Open Access Research

Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling

King-Hwa Ling1237, Chelsee A Hewitt19, Tim Beissbarth104, Lavinia Hyde114, Kakoli Banerjee5, Pike-See Cheah56, Ping Z Cannon1, Christopher N Hahn7, Paul Q Thomas5, Gordon K Smyth4, Seong-Seng Tan8, Tim Thomas1 and Hamish S Scott127*

Author Affiliations

1 Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia

2 The School of Medicine, The University of Adelaide, SA, 5005, Australia

3 Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia

4 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia

5 School of Molecular and Biomedical Science, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia

6 Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia

7 Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, Adelaide, SA 5000, Australia

8 Howard Florey Institute, The University of Melbourne, Parkville, Victoria 3010, Australia

9 Current address: Pathology Department, The Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria 3002, Australia

10 Current address: Department of Medical Statistics (Biostatistics), University of Göttingen, Humboldtalle 32, 37073 Göttingen, Germany

11 Current address: The Bioinformatics Unit, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia

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Genome Biology 2009, 10:R104  doi:10.1186/gb-2009-10-10-r104

Published: 2 October 2009

Additional files

Additional data file 1:

Analysis of SAGE, DETs, IPA, Sox4 and Sox11 genomic cluster analysis, and R script for implementing empirical Bayesian moderated t-test on multiple groups.

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Open Data

Additional data file 2:

SAGE tag information for 561 DETs.

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Open Data

Additional data file 3:

Functional annotations clustering analysis using DAVID.

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Open Data

Additional data file 4:

RT-qPCR validation of DETs based on multiple comparisons between two developmental stages (E versus Ad, PN1.5 versus Ad and E15.5 versus PN1.5).

Format: XLS Size: 53KB Download file

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Open Data

Additional data file 5:

RT-qPCR validation of gene clusters based on hierarchical clustering analysis.

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Open Data

Additional data file 6:

RT-qPCR validation of DETs based on the rostral versus caudal E15.5 cerebral cortex comparison.

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Open Data

Additional data file 7:

Statistically significant over-represented genomic loci based on genomic clustering of tags.

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Open Data

Additional data file 8:

Primers, probes, clones and assays designed for RT-qPCR, RACE, Southern, Northern and ISH analysis.

Format: XLS Size: 89KB Download file

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Open Data