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
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
pPRSK9 construct. Details on the myo-3::FLAG::PABP
(pPRSK9) construct.
mRNA-Tagging.
SD1075 Lysis, co-Immunoprecipitation of RNA, and Linear RNA Amplification.
Detailed
Protocols
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).
