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Gene expression profiling of hESC derived eGFP-SOX17+ endoderm cells - Study GBCO4216


Genomics Study Specifications

Study Name Gene expression profiling of hESC derived eGFP-SOX17+ endoderm cells
Contact Name Seung Kim (Stanford University)
Publication http://www.ncbi.nlm.nih.gov/pubmed/21362573
My Strategies Return to My Strategies page
Classification Cell differentiation
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BCBC Release Date July 29, 2011
Public Release Date July 29, 2011
Citation Wang P, Rodriguez RT, Wang J, Ghodasara A, Kim SK. Targeting SOX17 in human embryonic stem cells creates unique strategies for isolating and analyzing developing endoderm. Cell Stem Cell. 2011. 8:335-46
Synopsis
Using homologous recombination in human ESC, we inserted an enhanced green fluorescent protein (eGFP) transgene into a locus encoding a postulated marker of human endoderm, SOX17 in H9 human embryonic stem cells. This allowed purification of SOX17+ hESC endodermal progeny by fluorescence activated cell sorting (FACS) to generate microarray gene expression profile. Using Wnt3 and Activin to differentiate hSOX17-2 to stage 1 cells, and subsequently FGF10 and cyclopamine to stage 2 cells, we isolated eGFP+ cells by FACS at each stage, performed microarray analysis.
Identify a cell surface marker signature for human endodermal cells
Gene expression patterns of undifferentiated hS17 ESCs and their FACS-sorted eGFP+ progeny at stage 1 and stage 2 were compared by microarray analysis. Three replicates for each sample were analyzed using the Affymetrix Human Genome U133 Plus 2.0 arrays. To identify new cell surface markers for endoderm, transmembrane proteins (GO:000588 'integral to plasma membrane') were selected whose expression changed in SOX17-eGFP+ cells at stage 1 and 2. Findings were validated using commercially available antibodies for cluster of differentiation (CD) antigens.
A total of 13,209 genes showed statistically significant differential expression among the three samples. These included 608 genes encoding adhesion molecules, receptors, transporters, and ion channels, which were differentially expressed between undifferentiated hESCs and SOX17-eGFP+ endodermal cells. Antibodies to three molecules induced in stage 2 SOX17-eGFP+ cells were identified: CD49e (biolegend: 328005), CD141 (BD: 559780 and 559781), and CD238 (AbDSerotec:MCA1987T).
Microarray-based analysis of SOX17-eGFP+ cells identified cell surface markers for isolating endodermal progeny from hESC cultures.
Platform types Expression, Expression microarray
Platforms Show platform Affymetrix HG-U133_Plus_2
Study Design Type
  • cell_type_comparison_design
  • development_or_differentiation_design
  • is_expressed_design
Study Factors Show study factors
Study Assays Show study assays


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Repositories

Kim Lab
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Primary contributor: Kim Lab

Resource Tags

Affymetrix Human Genome U133 Plus 2.0, CD141, CD238, CD49e, ITGA5, KEL, SOX17, THBD

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Resource History & Actions

Approved on Jul 29, 2011
Last modified on Jan 17, 2012
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