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| Status |
Public on Dec 26, 2018 |
| Title |
Maternally Expressed Genes Identified by Single-cell RNA Sequencing in Pre-implantation Development of Buffalo Parthenogenesis |
| Organism |
Bubalus bubalis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
We collected the oocytes and early parthenogenetic activated embryos of buffalo in vitro （GV、MII、2cells、4cells、8cells、16cells、morula、blastocyst）to explore the dynamic changes of the maternal transcripts by single-cell RNA sequencing,using IlluminaHiSeq platform.
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| Contributor(s) |
Chen FM, Zhang M, Fu Q, Pu LP, Hou Z, Xu ZZ, Zhang PF, Zhao XL |
| Citation(s) |
30002204 |
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| Submission date |
Dec 27, 2017 |
| Last update date |
Dec 26, 2018 |
| Contact name |
F.M Chen |
| E-mail(s) |
[email protected]
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| Phone |
15296575023
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| Organization name |
Guangxi University
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| Department |
Animal Science and Technology
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| Lab |
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
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| Street address |
No. 100, East University Road
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| City |
Nanning |
| State/province |
GuangXi |
| ZIP/Postal code |
530004 |
| Country |
China |
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| Platforms (1) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA427717 |
| SRA |
SRP127629 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE108578_All_Gene.longest_transcript.fa.gz |
14.3 Mb |
(ftp)(http) |
FA |
| GSE108578_All_gene.fa.gz |
347.6 Mb |
(ftp)(http) |
FA |
| GSE108578_All_gene_fpkm.list.xls.gz |
2.2 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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