Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis

ABSTRACT: This study provides a first large-scale cloning and characterization of Porphyra miRNAs and their predicted targets. These miRNAs belong to 224 conserved miRNA families and 7 are novel in Porphyra. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in the regulation of Porphyra yezoensis development. We constructed a small RNA library from Porphyra yezoensis.

ORGANISM(S): Pyropia yezoensis

SUBMITTER: Naihao Ye

PROVIDER: E-GEOD-20534 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis.

Liang Chengwei C Zhang Xiaowen X Zou Jian J Xu Dong D Su Feng F Ye Naihao N

PloS one 20100519 5

<h4>Background</h4>miRNAs are a class of non-coding, small RNAs that are approximately 22 nucleotides long and play important roles in the translational level regulation of gene expression by either directly binding or cleaving target mRNAs. The red alga, Porphyra yezoensis is one of the most important marine economic crops worldwide. To date, only a few miRNAs have been identified in green unicellar alga and there is no report about Porphyra miRNAs.<h4>Methodology/principal findings</h4>To iden ...[more]

PMID: 20502668

Similar Datasets

Identification and Characterization of MicroRNAs from Phaeodactylum tricornutum by High-throughput Sequencing and Bioinformatics Analysis

Project description:Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatomsâ mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions. A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were differentially expressed in PT1, PT2 and PT3, and their potential targets were involved in various processes. Our results indicated that P. tricornutum contained novel miRNAs that differed from miRNAs of other organisms and that they might play important regulator roles in P. tricornutum metabolism. Constructing and sequencing small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions

2011-08-08 | E-GEOD-29321 | biostudies-arrayexpress

Identification of miRNA-like RNAs in a plant pathogen fungus Sclerotinia sclerotiorum by High-throughput sequencing

Project description:This study provides a first large-scale cloning and characterization of Sclerotinia sclerotiorum milRNAs and milRNAs candidates. Two microRNA-like RNAs (milRNAs) and 42 milRNA candidates were identified by sequence analysis. These milRNAs and candidates provide new insights into the functional roles of small RNAs and adds new resources for the study of plant pathogenic fungi. We constructed a small RNA library from Sclerotinia sclerotiorum.

2012-05-17 | E-GEOD-28730 | biostudies-arrayexpress

Small RNA sequencing and analysis of two ants: Camponotus floridanus and Harpegnathos saltator

Project description:Deep sequencing of small RNA from two Ants: Camponotus floridanus and Harpegnathos saltator Analysis of small RNA expression profile from different specimens: egg,larva,male,minor and major for Camponotus floridanus while egg,larva,male,worker and gammergate for Harpegnathos saltator

2010-08-26 | E-GEOD-22679 | biostudies-arrayexpress

High-throughput sequencing analyses of two ants: Camponotus floridanus and Harpegnathos saltator

Project description:This SuperSeries is composed of the following subset Series: GSE22678: Transcriptome sequencing and analysis of two ants: Camponotus floridanus and Harpegnathos saltator GSE22679: Small RNA sequencing and analysis of two ants: Camponotus floridanus and Harpegnathos saltator Refer to individual Series

2010-08-26 | E-GEOD-22680 | biostudies-arrayexpress

mRNA and sRNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation for Allopolyploid Heterosis in Nascent Hexaploid Wheat

Project description:Nascent allohexaploid wheat may represent the initial genetic state for the evolution and domestication of common wheat, which arose by combining the AB genomes of tetraploid Triticum turgidum with the D genome from Aegilops tauschii and out-competed its parents in growth vigor and adaptability. To better understand the molecular basis for this success, we performed mRNA and small RNA expression analyses in three tissues of nascent allohexaploid wheat and its following generations, their progenitors, and Chinese Spring, with the assistance of newly released A and D genome sequences. We found that nonadditive expression was rare among protein-coding genes which exhibited profound parental expression level dominance, with genes of total homoeolog expression level in nascent allohexaploid progeny similar to their expression levels in T. turgidum functionally enriched for development and those to Ae. tauschii distinctively for adaptation. In contrast, miRNAs appeared to be sensitive to polyploidization, with nonadditively expressed miRNAs potentially involved in growth vigor and adaptation. Meanwhile, siRNAs may contribute to biased repression of D homoeolog, possibly due to increased siRNA density on transposable element (TE)-associated D homoeologs. Together, our data provide new insights into homoeolog regulatory mechanisms that may be essential to heterosis in nascent hexaploid wheat. We performed mRNA and small RNA analyses in three tissues of nascent allohexaploid wheat and its following generations, their progenitors, and Chinese Spring.Among these samples, Samples 1-6 and 26-31, tetraploid progenitors; Samples 7-12 and 32-37, diploid progenitors; Samples 13-22 and 38-47, following generations; Samples 23-25 and 48-50, Chinese Spring.

2014-10-20 | E-GEOD-56587 | biostudies-arrayexpress

Identification of microRNAs involved in cold stress response in grapevine.

Project description:Two small RNA libraries were generated from micropropagated â??Muscat Hamburgâ?? (Vitis vinifera) plantlets under normal and low temperatures (4 Â°C). A total of 163 known miRNAs and 299 putative novel miRNAs were detected from two small RNA libraries by Solexa sequencing. Forty-four cold-inducible miRNAs were identified through differentially expressed miRNAs (DEMs) analysis; among which, 13 belonged to upregulated DEMs while 31 belonged downregulated DEMs. This study indicated that a diverse set of miRNAs in V. vinifera are cold-inducible and may play an important role in cold stress response. Examination of small RNA populations in grapevine under cold treatment and none cold treatment.

2016-06-14 | E-GEOD-68970 | biostudies-arrayexpress

Profile of small RNA transcriptome during cortical development in the Rat

Project description:Small non-coding RNAs play important roles in regulating gene expression during development and disease. However, a comprehensive analysis of small RNAs in developing brain is largely lacking. By using next-generation sequencing technique, we carried out a systematic analysis of small RNA transcriptome of rat neocortex from early developmental stage till adult. Our results revealed an extraordinary degree of stage-specific profiling of miRNA, and other classes of small RNAs including snoRNA, rasRNA, scRNA and unexpectedly piRNA, which was considered to be solely expressed in germline tissues. Developmentally regulated miRNA editing was also observed. This study further showed the effectiveness of the high through-put sequencing in genome-wide analysis of small RNAs. The dataset described here will greatly contribute to our understanding of the divergence, variation, and function of small RNAs and may be a valuable resource in clarifying new regulatory mechanisms of cortical development. Identification and quantification of small RNA: forebrain and cortex from E10 to P28

2012-06-25 | E-GEOD-27576 | biostudies-arrayexpress

Expression profiling of small RNAs in control and H2O2-treated rice seedlings

Project description:We aimed to identify putative H2O2-regulated miRNAs expressed in rice seedlings under oxidative stress by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from H2O2-treated and control rice seedlings, and more than five million small RNA sequence reads were generated for each library. We identified seven H2O2-responsive miRNA families via expression profiling of the miRNAs based on a comparative miRNAomic analysis in combination with experimental validation. Furthermore, 32 miRNAs, 17 from known miRNA loci and 15 from novel miRNA loci, were also newly identified from the sequencing data. To the best of our knowledge, this is the first report of a systematic investigation of H2O2-regulated miRNAs and their targets in plants. Examination of 2 different small RNA expression profilings in the control and H2O2 treated rice samples.

2010-08-15 | E-GEOD-23217 | biostudies-arrayexpress

Dynamic and Parent-of-Origin Expression of Small RNAs in the Developing Maize Endosperm

Project description:In angiosperms, endosperm plays a crucial role in coordinating seed development through genetic balance and molecular interaction, and is the primary tissue where genomic imprinting occurs. To identify small interfering RNA (siRNA) “imprintome” and its paternal transcriptome activation in early developing maize endosperms, we performed high-throughput small RNA sequencing of whole kernels at 0, 3 and 5 days after pollination (DAP) and endosperms at 7, 10 and 15 DAP, using B73 by Mo17 reciprocal crosses. We observed gradually increased expression of paternal siRNAs in 3- and 5-DAP kernels and balanced contribution of parental siRNA transcriptome in 7-DAP endosperm, followed by identification 460 imprinted siRNA loci with majority (456/460, 99.1%) being maternally expressed that occurred at 10 DAP. Genome-wide scanning found 13 imprinted genes harboring imprinted siRNA loci within their 2-Kb flanking regions, which was significantly different from random probability based on simulation analysis. Finally, gene ontology categories of “response to auxin stimulus”, “response to brassinosteroid stimulus” and “regulation of gene expression” for genes harboring 10-DAP specific siRNAs and “nutrient reservoir activity”, “protein localization to vacuole” and “secondary metabolite biosynthetic process” for genes harboring 15-DAP specific siRNAs indicated that siRNAs could be involved in influencing specific cellular or biochemical processes that are essential for endosperm development, e.g. nutrient uptake and allocation. Although the mechanism of how these siRNAs regulating endosperm key events remains unclear, this study provided us an alternative perspective of siRNA function in plant. The unpollinated kernels (0 DAP), the kernels of 3, 5 DAP and endosperms of 7 10, 15 DAP from the B73 and Mo17 reciprocal crosses were used to perform high-throughput sequencing using the Illumina HiSeq2000 platform

2013-11-26 | E-GEOD-52726 | biostudies-arrayexpress

Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells

Project description:Background: Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). These ncRNAs are functionally important in the genome, however, the identification and annotation of ncRNAs in a genome is challenging. The aim of this study was to identify different types of small ncRNAs particularly piRNAs, and the role of piRNA pathway genes in the protection of chicken primordial germ cells (PGCs). Results: At first, we performed next-generation sequencing to identify ncRNAs in chicken PGCs, and we performed ab initio predictive analysis to identify putative piRNAs in PGCs. Then, we examined the expression of three repetitive sequence-linked piRNAs and 14 genic-transcript-linked piRNAs along with their linked genes using real-time PCR. All piRNAs and their linked genes were highly expressed in PGCs. Subsequently, we knocked down two known piRNA pathway genes of chicken, PIWI-like protein 1 (CIWI) and 2 (CILI), in PGCs using siRNAs. After knockdown of CIWI and CILI, we examined their effects on the expression of six putative piRNA-linked genes and DNA double-strand breakage in PGCs. The knockdown of CIWI and CILI upregulated chicken repetitive 1 (CR1) element and RAP2B, a member of RAS oncogene family, and increased DNA double-strand breakage in PGCs. Conclusions: Our results increase the understanding of PGC-expressed ncRNAs and the role of piRNA pathway genes in the protection of germ cells. Small ncRNA expression profiling in SSEA-1 positive PGCs, SSEA-1 negative gonadal stromal cells (GSCs), Stage X blastoderms, and chicken embryonic fibroblast (CEFs)

2015-04-27 | E-GEOD-60400 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data