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| Status |
Public on Nov 01, 2012 |
| Title |
Microarray data Ptf1a gain-of-function Xenopus pancreas development |
| Organism |
Xenopus laevis |
| Experiment type |
Expression profiling by array
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| Summary |
The Ptf1a gene has essential functions during several stages of pancreas development. It is expressed in the naïve endoderm and required pancreas cell fate specification; it is also required later in the differentiation and maintenance of acinar cells. To identify the regulatory genetic program downstream of Ptf1a required for early pancreatic fate acquisition, we used microarrays to perform a comprehensive gene expression analysis of Ptf1a overexpressing endodermal tissue at NF32 and NF36.
The results revealed an up-regulation on 1142 probe sets over 2-fold. Additional analyses, by in situ hybridizations, identified 9 genes that were endodermally expressed after the onset of endogenous Ptf1a; STXBP1, putative transmembrane protein TA-2, C25H, IGFBP1, IRF1, HALPN3, Hey1, sestrin 1, syndecan-4. These results provide insight into the regulatory network activated by Ptf1a during early pancreas development.
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| Overall design |
In order to identify downstream targets of Ptf1a, two microarrays were performed at different time-points. The two microarrays compared control pancreatic tissue (GFP) and pancreatic tissue over-expressing Ptf1a (Ptf1a+GFP). The first microarray was performed at NF32, hence renamed MA32, 8 hours after the initial expression of endogenous Ptf1a. A second microarray was performed at NF36 (MA36), 8 hours after the first one. Ptf1a+gfp mRNA or gfp mRNA alone was injected into the two dorso-vegetal blastomeres of eight-cell embryos, targeting the anterior endoderm, and 40/48 hours later the anterior endoderm was dissected out. Approximated 15 endoderm explants were pooled for each RNA preparation, and both control and experimental samples were collected from the same batch of embryos; this was done in triplicate at NF32 and in quadruplicate at NF36 (Fig. 1A). For the NF32 microarray, we used the Affymetrix 3’ Xenopus laevis Genome 2.0 GeneChip, whereas for the NF36 microarray we used the Affymetrix 3’ Xenopus laevis Genome 1.0 GeneChip; the NF36 microarray was performed prior to the release of the 2.0 GeneChip.
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| Contributor(s) |
Bilogan CK, Horb ME |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 06, 2011 |
| Last update date |
Oct 02, 2015 |
| Contact name |
Cassandra Kathryn Bilogan |
| E-mail(s) |
cbilogan@mbl.edu
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| Phone |
508-289-7370
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| Organization name |
Marine Biology Laboratory
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| Department |
Eugene Bell Center for Regenerative Biology and Tissue Engineering
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| Street address |
7 MBL St
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| City |
Woods Hole |
| State/province |
MA |
| ZIP/Postal code |
02543 |
| Country |
USA |
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| Platforms (1) |
| GPL10756 |
[X_laevis_2] Affymetrix Xenopus laevis Genome 2.0 Array |
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| Samples (14)
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| GSM843821 |
GFP-injected embryos NF32, biological rep 1 |
| GSM843822 |
GFP-injected embryos NF32, biological rep 2 |
| GSM843823 |
GFP-injected embryos NF32, biological rep 3 |
| GSM843824 |
Ptf1a-injected embryos NF32, biological rep 1 |
| GSM843825 |
Ptf1a-injected embryos NF32, biological rep 2 |
| GSM843826 |
Ptf1a-injected embryos NF32, biological rep 3 |
| GSM843827 |
GFP-injected embryos NF36, biological rep 1 |
| GSM843828 |
GFP-injected embryos NF36, biological rep 2 |
| GSM843829 |
GFP-injected embryos NF36, biological rep 3 |
| GSM843830 |
GFP-injected embryos NF36, biological rep 4 |
| GSM843831 |
Ptf1a-injected embryos NF36, biological rep 1 |
| GSM843832 |
Ptf1a-injected embryos NF36, biological rep 2 |
| GSM843833 |
Ptf1a-injected embryos NF36, biological rep 3 |
| GSM843834 |
Ptf1a-injected embryos NF36, biological rep 4 |
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| Relations |
| BioProject |
PRJNA149829 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE34193_RAW.tar |
59.8 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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