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Total RNA from four independent biological replicates was processed and hybridized to Agilent Human miRNA microarrays using standard protocols.
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From each strain, two biological replicates were processed.
Two biological replicates were processed separately, and only sequence reads presented in both biological replicates were considered for further processing.
Each sample was run twice as a technical replicate, and five biological replicates were processed per experiment.
Four biological replicates were processed per species for all analyses except targeted HPLC-MS/MS, in which case only one replicate was performed.
The two biological replicates were processed separately, and only sequence reads present in both replicates and aligned to unique genomic location were considered for further study.
Four separate biological replicates were processed for control and each of the blastema samples across the time course, and two were processed for the "opposite side" samples.
RNA samples from three independent biological replicates were processed using the Truseq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer's protocol.
The biological replicates were prepared and processed on 4 separate occasions, hence acting as independent replicates, too.
The biological replicates were merged and the reads were processed using the SICTIN [ 38] tool build_binary into a binary format in which the number of reads at each genomic position is explicitly saved.
Three biological replicates were collected at each stage and were processed to generate indexed RNA-seq libraries, which were sequenced using an Illumina HiSeq 1000.
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