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Sampling strategies for sugarcane using either clonal replicates or diverse genotypes can bias the conclusions of RNA-seq studies

ABSTRACT: Sampling strategies for sugarcane using either clonal replicates or diverse genotypes can bias the conclusions of RNA-seq studies

PROVIDER: PRJEB44302 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5718910_1.fastq.gz	Fastqsanger.gz
	ERR5718910_2.fastq.gz	Fastqsanger.gz
	ERR5718911_1.fastq.gz	Fastqsanger.gz
	ERR5718911_2.fastq.gz	Fastqsanger.gz
	ERR5718912_1.fastq.gz	Fastqsanger.gz

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Sampling strategies for sugarcane using either clonal replicates or diverse genotypes can bias the conclusions of RNA-Seq studies.

Project description:A key procedure for ensuring statistical confidence in differential gene expression analyses is to use biological replicates to compare distinct groups. Biological replicates allow the estimation of the residual variation in the gene expression levels among samples of a given experimental condition. In sugarcane, it is possible to obtain an estimate of residual variability at two levels: among samples of distinct genotypes of the same experimental treatment, or clonal replicates of the same genotype. The sequencing costs are often a limitation to leveraging both these levels in the same study, stressing the relevance of efforts to determine an appropriate experimental design. We aim to investigate this question by comparing the transcriptional profiles of young sugarcane culms with different sucrose levels using both sampling strategies. Our results show that clonal replicates provided enough statistical power to identify nearly three times more deferentially expressed genes than the more diverse strategy. However, it resulted in potentially less meaningful biological results, because many of the significant genes were likely related to the particular genotype of choice, rather than representing a common expression profile for the compared groups. This study supports the development of sound experimental designs in new studies regarding differential expression for sugarcane.

| S-EPMC10075064 | biostudies-literature

Time of Day Bias for Biological Sampling in Studies of Mammary Cancer

Project description:Despite its demonstrated biological significance, time of day is a broadly overlooked biological variable in preclinical and clinical studies. How time of day affects the influence of peripheral tumors on central (brain) function remains unspecified. Thus, we tested the hypothesis that peripheral mammary cancer tumors alter the transcriptome of immune responses in the brain and that these responses vary based on time of day; we predicted that time of day sampling bias would alter the interpretation of the results. Brain tissues collected at mid dark and mid light from mammary tumor-bearing and vehicle injected mice were analyzed using the Nanostring nCounter Mouse Neuroinflammation Panel V1. Peripheral mammary tumors significantly affected expression within the brain of over 100 unique genes of the 770 represented in the panel, and fewer than 25% of these genes were affected similarly across the day. Indeed, between 65-75% of GO biological processes represented by the differentially expressed genes were dependent upon time of day of sampling. The implications of time-of-day sampling bias in interpretation of research studies cannot be understated. We encourage considering time of day as a significant biological variable in studies and to appropriately control for it and clearly report time of day in findings.

2024-01-09 | GSE249022 | GEO

Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions

Project description:Transcriptional profiling of sugarcane leaf (+1) was collected from drought-prone areas at 42 and 117 days after the last rainfall when plants were 6- and 9-month-old, respectively. Sample hybridization (non-irrigated treatment against irrigated control) was performed to monitor gene expression in a two-color Agilent custom microarray. Our goal was to investigate the effect of mild and severe water stress on the transcriptomes of drought-sensitive (IACSP97-7065) and -tolerant (IACSP94-2094) sugarcane genotypes.

2021-11-05 | GSE187416 | GEO

Time of Day Bias for Biological Sampling in Studies of Mammary Cancer

Project description:Time of Day Bias for Biological Sampling in Studies of Mammary Cancer

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Analysis of Protein Profiles in Mature Sugarcane and Identification of Differentially Expressed Protein

Project description:High sugar character is one of the important assessment indexes for selecting and breeding excellent sugarcane varieties. In order to screen important proteins that may be involved in sugar synthesis and accumulation during the ripening process of different sugarcane varieties, and to provide theoretical basis for future breeding of sugarcane varieties with high sugar maturity, the early-maturing sugarcane variety GL05-136 and late-maturing sugarcane variety GR2 were used as experimental materials. iTRAQ technique was used to identify the intraspecific and interspecific proteomic differences between the two sugarcane varieties at different sampling periods.

2024-12-12 | PXD058835 |

Transcripts associated with cell wall metabolism and development in the sugarcane stem by GeneChip expression profiling

Project description:Sugarcane is an important crop in tropical regions of the world, producing a very large biomass and accumulating large amounts of sucrose in the stem. In this study, we present the first report of transcript profiling using the GeneChip Sugarcane Genome Array. We have identified transcripts that are differentially expressed in the sugarcane stem during development by expression profiling using the array and total RNA derived from three disparate stem tissues (meristem, internodes 1-3; internode 8; internode 20) from four replicates of the sugarcane variety Q117 grown in the field. We have identified 119 transcripts that were highly differentially expressed with stem development and have characterised members of the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families which displayed coordinated expression during stem development. In addition, we determined that many other transcripts involved in cell wall metabolism and lignification were also co-expressed with members of the CesA and Csl gene families, offering additional insights into the dynamics of primary and secondary cell wall synthesis in the developing sugarcane stem. Keywords: stem development profile

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Project description:Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to the phytormone methyl jasmonate (MeJA) for 0-12 h. 26 ESTs were differentially expressed, including novel genes and also genes that had not previously been reported as being MeJA-inducible. Data are for two independent experiments. Keywords = sugarcane Keywords = methyl jasmonate Keywords = nylon arrays

2010-10-08 | E-GEOD-1546 | biostudies-arrayexpress

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Community metabarcoding is robust to sampling device bias. A case study comparing Multicorer vs Van Veen Grab samples for monitoring marine meiofauna in the North Sea

Project description:Community metabarcoding is robust to sampling device bias

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