Computational protocol: Family-Wide Survey of miR169s and NF-YAs and Their Expression Profiles Response to Abiotic Stress in Maize Roots

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Protocol publication

[…] We obtained NFYA family and miR169 family sequence data separately from the Plant Transcription Factor Database v2.0 (Center for Bioinformatics, Peking University, China, http://planttfdb_v3.cbi.edu.cn/) and the miRBase (University of Manchester, http://www.mirbase.org/), respectively. Sequence alignments were conducted using DNAMAN software (Lynnon Biosoft, Pointe-Claire, Quebec, Canada), and MEGA5 software was used to generate the NFYA phylogenetic tree analysis and reliability values at each branch representing bootstrap samples (1000 replicates). Prediction of mature miR169 family member targets was performed online with the PsRNA server using relatively strict rules (http://plantgrn.noble.org/psRNATarget/), including a maximum expectation value of 3.5, a length for complementarity scoring (hsp size) of 21 bp, a target accessibility (UPE) of 25, a flanking sequence length around the target site of 17 bp in upstream/13 bp in downstream for target accessibility analysis, and a range of 9–11 nt central mismatch leading to translational inhibition. […]

Pipeline specifications

Software tools DNAMAN, MEGA, PsRNA, psRNATarget
Databases PlantTFDB PlnTFDB miRBase
Applications Phylogenetics, RNA-seq analysis
Organisms Zea mays
Chemicals Abscisic Acid, Polyethylene Glycols, Sodium Chloride