Detailed feature profile of MirGeneDB highly and lowly expressed miRNA precursors
datasetposted on 18.08.2021, 14:52 by Wenjing KangWenjing Kang, Bastian Fromm, Inna Biryukova, Marc FriedländerMarc Friedländer
This is the Supplementary Data 9 of the MapToCleave study.
The file folder contains detailed feature information of MirGeneDB highly and lowly expressed miRNA precursors of 20 species. There are six feature files for each miRNA precursor. The file with the suffix “.statistics” provides basic information on the hairpin. The file with the suffix “.fold” provides RNA secondary structure in dot bracket format predicted by RNAfold. The file with suffix “.unopened_5p_ref” and “.unopened_3p_ref” provides positional information of base pairing indicated by “-” and symmetric mismatch bulge indicated by “*”, “>” asymmetric bulge with more nucleotides at the 5p strand or “<” asymmetric bulge with more nucleotides at the 3p strand. The file with suffix “.bulgefeatures_unopened_5p_ref” and “.bulgefeatures_unopened_3p_ref” provides detailed information on bulges with columns for identity, bulge name, maximum size of the bulge, start position of the bulge, end position of the bulge, type of bulge, nucleotides at the 5p strand, nucleotides at the 3p strand, the adjacent base pair at the 5’ side of the bulge and the adjacent base pair at the 3’ side of the bulge. The 5p and 3p in the file names mean that the features are counted respectively at the 5p and 3p strand of the hairpin. All the features were counted based on the 5’ side of Drosha cleavage site annotated from MirGeneDB.
The identify information of the highly and lowly expressed MirGeneDB miRNAs are available at “in_vivo_highly_expressed_miRNA_precursor_IDs.txt” and “in_vivo_lowly_expressed_miRNA_precursor_IDs.txt” respectively. The data frame of 7-mer window free energy used for Figure 4C-D is available at “local_free_energy_7-mer_of_MirGeneDB_miRNA_precursors.txt” with columns showing the position relative to 5’ side of Drosha cleavage site and rows showing MirGeneDB ID.