GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE69970 Query DataSets for GSE69970
Status Public on Oct 11, 2016
Title Transcriptome of mouse preimplantation development [Rlim KO]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goals of this study are to establish a roadmap of XCI and compare the transcriptomes of WT and Rlim KO embryos during X chromosome inactivation.

Methods: mRNA profiles of 175 preimplantation embryos WT and KO for Rlim were elucidated by RNA-seq at various stages. Trophoblasts isolated from blastocyst outgrowths were also included. The sequence reads that samples where gender could be determined and that passed quality filters were analyzed at the level of autosomes, X xhromosomes as well as single genes.

Results: Using single cell RNA-seq technology on 175 whole preimplantation embryos, we obtained about 2.95 million sequence reads per sample. Reads were normalized to autosomal gene expression. Gender of each embryo was determined by expression of Y-linked genes and Xist. Data analysis showed normal expression profiles of marker genes for epiblast and trophoblast cell types during preimplantation development. Comparing Xist expression profiles in embryos WT and KO shows that Rlim is not required for initiation of Xist transcription but for upregulation of Xist expression. Moreover, our results identify two waves of XCI during preimplantation development: One that occurs at Morula stages that is Rlim-independent and one at blastocyst stages that in dependent on Rlim.

Conclusions: Our study represents the first detailed mouse preimplantation transcriptome. Our results show that Rlim is required for a second wave of imprinted XCI that occurs in female embryos at blastocyst stages.
Overall design Global mRNA profiles of whole preimplantation embryos were generated by deep sequencing.
Contributor(s) Bach I
Citation(s) 27642011
Submission date Jun 17, 2015
Last update date May 15, 2019
Contact name Ingolf Bach
Organization name University of Massachusetts Medical School
Department Molecular, Cell and Cancer Biology
Street address 364 Plantation St
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (175)
GSM1714220 WT male 4 cell, repeat 1 [Rlim KO]
GSM1714221 WT male 4 cell, repeat 2 [Rlim KO]
GSM1714222 WT male 4 cell, repeat 3 [Rlim KO]
This SubSeries is part of SuperSeries:
GSE71442 Transcriptome of mouse preimplantation development
BioProject PRJNA287292
SRA SRP059611

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
GSE69970_htseq_counts.txt.gz 2.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap