Ontology highlight
ABSTRACT:
PROVIDER: PRJNA432364 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR6657770_1.fastq.gz | Fastqsanger.gz | |||
| SRR6657770_2.fastq.gz | Fastqsanger.gz | |||
| SRR6657771_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Investigation of whole genome gene expression level changes in Pichia stipitis CBS 6054 grown aerobically in xylose, compared to the same strain grown aerobically in glucose. A six array study using total RNA recovered from three separate cultures of Pichia stipitis CBS 6054 grown in glucose and three separate cultures of Pichia stipitis CBS 6054 grown in xylose. Each array measures the expression level of 374,100 probes (average probe length 53.6 +/- 4.1 nt) tiled across the Pichia stipitis CBS 6054 genome with a median spacing distance of 33 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.
2011-10-19 | E-GEOD-24854 | biostudies-arrayexpress
Project description:In Scheffersomyces stipitis and related fungal species the genes for L-rhamnose catabolism RHA1, LRA2, LRA3 and LRA4 but not LADH are clustered. We find that located next to the cluster is a transcription factor, TRC1, which is conserved among related species.Our transcriptome analysis shows that all the catabolic genes and all genes of the cluster are up-regulated on L-rhamnose. Among the genes that were also up-regulated on L-rhamnose were two transcription factors including the TRC1. In addition, in 16 out of the 32 analysed fungal species only RHA1, LRA2 and LRA3 are in a cluster. The clustering of RHA1, LRA3 and TRC1 is also conserved in species not closely related to S. stipitis. Since the LRA4 is often not part of the cluster and it has several paralogs in L-rhamnose utilising yeasts we analysed the function of one of the paralogs, RHA41 by heterologous expression and biochemical characterization. Rha41p has similar catalytic properties but the transcript was not up-regulated on L-rhamnose. The RHA1, LRA2, LRA4 and LADH genes were previously characterized in Sheffersomyces (Pichia) stipitis. We expressed the L-rhamnonate dehydratase, Rha3p, in S. cerevisiae, estimated the kinetic constants of the protein and showed that it indeed has activity with L-rhamnonate. A six chip study using total RNA recovered from three separate cultures of S. stipitis CBS 6054 grown glucose and respectively three separate cultures grown on rhamnose
2011-11-23 | E-GEOD-28557 | biostudies-arrayexpress
Project description:Liu2012 - Genome-scale metabolic network of Scheffersomyces stipitis (iTL885)
This model is described in the article:
A constraint-based model of
Scheffersomyces stipitis for improved ethanol production.
Liu T, Zou W, Liu L, Chen J.
Biotechnol Biofuels 2012; 5(1):
72
Abstract:
UNLABELLED: BACKGROUND: As one of the best xylose
utilization microorganisms, Scheffersomyces stipitis exhibits
great potential for the efficient lignocellulosic biomass
fermentation. Therefore, a comprehensive understanding of its
unique physiological and metabolic characteristics is required
to further improve its performance on cellulosic ethanol
production. RESULTS: A constraint-based genome-scale metabolic
model for S. stipitis CBS 6054 was developed on the basis of
its genomic, transcriptomic and literature information. The
model iTL885 consists of 885 genes, 870 metabolites, and 1240
reactions. During the reconstruction process, 36 putative sugar
transporters were reannotated and the metabolisms of 7 sugars
were illuminated. Essentiality study was conducted to predict
essential genes on different growth media. Key factors
affecting cell growth and ethanol formation were investigated
by the use of constraint-based analysis. Furthermore, the
uptake systems and metabolic routes of xylose were elucidated,
and the optimization strategies for the overproduction of
ethanol were proposed from both genetic and environmental
perspectives. CONCLUSIONS: Systems biology modelling has proven
to be a powerful tool for targeting metabolic changes. Thus,
this systematic investigation of the metabolism of S. stipitis
could be used as a starting point for future experiment designs
aimed at identifying the metabolic bottlenecks of this
important yeast.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180026.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180026 | BioModels
Project description:Scheffersomyces stipitis Genome sequencing and assembly
| PRJNA609885 | ENA
Project description:Scheffersomyces stipitis NRRL Y-7124 Standard Draft genome sequencing
| PRJNA460958 | ENA
Project description:New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. We developed a computational pipeline to strand long-read cDNA libraries that markedly improves assembly of transcripts from long-reads. Incorporating stranded long-reads in a new hybrid assembly approach, we demonstrate its efficacy for improved characterization of challenging lncRNA transcripts. Our workflow can be applied to a wide range of transcriptomics datasets for superior demarcation of transcript ends and refined isoform structure, which can enable better differential gene expression analyses and molecular manipulations of transcripts.
2023-10-14 | GSE215355 | GEO
Project description:New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. We developed a computational pipeline to strand long-read cDNA libraries that markedly improves assembly of transcripts from long-reads. Incorporating stranded long-reads in a new hybrid assembly approach, we demonstrate its efficacy for improved characterization of challenging lncRNA transcripts. Our workflow can be applied to a wide range of transcriptomics datasets for superior demarcation of transcript ends and refined isoform structure, which can enable better differential gene expression analyses and molecular manipulations of transcripts.
2023-10-14 | GSE215357 | GEO
Project description:Investigation of whole genome gene expression level changes in Pichia stipitis CBS 6054 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.
2011-10-20 | GSE24854 | GEO
Project description:Evaluation of short-read-only, long-read-only, and hybrid assembly approaches on metagenomic samples demonstrating how they affect gene and protein prediction which is relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic-based protein predictions.
2022-02-17 | PXD025505 | Pride
Project description:Draft hybrid long-read assembly of Candida metapsilosis ATCC 96143
| PRJNA432377 | ENA