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Populus trichocarpa

ABSTRACT: RNA-seq of major tissues and xylem cell types of Populus trichocarpa

PROVIDER: PRJNA320431 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3473000.fastq.gz	Fastqsanger.gz
	SRR3473010.fastq.gz	Fastqsanger.gz
	SRR3472991.fastq.gz	Fastqsanger.gz
	SRR3473001.fastq.gz	Fastqsanger.gz
	SRR3473011.fastq.gz	Fastqsanger.gz

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High-throughput sequencing of small RNAs in Populus trichocarpa

Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Populus trichocarpa tissues (including leaves, xylem and mechanically-treated xylem). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, xylem and mechanically-treated xylem of Populus trichocarpa, Nisqually-1 genotype. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Vincent Chiang for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

2011-05-09 | E-GEOD-28984 | biostudies-arrayexpress

High-throughput sequencing of small RNAs in Populus trichocarpa

2011-05-10 | GSE28984 | GEO

E-GEOD-81077

Project description:RNA-seq of different tissues and xylem cell types of Populus trichocarpa to study wood formation

2019-01-09 | E-GEOD-81077 | ExpressionAtlas

RNAseq of transfected protoplasts of Populus trichocarpa

Project description:PtrHSFB3-1 and PtrMYB092 are xylem specific genes in xylem of P. trichocarpa, and their expression levels are down regulated most significantly in tension wood. These two transcription factors were transiently overexpressed in stem differentiating xylem (SDX) of P. trichocarpa , and transcriptomic sequencing was performed to identify the regulatory effects of the two transcription factors on wood formation related genes.

2020-07-11 | GSE154167 | GEO

Ozone exposure of Populus deltoides and Populus trichocarpa

Project description:Populus deltoides and Populus trichocarpa were exposed to either ambient air or an acute ozone exposure of 200 ppb for 9 hrs and ozone response was profiled for each genotype by hybridising control against ozone-exposed samples per genotype. Keywords: stress response, genotype comparrison, ozone exposure

2009-04-01 | GSE10874 | GEO

Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza

Project description:Illumina HiSeq2000 technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after 3 months of contact in order to identify mycorrhiza-regulated transcripts. 100bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) reference genome.

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RNAseq of bending treated Populus trichocarpa

Project description:We treated 6 month Populus trichocarpa by bending for 0, 3, and 7 days to see effects of bending treatment on wood formation at transcript level

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Project description:Phloem proteins (P-proteins) may play crucial role in phloem transporting cell function. We used single-nucleus RNA sequencing (snRNA seq) to analyze P-protein expression in Populus trichocarpa root.

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Gene expression in leaves of a Populus trichocarpa and Populus deltoides pseudo-backcross population

Project description:A microarray analysis of whole-genome gene expression in leaves was carried out in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Resultant data contributed to the analysis of the genetic architecture of gene expression in leaves of Populus.

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