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Series GSE44183 Query DataSets for GSE44183
Status Public on Jul 29, 2013
Title Genetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-Sequencing
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Mammalian 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.
Overall design single-cell RNA-seq of human and mouse blastomeres
Contributor(s) Huang K, Zhigang X, Fan G
Citation(s) 23892778
Submission date Feb 08, 2013
Last update date May 15, 2019
Contact name Kevin Huang
Phone 310-267-0438
Organization name UCLA
Department Human Genetics
Lab Guoping Fan
Street address Gonda BLDG Rm. 6554, P.O.Box 957088
City Los Angeles
State/province CA
ZIP/Postal code 90095-7088
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (47)
GSM1080195 mouse oocyte 1
GSM1080196 mouse oocyte 2
GSM1080197 mouse pronuclei 1
BioProject PRJNA189204
SRA SRP018525

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Supplementary file Size Download File type/resource
GSE44183_RAW.tar 46.4 Mb (http)(custom) TAR (of WIG)
GSE44183_human_expression_mat.txt.gz 783.0 Kb (ftp)(http) TXT
GSE44183_mouse_expression_mat.txt.gz 343.7 Kb (ftp)(http) TXT
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Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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