RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

Lohse, Marc; Bolger, Anthony; Nagel, Axel; Fernie, Alisdair R.; Lunn, John E.; Stitt, Mark; Usadel, Björn

doi:10.1093/nar/gks540

Cited by 726 publications

(616 citation statements)

References 27 publications

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“…Each sample was sequenced to produce ∼60 million, 100-bp, paired-end reads (SI Appendix, Table 1). Raw sequence data quality was visualized using FastQC (73) and then cleaned and trimmed using Trimmomatic version 0.27 (paired-end mode; 6-bp-wide sliding window for quality below 20; minimum length of 25 bp) (74). All project sequence reads are available at the National Center for Biotechnology Information (NCBI) under accession number SRP055134.…”

Section: Methodsmentioning

confidence: 99%

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Alexander

Jenkins

Rynearson

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

156

160

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Diverse communities of marine phytoplankton carry out half of global primary production. The vast diversity of the phytoplankton has long perplexed ecologists because these organisms coexist in an isotropic environment while competing for the same basic resources (e.g., inorganic nutrients). Differential niche partitioning of resources is one hypothesis to explain this "paradox of the plankton," but it is difficult to quantify and track variation in phytoplankton metabolism in situ. Here, we use quantitative metatranscriptome analyses to examine pathways of nitrogen (N) and phosphorus (P) metabolism in diatoms that cooccur regularly in an estuary on the east coast of the United States (Narragansett Bay). Expression of known N and P metabolic pathways varied between diatoms, indicating apparent differences in resource utilization capacity that may prevent direct competition. Nutrient amendment incubations skewed N/P ratios, elucidating nutrient-responsive patterns of expression and facilitating a quantitative comparison between diatoms. The resource-responsive (RR) gene sets deviated in composition from the metabolic profile of the organism, being enriched in genes associated with N and P metabolism. Expression of the RR gene set varied over time and differed significantly between diatoms, resulting in opposite transcriptional responses to the same environment. Apparent differences in metabolic capacity and the expression of that capacity in the environment suggest that diatom-specific resource partitioning was occurring in Narragansett Bay. This high-resolution approach highlights the molecular underpinnings of diatom resource utilization and how cooccurring diatoms adjust their cellular physiology to partition their niche space.phytoplankton | diatom | nutrient physiology | niche partitioning | metatranscriptomics T he stability and primary productivity of ecosystems have long been linked to the diversity of primary producers (1, 2). This linkage is well documented in terrestrial systems (3-7) and is increasingly being established for marine systems (8-11). Marine phytoplankton generate roughly half of global primary production (12-14) and play a critical role in oceanic ecosystem structure and function. Within the phytoplankton, the diatoms generate an estimated 40% of primary production (15). Thus, diatoms alone exert a profound influence over marine primary production and global carbon (C) cycling, particularly in coastal margins and estuaries.Phytoplankton are extremely diverse, with estimates of over 200,000 extant species (16,17). This dramatic level of taxonomic diversity in the plankton is difficult to resolve with the apparently limited number of niches in the pelagic habitat because these organisms compete for the same two basic resources: light and nutrients. As was highlighted by Hutchinson (18), the phytoplankton violate Gause's law of competitive exclusion, which posits that two organisms competing for the same resources cannot coexist. Much thought has gone toward identifying the cause of the "pa...

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Section: Methodsmentioning

confidence: 99%

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Alexander

Jenkins

Rynearson

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

156

160

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“…Potential PCR duplicates were marked using the MarkDuplicates v1.98 utility (Broad Institute, Cambridge, MA, USA). Adaptive quality trimming was performed using a Trimmomatic v0.30 algorithm (The Usadel lab, Aachen, Germany) [18]. About 83.7 % reads were retained at length of >75 bp.…”

Section: Rna Sequencing Analysesmentioning

confidence: 99%

Anti-Müllerian hormone is produced heterogeneously in primate preantral follicles and is a potential biomarker for follicle growth and oocyte maturation in vitro

Letaw

et al. 2016

J Assist Reprod Genet

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Purpose The main goals of this study were to investigate the expression of anti-Müllerian hormone (AMH) and its receptor (AMHR2) during follicular development in primates, and to evaluate the potential of AMH as a biomarker for follicle growth and oocyte maturation in vitro. Methods The mRNA and protein expression of AMH and AMHR2 were determined using isolated follicles and ovarian sections from rhesus macaques (n = 4) by real-time PCR and immunohistochemistry, respectively. Isolated secondary follicles were cultured individually. Follicle growth and media AMH concentrations were assessed by ELISA. The mRNA expression profiles, obtained from RNA sequencing, of in vitro-and in vivo-developed antral follicles were compared. Secondary follicles from additional animals (n = 35) were cultured. Follicle growth, oocyte maturation, and media AMH concentrations were evaluated for forecasting follicular development in vitro by AMH levels. Results AMH immunostaining was heterogeneous in the population of preantral follicles that were also stained for AMHR2. The mRNA expression profiles were comparable between in vivo-and in vitro-developed follicles. AMH levels produced by growing follicles were higher than those of nongrowing follicles in culture. With a cutoff value of 1.40 ng/ml, 85 % of nongrowing follicles could be identified while eliminating only 5 % of growing follicles. Growing follicles that generated metaphase II-stage oocytes secreted greater amounts of AMH than did those yielding immature germinal vesicle-stage oocytes. Conclusions AMH, co-expressed with AMHR2, was produced heterogeneously by preantral follicles in macaques with levels correlated positively with follicle growth and oocyte maturation. AMH may serve as a biomarker for primate follicular development in vitro.

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“…For each sample (six conditions, three replicates) an average of 12.1 (±1.7 standard deviation) million fragments was obtained. The minimum fragment number was 10.1 million.Trimmomatic 0.22 (Lohse et al 2012) was used to remove adapters and leading/ trailing bases below quality 3. Reads were cut when a four base stretch had an average quality below 15 and they were removed when they had a length\36 bases.…”

Section: Southern Blottingmentioning

confidence: 99%

FluG affects secretion in colonies of Aspergillus niger

Wang

Krijgsheld

Hulsman

et al. 2014

Antonie van Leeuwenhoek

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Colonies of Aspergillus niger are characterized by zonal heterogeneity in growth, sporulation, gene expression and secretion. For instance, the glucoamylase gene glaA is more highly expressed at the periphery of colonies when compared to the center. As a consequence, its encoded protein GlaA is mainly secreted at the outer part of the colony. Here, multiple copies of amyR were introduced in A. niger. Most transformants over-expressing this regulatory gene of amylolytic genes still displayed heterogeneous glaA expression and GlaA secretion. However, heterogeneity was abolished in transformant UU-A001.13 by expressing glaA and secreting GlaA throughout the mycelium. Sequencing the genome of UU-A001.13 revealed that transformation had been accompanied by deletion of part of the fluG gene and disrupting its 3 0 end by integration of a transformation vector. Inactivation of fluG in the wild-type background of A. niger also resulted in breakdown of starch under the whole colony. Asexual development of the DfluG strain was not affected, unlike what was previously shown in Aspergillus nidulans. Genes encoding proteins with a signal sequence for secretion, including part of the amylolytic genes, were more often downregulated in the central zone of maltose-grown DfluG colonies and upregulated in the intermediate part and periphery when compared to the wild-type. Together, these data indicate that FluG of A. niger is a repressor of secretion.Keywords Fungus Á Conidiogenesis Á Asexual development Á Aspergillus fluG Á Secretion Á Heterogeneity Electronic supplementary material The online version of this article

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RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

Cited by 726 publications

References 27 publications

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Anti-Müllerian hormone is produced heterogeneously in primate preantral follicles and is a potential biomarker for follicle growth and oocyte maturation in vitro

FluG affects secretion in colonies of Aspergillus niger

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