Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

ABSTRACT: Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

PROVIDER: PRJNA691566 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13419176_1.fastq.gz	Fastqsanger.gz
	SRR13419176_2.fastq.gz	Fastqsanger.gz
	SRR13419177_1.fastq.gz	Fastqsanger.gz
	SRR13419177_2.fastq.gz	Fastqsanger.gz
	SRR13419178_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

Project description:In present study, we first tried to reveal the transcriptome-wide m6A methylation pattern in boar fresh sperm (Fs) and frozen-thawed sperm (Fts) through MeRIP-seq, which demonstrates occurrence the diverse m6A modiﬁcation patterns during cryopreservation. Results: the expression of m6A modification enzymes were significantly dysregulated in sperm during cryopreservation. Furthermore, the m6A peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. In Fts, a total of 1754 differentially methylated m6A genes containing 1928 differentially methylated peaks were identified as compared to Fs. Bioinformatics analysis revealed the role of these genes containing significantly altered m6A peaks (DMMGs) were significantly enriched in terms of metabolism and transcription, as well as a number of DMMGs were annotated to ubiquitin mediated proteolysis, AMPK, mTOR and MAPK signaling pathways. Furthermore, the joint analysis of DMMGs and differentially expressed genes indicated that both of these play a vital role in sperm energy metabolism and apoptosis. Conclusion: Our study is first to reveal the dynamic m6A modification in mRNAs of boar sperm during cryopreservation, and provides a new evidence regarding the potential roles of m6A in modulating sperm motility, apoptosis and metabolism. Keywords: N6-methyladenosine (m6A); Boar sperm; Cryopreservation; MeRIP-seq

2021-06-09 | GSE164691 | GEO

Comparative analysis of piRNA profiles reveals cryoinjury or freezability between boar (Sus scrofa) and giant panda (Ailuropoda melanoleuca) sperm during cryopreservation

Project description:In this study, differentially expressed (DE)piRNAs of fresh and frozen-thawed sperm with different freeze tolerance compacity from giant panda and boar were evaluated. The results showed 1160 (22 down-regulated and 1138 up-regulated) and 384 (110 up-regulated and 274 down-regulated) differentially expressed (DE) piRNAs were identified in giant panda and boar sperm, respectively. Gene ontology (GO) enrichment analysis revealed that the target DE mRNAs of DE piRNAs were mainly enriched in biological regulation, cellular process and metabolic process in giant panda and boar sperm. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the target DE mRNAs of DE piRNAs were only distributed on DNA replication and cAMP signaling pathway in giant panda, but cAMP, cGMP and MAPK signaling pathway in boar sperm which were considered as part of olfactory transduction pathway.Conclusion:Olfactory transduction related pathways maybe contributed to different freeze tolerance compacity between giant panda and boar sperm, which will benefit to further understand the molecular mechanism of sperm cryoinjury and freezability.

2021-04-19 | GSE163128 | GEO

Effect of cryopreservation on bull sperm proteins

Project description:In the present study, we evaluated the alteration of protein profile of spermatozoa during the different stages of cryopreservation i.e., freshly ejaculated sperm, equilibrated sperm, and cryopreserved sperm in crossbred bulls (Bos taurus * Bos indicus). It was found that the equilibration step of cryopreservation itself caused major changes in the proteome of spermatozoa. Therefore, cryopreservation protocols should be tailored in such a way that it minimize sperm proteome alterations.

2022-02-25 | PXD031895 | JPOST Repository

Transcriptome analysis reveals key gene expression changes in blue catfish sperm in response to cryopreservation

Project description:Cryopreservation of blue catfish sperm can cause variable embryo hatch rates, which is the limiting factor for hybrid catfish breeding. In this study, we investigated gene expression changes caused by cryopreservation using transcriptome profiles of fresh sperm samples and cryopreserved sperm from the same set of blue catfish.

2022-06-26 | GSE204687 | GEO

Improving sperm cryopreservation with type III antifreeze proteins: effect on proteomic profiles of Cynomolgus macaque sperm

Project description:Antifreeze protein III (AFP III) has been used in the cryopreservation of germ cells in several kinds of animals, but it is not yet known what the specific cryoprotective mechanism of AFP III is, except for reducing the formation of ice crystals during cryopreservation. In order to study the cryoprotective mechanism of AFP III on sperm cryopreservation, the proteomic profile of Cynomolgus macaques sperm were identified after cryopreservation. Compared to fresh sperm, 141 and 32 proteins were differentially identified in Cynomolgus macaques sperm cryopreserved without and with 0.1µg/ml AFP III, respectively. These proteins were mainly involved in mitochondrial production of reactive oxygen species (ROS), glutathione (GSH) synthesis and cell apoptosis. According to the differential proteins, we supposed that AFP Ⅲ mainly reduce sperm lipid, protein and DNA damage, as well as the release of cytochrome c, and thereby reduce sperm apoptosis by modulating the production of ROS in mitochondria. The molecular mechanism that how AFP III acts with sperm proteins and protects cell from cryoinjuries needs further study.

2022-02-17 | PXD024836 | Pride

m6A RNA modification controls cell fate transition in mammalian embryonic stem cells

Project description:N6-methyl-adenosine (m6A) is the most abundant modification on messenger RNAs and is linked to human diseases, but its functions in mammalian development are poorly understood. Here we reveal the evolutionary conservation and function of m6A by mapping the m6A methylome in mouse and human embryonic stem cells. Thousands of messenger and long noncoding RNAs show conserved m6A modification, including transcripts encoding core pluripotency transcription factors. m6A is enriched over 3M-bM-^@M-^Y untranslated regions at defined sequence motifs, and marks unstable transcripts, including transcripts turned over upon differentiation. Genetic inactivation or depletion of mouse and human Mettl3, one of the m6A methylases, led to m6A erasure on select target genes, prolonged Nanog expression upon differentiation, and impaired ESCM-bM-^@M-^Ys exit from self-renewal towards differentiation into several lineages in vitro and in vivo. Thus, m6A is a mark of transcriptome flexibility required for stem cells to differentiate to specific lineages. Examing m6A modification differences in two different cell types

2014-10-20 | E-GEOD-52600 | biostudies-arrayexpress

m6A modification profile in primary microglia with/without Igf2bp1 knockdown

Project description:Our study demonstrated that the expression of Igf2bp1 in activated microglia was significantly up-regulated, implying a role of Igf2bp1 in LPS-induced m6A modifications in microglia. To understand the roles of Igf2bp1 on LPS-induced m6A modification in microglia, we performed Igf2bp1 loss-of-function (LOF) approach. Microglia stimulated by LPS were transfected with either scrambled siRNA control or Igf2bp1 siRNA for 48 hours. To m6A modification profiles in control and Igf2bp1 LOF microglia were determined by MeRIP-seq analysis.

2022-12-31 | E-MTAB-11411 | biostudies-arrayexpress

DIA of boar sperm with different treatment

Project description:DIA of boar sperm with different treatment and PRM validation

2021-09-06 | PXD028213 |

Construction of N6 Methyladenosine Atlas in Yak Epididymis Reveals the Process of Sperm Maturation Modification

Project description:The epididymis is an important component of the male reproductive system and a crucial site for sperm maturation. During the process of sperm maturation through the epididymis, the effective payload of SncRNA significantly changes, which may be related to epigenetic modifications. Unfortunately, the N6 Methyladenosine (m6A) modification profile of the epididymis has not yet been established. In this study, the MeRIP seq combined with RNA seq method was used to analyze the m6A modification levels in the head, body, and tail of yak epididymis. It was found that the level of m6A in the epididymis significantly increased, and differentially methylated RNAs (DMRs) in the proximal end of the epididymis were significantly enriched in Gap junction, ErbB signaling pathway, and mTOR signaling pathway, participating in cell communication and sperm maturation processes. In the distal epididymis, DMRs are enriched in Apoptosis, FoxO signaling pathway, PI3K Akt signaling pathway, and TNF signaling pathway, which are involved in sperm autophagy, oxidative stress, and sperm maturation. In addition, we identified key genes with significant changes in m6A levels but no differences in RNA levels, including YY1 associated factor 2 (YAF2), Fork head box J2 (FOXJ2), and Fork head box O1 (FOXO1), suggesting that these genes are modified by m6A to affect translation processes and participate in sperm maturation. In summary, our study established an m6A map of the epididymis, which is beneficial for further understanding the maturation process of sperm and revealing more information related to male infertility.

2024-06-01 | GSE264337 | GEO

m6A RNA modification controls cell fate transition in mammalian embryonic stem cells (RNA methylation)

Project description:Here we determine the map of RNA methylation (m6A) in mouse embrionic stem cells, and Mettl3 knock out cells Examination of m6A modification sites on the transcriptome of mouse Embryonic stem cells and Embryonic Mettl3 knock out cells, using a m6A specific antibody.

2014-10-16 | E-GEOD-52662 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data