Hi!

If I get it right, then the supplemental data comes from the Nature article "Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs" where the authors carried out experiments on human cell lines, so I assume that the gene names are HGNC symbols (cannot access the full-text right now). Below I describe what I did to get 18,457 3'UTRs from Ensembl's BioMart installation:

1. Go to http://www.ensembl.org/biomart/martview
2. Choose "Ensembl Genes 66" as database
3. Choose "Homo sapiens genes" as dataset
4. Click on "Attributes", select "Sequences"
5. In the tabs below select "3'UTR", "Ensembl Gene ID" and "Associated Gene Name"
6. Click on "Filters", in the "Gene" tab set the "ID list limit" filter to "HGNC symbol(s)"
7. Upload the file with the gene names (as you did beforehand)
8. Click on "Results"

9. Select "Export all results to" "File", "FASTA" and "Unique results only", press "Go"

   The downloaded file was named "mart_export.txt", where I counted the returned results as follows:

   grep \> mart_export.txt | sort | uniq | wc -l

   The number of associated gene names in the FASTA file came down to 17,375, which I counted via:

   grep \> mart_export.txt | cut -d '|' -f 2 | sort | uniq | wc -l

   Unfortunately, the sequence download in BioMart 0.7 is not very reliable and I suggest you try downloading the same information multiple times until you have a couple of files that are of the same size. The file I got was 55,288,206 bytes in size, contained 18,457 entries, where the gene name list from the Excel files contains 20,401 gene names.

   Hope this helps.

Joachim