scholarly journals Sequence Verification as Quality-Control Step for Production of cDNA Microarrays

BioTechniques ◽  
2001 ◽  
Vol 31 (1) ◽  
pp. 62-65 ◽  
Author(s):  
E. Taylor ◽  
D. Cogdell ◽  
K. Coombes ◽  
L. Hu ◽  
L. Ramdas ◽  
...  
Keyword(s):  
Quality Control ◽  
Cdna Microarrays ◽  
Control Step ◽  
Quality Control Step

scholarly journals Vectorial Import via a Metastable Disulfide-Linked Complex Allows for a Quality Control Step and Import by the Mitochondrial Disulfide Relay

Cell Reports ◽  
2019 ◽  
Vol 26 (3) ◽  
pp. 759-774.e5 ◽  
Author(s):  
Markus Habich ◽  
Silja Lucia Salscheider ◽  
Lena Maria Murschall ◽  
Michaela Nicole Hoehne ◽  
Manuel Fischer ◽  
...  
Keyword(s):  
Quality Control ◽  
Control Step ◽  
Quality Control Step

scholarly journals An Internally Consistent Dataset of δ<sup>13</sup>C-DIC in the North Atlantic Ocean – NAC13v1

2016 ◽  
Author(s):  
Meike Becker ◽  
Nils Andersen ◽  
Helmut Erlenkeuser ◽  
Matthew. P. Humphreys ◽  
Toste Tanhua ◽  
...  
Keyword(s):  
Quality Control ◽  
North Atlantic ◽  
Inorganic Carbon ◽  
Dissolved Inorganic Carbon ◽  
Stable Carbon Isotope ◽  
The North ◽  
Crossover Analysis ◽  
Control Step ◽  
The North Atlantic ◽  
Quality Control Step

Abstract. The stable carbon isotope composition of dissolved inorganic carbon (δ13C-DIC) can be used to quantify fluxes within the carbon system. For example, knowing the δ13C-DIC signature of the inorganic carbon pool can help to describe the exchange between ocean and atmosphere as well as the amount of anthropogenic carbon in the water column. The measurements can also be used for evaluating modeled carbon fluxes, for making basin wide estimates, studying seasonal and interannual variability or decadal trends in interior ocean biogeochemistry. For all these purposes, it is not only important to have a sufficient amount of data, but these data must also be internally consistent and of high quality. In this study, we present a δ13C-DIC dataset for the North Atlantic, which has undergone secondary quality control. The data originate from oceanographic research cruises between 1981 and 2012. During a primary quality control step based on simple range tests obviously bad data were flagged. In a second quality control step, biases between measurements from different cruises were quantified through a crossover analysis using nearby data of the respective cruises and absolute values of biased cruises were adjusted in the data product. the crossover analysis was possible for 22 of the 29 cruises in our dataset and adjustments were applied to 10 of these. The internal accuracy of this dataset is 0.017 ‰. The dataset is available via CDIAC at http://cdiac.ornl.gov/oceans/ndp_096/NAC13v1.html, doi:10.3334/CDIAC/OTG.NAC13v1.

scholarly journals Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies

2019 ◽  
pp. g3.200745.2018 ◽  
Author(s):  
Alexander P. Douglass ◽  
Caoimhe E. O'Brien ◽  
Benjamin Offei ◽  
Aisling Y. Coughlan ◽  
Raúl A. Ortiz-Merino ◽  
...  
Keyword(s):  
Quality Control ◽  
Genome Sequence ◽  
De Novo ◽  
Yeast Genome ◽  
Control Step ◽  
Quality Control Step

scholarly journals An internally consistent dataset of <i>δ</i><sup>13</sup>C-DIC in the North Atlantic Ocean – NAC13v1

2016 ◽  
Vol 8 (2) ◽  
pp. 559-570 ◽  
Author(s):  
Meike Becker ◽  
Nils Andersen ◽  
Helmut Erlenkeuser ◽  
Matthew P. Humphreys ◽  
Toste Tanhua ◽  
...  
Keyword(s):  
Quality Control ◽  
North Atlantic ◽  
Inorganic Carbon ◽  
Dissolved Inorganic Carbon ◽  
The North ◽  
Anthropogenic Carbon ◽  
Crossover Analysis ◽  
Control Step ◽  
The North Atlantic ◽  
Quality Control Step

Abstract. The stable carbon isotope composition of dissolved inorganic carbon (δ13C-DIC) can be used to quantify fluxes within the carbon system. For example, knowing the δ13C signature of the inorganic carbon pool can help in describing the amount of anthropogenic carbon in the water column. The measurements can also be used for evaluating modeled carbon fluxes, for making basin-wide estimates of anthropogenic carbon, and for studying seasonal and interannual variability or decadal trends in interior ocean biogeochemistry. For all these purposes, it is not only important to have a sufficient amount of data, but these data must also be internally consistent and of high quality. In this study, we present a δ13C-DIC dataset for the North Atlantic which has undergone secondary quality control. The data originate from oceanographic research cruises between 1981 and 2014. During a primary quality control step based on simple range tests, obviously bad data were flagged. In a second quality control step, biases between measurements from different cruises were quantified through a crossover analysis using nearby data of the respective cruises, and values of biased cruises were adjusted in the data product. The crossover analysis was possible for 24 of the 32 cruises in our dataset, and adjustments were applied to 11 cruises. The internal accuracy of this dataset is 0.017 ‰. The dataset is available via the Carbon Dioxide Information Analysis Center (CDIAC) at http://cdiac.ornl.gov/oceans/ndp_096/NAC13v1.html, doi:10.3334/CDIAC/OTG.NAC13v1.

scholarly journals Crowdsourced MRI quality metrics and expert quality annotations for training of humans and machines

2018 ◽  
Author(s):  
Oscar Esteban ◽  
Ross W Blair ◽  
Dylan M Nielson ◽  
Jan C Varada ◽  
Sean Marrett ◽  
...  
Keyword(s):  
Quality Control ◽  
Image Quality ◽  
Visual Assessment ◽  
Quality Metrics ◽  
Machine Learning Algorithms ◽  
Mr Images ◽  
Image Quality Metrics ◽  
Control Step ◽  
Automated Quality Control ◽  
Expert Ratings

AbstractThe neuroimaging community is steering towards increasingly large sample sizes, which are highly heterogeneous because they can only be acquired by multi-site consortia. The visual assessment of every imaging scan is a necessary quality control step, yet arduous and time-consuming. A sizeable body of evidence shows that images of low quality are a source of variability that may be comparable to the effect size under study. We present the MRIQC Web-API, an open crowdsourced database that collects image quality metrics extracted from MR images and corresponding manual assessments by experts. The database is rapidly growing, and currently contains over 100,000 records of image quality metrics of functional and anatomical MRIs of the human brain, and over 200 expert ratings. The resource is designed for researchers to share image quality metrics and annotations that can readily be reused in training human experts and machine learning algorithms. The ultimate goal of the database is to allow the development of fully automated quality control tools that outperform expert ratings in identifying subpar images.

scholarly journals Toward Automated Additive Manufacturing of Living Bio-Tubes Using Ring-Shaped Building Units

2020 ◽  
Vol 25 (6) ◽  
pp. 608-620
Author(s):  
Kali L. Manning ◽  
Jacob Feder ◽  
Marianne Kanellias ◽  
John Murphy ◽  
Jeffrey R. Morgan
Keyword(s):  
Quality Control ◽  
Additive Manufacturing ◽  
Real Time ◽  
Academic Research ◽  
Manufacturing Method ◽  
Liquid Handling ◽  
Air Interface ◽  
Morphological Criteria ◽  
Control Step ◽  
Liquid Handling Robot

Tissue engineering has been largely confined to academic research institutions with limited success in commercial settings. To help address this issue, more work is needed to develop new automated manufacturing processes for tissue-related technologies. In this article, we describe the automation of the funnel-guide, an additive manufacturing method that uses living tissue rings as building units to form bio-tubes. We developed a method based on 96-well plates and a modified off-the-shelf liquid-handling robot to retrieve, perform real-time quality control, and transfer tissue rings to the funnel-guide. Cells seeded into 96-well plates containing specially designed agarose micromolds self-assembled and formed ring-shaped microtissues that could be retrieved using a liquid-handling robot. We characterized the effects of time, cell type, and mold geometry on the morphology of the ring-shaped microtissues to inform optimal use of the building parts. We programmed and modified an off-the-shelf liquid-handling robot to retrieve ring-shaped microtissues from the 96-well plates, and we fabricated a custom illuminated pipette to visualize each ring-shaped microtissue prior to deposit in the funnel guide. Imaging at the liquid-air interface presented challenges that were overcome by controlling lighting conditions and liquid curvature. Based on these images, we incorporated into our workflow a real-time quality control step based on visual inspection and morphological criteria to assess each ring prior to use. We used this system to fabricate bio-tubes of endothelial cells with luminal alignment.

scholarly journals Comparative poly(A)+ RNA interactome capture of fission yeast RNA exosome mutants reveals insights into RNA biogenesis

2020 ◽  
Author(s):  
Adrien Birot ◽  
Cornelia Kilchert ◽  
Krzysztof Kus ◽  
Emily Priest ◽  
Ahmad Al Alwash ◽  
...  
Keyword(s):  
Quality Control ◽  
Rna Polymerase Ii ◽  
Rna Binding ◽  
Zinc Finger Protein ◽  
Rna Binding Proteins ◽  
Protein Coding ◽  
Multiple Protein ◽  
Nuclear Rna ◽  
Control Step ◽  
Rna Exosome

ABSTRACTThe nuclear RNA exosome plays a key role in quality control and processing of multiple protein-coding and non-coding transcripts made by RNA polymerase II. A mechanistic understanding of exosome function remains a challenge given it has multiple roles in RNA regulation. Here we have analysed changes in the poly(A)+ RNA transcriptome and interactome provoked by mutations in three distinct subunits of the nuclear RNA exosome. We have identified multiple proteins whose occupancy on RNA is altered in the exosome mutants. We demonstrate that the Zinc-finger protein Mub1 regulates exosome dependent transcripts that encode stress-responsive proteins. Furthermore, we assess impact of the exosome inactivation upon RNA binding of the components of the mRNA processing machineries such as spliceosome and mRNA cleavage polyadenylation complex. We show that mutations in the exosome lead to accumulation of the components of U1 and U2 snRNPs on poly(A)+ RNA and depletion of the components of the activated spliceosome from RNA suggesting that the early stages of spliceosome assembly might provide a critical quality control step. Collectively, our data provide a global view of how RNA metabolism is affected in the exosome-deficient cells and reveal RNA-binding proteins that may act as novel exosome cofactors.

scholarly journals Rapid, robust plasmid verification by de novo assembly of short sequencing reads

2020 ◽  
Vol 48 (18) ◽  
pp. e106-e106 ◽  
Author(s):  
Jenna E Gallegos ◽  
Mark F Rogers ◽  
Charlotte A Cialek ◽  
Jean Peccoud
Keyword(s):  
Quality Control ◽  
Synthetic Biology ◽  
De Novo Assembly ◽  
Life Science ◽  
De Novo ◽  
Science Research ◽  
Application Security ◽  
Security Issues ◽  
Control Step ◽  
Basic And Applied Research

Abstract Plasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and—depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.

scholarly journals Quality Control and Robust Estimation for cDNA Microarrays With Replicates

2006 ◽  
Vol 101 (473) ◽  
pp. 30-40 ◽  
Author(s):  
Raphael Gottardo ◽  
Adrian E Raftery ◽  
Ka Yee Yeung ◽  
Roger E Bumgarner
Keyword(s):  
Quality Control ◽  
Robust Estimation ◽  
Cdna Microarrays
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