Dataset View [GSE44183]

TitleGenetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-Sequencing
ArticleFan G,Horvath S,Liu JY,Sun YE,Cheng L,Zeng Q,Liu Z,Feng Y,Jiang CY,Cai L,Cai C,Huang K,Xue Z.Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.Nature.2013 Aug 29
Bio ProjectBioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA189204
SraSRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP018525
Overall Desginsingle-cell RNA-seq of human and mouse blastomeres
SummaryMammalian preimplantation development is a complex process involving dramatic changes in the transcriptional architecture. Through single-cell RNA-sequencing (RNA-seq), we report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos. Based on single nucleotide variants (SNVs) in blastomere mRNAs and paternal-specific SNPs, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25-53%). By weighted gene co-expression network analysis (WGCNA), we find that each developmental stage can be concisely delineated by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation, and metabolism in a step-wise fashion from cleavage to morula. Cross-species comparisons reveal that the majority of human stage-specific modules (7 out of 9) are remarkably preserved, only to diverge in developmental specificity and timing in mice. We further identify conserved key members (or hub genes) of the human and mouse networks. These genes represent novel candidates that are likely key players in driving mammalian preimplantation development. Collectively, we demonstrate that mammalian preimplantation development is orchestrated by evolutionarily conserved genetic programs that diverge in developmental timing. Our results provide a valuable resource to dissect gene regulatory mechanism underlying progressive development of early mammalian embryos.
Experimental ProtocolTargeted enrichment was performed with Agilent 50M kit; Libraries were prepared using an Illumina paired-end DNA sample prep kit (Illumina) following the manufacturer's protocols
RNA was isolated from single cells or single morula embryos and amplified as previously described (Tang et al., 2010, Nat Protoc); Library construction was performed following Illumina manufacturer suggestions.
Data processingLibrary strategy: Exome-Seq; Raw reads from the Illumina HiSeq2000 were mapped to the hg19 genome using default parameters in BWA; hg19; exome.wig: wiggle files represent the read depth every 10bp along the hg19 genome
Raw reads from the Illumina HiSeq2000 were mapped to the hg19 genome using default parameters in BWA; Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric; Genes with low expression in all stages (average RPKM<0.5) were filtered out, followed by quantile normalization.; Genome_build: hg19; Supplementary_files_format_and_content: human_expression_mat.txt: matrix listing normalized RPKM
Public OnPublic on Jul 29 2013

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