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
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
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.
Description of columns in the master data file.
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]
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.
S-Note 1. There is no evidence to suggest that clustered muscle genes are expressed differently than non-clustered muscle genes.
pPRSK9 construct. Details on the myo-3::FLAG::PABP (pPRSK9) construct.
mRNA-Tagging. SD1075 Lysis, co-Immunoprecipitation of RNA, and Linear RNA Amplification.
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).