scholarly journals Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Mitsutaka Kadota ◽  
Osamu Nishimura ◽  
Hisashi Miura ◽  
Kaori Tanaka ◽  
Ichiro Hiratani ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Best Practice ◽  
De Novo ◽  
Third Party ◽  
Chromosome Conformation ◽  
Preparation Methods ◽  
Preparation Conditions ◽  
Genome Scaffolding ◽  
Multiple Sample ◽  
Softshell Turtle

Abstract Background Hi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomic scale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number. Despite its prevalent use, the sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding. Results To gain insight into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we identified several key factors that helped improve Hi-C scaffolding, including the choice and preparation of tissues, library preparation conditions, the choice of restriction enzyme(s), and the choice of scaffolding program and its usage. Conclusions This study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding by an academic third party. We introduce a customized protocol designated “inexpensive and controllable Hi-C (iconHi-C) protocol,” which incorporates the optimal conditions identified in this study, and demonstrate this technique on chromosome-scale genome sequences of the Chinese softshell turtle Pelodiscus sinensis.

scholarly journals Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

2019 ◽  
Author(s):  
Mitsutaka Kadota ◽  
Osamu Nishimura ◽  
Hisashi Miura ◽  
Kaori Tanaka ◽  
Ichiro Hiratani ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Best Practice ◽  
De Novo ◽  
Third Party ◽  
Chromosome Conformation ◽  
Preparation Methods ◽  
Preparation Conditions ◽  
Genome Scaffolding ◽  
Multiple Sample ◽  
Softshell Turtle

AbstractBackgroundHi-C, a derivative of chromosome conformation capture (3C) targeting the whole genome, was originally developed as a means for characterizing chromatin conformation. More recently, this method has also been frequently employed in elongating nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converge into the chromosome number. Despite the prevailing and irreplaceable use, sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding.ResultsTo gain insights into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we have identified some key factors that help improve Hi-C scaffolding including the choice and preparation of tissues, library preparation conditions, and restriction enzyme(s), as well as the choice of scaffolding program and its usage.ConclusionsThis study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding, by an academic third party. We introduce a customized protocol designated the ‘inexpensive and controllable Hi-C (iconHi-C) protocol’, in which the optimal conditions revealed by this study have been incorporated, and release the resultant chromosome-scale genome assembly of the Chinese softshell turtle Pelodiscus sinensis.

scholarly journals Assessment of human plasma and urine sample preparation for reproducible and high-throughput UHPLC-MS clinical metabolic phenotyping

The Analyst ◽  
2020 ◽  
Vol 145 (20) ◽  
pp. 6511-6523 ◽  
Author(s):  
Andrew D. Southam ◽  
Liam D. Haglington ◽  
Lukáš Najdekr ◽  
Andris Jankevics ◽  
Ralf J. M. Weber ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Human Plasma ◽  
Urine Sample ◽  
High Throughput ◽  
Human Urine ◽  
Metabolic Phenotyping ◽  
Preparation Methods ◽  
Human Plasma And Urine ◽  
Multiple Sample ◽  
Sample Preparation Methods

In this study we assess multiple sample preparation methods for UHPLC-MS metabolic phenotyping analysis of human urine and plasma. All methods are discussed in terms of metabolite and lipid coverage and reproducibility.

Improving Sample Preparation Methods For Cannabis-Infused Edible And Topical Products

Planta Medica ◽  
2016 ◽  
Vol 82 (05) ◽  
Author(s):  
M Wilcox ◽  
M Jacyno ◽  
J Marcu ◽  
J Neal-Kababick
Keyword(s):  
Sample Preparation ◽  
Preparation Methods ◽  
Sample Preparation Methods

Methodology for TEM Analysis of Barrier Profiles

2002 ◽  
Author(s):  
Tan-Chen Lee ◽  
Jui-Yen Huang ◽  
Li-Chien Chen ◽  
Ruey-Lian Hwang ◽  
David Su
Keyword(s):  
Sample Preparation ◽  
Profile Analysis ◽  
Image Interpretation ◽  
Sample Thickness ◽  
Image Resolution ◽  
Specimen Preparation ◽  
Tem Analysis ◽  
Preparation Methods ◽  
High Image Resolution ◽  
Common Technique

Abstract Device shrinkage has resulted in thinner barriers and smaller vias. Transmission Electron Microscopy (TEM) has become a common technique for barrier profile analysis because of its high image resolution. TEM sample preparation and image interpretation becomes difficult when the size of the small cylindrical via is close to the TEM sample thickness. Effects of different sample thickness and specimen preparation methods, therefore, have been investigated. An automatic FIB program has been shown to be useful in via sample preparation. Techniques for imaging a TEM specimen will be discussed in the paper. Conventional TEM bright field (BF) image is adequate to examine the barrieronly via; however, other techniques are more suitable for a Cu filled via.

Thin-Die Flip Chip Physical-FA Process Flow

2002 ◽  
Author(s):  
Andrew J. Komrowski ◽  
N. S. Somcio ◽  
Daniel J. D. Sullivan ◽  
Charles R. Silvis ◽  
Luis Curiel ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Failure Analysis ◽  
Flip Chip ◽  
Semiconductor Industry ◽  
Organic Substrate ◽  
Fault Isolation ◽  
Preparation Methods ◽  
Chip Technology ◽  
Isolation Test ◽  
Sample Preparation Methods

Abstract The use of flip chip technology inside component packaging, so called flip chip in package (FCIP), is an increasingly common package type in the semiconductor industry because of high pin-counts, performance and reliability. Sample preparation methods and flows which enable physical failure analysis (PFA) of FCIP are thus in demand to characterize defects in die with these package types. As interconnect metallization schemes become more dense and complex, access to the backside silicon of a functional device also becomes important for fault isolation test purposes. To address these requirements, a detailed PFA flow is described which chronicles the sample preparation methods necessary to isolate a physical defect in the die of an organic-substrate FCIP.

Influence of Sample Preparation on Intrinsic Stress Inside a Model Chip—Comparison of Results from Electric Read-Out and Raman Spectroscopy

2017 ◽  
Author(s):  
T. Schaffus ◽  
H. Pfaff ◽  
P. Albert ◽  
M. Schaffus ◽  
F. Kroninger ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Sample Preparation ◽  
Intrinsic Stress ◽  
Stress Monitoring ◽  
Preparation Methods ◽  
Comparison Of Results ◽  
The Given

Abstract The given project is to benchmark typical preparation methods under the aspect of the influence of initial intrinsic stresses inside electric components. Raman spectroscopy has been applied as well as the piezo resistive readout on a specifically designed model stress monitoring chip.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

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