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Vienna Biocenter Core Facilities GmbH next-generation sequencing
Next Generation Sequencing, supplied by Vienna Biocenter Core Facilities GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/next+generation+sequencing+data/next+generation+sequencing/pm37683092-591-12-6
Average 90 stars, based on 1 article reviews
next-generation sequencing - by Bioz Stars, 2026-09
90/100 stars

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Related Articles

Confocal Microscopy:

Article Title: ANAC044 orchestrates mitochondrial stress signaling to trigger iron-induced stem cell death in root meristems.
Article Snippet: Iron toxicity is a frequent environmental stress induced by flooded soil conditions that can cripple root growth and harm crop production.. S-nitrosoglutathione reductase (GSNOR) has emerged as a crucial gene in safeguarding root growth from iron toxicity in various plant species, yet the underlying mechanism remains unclear.. Our study exposes the mitochondrial retrograde signaling pathway that involves the transcription factor ANAC044, which constitutes the primary mechanism downstream of GSNOR.

Next-Generation Sequencing:

Article Title: ANAC044 orchestrates mitochondrial stress signaling to trigger iron-induced stem cell death in root meristems.
Article Snippet: Iron toxicity is a frequent environmental stress induced by flooded soil conditions that can cripple root growth and harm crop production.. S-nitrosoglutathione reductase (GSNOR) has emerged as a crucial gene in safeguarding root growth from iron toxicity in various plant species, yet the underlying mechanism remains unclear.. Our study exposes the mitochondrial retrograde signaling pathway that involves the transcription factor ANAC044, which constitutes the primary mechanism downstream of GSNOR.

Article Title: LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regions.
Article Snippet: We are grateful to Egon Ogris, Max Perutz Labs, Vienna, for providing the lamin A / C 3A6 antibody and to Gerhard Wiche, University of Vienna, for contributing the immortalized p53 knockout myoblasts. .. We thank the Next Generation sequencing facility at the Vienna Biocenter Core Facilities for technical support with NGS sequencing and the Max Perutz Labs Biooptics facility for performing FACS sorting. ..

Article Title: Regulation of somatic hypermutation by higher-order chromatin structure.
Article Snippet: We are grateful to Marieke Oudelaar (Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Gö ttingen, Germany) for exten- sive discussions and feedback on all aspects of Tri-C. We thank Johannes Zuber (IMP, Vienna) for the plasmid expressing rtTA3 and ecotropic receptor, Christoph Neumayr and Alexander Stark (IMP) for osTIR plasmids, and Wen Tang and Jan-Michael Peters (IMP) for the RAD21 auxin-inducible degron fusion constructs. .. We are grateful to the Vienna Biocenter Core Facilities (VBCF) for next-generation sequencing and the IMP/IMBA core facilities, especially the Molecular Biology Service and Bio-optics services. .. This work was funded by Boehringer Ingelheim, The Austrian Industrial Research Promotion Agency (Headquarter Grant FFG-834223), and grants from the Austrian Science Fund to U.E.S. (FWF T 795-B30) and R.P. (FWF P 29163-B26 and FWF P35396-B).

Article Title: Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12.
Article Snippet: .. The team of the Vienna BioCenter Core Facilities (https://www.vbcf.ac.at) performed next generation sequencing services. ..

Article Title: Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing.
Article Snippet: .. We would like to thank the Vienna Biocenter Core Facilities GmbH (VBCF) Next-Generation Sequencing for NGS services; VBCF Plant Sciences for the excellent growth chambers; IMBA-IMP-GMI Molecular Biology Services for providing the access to instruments, molecular biology reagents, and support; and the VBC Ethics, Health and Safety team for their support during the COVID-19 pandemic. ..

Article Title: Enhancer cooperativity can compensate for loss of activity over large genomic distances.
Article Snippet: The BioOptics-FACS facility at the Max Perutz labs was instrumental in the success of this project. .. Cas9-seq and ATAC-seq were performed by the Next Generation Sequencing facility at the Vienna BioCenter Core Facilities (VBCF), a member of the Vienna BioCenter (VBC). ..

Sequencing:

Article Title: LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regions.
Article Snippet: We are grateful to Egon Ogris, Max Perutz Labs, Vienna, for providing the lamin A / C 3A6 antibody and to Gerhard Wiche, University of Vienna, for contributing the immortalized p53 knockout myoblasts. .. We thank the Next Generation sequencing facility at the Vienna Biocenter Core Facilities for technical support with NGS sequencing and the Max Perutz Labs Biooptics facility for performing FACS sorting. ..

FACS:

Article Title: LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regions.
Article Snippet: We are grateful to Egon Ogris, Max Perutz Labs, Vienna, for providing the lamin A / C 3A6 antibody and to Gerhard Wiche, University of Vienna, for contributing the immortalized p53 knockout myoblasts. .. We thank the Next Generation sequencing facility at the Vienna Biocenter Core Facilities for technical support with NGS sequencing and the Max Perutz Labs Biooptics facility for performing FACS sorting. ..

other:

Article Title: Cytoplasmic mRNA decay controlling inflammatory gene expression is determined by pre-mRNA fate decision.
Article Snippet: Library preparation, quality control and sequencing were performed by the VBCF (Vienna BioCenter Core Facilities) Next Generation Sequencing (NGS) Facility (www.viennabiocenter.org/facilities).

Article Title: Multi-chamber cardioids unravel human heart development and cardiac defects.
Article Snippet: Then the RNA-seq library was submitted to the Vienna Biocenter Core Facilities (VBCF) Next-Generation-Sequencing (NGS) facility for sequencing.



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Data preprocessing workflow. When analyzing NGS datasets with KPop, one can optionally pre-process sequencing reads in order to eliminate biases and/or have the method focus on specific parts of the genome. For instance, one might align reads to a (pan-)genome and separate them into reads that align (likely to originate from the organism being studied) and reads that do not (likely to come from contaminations). Furthermore, reads that do map to the pan-genome might be separated into groups specific to different genomic features; for instance, one might align them to a set of MLST genes or AMR genes. Full k -mer spectra would then be separately obtained from each group of reads (contaminations, pan-genomic, MLST genes, AMR genes) and given as input to downstream/classification methods. The choice of the group of reads from which spectra are computed determines the set of sequences seen by the method, and hence the scope of the classification

Journal: Genome Biology

Article Title: KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings

doi: 10.1186/s13059-025-03585-8

Figure Lengend Snippet: Data preprocessing workflow. When analyzing NGS datasets with KPop, one can optionally pre-process sequencing reads in order to eliminate biases and/or have the method focus on specific parts of the genome. For instance, one might align reads to a (pan-)genome and separate them into reads that align (likely to originate from the organism being studied) and reads that do not (likely to come from contaminations). Furthermore, reads that do map to the pan-genome might be separated into groups specific to different genomic features; for instance, one might align them to a set of MLST genes or AMR genes. Full k -mer spectra would then be separately obtained from each group of reads (contaminations, pan-genomic, MLST genes, AMR genes) and given as input to downstream/classification methods. The choice of the group of reads from which spectra are computed determines the set of sequences seen by the method, and hence the scope of the classification

Article Snippet: In order to do so, simulated next-generation sequencing (NGS) data was generated for each genome using ART [ ], emulating Illumina HiSeq 2500 paired-end reads of length 150 bp with an average coverage of 20-fold.

Techniques: Sequencing