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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

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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

Poplar

Project description:Poplar Raw sequence reads

| PRJNA679064 | ENA

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

Project description: Not available

| S-EPMC6463665 | biostudies-literature

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

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