Chromosomal clustering of muscle-expressed genes in C. elegans 

Online Supplement

Peter J. Roy1, Joshua M. Stuart2, Jim Lund1, Stuart K. Kim1,3

1Departments of Developmental Biology and Genetics

Stanford University Medical Center

Stanford, CA, 94305

 

2Stanford Medical Informatics

251 Campus Drive, MSOB X-215

Stanford, California, 94305

 

3corresponding author

650-725-7671

650-725-7739 fax

kim@cmgm.stanford.edu


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The Manuscript

 

Access to Data

*   Download the data.  Zipped excel file containing all relevant raw data (same as S-Table1).

*   Explore the data.  Gene Explorer for the 1364 muscle expressed genes presented in Figure 3b.

 

Table from the Paper

*   Table 1.  Genes expressed in the same tissue tend to cluster along the chromosomes. [HTML] [TAB DELIMITED] [EXCEL]

 

Figures from the Paper (note: click on figure images to enlarge)

*   Figure 1.  An outline of the mRNA-tagging technique.

*   Figure 2.  Muscle mRNA-tagging.

*   Figure 3.  Genes enriched from L1 muscle by mRNA-tagging.

*   Figure 4.  Muscle gene positions are clustered in small groups of two to five genes along the chromosomes.

 

Supplemental Tables

*   S-Table 1.  The master data file. [ZIPPED EXCEL]

* Description of columns in the master data file.

*   S-Table 2.  A comparison of the genes identified as expressed in L1 muscle to muscle positive controls. [HTML] [TAB DELIMITED] [EXCEL]

*   S-Table 3.  Most Genes whose expression patterns were previously characterized in detail, and were identified as enriched in L1 muscle by mRNA tagging, are at least expressed in muscle.  [HTML] [TAB DELIMITED] [EXCEL]

*   S-Table 4.  A search of the Yuji Kohara expression data base (YKDB-http://dolphin.lab.nig.ac.jp/ ) for 51 randomly selected expression patterns. [HTML] [TAB DELIMITED] [EXCEL]

*   S-Table 5.  A list of 559 negative controls. [HTML] [TAB DELIMITED] [EXCEL]

*   S-Table 6.  A list of genes that show undetectable hybridization signals in DNA microarray experiments using RNA from L1 animals.  [HTML] [TAB DELIMITED] [EXCEL]

*   S-Table 7.  A comparison of the gene groups represented in the entire list of 1364 muscle genes and the 386 clustered muscle genes. [HTML] [TAB DELIMITED] [EXCEL]

*   S-Table 8.  The breakdown of the number of genes in each cluster type. [HTML] [TAB DELIMITED] [EXCEL]

 

 

Supplemental Figures (note: click on figure images to enlarge)

*   S-Figure 1.  A histogram showing that mRNA-tagging can enrich for both abundant mRNAs and rare mRNAs.

*   S-Figure 2.  Distribution of all muscle genes along the chromosomes.

*   S-Figure 3.  An introduction to what is considered a chromosomally clustered gene.

*   S-Figure 4.  The order of operations used in the chromosomal cluster analysis.

 

Supplemental Notes

*   S-Note 1.  There is no evidence to suggest that clustered muscle genes are expressed differently than non-clustered muscle genes.

 

 

Methods

*   Molecular Biology.

*   pPRSK9 construct.  Details on the myo-3::FLAG::PABP (pPRSK9) construct.

*   DNA sequences. 

*   Plasmid map.

*   mRNA-Tagging.  SD1075 Lysis, co-Immunoprecipitation of RNA, and Linear RNA Amplification.

*  Data Analysis.

 

 

Detailed Protocols

*   Linear Amplification.

*   co-Immunoprecipitation.


Access to the code

*   Matlab source code [ZIP]  Code for performing chromosome clustering analysis (unzipping creates a chrom_cluster_src sub-directory; see the README file in that directory for further instructions).