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Series GSE17984 Query DataSets for GSE17984
Status Public on Feb 24, 2011
Title Epiblast stem cell subpopulations represent mouse embryos of distinct pregastrulation stages
Organism Mus musculus
Experiment type Expression profiling by array
Summary Embryonic stem cells (ESCs) comprise at least two populations of cells with divergent states of pluripotency. Here, we show that epiblast stem cells (EpiSCs) also comprise two distinct cell populations that can be distinguished by the expression of a specific Oct4-GFP marker. These two subpopulations, Oct4-GFP positive and negative EpiSCs, are capable of converting into each other in vitro. Oct4-GFP positive and negative EpiSCs are distinct from ESCs with respect to global gene expression pattern, epigenetic profile, and Oct4 enhancer utilization. Oct4-GFP negative cells share features with cells of the late mouse epiblast and cannot form chimeras. However, Oct4-GFP positive EpiSCs, which only represent a minor EpiSC fraction, resemble cells of the early epiblast and can readily contribute to chimeras. Our findings suggest that the rare ability of EpiSCs to contribute to chimeras is due to the presence of the minor EpiSC fraction representing the early epiblast.
Overall design RNA samples to be analyzed on microarrays were prepared using Qiagen RNeasy columns with on-column DNA digestion. 300 ng of total RNA per sample was used as input into a linear amplification protocol (Ambion), which involved synthesis of T7-linked double-stranded cDNA and 12 hrs of in-vitro transcription incorporating biotin-labelled nucleotides. Purified and labelled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina) according to the manufacturer's instructions. After washing, as recommended, chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and accompanying software. Samples were hybridized as biological replicates.

6 samples were analyzed, five of them in duplicate and one of them (T9-EpiSC) a single time (11 total samples). ESC: Mouse ESC male; EpiSC: Mouse EpiSC male GOF18; Epi-Sox2: Mouse EpiSC Sox2 male GOF18 (Overexpressing WT Sox2) cultured in condition EpiSC medium (CM); EpiSC-GFP-: Mouse E3 EpiSC grown in CM and FACS-sorted for GFP-; EpiSC-GFP+: Mouse E3 EpiSC grown in CM and FACS-sorted for GFP+; T9-EpiSC: Mouse T9 EpiSC grown on medium-density CF1 MEFs in UM, 2d -Fgf2, harvested without MEFs.

The supplementary file 'GSE17984_non-normalized_data.txt' contains non-normalized data for Samples GSM450294-GSM450304.
Contributor(s) Han DW, Tapia N, Joo JY, Araúzo-Bravo MJ, Greber B, Bernemann C, Wu G, Stehling M, Ko K, Do JT, Schöler HR
Citation(s) 21056461
Submission date Sep 04, 2009
Last update date Jun 14, 2018
Contact name Marcos J Araúzo-Bravo
Organization name Max Planck Institute for Molecular Biomedicine
Department Cell and Developmental Biology
Lab Computational Biology and Bioinformatics
Street address Rontgenstr. 20
City Muenster
ZIP/Postal code 48149
Country Germany
Platforms (1)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
Samples (11)
GSM450294 ESC, rep1
GSM450295 ESC, rep2
GSM450296 EpiSC, rep1
BioProject PRJNA120015

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
GSE17984_RAW.tar 3.1 Mb (http)(custom) TAR
GSE17984_non-normalized_data.txt.gz 1.9 Mb (ftp)(http) TXT
Raw data are available on Series record
Processed data included within Sample table
Raw data provided as supplementary file

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