Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression changes in galls at 21 dai and corresponding uninfected roots from Poplar CAD and WT lines

ABSTRACT: Illumina technology was used to generate mRNA profiles of galls from root-knot nematodes infected and corresponding uninfected roots from Poplar CAD and WT lines. RNA was extracted from 3 replicates.TruSeq mRNA Stranded libraries were constructed and after pooling and normalization of libraries, sequencing was done on a NextSeq500 Sequencing System. Raw reads were trimmed for quality and mapped to the substituted genome sequence of P. tremula x P. alba 717-1B4 using CLC Genomics Workbench v9.5.2 and the primary transcripts only.

ORGANISM(S): Populus tremula x Populus alba

PROVIDER: GSE112673 | GEO | 2019/01/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of Methyl jasmonate of the Poplar root transcriptome

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Populus tremula x alba INRA 717-1B4 roots treated with Methyl jasmonate. Samples were harvested after two weeks either from untreated control roots or from Methyl jasmonate treated roots. Paired-end (2X100bp) reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) using CLC Genomics Workbench 6. mRNA profiles from Populus tremula x alba INRA 717-1B4 roots treated with Methyl jasmonate as well as from control roots were generated by paired-end (2X100bp) Illumina HiSeq sequencing. Four samples were sequenced per lane, two biological replicates per treatment.

2014-04-17 | E-GEOD-56864 | biostudies-arrayexpress

Effect of Methyl jasmonate of the Poplar root transcriptome

2014-04-17 | GSE56864 | GEO

Time Course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development

Project description:Illumina technology was used to generate mRNA profiles of a time course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development. Total RNA was extracted, TruSeq mRNA Stranded libraries were constructed and and sequenced in triplicates (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France). Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. bicolor v2 reference transcripts available at the JGI database https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html using CLC Genomics Workbench v8.

2021-12-15 | GSE190443 | GEO

Effect of MiSSP7 overexpression on the Poplar root transcriptome

Project description:The Poplar transcriptome was analyzed in Populus tremulaxPopulus alba clone 717-1B4 control roots and in two poplar lines overexpressing MiSSP7. We performed 9 hybridizations (NimbleGen) with samples derived from Populus tremulaxPopulus alba clone 717-1B4 control roots, as well as from roots of LINE1 and LINE2 MiSSP7 overexpressor poplars (3 biological replicates each). All samples were labeled with Cy3.

2014-04-17 | E-GEOD-56863 | biostudies-arrayexpress

Changes in gene expression in the bark of MIR15

Project description:Illumina HiSeq technology was used to generate mRNA profiles of bark from MIR15 compared to wildtype plants. Wild type (WT) and transgenic poplars (Populus tremula x P. alba, clone INRA 717-1B4) were grown aseptically on Woody Plant Medium. Total RNA was extracted using Tri-Reagent according to the manufacturer’s instructions. Reads of 2X100bp were generated and aligned to Populus trichocarpa v3.0 reference transcripts (http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa; Ptrichocarpa_210_transcript_primaryTranscriptOnly) using CLC Genomics Workbench 7.

2015-05-07 | GSE68595 | GEO

Effect of MiSSP7 overexpression on the Poplar root transcriptome

Project description:The Poplar transcriptome was analyzed in Populus tremulaxPopulus alba clone 717-1B4 control roots and in two poplar lines overexpressing MiSSP7.

2014-04-17 | GSE56863 | GEO

Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica

Project description:Root-knot nematodes (RKNs) induce inside the vascular cylinder the giant cells (GCs) imbibed into a gall. Gene-repression in early developing GCs could be facilitated by small RNAs (sRNA) as miRNAs. 24nt-sRNAs, rasiRNAs and 21-22nt-sRNAs can also mediate epigenetic mechanisms. Three sRNA libraries from 3dpi galls and three from uninfected root segments were sequenced following Illumina-Solexa technology. Three sRNA libraries from 3dpi galls and three from uninfected root segments were sequenced

2015-11-19 | E-GEOD-71563 | biostudies-arrayexpress

Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between Laccaria bicolor and Populus roots

Project description:The Poplar transcriptome was analyzed in mycorrhizal root tips in contact with Laccaria bicolor for 2 weeks. During mycorrhization the roots were treated with either 250M-BM-5m ACC, 10nM JA or 500M-BM-5M SA and compared to untreated mycorrhiza or control roots without contact to L. bicolor. In addition the poplar mutants 35S::PttACO1 and 35S::Atetr1 were used We performed 27 hybridizations (NimbleGen) with samples derived from Populus tremula x Populus alba clone 717-1B4 control roots, untreated mycorrhiza, SA-treated mycorrhiza, ACC-treated mycorrhiza and JA-treated mycorrhiza (3 biological replicates each) as well as Populus tremula x Populus tremuloides T89 control roots, mycorrhiza, 35S::PttACO1 mycorrhiza and 35S::Atetr1-1 mycorrhiza (3 biological replicates). All samples were labeled with Cy3.

2013-12-19 | E-GEOD-53475 | biostudies-arrayexpress

Changes in gene expression in the bark of MIR15

2015-05-07 | E-GEOD-68595 | biostudies-arrayexpress