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Effects of high cholesterol diet on sperm small RNA expression profile utilizing two different RNA-seq methods

ABSTRACT: Effects of high cholesterol diet on sperm small RNA expression profile utilizing two different RNA-seq methods

PROVIDER: PRJNA1055102 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27308370.fastq.gz	Fastqsanger.gz
	SRR27308371.fastq.gz	Fastqsanger.gz
	SRR27308372.fastq.gz	Fastqsanger.gz
	SRR27308373.fastq.gz	Fastqsanger.gz
	SRR27308374.fastq.gz	Fastqsanger.gz

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Effects of high cholesterol diet on sperm small RNA expression profile utilizing two different RNA-seq methods

Project description:Purpose: To reveal the small RNA profiles in the sperm using traitional and PANDORA-seq methods Methods: 3 week old LDLR-/- male mice were fed a high cholesterol or low cholesterol diet for 9 weeks. Sperm RNA was extracted via Trizol. Results: paternal HCD feeding can lead to sperm tsRNA/rsRNA landscape changes that are undetected by traditional RNA-seq

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Effects of DCHP exposure on sperm small RNA expression profile utilizing two different RNA-seq methods

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Effects of DCHP exposure on sperm small RNA expression profile utilizing two different RNA-seq methods

Project description:Purpose: To reveal the small RNA profiles in the sperm using traitional and PANDORA-seq methods Methods: 8 week male WT mice were exposed to DCHP by oral gavage for 4 weeks. Sperm RNA was extracted for further processing Results: PANDORA-seq revealed an abundant amount of tsRNA and rsRNA that were undetected by traditional-seq. Importantly, PANDORA-seq revealed that many differentially regulated sncRNAs also undetected with traditional-seq

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Effects of high cholesterol diet on intimal small RNA expression profile utilizing two different RNA-seq methods [Intima_small_RNA]

Project description:Effects of high cholesterol diet on intimal small RNA expression profile utilizing two different RNA-seq methods [Intima_small_RNA]

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Effects of high cholesterol diet on intimal small RNA expression profile utilizing two different RNA-seq methods [Intima_small_RNA]

Project description:Purpose: To reveal the small RNA profiles in the intima using traditional and PANDORA-seq methods. Methods: 3-week-old LDLR-/- male mice were fed a high cholesterol or low cholesterol diet for 9 weeks. Intimal RNA was extracted by injecting Trizol into the aorta and collecting the flow through for further processing. Results: PANDORA-seq revealed an abundant amount of tsRNA and rsRNA that were undetected by traditional-seq. Importantly, PANDORA-seq revealed that many differentially regulated sncRNAs also undetected with traditional-seq.

2023-02-08 | GSE213304 | GEO

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Project description:RNA-Seq technique was applied to investigate the effects of two semen collection methods (Pelleted vs Liquefied) and two sperm purification methods (SCLB vs PS) to the integrity of isolated RNAs at different perspectives. The same set of semen samples were applied to investigate the qualitative and quantitative effect of semen collection methods and sperm cell purification methods on sperm transcript profiling.

2013-12-09 | E-GEOD-43586 | biostudies-arrayexpress

Evaluation of the effectiveness of semen collection and sperm purification methods for spermatozoa transcript profiling

2013-12-09 | GSE43586 | GEO

RNA Isolation Methods - Diverse Biofluids

Project description:RNA Isolation Methods - Diverse Biofluids

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SpermBase - A database for sperm-borne RNA contents

Project description:Purpose: Sperm-borne RNA are particularly sensitive to degradation and methodology-induced bias, thus necessitating the use of a consistent, effective RNA extraction protocol for inter-species comparisons. To this end, we established SpermBase, an RNA expression database consisting of small and large RNA expression data obtained using consistent methodologies. Methods: Total RNA was extracted from total sperm and sperm head samples using an RNA extraction protocol that required only slight, species-specific alterations at the lysis stage. Total RNA was subjected to either RNA-Seq (large RNA) or sncRNA-Seq (small RNA). Results: By using a consistent methodology, we were able to perform a cross-species analysis on the conserved features of large and small sperm-borne RNAs. We identified conserved features in both populations of RNAs in the four mammalian species (i.e., mouse, rabbit, rat, and human) surveyed. Conclusions: Our study demonstrates an effective, near-universal approach to the study of sperm-borne RNAs, and identifies conserved characteristics in the large and small RNA populations of mammalian sperm.

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Project description:Purpose: In order to understand the functional significance of sperm transcriptome in stallion fertility, the aim of this study was to generate a detailed body of knowledge about the sperm RNA profile that defines a normal fertile stallion. Methods: The 50 bp single-end ABI SOLiD raw reads were directly aligned with the horse reference sequence EcuCab2 using ABI aligner software (NovoalignCS version 1.00.09, novocraft.com) which uses multiple indexes in the reference genome, identifies candidate alignment locations for each primary read, and allows completion of the alignment. Results: Next generation sequencing (NGS) of total RNA from the sperm of two reproductively normal stallions generated about 70 million raw reads and more than 3 Gb of sequence per sample; over half of these aligned with the EcuCab2 reference genome. Altogether, 19,257 sequence tags with average coverage ?1 (normalized number of transcripts) were mapped in the horse genome. Conclusion: The sequence of stallion sperm transcriptome is an important foundation for the discovery of transcripts of known and novel genes, and non-coding RNAs, thus improving the annotation of the horse genome sequence draft and providing markers for evaluating stallion fertility. Reproductively fertile Stallion sperm transcriptome as revealed by RNA sequencing

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