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3’ RNA-seq of whole organisms is superior to standard in cases of sparse data but inferior with respect to identified functions

ABSTRACT: 3’ RNA-seq of whole organisms is superior to standard in cases of sparse data but inferior with respect to identified functions

PROVIDER: PRJNA885491 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21758105.fastq.gz	Fastqsanger.gz
	SRR21758106.fastq.gz	Fastqsanger.gz
	SRR21758107.fastq.gz	Fastqsanger.gz
	SRR21758108.fastq.gz	Fastqsanger.gz
	SRR21758109.fastq.gz	Fastqsanger.gz

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3’ RNA-seq of whole organisms is superior to standard in cases of sparse data but inferior with respect to identified functions

Project description:Purpose: The goal of this study was to compare 3’ RNA-seq data to standard sequencing in samples collected from zebrafish exposed to control conditions or an elevated level of perfluorobutane sulfonamide (FBSA). Methods: Dechorionated embryonic zebrafish were statically exposed at 8 hours post fertilization (hpf) to either vehicle control (0.5% methanol) or to 47 µM perfluorobutane sulfonamide (FBSA) in 96-well plate format. Zebrafish embryos were sampled at 48 hpf, before morphological effects were observable but with samples phenotypically anchored to abnormal morphology at 120 hpf. At 48 hpf, 10 embryos were pooled per replicate (n = 3), euthanized via ice bath, and total RNA extracted using a Zymo Research Direct-zol RNA MiniPrep kit. For the standard RNA-seq, library preparation and sequencing was performed by Beijing Genomics Institute (BGI) on their BGISEQ-500 platform (raw data files previously submitted to GEO; GSE186576). For the 3' RNA-seq, library preparation and sequencing was performed by the Center for Quantitative Life Sciences (CQLS) at Oregon State University using the Lexogen QuantSeq 3' FWD library preparation kit and a HiSeq 3000. Both datasets were analyzed using the same RNA-seq analysis pipeline. Results: We found that 3’ RNA-seq and standard showed specific alignment advantages when focusing on annotated or unannotated regions of the genome, with 3’ RNA-seq showing better alignment to annotated regions. We also found that 3’ RNA-seq was far better at detecting DEGs under conditions of sparse data (fewer reads) but that DEGs identified by standard RNA-seq led to a greater number of statistically enriched biological functions.

2022-10-04 | GSE214481 | GEO

3' RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism.

Project description:Introduction: The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Methods and results: Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. Conclusions: These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.

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Differential expressions of microRNAs involve the development of superior and inferior spikelets in rice (Oryza sativa)

Project description:We aimed to identify differential expression of microRNAs between superior and inferior spikelets by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from superior and inferior spikelets at 18 days after fertilization, and more than nine million small RNA sequence reads were generated for each library. Totals of 351 and 312 known miRNAs were obtained from the superior and inferior spikelets, respectively. Analysis of the expression profiles of these miRNAs showed that 189 miRNAs were differentially expressed between superior spikelets and inferior spikelets. In addition, 43 novel miRNAs were identified mostly by the accumulations of miRNA*s were also expressed differentially. Further analysis shows that these miRNAs may individually participate in regulating hormone metabolism, carbohydrate metabolic pathways, and cell division during rice grain development. These results indicate that slow grain filling and low grain weight of rice inferior spikelets probably relation to the expression and function differences between superior and inferior spikelet miRNAs. Examination of 2 different small RNA expression profilings in superior and inferior spikelets at 18 days after fertilization.

2011-03-19 | E-GEOD-28028 | biostudies-arrayexpress

Identifying endogenous superior and inferior neural progenitor cells

Project description:Identifying endogenous superior and inferior neural progenitor cells

| PRJNA838936 | ENA

Differential expressions of microRNAs involve the development of superior and inferior spikelets in rice (Oryza sativa)

2011-03-19 | GSE28028 | GEO

Comparative proteomics analysis of superior and inferior spikelets in hybrid rice during grain filling and response of inferior spikelets to drought stress using isobaric tags for relative and absolute quantification

Project description:The biological functions of differently expressed proteins between superior and inferior spikelet grains were investigated based on the isobaric tags for relative and absolute quantification to further clarify the mechanism of rice grain filling at the proteomic level, as well as the response of inferior spikelets to drought dress (-20 kPa or -40 kPa). Compared with superior spikelets, inferior ones had lower sink strength due to the lower sink activities (lower expressions of ADP-glucose pyrophosphorylase, granule-bound starch synthase, starch branching enzyme and pullulanase) and smaller sink sizes (lower abundances of structural proteins). The slower and later grain filling resulted from the weaker decomposition and conversion of photoassimilate and the slower cell division. Moderate drought stress (-20 kPa) promoted the grain filling of inferior spikelets through regulating the proteins associated with photoassimilate supply and conversion. These proteins may be important targets for rice breeding programs that raise the rice yield under drought condition. The findings offer new insights into rice grain-filling and provide theoretical evidences for better quality control and scientific improvement of super rice in practice.

2015-08-05 | PXD001046 | Pride

Evidence of superior and inferior sinoatrial nodes in the mammalian heart [Rat]

Project description:We report the application of RNA sequencing technology for high-throughput profiling of regionally separated sinoatrial nodal tissues from rat hearts. We find that both the superior and inferior regions of these sinoatrial nodal tissues (termed sSAN and iSAN, respectively) possess statistically comparable levels of cardiac ion channels, receptors, neural proteins, and transcription factors. This study provides new insights into regional molecular expression of pacemaking tissue in the right atria.

2021-04-26 | GSE149542 | GEO

Evidence of superior and inferior sinoatrial nodes in the mammalian heart [Human]

Project description:We report the application of RNA sequencing technology for high-throughput profiling of regionally separated sinoatrial nodal tissues from human hearts. We find that both the superior and inferior regions of these sinoatrial nodal tissues (termed sSAN and iSAN, respectively) possess statistically comparable levels of cardiac ion channels, receptors, neural proteins, and transcription factors. This study provides new insights into regional molecular expression of pacemaking tissue in the right atria.

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Evidence of superior and inferior sinoatrial nodes in the mammalian heart

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microbiota of human inferior turbinate

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