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Mohammed, J., Lai, E.C. (2016.2.8). Lai lab miRNA expression and conservation data for Drosophila. 
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Data from 274 short RNA-seq assays from multiple, independent studies have been analyzed in parallel and consolidated into 44 conditions: 26 different cell lines, 13 developmental stages and 5 tissues.
To generate bigWig short RNA transcriptome profiles, reads for these assays were mapped to D. melanogaster Release 6 (FlyBase r6.09). Multiple libraries were consolidated per condition by summing the number of reads per genomic position and normalizing this count by dividing by the total number of reads summed over all libraries for this condition and multiplying by 1,000,000. Basically, this normalization is equivalent to reads per million (RPM), but on a per nucleotide basis. For reads mapping to multiple locations, the coverage values were equally weighted across all mapping sites.
miRNA expression was computed by first identifying all perfectly-mapped reads that reside entirely within the coordinates flanked by the miRNA sequences + 2nt flanking region; coordinates for the mature and star sequences are provided in "dmeMirnaInfoMature_dm6.bed" and "dmeMirnaInfoStar_dm6.bed".  For reads mapping to multiple locations, the coverage values were equally weighted across all mapping sites. The mapping results are provided in two files, "dmeMatureCoverage_v3.txt" and "dmeStarCoverage_v3.txt", that contain the number of mapped reads per library for the mature sequence and the star sequence, respectively. The "summarizeCoverage.R" R script combines data from all libraries for a given condition to calculate the expression for each miRNA in terms of mapped miRNA reads per million miRNA reads (RPMM).
We have also provided a conservation analysis for all D. melanogaster miRNAs to highlight the more highly conserved ("older") miRNAs that are more likely to have a biological impact. This analysis is based upon synteny evidence from alignment of first 12 sequenced Drosophila genomes (to be published in the near future). In some cases, an ortholog was not found in the genome assembly for a given species, but was supported by PCR or by bioinformatic searches of genomic trace databases. Note that some miRNAs on this list are in fact not miRNAs: we have not found evidence that mir-280, mir-287, mir-288 and mir-289 are products of any known miRNA biogenesis pathway; mir-997-1 and mir-997-2 were recently classified as siRNAs.
The age of each D. melanogaster miRNA is assigned based on the furthest clade away from D. melanogaster which contains an ortholog:
melanogaster-only: miRNA orthologs are absent from all other 11 Drosophilids.
simulans-subgroup: miRNA orthologs are found in either D. simulans or D. sechellia but in none of the other more distantly related Drosophilids.
melanogaster-subgroup: miRNA orthologs are found in D. erecta or D. yakuba, but in none of the other more distantly related Drosophilids.
melanogaster-group: miRNA ortholog is found in D. ananassae, but in none of the other more distantly related Drosophilids.
Sophophora-group: miRNA orthologs are found in D. pseudoobscura, D. persimilis, or D. willistoni, but in none of the other more distantly related Drosophilids.
Drosophila-group: miRNA orthologs are found in D. virilis, D. mojavensis, or D. grimshawi.
We typically use the term "conserved" to refer only to those miRNA that are present in D. pseudoobscura or more distantly related species, while miRNAs born within the melanogaster-group or earlier are labeled as “newly-evolved”. 
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Associated Information

Publications in which the 274 small RNA-Seq datasets reanalyzed here were originally described are listed in the "Related Publications" section of this Reference Report.

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File date: 2016.2.8 ; File size: 680041 ; File format: txt ; File name: Mohammed.2016.2.8.tar.gz
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