scholarly journals Targeted reduction of highly abundant transcripts using pseudo-random primers

BioTechniques ◽  
2016 ◽  
Vol 60 (4) ◽  
Author(s):  
Ophélie Arnaud ◽  
Sachi Kato ◽  
Stéphane Poulain ◽  
Charles Plessy
Keyword(s):  
Random Primers

scholarly journals The use of random amplified polymorphic DNA to evaluate the genetic variability of Ponkan mandarin (Citrus reticulata Blanco) accessions

2000 ◽  
Vol 23 (1) ◽  
pp. 169-172 ◽  
Author(s):  
Helvécio Della Coletta Filho ◽  
Marcos Antonio Machado ◽  
M. Luiza P.N. Targon ◽  
Jorgino Pompeu Jr.
Keyword(s):  
Genetic Variability ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Point Mutations ◽  
The Other ◽  
Citrus Reticulata ◽  
Random Primers ◽  
Citrus Reticulata Blanco ◽  
Ponkan Mandarin

RAPD analysis of 19 Ponkan mandarin accessions was performed using 25 random primers. Of 112 amplification products selected, only 32 were polymorphic across five accessions. The absence of genetic variability among the other 14 accessions suggested that they were either clonal propagations with different local names, or that they had undetectable genetic variability, such as point mutations which cannot be detected by RAPD.

scholarly journals Targeted reduction of highly abundant transcripts with pseudo-random primers

2015 ◽  
Author(s):  
Ophélie Arnaud ◽  
Sachi Kato ◽  
Stéphane Poulain ◽  
Charles Plessy
Keyword(s):  
Gene Expression ◽  
Reverse Transcription ◽  
Flexible Tool ◽  
Expression Levels ◽  
Random Primers ◽  
Sequencing Cost ◽  
Transcriptome Diversity ◽  
Gene Expression Levels ◽  
Selection Of

Transcriptome studies based on quantitative sequencing estimate gene expression levels by measuring the abundance of target RNAs in libraries of sequence reads. The sequencing cost is proportional to the total number of sequenced reads. Therefore, in order to cover rare RNAs, considerable quantities of abundant and identical reads have to be sequenced. This major limitation can be lifted by strategies used to deplete the library from some of the most abundant sequences. However, these strategies involve either an extra handling of the input RNA sample, or the use of a large number of reverse-transcription primers (termed "not-so-random primers"), which are costly to synthetize and customize. Here, we demonstrate that with a precise selection of only 40 "pseudo-random" reverse-transcription primers, it is possible to decrease the rate of undesirable abundant sequences within a library without affecting the transcriptome diversity. "Pseudo-random" primers are simple to design, and therefore are a flexible tool for enriching transcriptome libraries in rare transcripts sequences.

scholarly journals RAPD-based analysis of differences between male and female genotypes of Asparagus officinalis

2012 ◽  
Vol 39 (No. 1) ◽  
pp. 33-37 ◽  
Author(s):  
Y. Ii ◽  
A. Uragami ◽  
Y. Uno ◽  
M. Kanechi ◽  
N. Inagaki
Keyword(s):  
Molecular Markers ◽  
Sex Determination ◽  
Genomic Dna ◽  
Asparagus Officinalis ◽  
Breeding Line ◽  
Male And Female ◽  
Future Studies ◽  
Random Primers

Asparagus (Asparagus officinalis L.) plants are dioecious. All-male cultivars are desired because of their higher yields. To increase the proportion of male individuals planted in the field and expedite the breeding of all-male cultivars in asparagus, development of generally applicable molecular markers to distinguish male and female individuals is required. Bulked genomic DNA samples from ten male (XY) and ten female (XX) plants was screened with 10-bp random primers. Of the 188 primers tested, the primer T35R54 produced a 1600-bp fragment observed only in male individuals. The specificity of this T35R54-1600 marker was verified using DNA from one supermale (YY) and one female (XX) breeding line and their four F<sub>1</sub> progenies (XY). The T35R54-1600 marker fragment was observed in both supermale and all-male lines. The sequence of the T35R54 primer (5'-TTCACGGTGG-3') was absent among the sequences of primers or amplified fragments from previous studies. Therefore, this marker could be useful as a sex-related marker in future studies to increase the reliability of sex determination in asparagus.

scholarly journals A novel 3′ extension technique using random primers in RNA-PCR

1991 ◽  
Vol 19 (13) ◽  
pp. 3747-3747 ◽  
Author(s):  
J.D. Fritz ◽  
M.L. Greaser ◽  
J.A. Wolff
Keyword(s):  
Random Primers

scholarly journals LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens

2008 ◽  
Vol 9 (1) ◽  
pp. 368 ◽  
Author(s):  
Wah Lee ◽  
Christopher W Wong ◽  
Wan Leong ◽  
Lance D Miller ◽  
Wing Sung
Keyword(s):  
Fast Method ◽  
Amplification Bias ◽  
Random Primers

Genetic Relationships Among 22 Taxa of Bamboo Revealed by ISSR and EST-Based Random Primers

2010 ◽  
Vol 48 (11-12) ◽  
pp. 1015-1025 ◽  
Author(s):  
Arup K. Mukherjee ◽  
Shibani Ratha ◽  
Sujaya Dhar ◽  
Akhil K. Debata ◽  
Pradosh K. Acharya ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Random Primers

scholarly journals Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers

2015 ◽  
Vol 6 (6) ◽  
pp. 555-567 ◽  
Author(s):  
Zhiyu Peng ◽  
Chengfu Yuan ◽  
Lucas Zellmer ◽  
Siqi Liu ◽  
Ningzhi Xu ◽  
...  
Keyword(s):  
Homologous Sequence ◽  
Random Primers ◽  
Chimeric Rnas

scholarly journals Virus detection and identification using random multiplex (RT)-PCR with 3'-locked random primers

2007 ◽  
Vol 4 (1) ◽  
pp. 65 ◽  
Author(s):  
Amy L Clem ◽  
Jonathan Sims ◽  
Sucheta Telang ◽  
John W Eaton ◽  
Jason Chesney
Keyword(s):  
Virus Detection ◽  
Rt Pcr ◽  
Random Primers ◽  
Detection And Identification
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