GSE62023
GSE GEOIdentification of Sox9/Pdx1-coregulated Genes During Pancreas Organogenesis
Organism:
Mus musculus
Platform:
GPL7202
Samples:
9
Experiment Types:
Expression profiling by array
Submitted:
Oct 03 2014
Last Updated:
Jan 12 2017
Status:
Public on Aug 07 2015
Contact:
Maike,,Sander (UC San Diego)
Relations
SubSeries of: GSE61948
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA262969
Summary
Sox9/Pdx1 co-regulated target genes were identified by comparing gene expression in Sox9/Pdx1-double heterozygates versus Sox9- or Pdx1- heterozygates pancreata using microarray analysis.
Overall Design
Pdx1LacZko (herein designated Pdx1-/+) (Offield et al. 1996) and one Sox9 allele was conditionally deleted in the developing pancreas via recombination of a Sox9-flox allele (Kist et al., 2002) using the Foxa3-Cre transgene (Lee et al., 2005). Total RNA was isolated and pooled from dorsal pancreatic epithelia of e12.5 Sox9fl/+; Foxa3-Cre (Sox9 het), Pdx1-/+ (Pdx1 het) versus Sox9fl/+; Foxa3-Cre; Pdx1-/+ (Sox9/Pdx1 double hets) littermates for three biological replicates
Analysis (5 steps)
View Data Processing
Processing steps for GSE62023
- Mean foreground intensities were obtained for each spot and imported into the mathematical software package âRâ, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis.
- In outline, the Cy3 (green) intensities were not background corrected (this has been shown to only introduce noise), and corrected for the scanner offset (40 was subtracted for each intensity).
- The dataset was filtered to remove positive control elements and any elements that had been flagged as bad.
- Using the negative controls on the arrays, the background threshold was determined and all values less than this value were set to the threshold value.
- Finally, the data was normalized using the Limma Quantile Normalization package in âRâ (Smyth 2004, Bolstad et al., 2003).
GEO Samples (9)
Dataset Citations (1)
A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells.
PMID 26440894
· 2015
· Cell reports
Hung Ping Shih, Philip A Seymour, Nisha A Patel, Ruiyu Xie, Allen Wang, Patrick P Liu, Gene W Yeo, Mark A Magnuson, Maike Sander