Micro array analysis to study Xenopus laevis metamorphosis

Prepared by:

Biswajit Das, Liquan Cai and Donald D. Brown
Department of Embryology, Carnegie Institution of Washington, 3520 San Martin Drive, Baltimore, MD 21218

In collaboration with:

Mark G. Carter, Yu-Lan Piao, Alexei A. Sharov, Minoru S.H. Ko
Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224


For the description of Agilent micro arrays (AMADID#012454), probe preparation, and universal standard (see Das et al. Dev. Biol. 291: 342-355 (2006)). Accessible from this page are the supplementary tables of this paper. These micro arrays contain all of the 21654 Xenopus laevis Unigene entries of Build 48 (February 2004).


The gene expression data of the following organs and conditions are accessible:

Tail: Two thyroid hormone (TH)-induced time points at NF stage 54 (24 h and 48 h) and one developmental time point (NF stage 62). All of these are compared with NF54 control tails.
Hind limb from NF 54 tadpoles treated for 1 week with 1 mM methimazole to reduce endogenous TH: Three TH-induced time points (14 h, 24 h and 48 h) are compared with NF54 control (methimazole treated).
Brain from NF 54 tadpoles treated for 1 week with 1 mM methimazole to reduce endogenous TH: Two TH-induced time points at NF stage 54 (24 h and 48) are compared with NF54 control.


The complete gene expression data can be found in the Gene Expression Omnibus (GEO) database (NCBI):
Tail:   GSE3405
Limb: GSE3404
Brain: GSE3402


Gene Ontology (GO) analysis:

Tables 2 and 5 from the Dev. Biol. paper excerpt examples of functions that are altered by thyroid hormone as analyzed by the human Gene Ontology (GO) Program. All GO functions that are changed by TH as judged by a probability of 0.05 or lower are listed for each time point and sample (Note: All tables are in Microsoft Excel format):

Brain 48 down.xls   Tail 48 down.xls
Brain 48 up.xls Tail 48 up.xls
HL 48 down.xls Tail 62 down.xls
HL 48 up.xls Tail 62 up.xls


A second micro array study

Cai, L., Das, B., Brown, DD (2007) Changing a limb muscle growth program into a resorption  program. Dev. Biol. 304, 260-271. Supplementary tables are accessible from this paper. These micro arrays contain all of the 21654 Xenopus laevis Unigene entries of Build 48 (February 2004) in a  revised format (AMADID #013214).

Transgenic Xenopus laevis tadpoles were prepared expressing a dominant negative form of the thyroid receptor alpha fused to GFP and controlled by the Xenopus cardiac actin promoter. This reporter was itself controlled by the tetracycline system so that the transgene remains silent until the chemical inducer doxycycline is added to the rearing water. Four sets of limb samples were collected for microarray analysis:

1 and 2. Sibling control and induced transgenic tadpoles at NF56 after 2 weeks of induction with doxycycline.

3. Transgenic NF61 tadpoles after 6 weeks dox. Induction.

4. Control NF 66 froglets.

The complete gene expression data can be found in the Gene Expression Omnibus (GEO) database (NCBI):

GSE5249.
GPL3936     Carnegie Xenopus laevis 22k Micorarray


Annotated Gene Expression Data

We have found it convenient to place the gene expression data in a FileMaker Pro database. Each of the 21,000 genes on the array has a page that contains many links and annotations. A copy of the current database is available for download.

Download FileMaker Pro Database (20 MB)