Maternally Expressed Genes Identified by Single-cell RNA Sequencing in Pre-implantation Development of Buffalo Parthenogenesis
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ABSTRACT:
PROVIDER: PRJNA427717 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6425310_1.fastq.gz | Fastqsanger.gz | |||
| SRR6425310_2.fastq.gz | Fastqsanger.gz | |||
| SRR6425311_1.fastq.gz | Fastqsanger.gz | |||
| SRR6425311_2.fastq.gz | Fastqsanger.gz | |||
| SRR6425312_1.fastq.gz | Fastqsanger.gz |
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Project description:Background:Maternal mRNAs that accumulate in the oocyte during oogenesis play important roles during initial stages of embryonic development, before activation of the embryonic genome. Parthenogenesis of mammalian is a critical research modle for the function analysis of maternal genomics. Results:Here we report comprehensive maternal transcriptome dynamics of single matured oocytes and pre-implantation embryos of buffalo parthenogenesis.Notably, more than half of the estimated 28659 bovine genes,15331 involved in more than 280 pathways, is expressed in oocytes and early embryos of parthenogenesis .The total numbers of genes expressed across stages are from 908 genes (morula/16cells)to 2603 genes(blastocyst/morula), and the nature of the expressed genes is also greatly different. A total of 3567 unique genes were identified to be differentially expressed between all consecutive stages of development(FPKM>0),of which the biggest expressed change was detected between the 8-and 16-cell stages, which demonstrated that parthenogenetic activation of embryonic development exist an embryonic genome activation process which is the same as the normal fertilization of embryos,also occurs between 8cells-16cells, consistent with the time of the development of the normal fertilized embryonic development,which suggesting that parthenogenetic embryonic development and normal fertilization embryo development may have a similar genome activation transcription regulation process.Besides,2726 genes were identified as only expressed/highly enriched in particular stages of development, suggesting their stage-specific roles in maternal genome during embryogenesis.Using weighted gene co-expression network analysis, we found 11 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified 1530 hub genes of the maternally expressed gene networks. Methods:Maternal mRNA profiles of pre-implantation development in buffalo parthenogenesis,using single-cell RNA sequencing in IlluminaHiSeq platform. Sequencing adapters were trimmed using Cutadapt (https://code.google.com/p/cutadapt/) and the filtered reads were mapped to the reference genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/471/725/GCA_000471725.1_UMD_CASPUR_WB_2.0/)assembly using Tophat2 followed by Cufflinks.qRT–PCR validation was performed using SYBR Green assays. Conclusions:This study provides a comprehensive examination of maternally expressed gene activities in buffalo oocytes and pre-implantation embryos of parthenogenesis for the first time,and find the special “EGA”between 8cells-16cells for parthenogenetic embry,and the study screen a number of specific stages hub gene with potentially important function.
2018-12-26 | GSE108578 | GEO
Project description:Oocytes act as the genetic vector for zygote reprogramming, and stores a large amount of material that is required to regulate embryogenesis. However, to date, there is no report on the dynamic changes of maternal proteins and genes that occur during the early stages of the embryo, particularly studies that use proteomic techniques in buffalos. Here, an integrated single-cell RNA sequencing transcriptomic and quantitative proteomic analysis were employed to systematically explore the dynamic function of maternally-expressed proteins in parthenogenesis model of buffalo.The proteome of the buffalo was quantitatively analyzed during parthenogenesis of mature oocytes and the two-cell stage embryo. Of 1,908 quantified proteins, 123 differed significantly. The transcriptome was analyzed 8 stages (GV, MII, 2-cell,4-cell,8-cell,16-cell,morula,blastocyst)of buffalo using the single-cell RNA sequencing, and a total of 3567 unique genes were identified to be differently expressed between all consecutive stages of pre-implantation development. Bioinformatics studies and validated results indicated that maternal expression of the proteins possibly plays a role in the formation of cellular junctions firstly after parthenogenetic activation and the “maternal-to-zygotic transition” (MZT) process exists during parthenogenesis and occur between the 8-cell to 16-cell stage.
2018-07-17 | PXD008549 | Pride
Project description:Long non-coding RNAs (lncRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of lncRNAs across Guangxi native cattle and swamp buffalo muscle development has never been investigated. Here, we examine the expression of lncRNA in cattle and buffalo muscle at adult stage(12 months), exhibiting the first report of lncRNA in the Guangxi native cattle and swamp buffalo muscle development of a large animal. 16,236 lncRNA candidates were obtained from buffalo skeletal muscle samples, of which a number of lncRNAs were highly abundant, and 2,161 lncRNAs were differentially expressed between buffalo and cattle. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these lncRNAs, including several highly abundant lncRNAs, and a subset of differently expressed lncRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results indicate that abundant lncRNA is differentially expressed in bovine muscle, indicating important and diverse functions in mammalian muscle development.
2019-12-20 | GSE123869 | GEO
Project description:Buffalo breeding has become an important branch of beef cattle industry. It is of great significance to study buffalo meat production and meat quality. However, the important role of mRNA and lncRNA molecules in muscle stem cells (MuSCs) development in buffalo has not been explored. Then, we performed mRNA and lncRNA expression profiling analysis on the proliferation and differentiation of MuSCs in buffalo. The results showed that there were 4,820 differentially genes, 12,227 mRNAs, and 1,352 lncRNAs. These differentially expressed mRNAs are enriched in biological processes such as cell cycle, p53 signaling pathway, RNA transport, and Calcium signaling pathway and others. We also identified a number of genes, such as MCMC4, SERDINE1, ISLR, LOC102394806, and LOC102403551, and found that interference with MYLPF expression significantly inhibited the differentiation of MuSCs. In conclusion, our research revealed the role of mRNA and lncRNA expression in the differentiation of buffalo MuSCs. This study can be used as an important reference for the study of RNA regulation during muscle development in buffalo.
2021-07-28 | GSE164808 | GEO
Project description:We asked whether oocyte number could be amplified through parthenogenesis of mouse oocytes, without requiring creation of a paternal genome and a genetically unique genome. Parthenotes develop to a blastocyst-like stage, and from this parthenogenetic ESCs (pESCs) can be derived with high efficiency. Like ESCs, pESCs maintain unlimited self-renewal and pluripotency, as well as germline competence. Further, we demonstrate that their expression pattern of imprinted maternal genes resembles that observed in oocytes. pESCs can be directed to differentiate into primordial germ cell-like cells (PGCLCs) and form oocytes that produce fertile pups and reconstitute ovarian endocrine functions. The transcriptome and imprinting pattern of PGCLCs differentiated from pESCs more closely approximate those of in vivo produced embryonic PGCs, than PGCLCs produced from ESCs. Parthenogenesis offers a promising route for deriving PGCLCs and amplifying oocytes by faithfully maintaining maternal genes, without fertilization.
2019-11-28 | GSE141103 | GEO
Project description:We asked whether oocyte number could be amplified through parthenogenesis of mouse oocytes, without requiring creation of a paternal genome and a genetically unique genome. Parthenotes develop to a blastocyst-like stage, and from this parthenogenetic ESCs (pESCs) can be derived with high efficiency. Like ESCs, pESCs maintain unlimited self-renewal and pluripotency, as well as germline competence. Further, we demonstrate that their expression pattern of imprinted maternal genes resembles that observed in oocytes. pESCs can be directed to differentiate into primordial germ cell-like cells (PGCLCs) and form oocytes that produce fertile pups and reconstitute ovarian endocrine functions. The transcriptome and imprinting pattern of PGCLCs differentiated from pESCs more closely approximate those of in vivo produced embryonic PGCs, than PGCLCs produced from ESCs. Parthenogenesis offers a promising route for deriving PGCLCs and amplifying oocytes by faithfully maintaining maternal genes, without fertilization.
2023-10-26 | GSE141172 | GEO
Project description:Amplification of Oocytes through Parthenogenesis
| PRJNA592123 | ENA
Project description:Background: Intramuscular fat (IMF) content is highly valued as it improves meat product quality by enhancing taste, juiciness, and tenderness. IMF content can be significantly different between breeds. Thought many lipid metabolism-related genes are stated to be associated with IMF deposition, the molecular mechanism of IMF deposition is still poorly understood. To date, no gene or mutation loci responsible for the difference of IMF content among cattle breeds has been identified. To identify transcripts with potential regulatory role in lipid accumulated in muscle tissue, RNA sequencing was performed to compare the mRNAs, lncRNAs, and circRNAs expression patterns in the longissimus dorsi muscle and back fat between Chinese buffalo and cattle. Results: A total of 12 cDNA libraries were constructed. A total of 925,441,106 and 512,507,068 raw reads were obtained from buffalo and cattle, respectively. After filtering the adaptor and low quality reads, 909,040,352 and 491,967,820 clean reads were retained. In total, 19,917 mRNAs, 43,975 lncRNAs, and 10,701 circRNAs were identified in buffalo and 19,383 mRNAs, 8,265 lncRNAs, and 18,535 circRNAs were identified in cattle.
2020-10-20 | GSE139102 | GEO
Project description:The primary mammary epithelial cells of riverine buffalo were exposed to thermal stress condition at 42C for one hour. The cells were subsequently allowed to recover at 37C and harvested at different time intervals (30 min to 48 h) along with control samples (un-stressed). The study has identified several genes from different functional classes and biological pathways which could be termed as heat responsive in buffalo MEC
2016-08-26 | GSE84486 | GEO
Project description:Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. Results: Six small RNA libraries were constructed. A total of 66,128,645 and 70,974,347 raw reads were obtained from muscle and adipose groups, respectively. After filtering the adaptor and low quality reads, 60,765,257 and 67,327,095 clean reads were retained. In total, 721 miRNAs were identified.
2021-08-27 | GSE119064 | GEO