the input. cfMBD-seq demonstrated equivalent sequencing data quality as well as similar methylation profile when compared to cfMeDIP-seq. We showed that cfMBD-seq outperforms cfMeDIP-seq in the enrichment of CpG islands. This new bisulfite-free ultra-low input methylation profiling technology has a great potential in non-invasive and cost-effective cancer detection and classification.
2021-01-01 | GSE161331 | GEO
Project description:Soil eDNA and enrichment cultures
| PRJNA712947 | ENA
Project description:We provide raw gene sequences of 174 flowering time regulatory genes and gene othologs across a large barley population (895 barley lines) selected from a collection of landrace, cultivated barley, and research varieties of diverse origin. This set represents the whole variety of cultivated barley lifeforms, namely two- and six-row genotypes with winter, spring, and facultative growth habits. We applied a target capture method based on in-solution hybridization using the myBaits® technology (Arbor Biosciences, Ann Arbour, MI, USA) which is based on in-solution biotinylated RNA probes. Baits were designed for flowering time regulatory genes and gene othologs, and used for production of 80mer capture oligonucleotides for hybridization. Genomic DNA was extracted from leaves of a single two-week old barley plant per variety using the cetyl-trimethyl-ammonium bromide (CTAB) method. Physical shearing of genomic DNA was performed with an average size of 275 bp. Library preparation was conducted with KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA). Hybridization of customised RNA baits with capture pools was performed at 65°C for 24 hours. Each pooled sequence capture library was sequenced on an Illumina HiSeq3000 instrument using three lanes to generate paired-end reads per sample. Genome sequencing was conducted at AgriBio, (Centre for AgriBioscience, Bundoora, VIC, Australia).
2019-02-15 | E-MTAB-7362 | biostudies-arrayexpress
Project description:Dengue virus Raw sequence reads pre-capture using a capture based purification method
| PRJNA489518 | ENA