Open Access Highly Accessed Research article

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea

Chi Keung Cheng1, Chun Hang Au1, Sarah K Wilke2, Jason E Stajich3, Miriam E Zolan4, Patricia J Pukkila2 and Hoi Shan Kwan1*

Author Affiliations

1 Food Research Centre and Food and Nutrition Sciences Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, S.A.R., Hong Kong

2 Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

3 Department of Plant Pathology and Microbiology, University of California-Riverside, Riverside, United States of America

4 Department of Biology, Indiana University, Bloomington, Indiana, United States of America

For all author emails, please log on.

BMC Genomics 2013, 14:195  doi:10.1186/1471-2164-14-195

Published: 20 March 2013

Additional files

Additional file 1:

List of 3270 genes of which expression is detected in either Myc or S1-Pri stage. Expression level is evaluated by summing up the counts of all tags mapped to the putative 5-UTR, divided by the total tag counts in the respective stage, and expressed in tags per 100,000.

Format: XLSX Size: 439KB Download file

Open Data

Additional file 2:

List of 324 genes differentially expressed in the Myc stage. Expression level is evaluated by summing up the counts of all tags mapped to the putative 5-UTR, divided by the total tag counts in the Myc stage, and expressed in tags per 100,000. Differential expression is defined by p<0.05 in Fisher’s exact test.

Format: XLSX Size: 51KB Download file

Open Data

Additional file 3:

List of 716 genes differentially expressed in the S1-Pri stage. Expression level is evaluated by summing up the counts of all tags mapped to the putative 5-UTR, divided by the total tag counts in the S1-Pri stage, and expressed in tags per 100,000. Differential expression is defined by p<0.05 in Fisher’s exact test.

Format: XLSX Size: 110KB Download file

Open Data

Additional file 4:

Microarray data for the 8667 genes after quality filtering. M_006_z to M_009_z represent four replicate experiments. Values are given as log2 ratio of expression level of Myc divided by that of S1-Pri.

Format: XLSX Size: 1.1MB Download file

Open Data

Additional file 5:

Gene ontology terms assigned to the differentially expressed genes in both Myc and S1-Pri. We recommend viewing using Gene Ontology Browsing Utility, available at //gobu.iis.sinica.edu.tw. Run “gobuCmd.bat” in the “gobu” folder after extraction of the downloaded .zip file, wait for the program interface to pop up and load the .txt file into the program.

Format: TXT Size: 169KB Download file

Open Data

Additional file 6:

KEGG pathway maps assigned to S1-Pri DEGs. KEGG Orthology (KO) id and description can be found in the last two columns of additional file 2.

Format: XLSX Size: 19KB Download file

Open Data

Additional file 7:

KEGG pathway maps assigned to Myc DEGs. KEGG Orthology (KO) id and description can be found in the last two columns of additional file 1.

Format: XLSX Size: 12KB Download file

Open Data

Additional file 8:

Protein domains enriched in the Myc DEGs.

Format: XLSX Size: 24KB Download file

Open Data

Additional file 9:

Protein domains enriched in the S1-Pri DEGs.

Format: XLSX Size: 37KB Download file

Open Data

Additional file 10:

Myc and S1-Pri DEGs that are unique to at least two fruiting body-forming basidiomycetes. Ab: Agaricus bisporus; Le: Lentinula edodes; Lb: Laccaria bicolor; Po: Pleurotus ostreatus; Sc: Schizophyllum commune; Pc: Phanerochaete chrysosporium; Pp: Postia placenta.

Format: XLSX Size: 13KB Download file

Open Data

Additional file 11:

Myc and S1-Pri DEGs that are unique to C. cinerea.

Format: XLSX Size: 12KB Download file

Open Data

Additional file 12:

Primers used in real-time RT-PCR for cross-validation of 5-SAGE and microarray.

Format: XLSX Size: 13KB Download file

Open Data

Additional file 13:

Primers used in real-time RT-PCR for expression validation of additional selected genes.

Format: XLSX Size: 10KB Download file

Open Data