Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Validation of pilot transcriptomic study - Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

ABSTRACT: jc2013_sybiopop_2014-validation of pilot transcriptomic study-Which genes affect biomass yield in poplar

ORGANISM(S): Populus nigra

PROVIDER: GSE117347 | GEO | 2019/06/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Pilot transcriptomic study- Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

Project description:jc2013_sybiopop_2014-pilot transcriptomic study - Which genes affect biomass yield in poplar? RNA was extracted from young differentiating xylem and cambium collected on 24 4-year-old trees trialed in a common garden experiment at INRA Orléans. The trees corresponded to corresponding to 2 replicates of 12 genotypes from 6 natural populations. After RNA quantification, the RNA from xylem and cambium from the same tree were pooled and subjected to high-throughput sequencing on an Illumina HiSeq 2000 using 100 bp paired-ends reads indexing runs. All the samples were sequenced on one Illumina lane, yielding around 20 million of single-reads per sample.

2018-10-23 | GSE117346 | GEO

Large genotype and population comparisons in populus nigra-Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

Project description:jc2013_sybiopop_2014 Large genotype and population comparisons in populus nigra-Which genes affect biomass yield in poplar ?-Large genotype comparisons: 241 genotype from 11 populations. RNA was extracted from young differentiating xylem and cambium collected on 480 4-year-old trees trialed in a common garden experiment at INRA Orléans. The trees corresponded to corresponding to 2 replicates of 241 genotypes from 11 natural populations. After RNA quantification, the RNA from xylem and cambium from the same tree were pooled and subjected to high-throughput sequencing on an Illumina HiSeq2000 using 100 bp single-read indexing runs. All the samples were sequenced on one Illumina, yielding around 20 million of single-reads per sample.

2020-06-03 | GSE128482 | GEO

Pilot transcriptomic study- Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

Project description:Pilot transcriptomic study- Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

| PRJNA481792 | ENA

validation of pilot transcriptomic study - Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

Project description:validation of pilot transcriptomic study - Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

| PRJNA481791 | ENA

Project description:Large genotype and population comparisons in populus nigra-Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

| PRJNA527833 | ENA

Lignocellulosic biomass deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus

Project description:The ideal microorganism for consolidated biomass processing to biofuels has the ability to breakdown of lignocellulose. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on lignocellulose samples as well as model hemicellulose components. Identification of the enzymes utilized by the cell in lignocellulose saccharification was done using whole-genome transcriptional response analysis and comparative genomics. C. saccharolyticus was subcultured (overnight) seven times on the substrate of interest in modified DSMZ 640 medium before inoculating a 1-liter batch containing 0.5 gram substrate per liter. Cells were grown at 70 Â°C until mid-logarithmic phase (3-5*107) and harvested by rapid cooling to 4 Â°C and centrifugation and then stored at -80 Â°C. To elucidate the transporters plus the central carbon metabolic pathways and their regulation utilized on the different sugars, transcriptome analysis was performed after growth on switchgrass, poplar, glucose and xylose.

2010-05-14 | E-GEOD-18856 | biostudies-arrayexpress

Desirable plant cell wall traits for higher-quality miscanthus lignocellulosic biomass.

Project description:BackgroundLignocellulosic biomass from dedicated energy crops such as Miscanthus spp. is an important tool to combat anthropogenic climate change. However, we still do not exactly understand the sources of cell wall recalcitrance to deconstruction, which hinders the efficient biorefining of plant biomass into biofuels and bioproducts.ResultsWe combined detailed phenotyping, correlation studies and discriminant analyses, to identify key significantly distinct variables between miscanthus organs, genotypes and most importantly, between saccharification performances. Furthermore, for the first time in an energy crop, normalised total quantification of specific cell wall glycan epitopes is reported and correlated with saccharification.ConclusionsIn stems, lignin has the greatest impact on recalcitrance. However, in leaves, matrix glycans and their decorations have determinant effects, highlighting the importance of biomass fine structures, in addition to more commonly described cell wall compositional features. The results of our interrogation of the miscanthus cell wall promote the concept that desirable cell wall traits for increased biomass quality are highly dependent on the target biorefining products. Thus, for the development of biorefining ideotypes, instead of a generalist miscanthus variety, more realistic and valuable approaches may come from defining a collection of specialised cultivars, adapted to specific conditions and purposes.

| S-EPMC6463665 | biostudies-literature

Poplar

Project description:Poplar Raw sequence reads

| PRJNA679064 | ENA

Poplar tissue types 1

Project description:Global gene expression pattern of different poplar tissue types were determined using a Nimblegen microarray based on JGI v1.1 gene models. All tissue except reproductive tissue were obtained from the same clone used for the poplar genome sequencing project (Populus trichocarpa Nisqually-1). Reproductive tissue were from wild Populus trichocarpa trees.

2010-08-01 | GSE21481 | 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

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