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Keywords small rna discovery short read...

small rna discovery short read sequencing

https://read.qxmd.com/read/23324106/transcriptomic-profiling-of-the-salt-stress-response-in-the-wild-recretohalophyte-reaumuria-trigyna
#21
JOURNAL ARTICLE
Zhen-hua Dang, Lin-lin Zheng, Jia Wang, Zhe Gao, Shu-biao Wu, Zhi Qi, Ying-chun Wang
BACKGROUND: Reaumuria trigyna is an endangered small shrub endemic to desert regions in Inner Mongolia. This dicotyledonous recretohalophyte has unique morphological characteristics that allow it to tolerate the stress imposed by semi-desert saline soil. However, it is impossible to explore the mechanisms underlying this tolerance without detailed genomic information. Fortunately, newly developed high-throughput sequencing technologies are powerful tools for de novo sequencing to gain such information for this species...
January 16, 2013: BMC Genomics
https://read.qxmd.com/read/23061771/deep-sequencing-discovery-of-novel-and-conserved-micrornas-in-strawberry-fragaria%C3%A3-ananassa
#22
JOURNAL ARTICLE
Anjing Ge, Lingfei Shangguan, Xi Zhang, Qinghua Dong, Jian Han, Hong Liu, Xicheng Wang, Jinggui Fang
In plants, microRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new miRNAs in cultivated strawberry (Fragaria×ananassa)...
July 2013: Physiologia Plantarum
https://read.qxmd.com/read/23044543/ncpro-seq-a-tool-for-annotation-and-profiling-of-ncrnas-in-srna-seq-data
#23
JOURNAL ARTICLE
Chong-Jian Chen, Nicolas Servant, Joern Toedling, Alexis Sarazin, Antonin Marchais, Evelyne Duvernois-Berthet, Valérie Cognat, Vincent Colot, Olivier Voinnet, Edith Heard, Constance Ciaudo, Emmanuel Barillot
SUMMARY: Non-coding RNA (ncRNA) PROfiling in small RNA (sRNA)-seq (ncPRO-seq) is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on sRNAs derived from annotated non-coding regions in miRBase, Rfam and RepeatMasker, as well as specific regions defined by users. The ncPRO-seq pipeline performs both gene-based and family-based analyses of sRNAs. It also has a module to identify regions significantly enriched with short reads, which cannot be classified under known ncRNA families, thus enabling the discovery of previously unknown ncRNA- or small interfering RNA (siRNA)-producing regions...
December 1, 2012: Bioinformatics
https://read.qxmd.com/read/22493715/discovery-of-potential-pirnas-from-next-generation-sequences-of-the-sexually-mature-porcine-testes
#24
JOURNAL ARTICLE
Gang Liu, Bin Lei, Yan Li, Keya Tong, Yi Ding, Lifan Luo, Xuanyan Xia, Siwen Jiang, Changyan Deng, Yuanzhu Xiong, Fenge Li
Piwi-interacting RNAs (piRNAs), a new class of small RNAs discovered from mammalian testes, are involved in transcriptional silencing of retrotransposons and other genetic elements in germ line cells. In order to identify a full transcriptome set of piRNAs expressed in the sexually mature porcine testes, small RNA fractions were extracted and were subjected to a Solexa deep sequencing. We cloned 6,913,561 clean reads of Sus Scrofa small RNAs (18-30 nt) and performed functional characterization. Sus Scrofa small RNAs showed a bimodal length distribution with two peaks at 21 nt and 29 nt...
2012: PloS One
https://read.qxmd.com/read/22454452/characterization-of-the-longissimus-lumborum-transcriptome-response-to-adding-propionate-to-the-diet-of-growing-angus-beef-steers
#25
JOURNAL ARTICLE
Ransom L Baldwin, Robert W Li, Cong-jun Li, Jennifer M Thomson, Brian J Bequette
Development of management paradigms that enhance the rate of gain and qualitative characteristics of beef carcass development has the potential to impact production and nutrient use efficiency but also mitigate losses to the environment. We used eight Black Angus beef steers (272.5 ± 17.6 kg initial body wt) fed a forage-based pelleted diet alone (n = 4) or supplemented with sodium propionate included (n = 4) for 42 days. High-quality RNA was extracted from the longissimus lumborum and subjected to transcriptome sequencing using RNA-seq technology...
May 1, 2012: Physiological Genomics
https://read.qxmd.com/read/22307312/novel-high-rank-phylogenetic-lineages-within-a-sulfur-spring-zodletone-spring-oklahoma-revealed-using-a-combined-pyrosequencing-sanger-approach
#26
JOURNAL ARTICLE
Noha Youssef, Brandi L Steidley, Mostafa S Elshahed
The utilization of high-throughput sequencing technologies in 16S rRNA gene-based diversity surveys has indicated that within most ecosystems, a significant fraction of the community could not be assigned to known microbial phyla. Accurate determination of the phylogenetic affiliation of such sequences is difficult due to the short-read-length output of currently available high-throughput technologies. This fraction could harbor multiple novel phylogenetic lineages that have so far escaped detection. Here we describe our efforts in accurate assessment of the novelty and phylogenetic affiliation of selected unclassified lineages within a pyrosequencing data set generated from source sediments of Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma...
April 2012: Applied and Environmental Microbiology
https://read.qxmd.com/read/21729735/coding-vs-non-coding-translatability-of-short-orfs-found-in-putative-non-coding-transcripts
#27
REVIEW
Yuji Kageyama, Takefumi Kondo, Yoshiko Hashimoto
Genome analysis has identified a number of putative non-protein-coding transcripts that do not contain ORFs longer than 100 codons. Although evidence strongly suggests that non-coding RNAs are important in a variety of biological phenomena, the discovery of small peptide-coding mRNAs confirms that some transcripts that have been assumed to be non-coding actually have coding potential. Their abundance and importance in biological phenomena makes the sorting of non-coding RNAs from small peptide-coding mRNAs a key issue in functional genomics...
November 2011: Biochimie
https://read.qxmd.com/read/21554183/association-of-a-novel-dna-virus-with-the-grapevine-vein-clearing-and-vine-decline-syndrome
#28
JOURNAL ARTICLE
Yu Zhang, Kashmir Singh, Ravneet Kaur, Wenping Qiu
A severe vein-clearing and vine decline syndrome has emerged on grapevines (Vitis vinifera) and hybrid grape cultivars in the Midwest region of the United States. The typical symptoms are translucent vein-clearing on young leaves, short internodes and decline of vine vigor. Known viral pathogens of grapevines were not closely associated with the syndrome. To obtain a comprehensive profile of viruses in a diseased grapevine, small RNAs were enriched and two cDNA libraries were constructed from a symptomatic grapevine and a symptomless grapevine, respectively...
September 2011: Phytopathology
https://read.qxmd.com/read/21525786/genome-wide-discovery-and-analysis-of-micrornas-and-other-small-rnas-from-rice-embryogenic-callus
#29
JOURNAL ARTICLE
Chong-Jian Chen, Qing liu, Yu-Chan Zhang, Liang-Hu Qu, Yue-Qin Chen, Daniel Gautheret
Small RNAs constitute a new and unanticipated layer of gene regulation present in the three domains of life. In plants, all organs are ultimately derived from a few pluripotent stem cells localized in specialized structures called apical meristems. The development of meristems involves a coordinated balance between undifferentiated growth and differentiation, a phenomenon requiring a tight regulation of gene expression. We used in vitro cultured embryogenic calli as a model to investigate the roles of meristem-associated small RNAs...
May 2011: RNA Biology
https://read.qxmd.com/read/21367939/discovery-and-annotation-of-small-proteins-using-genomics-proteomics-and-computational-approaches
#30
JOURNAL ARTICLE
Xiaohan Yang, Timothy J Tschaplinski, Gregory B Hurst, Sara Jawdy, Paul E Abraham, Patricia K Lankford, Rachel M Adams, Manesh B Shah, Robert L Hettich, Erika Lindquist, Udaya C Kalluri, Lee E Gunter, Christa Pennacchio, Gerald A Tuskan
Small proteins (10-200 amino acids [aa] in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained ~2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences...
April 2011: Genome Research
https://read.qxmd.com/read/21352554/discovery-of-barley-mirnas-through-deep-sequencing-of-short-reads
#31
JOURNAL ARTICLE
Andreas W Schreiber, Bu-Jun Shi, Chun-Yuan Huang, Peter Langridge, Ute Baumann
BACKGROUND: MicroRNAs are important components of the regulatory network of biological systems and thousands have been discovered in both animals and plants. Systematic investigations performed in species with sequenced genomes such as Arabidopsis, rice, poplar and Brachypodium have provided insights into the evolutionary relationships of this class of small RNAs among plants. However, miRNAs from barley, one of the most important cereal crops, remain unknown. RESULTS: We performed a large scale study of barley miRNAs through deep sequencing of small RNAs extracted from leaves of two barley cultivars...
2011: BMC Genomics
https://read.qxmd.com/read/21127032/mtr-taxonomic-annotation-of-short-metagenomic-reads-using-clustering-at-multiple-taxonomic-ranks
#32
JOURNAL ARTICLE
Fabio Gori, Gianluigi Folino, Mike S M Jetten, Elena Marchiori
MOTIVATION: Metagenomics is a recent field of biology that studies microbial communities by analyzing their genomic content directly sequenced from the environment. A metagenomic dataset consists of many short DNA or RNA fragments called reads. One interesting problem in metagenomic data analysis is the discovery of the taxonomic composition of a given dataset. A simple method for this task, called the Lowest Common Ancestor (LCA), is employed in state-of-the-art computational tools for metagenomic data analysis of very short reads (about 100 bp)...
January 15, 2011: Bioinformatics
https://read.qxmd.com/read/20626894/deep-sequencing-discovery-of-novel-and-conserved-micrornas-in-trifoliate-orange-citrus-trifoliata
#33
JOURNAL ARTICLE
Changnian Song, Chen Wang, Changqing Zhang, Nicholas Kibet Korir, Huaping Yu, Zhengqiang Ma, Jinggui Fang
BACKGROUND: MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. RESULTS: In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata) which is an important rootstock of citrus...
2010: BMC Genomics
https://read.qxmd.com/read/20565853/designing-deep-sequencing-experiments-detecting-structural-variation-and-estimating-transcript-abundance
#34
JOURNAL ARTICLE
Ali Bashir, Vikas Bansal, Vineet Bafna
BACKGROUND: Massively parallel DNA sequencing technologies have enabled the sequencing of several individual human genomes. These technologies are also being used in novel ways for mRNA expression profiling, genome-wide discovery of transcription-factor binding sites, small RNA discovery, etc. The multitude of sequencing platforms, each with their unique characteristics, pose a number of design challenges, regarding the technology to be used and the depth of sequencing required for a particular sequencing application...
June 18, 2010: BMC Genomics
https://read.qxmd.com/read/20478827/mirtools-microrna-profiling-and-discovery-based-on-high-throughput-sequencing
#35
JOURNAL ARTICLE
Erle Zhu, Fangqing Zhao, Gang Xu, Huabin Hou, Linglin Zhou, Xiaokun Li, Zhongsheng Sun, Jinyu Wu
miRNAs are small, non-coding RNA that negatively regulate gene expression at post-transcriptional level, which play crucial roles in various physiological and pathological processes, such as development and tumorigenesis. Although deep sequencing technologies have been applied to investigate various small RNA transcriptomes, their computational methods are far away from maturation as compared to microarray-based approaches. In this study, a comprehensive web server mirTools was developed to allow researchers to comprehensively characterize small RNA transcriptome...
July 2010: Nucleic Acids Research
https://read.qxmd.com/read/19332473/expression-profiling-of-micrornas-by-deep-sequencing
#36
REVIEW
Chad J Creighton, Jeffrey G Reid, Preethi H Gunaratne
MicroRNAs are short non-coding RNAs that regulate the stability and translation of mRNAs. Profiling experiments, using microarray or deep sequencing technology, have identified microRNAs that are preferentially expressed in certain tissues, specific stages of development, or disease states such as cancer. Deep sequencing utilizes massively parallel sequencing, generating millions of small RNA sequence reads from a given sample. Profiling of microRNAs by deep sequencing measures absolute abundance and allows for the discovery of novel microRNAs that have eluded previous cloning and standard sequencing efforts...
September 2009: Briefings in Bioinformatics
https://read.qxmd.com/read/18227114/soap-short-oligonucleotide-alignment-program
#37
JOURNAL ARTICLE
Ruiqiang Li, Yingrui Li, Karsten Kristiansen, Jun Wang
SUMMARY: We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets...
March 1, 2008: Bioinformatics
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