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Fig. 9 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 9. Distribution map of Ngirhaphium meieri, new species and Ngirhaphium thaicum, new species.

Fig. 7 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 7. Ngirhaphium meieri, new species, female habitus. Scale = 1 mm.

Fig. 6 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 6. Ngirhaphium meieri, new species, male habitus (photo: Abdulloh Samoh). Scale = 1 mm.

Fig. 3 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 3. Ngirhaphium thaicum, new species male habitus. Scale = 1 mm.

Fig. 4 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 4. Ngirhaphium thaicum, new species habitus female. Scale = 1 mm.

opencc-zeroNov 2022View details →

NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations

We developed a method to detect copy number variation and loss of heterozygosity in genome-edited cell lines by only sequencing the edited site. We introduced different substitutions on both chromosomes of diploid H9 human embryonic stem cells using CRISPR/Cas9 and a mixture of homology-directed repair donor DNAs carrying different substitutions. Here, we deposit the associated sequencing data (BAM-files) generated by extracting genomic DNA from genome-edited H9 cells, PCR amplifying the region of interest and sequencing on a MiSeq platform. We sequenced the edited site of cell bulks to investigate the editing efficiencies of individual donors from the donor mixtures. For proof of concept, we isolated over 850 cellular clones from the edited cell bulks and sequenced the edited site and heterozygous positions flanking the edited site to determine the number of alleles at the edited site and detect copy-neutral loss of heterozygosity. Additionally, we sequenced the DNA donors to assess, the distribution of individual donors in the mixtures.

opencc-by-4.0Apr 2022View details →

Real-time Alignments for Predicting Decision-Making Time for Diagnostics over NGS Cycles

Input datasets for an interpretable learning approach to predict decision-making time for diagnostics over NGS cycles. The dataset contains alignment files of two clinical sputum samples sequenced with an Illumina MiSeq sequencing device, and following a real-time sequencing protocol. The datasets consist of real-time alignment files for specific sequencing cycle intervals. The alignment has been performed to a database of respiratory microbes. Data preprocessing, including the removal of human host DNA, is integrated into the real-time alignment approach that has been applied to generate the alignments.

opencc-by-4.0Jan 2023View details →

Dataset incr1 - NGS-based S. aureus typing and outbreak analysis in clinical microbiology laboratories: lessons learned from a Swiss-wide proficiency test

Supplemental material of article "NGS-based S. aureus typing and outbreak analysis in clinical microbiology laboratories: lessons learned from a Swiss-wide proficiency test" by D. Dylus et al. Please refer to Methods therein. FASTQ datasets for increment 1.

opencc-by-4.0Jan 2023View details →

N-TIMP2 CD loop extension NGS data and analysis script

NGS data and analysis script for the YSD sorts described in Bonadio et al. "Using designed loop extension and combinatorial screening to enhance specificity of a broad matrix metalloproteinase inhibitor"

opencc-zeroFeb 2023View details →

Sequences of bacterial and fungal communities by Next-Generation Sequencing (NGS) associated to wall patinas

These data are the DNA sequences obtained from samples of house plaster with chromatic alteration facies. Three areas (VA1, VA3 and VNA6) of the wall were sampled. the DNA was extracted using the Spin Kit For Soil MPBio. The DNA extracts were sequenced by NGS using Illumina MiSeq Two regions were selected V3V5 16S for Bacteria and ITS1 ITS for Fungi.

opencc-zeroJul 2023View details →

NGS data from: Deploying synthetic coevolution and machine learning to engineer protein-protein interactions

Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a synthetic platform for protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain-affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pre-trained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. The integration of these approaches provides a means of generating protein complexes with diverse molecular recognition properties as tools for biotechnology and synthetic biology.

ClinicalTrials.gov36/100

Study of Plasma NGS for Assessment, Characterization, Evaluation of Patients With ALK Resistance

ClinicalTrials.gov study NCT03833934. IPD Sharing: NO. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →