Contamination genomic or cdna oligonucleotide array sequence analysis. Medical search. Frequent questions

Every PCR primer pair was experimentally validated using Bio-Rad's iScript™ advanced cDNA synthesis kit and SsoAdvanced™ SYBR ® Green supermix. (bio-rad.com)
Thus, many of the basic functionalities for microfluidic single cell gene expression analysis have been demonstrated in isolation, including cell manipulation and trapping (9, 10), RNA purification and cDNA synthesis (11-13), and microfluidic qPCR (14) following off-chip cell isolation cDNA synthesis and preamplification. (justia.com)
This allows for the simultaneous preparation of multiple cells by pooling them after cDNA synthesis, increasing the throughput and efficiency of scRNA-seq library preparation. (molcells.org)
Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)
Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)
Three specific modifications, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and N1-methylguanosine (m1G), are abundant in eukaryotic tRNAs and are particularly problematic for reverse transcriptases (RTs) by causing cDNA synthesis to stop or misincorporate. (cdc.gov)
Following the whole workflow of a RT-PCR quantitative analysis, it starts with the sampling step, followed by nucleic acid extraction and stabilization, cDNA synthesis and finally the qPCR where the mRNA quantification takes place. (gene-quantification.org)

Existing methods for measuring transcript levels in single cells include RT-qPCR (1), single molecule counting using digital PCR (2) or hybridization probes (3, 4), and next generation sequencing (5). (justia.com)
In particular, microfluidic qPCR devices (Biomark Dynamic Array, Fluidigm) have recently been applied to single cell studies (15, 16). (justia.com)
Although these systems provide a high-throughput qPCR readout, they do not address the front end sample preparation and require single cell isolation by FACS or micropipette followed by off-chip processing and pre-amplification of starting template prior to analysis. (justia.com)
Traditional methods for tumor characterization are tumor-type specific and include assays such as immunohistochemistry (IHC), in situ hybridization (ISH), quantitative PCR (qPCR), Sanger sequencing and gene signature microarrays [ 1 - 8 ]. (oncotarget.com)
Overexpression was confirmed by RT-qPCR analyses of patient tissues from two independent cohorts. (biomedcentral.com)
By RT-qPCR analysis we furthermore detected stronger CASC9 overexpression in pure SCC of the urinary bladder and mixed urothelial carcinoma with squamous differentiation than in pure urothelial carcinomas. (biomedcentral.com)
The real-time reverse transcription polymerase chain reaction (RT-qPCR) addresses the evident requirement for quantitative data analysis in molecular medicine, biotechnology, microbiology and diagnostics and has become the method of choice for the quantification of mRNA. (gene-quantification.org)
Additionally, we constructed a real-time quantitative PCR (qPCR) array to fill the qPCR technical gap in differentiation and to facilitate the quarantine departments. (bvsalud.org)

Use the PrimePCR DNA contamination control assay to determine if genomic DNA (gDNA) is present in a sample at a level that may affect PCR results. (bio-rad.com)
This assay may also be used to compare relative levels of gDNA contamination present in different samples to determine if PCR results may be affected. (bio-rad.com)
Phylogenetic analyses using Complete Genome Hybridization and Multi Locus VNTR Assay showed that CF-Marseille was closely related to strain Mu50, representing vancomycin-resistant S. aureus . (biomedcentral.com)
The significant problems caused by variability of RNA templates, assay designs and protocols, as well as inappropriate data normalization and inconsistent data analysis, are widely known but also widely disregarded. (gene-quantification.org)
Apply TopSeal to the top surface of the plate to prevent evaporation or radioactive contamination during assay incubation steps and/or plate reading measurements. (horizondiscovery.com)

To ease future molecular studies, this study compares first- (partial sequencing via Sanger), second- (Illumina), and third-generation (MinION Nanopore) sequencing platforms for USUV. (frontiersin.org)
Sanger sequencing was performed on the amplified DNA to confirm the results obtained from dPCR KRAS mutation analysis. (takarabio.com)

Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells. (takarabio.com)
The PicoPLEX DNA-seq Kit did not require a separate library preparation step as the kit performs whole genome amplification (WGA) and library construction simultaneously, resulting "in a sequencing-ready library, using a single-tube reaction. (takarabio.com)
The study concluded that "PicoPLEX showed the best performance in the quality of sequencing data, uniformity of read depth, amplification reproducibility and fidelity," and "recommended [PicoPLEX] for CNV calling on Ion Proton platform. (takarabio.com)
Limitations on the number and type of genomic analyses that can be performed due to insufficient quantities of genomic DNA can be overcome by global amplification of all DNA within a sample (whole genome amplification). (qiagen.com)
REPLI‑g Kits provide DNA polymerase, buffers and reagents for highly uniform whole genome amplification with minimal sequence bias and can be used with various starting materials, including genomic DNA, fresh or dried blood, buccal swabs, fresh or frozen tissue and cells. (qiagen.com)
Indeed, if the sequence of interest is present in the DNA extract, it is possible to selectively replicate it (we speak of amplification) in very large numbers. (intechopen.com)
We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). (biomedcentral.com)
Using two pairs of primers one after another, it improved precision by lowering the probability of magnifying several target zones, which was completely free of contamination by nonspecific amplification. (bvsalud.org)
Here, we established a sensitive CRISPR/Cas12a array based on Multiple-recombinase polymerase amplification (M-RPA) for CaPV differentiation, which provided a more comprehensive and accurate differentiation mode targeting VARV B22R and RPO30 genes. (bvsalud.org)

We concluded that depending on the focus of a research project, amplicon-based MinION Nanopore sequencing can be an ideal cost- and time-effective alternative to Illumina in producing optimal genome coverage. (frontiersin.org)
The amplified DNA underwent exome capturing, followed by sequencing on both Illumina HiSeq® 2000 and Thermo Fisher Ion Proton platforms. (takarabio.com)
Cells were whole-genome amplified, followed by PCR-free library preparation and Illumina sequencing. (takarabio.com)
3 , except that primers and adaptors are designed for the Illumina platform, thus allowing multiplexing sequencing. (researchsquare.com)

Using Affymetrix Gene Chip analysis, we have identified genes linked to regenerative success downstream of BMP signalling, including the BMP inhibitor Gremlin and the stress protein Hsp60 ( no blastema in zebrafish). (biomedcentral.com)
Gene Ontology analysis showed that genes involved in embryonic development and growth are significantly over-represented in regenerating early hindlimb buds and that successful regeneration in the Xenopus hindlimb correlates with the induction of stress response pathways. (biomedcentral.com)
Microarrays, by making use of the sequence resources created in genomic projects, are a powerful technology capable of measuring the expression levels of thousands of genes simultaneously and have dramatically expedited comprehensive understanding of gene expression profiles for disease development. (biomedcentral.com)
TFs are known as master switch in plant stress response, and genetic transformation of the genes encoding TFs has been suggested as a possible approach for engineering stress tolerance as manipulation of a single TF can alter expression of a wide array of target genes [ 7 ]. (biomedcentral.com)
The selected pathways were used to design panels of real-time PCR primers tailored for the top-ranked genes for differential gene expression analysis. (bio-rad.com)
Reference genes are used in relative gene expression analysis to normalize for variation in the amount of input messenger RNA (mRNA) among samples. (bio-rad.com)
A study of Escherichia coli physiology during growth on glycerol was performed combining transcriptional-proteomic analysis as well as kinetic and stoichiometric evaluations in the strain JM101 and certain derivatives with important inactivated genes. (biomedcentral.com)
CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. (frontiersin.org)
For example, single cell analysis allows for the direct measurement of gene expression kinetics, or for the unambiguous identification of co-regulated genes, even in the presence of de-synchronization and heterogeneity that could obscure population-averaged measurements. (justia.com)
Third, even using currently available comprehensive arrays, tissue-specific genes are still under-represented, including alternatively spliced variants or genes that are only briefly expressed in a tissue-specific pattern. (biomedcentral.com)

developed the first microarray containing splice-junction oligonucleotides to analyze splice events in yeast [ 16 ]. (biomedcentral.com)
In the realm of statistical analysis, the various available methods of the probe level normalization for microarray analysis may result in distinctly different target selections and variation in the scores for the correlation between microarray and Q-RT-PCR. (biomedcentral.com)
The REPLI-g Screening kit is intended for rapid screening using a range of genotyping, PCR, sequencing or microarray assays. (qiagen.com)
A tissue-specific cDNA microarray was generated using a set of sequence non-redundant EST clones collected from mouse retina. (biomedcentral.com)
Gene microarray analyses represent potentially effective means for high-throughput gene expression profiling in non-human primates. (gene-quantification.de)

Rigorous contamination mitigation to ensure the reliability of your assays. (biosearchtech.com)

16S rRNA gene sequence evaluation said that the particular isolate displayed a previously uncultured family tree with the subphylum degree from the phylum Lentisphaerae called 'WWE2 subgroup I ha. (erk-signal.com)

We applied two strategies to eliminate or substantially reduce the obstacles of tRNA modification and structure for efficient and quantitative tRNA sequencing ( Fig. 1a ). (cdc.gov)

Some of its major applications include genomics, proteomics, molecular diagnostics, point-of-care diagnostics, tissue engineering, single cell analysis and implantable microdevices. (wikipedia.org)
The study of biological complexity is a new frontier that requires high-throughput molecular technology, high speed computer memory, new approaches to data analysis, and the integration of interdisciplinary skills. (intechopen.com)
The purified nucleic acids can be used in downstream applications in biomedical research, molecular diagnostics and gene expression analyses. (hseag.com)

One of the most recent advancements in this field includes in situ combinatorial indexing, which fixes cells to confine the RNA within them, then uses a split-and-pool technique (the cells are sequentially divided into well plates then recombined several times) to attach barcodes and adapter sequences in several combinations. (molcells.org)

The array consisted of exon probes and thermodynamically balanced junction probes. (biomedcentral.com)
Suboptimal probes were tagged and considered in the final analysis. (biomedcentral.com)
These arrays contain oligonucleotide probes that span exon-exon junctions, and probes positioned within exons to determine individual exon levels and overall transcript expression. (biomedcentral.com)
The short-oligonucleotide-based Affymetrix GeneChip ® arrays utilize multiple probes for each gene with an automated control for the experimental process from hybridization to quantification and thus provide reliable and comparable data [ 2 ]. (biomedcentral.com)

Moreover, Lateral flow dipstick (LFD) array based on CRISPR/Cas12a achieved portable and intuitive detection, making it suitable for point-of-care testing. (bvsalud.org)
Therefore, CRISPR/Cas12a array and LFD array paved the way for CaPV differentiation in practice. (bvsalud.org)

PCR analysis of exon utilization reveals massive alternative mRNA splicing of Sec31B, with just 16 exons being constitutively utilized in all transcripts. (biologists.com)
Since the introduction of RNA sequencing (RNA-seq) as a high-throughput mRNA expression analysis tool, this procedure has been increasingly implemented to identify cell-level transcriptome changes in a myriad of model systems. (molcells.org)

These kits generate high yields of genomic DNA, total cellular DNA or total nucleic acids (TNA) in under 60 minutes. (biosearchtech.com)
Analysis of nucleic acids and proteins from biological samples are often a crucial part of medical and biochemical applications. (hseag.com)

Similarly, micro total analysis systems may not have biological applications in mind, and are usually dedicated to chemical analysis. (wikipedia.org)

We can therefore amplify nucleotide sequences from infinitesimal amounts of DNA extract. (intechopen.com)
In another embodiment, the present invention relates to a gene comprising a DNA sequence having at least a portion of the nucleotide sequence set forth in SEQ ID NO: 1. (justia.com)
In one embodiment, the nucleic acid comprises a nucleotide sequence having at least a portion of the sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 41, and SEQ ID NO: 43. (justia.com)

With emphasis on MinION Nanopore sequencing, cDNA-direct and target-enrichment (amplicon-based) sequencing approaches were validated in parallel. (frontiersin.org)

The absence of DNA contamination in RNA samples was confirmed by PCR of GAPDH with primers specific to genomic DNA. (biomedcentral.com)

strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. (frontiersin.org)

Analysis of TCGA pan-cancer data revealed significant overexpression of CASC9 across different other entities including bladder, liver, lung and stomach cancers and especially in squamous cell carcinoma (SCC) of the lung. (biomedcentral.com)

Our applications expertise covers a wide range of technologies such as capillary electrophoresis, real-time PCR, Pyrosequencing, and next-generation sequencing. (hseag.com)

Our mag kits are a high-throughput and cost-effective DNA isolation method suitable for PCR, sequencing and genotyping. (biosearchtech.com)

However, compared to other flaviviruses, USUV has received less research attention and there is therefore limited access to whole-genome sequences and also to in-depth phylogenetic and phylodynamic analyses. (frontiersin.org)
Phylogenetic analysis of phenotypically similar h-GISA in our study also suggests that CF patients are colonized by polyclonal populations of MRSA that represents an incredible reservoir for lateral gene transfer. (biomedcentral.com)

Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups. (frontiersin.org)

This method can generate tens of billions of copies of a particular DNA fragment (the sequence of interest, DNA of interest, or target DNA) from a DNA extract (DNA template). (intechopen.com)

In recent years, powerful techniques for genome-wide identification and analysis of alternative splicing isoforms have been developed. (biomedcentral.com)
Therefore, this review will discuss the current status of cell engineering toolkits and their contributions to single-cell and genome-wide data collection and analyses. (molcells.org)

Firstly, drug discovery in the last decades leading up to the 1990s had been limited due to the time and cost of running many chromatographic analyses in parallel on macroscopic equipment. (wikipedia.org)

Nonetheless, the recent and continuous development of new single-cell RNA sequencing (scRNA-seq) toolkits has enabled researchers to compare transcriptomes at a single-cell resolution, thus facilitating the analysis of individual cellular features and a deeper understanding of cellular functions. (molcells.org)
Author Manuscript class of cellular RNA for which the standard sequencing methods cannot yet be applied efficiently and quantitatively, although attempts have been made (e.g. ref 2). (cdc.gov)

The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. (biomedcentral.com)
Various clinical and non-clinical research samples can be used with REPLI-g Mini and Midi Kits, including genomic DNA, fresh or dried blood, fresh or frozen tissue and cells. (qiagen.com)
The virus was recovered from acute-phase serum samples from both case-patients and identified with cardiovirus-specific reverse transcription-PCR and sequencing. (cdc.gov)

Minimal primer dimer formation and genomic DNA cross reactivity. (bio-rad.com)

Researchers are still confronted with challenging questions after completing the expression profiling and these include how to validate and standardize the data processing using proper statistical analysis. (biomedcentral.com)
The GEO accession number for the sequencing data reported in this paper is GSE66550. (cdc.gov)
This article focuses on effective experimental design while the companion article focuses on methodology and data analysis. (gene-quantification.de)

The new challenge in gene quantification analysis is how to explicitly incorporate statistical estimation in such studies. (biomedcentral.com)

In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. (biomedcentral.com)

PtrABF had a complete open reading frame of 1347 bp, encoding a 448 amino acid peptide, and shared high sequence identities with ABFs from other plants. (biomedcentral.com)
Obtaining uniform DNA yields from varying template concentrations is always important, but particularly essential for high-throughput applications, which require subsequent genetic analyses to be possible without additional measurement or adjustment of DNA concentration. (qiagen.com)
Unfortunately, such devices do not allow for high throughput analysis due to the manual effort involved in operating the valving mechanisms. (justia.com)
High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)
We also describe the validation of the Affymetrix OncoScan platform, an array technology for high resolution copy number variant detection for use in parallel with the NGS panel that can detect single copy amplifications and hemizygous deletions. (oncotarget.com)
In order to investigate the high resolution capability of nitrocellulose resist, periodic line array with a period of 600 nm was exposed at 20 keV over a broad line dose range and subsequently coated with 30 nm Cr for SEM imaging. (kinasepathway.com)
One major limitation for its application to mammalian systems resides in their genome size and complexity, rendering challenging the preparation of representative libraries and requiring very high sequencing depth. (researchsquare.com)
To circumvent this problem, we developed CapStarr-seq, a technique capturing genomic sequences of interest for high-throughput assessment of enhancer activity in mammals 3 . (researchsquare.com)

First, a suitable shRNA sequence must be identi﫿ed. (berterolab.com)

This in turn allows for contamination events, and further limits the downstream applications of the device. (justia.com)
Pol IV is needed to produce the small RNA trigger for methylation whereas Pol V acts downstream of small RNA biogenesis to facilitate de novo methylation of genomic DNA at the small RNA-targeted site. (biomedcentral.com)

In some embodiments, the present invention provides a protein which consists of the amino acid sequence shown in SEQ ID NO: 2 having a deletion, substitution, or addition of at least one amino acid and which has neurogenesis inducing activity. (justia.com)
The 﫿rst step in generating OPTiKD hPSCs consists in obtaining oligonucleotides to be used to clone the shRNA sequence in the targeting vector. (berterolab.com)

The study found that PicoPLEX DNA-seq libraries "detected 100% of the CNVs that were also detected in the sequenced bulk sample. (takarabio.com)
NGS libraries were constructed for sequencing on the Ion Proton platform. (takarabio.com)

Because of the clinical importance of the spread of such strain among CF patients we decided to sequence the genome of one representative isolate (strain CF-Marseille) to compare this to the published genome sequences. (biomedcentral.com)

The use of splice-junction oligonucleotides to analyze splice events was proposed as early as 1986, when Morgan and Ward used them to identify differential splice forms of minute virus in mice cDNA [ 14 ]. (biomedcentral.com)

Initial annotation of the rhesus genome array was based on Affymetrix human GeneChips. (gene-quantification.de)

In one embodiment, the present invention relates to a recombinant protein having a protein comprising at least a portion of the amino acid sequence set forth in SEQ ID NO:2. (justia.com)
The present invention also relates to a gene which hybridizes with the neurogenesis inducing gene encoding for a protein comprising at least a portion of the amino acid sequence set forth in SEQ ID NO:2. (justia.com)
In another embodiment, the present invention relates to an isolated nucleic acid encoding a protein having at least a portion of the amino acid sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 42 and in SEQ ID NO: 44. (justia.com)

An optimised reverse transcriptase for production of full-length cDNA from as little as 100pg of total RNA/low abundance RNA. (biosearchtech.com)

Considerable effort over the last decade has been directed towards developing integrated and scalable single cell genetic analysis on chip (7, 8). (justia.com)

This paper compared the performance of the PicoPLEX DNA-seq Kit , the DOPlify WGA Kit, the REPLI-g Single Cell Kit, and the Ampli1 WGA Kit for aneuploidy screening and copy number analysis using shallow whole genome sequencing, starting from one, three, or five cells isolated from the Loucy cell line. (takarabio.com)
Analysis of PicoPLEX WGA products provided a correct diagnosis for 16/16 cells, with detection of 16/16 individual aneuploidies. (takarabio.com)
Moreover, the device does not allow isolated cells to be washed from the supernatant prior to treatment or analysis. (justia.com)
Accordingly, a goal of microfluidics research has been the development of integrated technology for scalable analysis of transcription in single cells. (justia.com)
The critical step of integrating all steps of single cell analysis into a robust system capable of performing measurements on large numbers of cells has yet to be reported. (justia.com)

13. The apparatus of claim 12, wherein the array of conductors comprises a periodic array of equally spaced electrodes, and wherein an extent of the thin region from and normal to a surface of the substrate is based at least in part on a spacing between adjacent electrodes of the periodic array. (patentsencyclopedia.com)
15. The apparatus of claim 13, further comprising at least one signal generator coupled to the equally spaced electrodes, such that when the at least one signal generator is energized, adjacent electrodes of the periodic array have opposite polarities. (patentsencyclopedia.com)
16. The apparatus of claim 15, wherein adjacent electrodes of the periodic array have equal and opposite potentials. (patentsencyclopedia.com)

The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. (biomedcentral.com)

Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.com)
Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. (researchsquare.com)

Microfluidic systems provide numerous advantages for single cell analysis: economies of scale, parallelization and automation, and increased sensitivity and precision that comes from small volume reactions. (justia.com)
Particularly, this issue could be addressed by coupling cell engineering techniques with single-cell sequencing. (molcells.org)
Brie﫿y, two single-stranded oligonucleotides are annealed to form a double-stranded DNA sequence containing the shRNA sequence followed by a Pol III terminator (consisting of a stretch of four or more thymidines), as well as 5'- and 3'-end "sticky" overhangs that are complementary to those generated in the targeting vector following restriction digestion with BglII and SalI (Figures 3E and 4C). (berterolab.com)

Since AsCas12a contains RNA processing activity, we used arrayed dual-gRNAs to improve AsCas12a and CHyMErA applications. (nature.com)

RNA-directed DNA methylation results in a characteristic modification pattern that is typified by methylation of cytosines in all sequence contexts (CG, CHG and CHH, where H is A, T or C) within the region of small RNA-DNA sequence homology [ 4 ]. (biomedcentral.com)

Secondly, the Human Genome Project (HGP), which started in October 1990, created demand for improvements in DNA sequencing capacity. (wikipedia.org)

Anatomy8

Organisms13

Diseases3

Chemicals and Drugs57

Analytical, Diagnostic and Therapeutic Techniques and Equipment49

Phenomena and Processes99

Disciplines and Occupations8

Anthropology, Education, Sociology and Social Phenomena2

Technology, Industry, Agriculture8

Information Science9

Health Care26

Synthesis8

QPCR8

Assay5

Sanger2

Amplification9

Illumina4

Genes10

Microarray5

Assays1

RRNA gene1

Quantitative1

Molecular3

Adapter1

Probes4

CRISPR2

MRNA2

Nucleic acids2

Biological1

Nucleotide3

Approaches1

Primers1

Comparative1

Overexpression1

Capillary1

Isolation1

Phylogenetic2

Genomes1

Generate1

Genome-wide2

1990s1

Cellular2

Samples3

Minimal1

Data3

Quantification1

Procedure1

High8

Suitable1

Downstream2

Consists2

Libraries2

Strain1

Differential1

Annotation1

Amino3

Full-length1

Genetic analysis1

Cells5

Periodic3

Control1

Specific2

Single3

Applications1

Results1

Human1