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Pooling DNA
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We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity.
11p
vibransone
28-03-2024
5
2
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DNA methylation changes that accrue in the stem cell pool of an adult tissue in line with the cumulative number of cell divisions may contribute to the observed variation in cancer risk among tissues and individuals. Thus, the construction of epigenetic “mitotic” clocks that can measure the lifetime number of stem cell divisions is of paramount interest.
17p
vibransone
28-03-2024
3
2
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The long introns of mammals are pools of evolutionary potential due to the multiplicity of sequences that permit the acquisition of novel exons. However, the permissibility of genes to this type of acquisition and its influence on the evolution of cell regulation is poorly understood.
13p
vigalileogalilei
27-02-2022
10
1
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Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases associated with copy number alterations, the effects of sgRNAs co-targeting multiple genomic loci in CRISPR screens have not been discussed.
25p
vigalileogalilei
27-02-2022
16
1
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Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such “functional metagenomics” experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications.
10p
vilarryellison
29-10-2021
9
1
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Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes. The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of protein-coding gene function.
15p
vijeeni2711
24-07-2021
1
0
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Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable breeding. Discovery of DNA variations is an important step in the efficient use of these resources.
16p
vijeeni2711
30-06-2021
10
0
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Ataxia telangiectasia-mutated (ATM) gene contributes to repair damaged DNA and to regulate cell cycle; therefore, ATM variants seem to increase breast cancer risk; however, the results are controversial. So we conducted a systematic review and meta-analysis to clarify the pooled association between various ATM variants and the risk of breast cancer.
12p
vianrose2711
27-04-2021
11
1
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DNA pooling constitutes a cost effective alternative in genome wide association studies. In DNA pooling, equimolar amounts of DNA from different individuals are mixed into one sample and the frequency of each allele in each position is observed in a single genotype experiment.
10p
viwyoming2711
16-12-2020
5
0
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Short oligonucleotides can be used as markers to tag and track DNA sequences. For example, barcoding techniques (i.e. Multiplex Identifiers or Indexing) use short oligonucleotides to distinguish between reads from different DNA samples pooled for high-throughput sequencing.
7p
vikentucky2711
26-11-2020
12
1
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Despite ongoing reduction in genotyping costs, genomic studies involving large numbers of species with low economic value (such as Black Tiger prawns) remain cost prohibitive. In this scenario DNA pooling is an attractive option to reduce genotyping costs.
11p
vikentucky2711
24-11-2020
9
1
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Despite the tremendous drop in the cost of nucleotide sequencing in recent years, many research projects still utilize sequencing of pools containing multiple samples for the detection of sequence variants as a cost saving measure. Various software tools exist to analyze these pooled sequence data, yet little has been reported on the relative accuracy and ease of use of these different programs.
9p
vikentucky2711
24-11-2020
9
2
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Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously.
6p
viconnecticut2711
28-10-2020
14
1
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Genome-wide high-throughput sequencing (HTS) time series experiments are a powerful tool for monitoring various genomic elements over time. They can be used to monitor, for example, gene or transcript expression with RNA sequencing (RNA-seq), DNA methylation levels with bisulfite sequencing (BS-seq), or abundances of genetic variants in populations with pooled sequencing (Pool-seq).
6p
viconnecticut2711
28-10-2020
10
0
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Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. (PLoS ONE 13:0195090, 2018) proposed a pooling strategy without the use of barcodes.
11p
viconnecticut2711
28-10-2020
9
1
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Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequencing. In cases of single-cell and low-input RNAseq methods, the library is further amplified by PCR after the pooling.
9p
vicolorado2711
23-10-2020
11
0
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Duplex sequencing is the most accurate approach for identification of sequence variants present at very low frequencies. Its power comes from pooling together multiple descendants of both strands of original DNA molecules, which allows distinguishing true nucleotide substitutions from PCR amplification and sequencing artifacts.
10p
vicolorado2711
22-10-2020
10
0
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MYC family members are among the most frequently deregulated oncogenes in human cancers, yet direct therapeutic targeting of MYC in cancer has been challenging thus far. Synthetic lethality provides an opportunity for therapeutic intervention of MYC-driven cancers.
13p
vialabama2711
21-09-2020
7
1
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Physical maps created from large insert DNA libraries, typically cloned in BAC vector, are valuable resources for map-based cloning and de novo genome sequencing. The maps are most useful if contigs of overlapping DNA clones are anchored to chromosome(s), and ordered along them using molecular markers.
13p
viminato2711
22-05-2020
15
0
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Molecular variation in chilli fruit rot pathogen (Alternata alternata) was analyzed by using six isolates collected from major chilli growing region of Maharashtra. The genomic DNA extracted from each isolate of A. alternata was subjected to polymerase chain reaction using 15 primers of OPA and OPB series off which 10 primers produced 83 scorable bands with size ranging from Among the RAPD primer 83 bands 80 bands were polymorphic and level of polymorphism was 96.38%. Molecular diversity using RAPD marker showed that the Aa2 (Satara) having higher similarity index with Aa4 (Akola).
7p
trinhthamhodang1212
06-04-2020
10
1
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