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Series GSE57249 Query DataSets for GSE57249
Status Public on Jul 29, 2014
Title Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary It remains an open question when and how the first cell fate decision is made in mammals. Using deep single-cell RNA-seq of matched sister blastomeres, we report highly reproducible interblastomere differences among ten 2-cell and five 4-cell mouse embryos. Inter-blastomere gene expression differences dominated between-embryo differences and noises, and were sufficient to cluster sister blastomeres into distinct groups. Dozens of protein-coding genes exhibited reproducible bimodal expression in sister blastomeres (0 vs. 1e3-1e6 of FPKM), which cannot be explained by random fluctuations. The protein expression of one of these bimodal genes, Gadd45a, exhibited clear inter-blastomeric contrasts. We traced some of the bimodal mRNA expressions to embryonic genome activation, and others to blastomere-specific RNA depletion. Inter-blastomere differences created co-expression gene networks that were much stronger and larger than those that can be possibly created by random noises. The highly correlated gene pairs at the 4-cell overlapped with those showing the same directions of differential expression between inner cell mass (ICM) and trophectoderm (TE). These data substantiate the hypothesis of inter-blastomere differences in 2- and 4-cell mouse embryos, and associate these differences with ICM/TE differences.
 
Overall design 9 zygotes, 10 2-cell, and 5 4-cell mouse (C57BL/6) embryos were collected and multi-cell embryos were separated into blastomeres. 4 inner cell mass (ICM) and 3 trophectoderm (TE) samples are also extracted from mouse blastocysts. Transcriptome profiles for all samples are obtained via Smart-seq protocol.
Web link http://singlecell.cepbrowser.org/
 
Contributor(s) Biase FH, Cao X, Zhong S
Citation(s) 25096407
Submission date May 02, 2014
Last update date May 15, 2019
Contact name Fernando H Biase
E-mail(s) fbiase@auburn.edu
Phone 334-844-1680
Organization name Auburn University
Department Animal Sciences
Lab Biase lab
Street address 559 Devall Drive
City Auburn
State/province AL
ZIP/Postal code 36849
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (56)
GSM1377859 Zygote 1
GSM1377860 Zygote 2
GSM1377861 Zygote 3
Relations
BioProject PRJNA246056
SRA SRP041618

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE57249_RAW.tar 2.2 Gb (http)(custom) TAR (of BIGWIG)
GSE57249_fpkm.txt.gz 2.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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