Email updates

Keep up to date with the latest news and content from BMC Developmental Biology and BioMed Central.

Open Access Highly Accessed Research article

Microarrays and RNA-Seq identify molecular mechanisms driving the end of nephron production

Eric W Brunskill1, Hsiao L Lai2, D Curtis Jamison3, S Steven Potter1 and Larry T Patterson2*

Author Affiliations

1 Division of Developmental Biology, Cincinnati Children's Hospital Medical Center and the University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229 USA

2 Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center and the University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229 USA

3 Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center and the University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229 USA

For all author emails, please log on.

BMC Developmental Biology 2011, 11:15  doi:10.1186/1471-213X-11-15

Published: 12 March 2011

Additional files

Additional file 1:

Optical section of Tg(Crym-EGFP)82Gsat/Mmcd transgenic mouse kidney. a) Strong GFP expression is seen in both the Cited1(+) (red) and Cited1(-) (arrows) capping mesenchyme at P2 in the Tg(Crym-EGFP)82Gsat/Mmcd mouse. GFP (green) is seen in the cap surrounding the branch tips of the ureteric bud and does not extend into the stroma. Ecadherin (blue); b) The abrupt change in character of the cap between P2 and P3 is accompanied by loss of Cited1 immunostaining.

Format: TIFF Size: 12.6MB Download file

Open Data

Additional file 2:

Optical section through transgenic mouse kidney at P0. GFP is expressed at birth at lower intensity in the renal vesicles of the Tg(Crym-EGFP)82Gsat/Mmcd mouse than in the capping mesenchyme. The optical section through the nephrogenic region shows a portion of a renal vesicle (encircled), defined by morphological criteria of a central cavity in a deeper plane.

Format: TIFF Size: 5MB Download file

Open Data

Additional file 3:

Image of the FACS plot of cells collected for RNA measurements. The GFP-positive cells with the highest level of expression were collected by FACS. Gating was set at a constant level as seen from birth to P3. After birth, both the fraction of GFP cells and the level of GFP intensity (peak shifts to the left) decreased.

Format: TIFF Size: 470KB Download file

Open Data

Additional file 4:

List of genes with changing levels of expression by microarray after birth. Relative expression levels of 2000 genes with significant change in level of expression by ANOVA in the multi-potential progenitors after birth in mice. Levels of expression obtained in triplicate at birth (P0) and each 24-hour interval afterwards (P1-P4) were combined. The data is Log2 transformed.

Format: XLS Size: 392KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

List of genes with a change in level of expression by RNA-Seq between P0 and P2. RNA-Seq raw counts, normalized counts, fold change, and level of significance are shown for those genes with a significant difference in expression between P0 and P2.

Format: XLS Size: 76KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Functional sets of genes with a change in level by RNA-Seq between P0 and P2. Genes identified by Partek Genomic Suites to significantly change were analyzed by ToppGene to identify functional classes.

Format: XLS Size: 182KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

List of genes with changes in transcript levels between P1 and P4. List of genes identified by GeneSpring analysis of microarrays.

Format: XLS Size: 71KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Functional sets of genes with transcript levels that decrease or increase between P1 and P4. Genes identified by GeneSpring to significantly change were analyzed by ToppGene to identify functional classes.

Format: XLS Size: 280KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data