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README
Taft et al Nature Genetics 2009 
tiRNA BED, FASTA, and REFGENE files
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Transcription initiation RNAs (tiRNAs) from human, chicken, and Drosophila can be found here as UCSC compatible BED (*.bed) and standard FASTA (*.fa) files.

The FASTA name header, or the name field (4th column) of the BED file, follows the following convention:

<library identifier>_<set identifier>_<tag identifier>_<tag count/abundance>

The <Tag identifier> is simply a number we used to keep track of the tag - it has no external reference or meaning. For all chicken and Drosophila tags the first two fields will be the NCBI GEO library and set IDs. For example, every chicken <library identifier will be GSE10686 and the set identifiers will refer to the different embryonic time points.

For human tiRNAs we've simply used "FANTOM4" and "THP-1" for the first two fields, since all the small RNA data is available here, on the FANTOM4 website.

You can also find a list of Refgene identifiers for all genes with tiRNAs in our human and chicken datasets. Please note that the human data is a single column of names, while the chicken data is two columns - <set identifier> <refGene id>.

The tiRNAs listed in these file are "high confidence" small RNAs. They occur in the same strand as a TSS or deepCAGE tag, and are located between -60 and +120 nt relative to the TSS.


Please contact me if you have any questions.

List of files and brief descriptions:
FILES :: Description
Drosophila_GSE11624_tiRNAs.bed :: mapped coordinates of fruit fly tiRNAs (UCSC dm3) from GSE11624
Drosophila_GSE11624_tiRNAs.fa :: FASTA file of fruit fly tiRNAs from GSE11624
Drosophila_GSE7448_tiRNAs.bed :: mapped coordinates of fruit fly tiRNAs (UCSC dm3) from GSE7448
Drosophila_GSE7448_tiRNAs.fa :: FASTA file of fruit fly tiRNAs from GSE7448
chicken_GSE10686_tiRNAs.bed :: mapped coordinates of chicken tiRNAs (UCSC galGal3) from GSE10686
chicken_GSE10686_tiRNAs.fa :: FASTA file of chicken tiRNAs (UCSC galGal3) from GSE10686
chicken_GSE10686_tiRNAs_refGenes.txt :: list of all chicken genes with tiRNAs
human_FANTOM4_tiRNAs.bed :: mapped coordinates of human tiRNAs (UCSC hg18) from the FANTOM4 small RNA dataset (see README_allSmallRNAsequences.txt)
human_FANTOM4_tiRNAs.fa :: FASTA file of human tiRNAs (UCSC hg18) from the FANTOM4 small RNA dataset
human_FANTOM4_tiRNAs_refGenes.txt :: list of all human genes with tiRNAs

Ryan J Taft
Mattick Laboratory
Institute for Molecular Bioscience
University of Queensland
Australia
r.taft@imb.uq.edu.au