Supplementary information

From the following article:

The impact of microRNAs on protein output

Daehyun Baek, Judit Villén, Chanseok Shin, Fernando D. Camargo, Steven P. Gygi & David P. Bartel

Nature 455, 64-71(4 September 2008)

doi:10.1038/nature07242

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Supplementary Information 1

The file contains Supplementary Discussion; Supplementary Tables 1-2; Supplementary Figures 1-8 with Legends. Supplementary Discussion discusses potential caveats of ectopically introduced miRNAs in investigating miRNA targeting and corresponding advantages of examining miRNA-deficient cells. Supplementary Table 1 lists 3'UTR motifs overrepresented in messages of proteins most upregulated in miR-223-/Y neutrophils. Supplementary Table 2 lists the top 20 miRNAs co-expressed with miR-223 in wild-type neutrophils cultured in vitro. Supplementary Figure 1 shows the schematic of our quantitative proteomics approach using SILAC in experiments transfecting miR-1, 124, and 181 into HeLa cells.Supplementary Figure 2 illustrates the quantification of peptides from two proteins that respond the loss of miR-223 and two proteins that do not. Supplementary Figure 3 illustrates the reproducibility of the quantification when comparing technical replicates and when comparing different peptides representing the same protein. Supplementary Figure 4 shows additional characterization of the neutrophils differentiated in vitro. Supplementary Figure 5 shows the response of proteins predicted to be miR-223 targets after deleting miR-223. Supplementary Figure 6 illustrates the protein and mRNA changes for the additional cohorts of genes lacking 3'UTR sites. Supplementary Figure 7 shows comparative immunoblots illustrating the consequences of losing miR-223 in neutrophils differentiated in vitro and those isolated from the mouse. Supplementary Figure 8 shows the protein repression of genes predicted to be miR-124, miR-1, and miR-181 targets from experiments transfecting those miRNAs into HeLa cells.

nature07242-s2.xls

This file contains Supplementary Data 1. This Excel file lists the number of uniquely quantified peptides, the number of independent measurements, the median log2-fold-change in quantified protein (with 25th and 75th percentiles), and the log2-fold-change in mRNA (with error) for each human message in our dataset after transfecting miR-124. Also listed is the number of miR-124 sites in the UTRs and ORF of each message.

nature07242-s3.xls

This file contains Supplementary Data 2. This Excel file lists the number of uniquely quantified peptides, the number of independent measurements, the median log2-fold-change in quantified protein (with 25th and 75th percentiles), and the log2-fold-change in mRNA (with error) for each human message in our dataset after transfecting miR-1. Also listed is the number of miR-1 sites in the UTRs and ORF of each message.

nature07242-s4.xls

This file contains Supplementary Data 3. This Excel file lists the number of uniquely quantified peptides, the number of independent measurements, the median log2-fold-change in quantified protein (with 25th and 75th percentiles), and the log2-fold-change in mRNA (with error) for each human message in our dataset after transfecting miR-181. Also listed is the number of miR-181 sites in the UTRs and ORF of each message.

nature07242-s5.xls

This file contains Supplementary Data 4. This Excel file lists the number of uniquely quantified peptides, the number of independent measurements, the median log2-fold-change in quantified protein (with 25th and 75th percentiles), and the mean log2-fold-change in mRNA (with s.e.m.) for each mouse message in our dataset, comparing neutrophils with and without miR-223. Also reported are the profiling data for sorted progenitors and sorted neutrophils, and the number of miR-223 sites in the UTRs and ORF of each message.

nature07242-s6.zip

This file contains Supplementary Data 5a. This fasta file lists the complete 5' UTR, ORF, and 3' UTR sequences of our human reference cDNAs.

nature07242-s7.zip

This file contains Supplementary Data 5b. This fasta file lists the complete 5' UTR, ORF, and 3' UTR sequences of our mouse reference cDNAs.

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