Study of MicroRNAs Related to the Liver Regeneration of the Whitespotted Bamboo Shark, Chiloscyllium plagiosum

Table 1

Criteria used for miRNAs annotation and hairpin structure determination.

miRNAs annotation
The miR_name is composed of the known miR name in a cluster, an underscore, and a matching annotation such as
L−𝑛 means that the miRNAs_seq (detected) is 𝑛 base less than known rep_miRSeq in the left side;
R−𝑛 means that the miRNAs_seq (detected) is 𝑛 base less than known rep_miRSeq in the right side;
L+𝑛 means that the miRNAs_seq (detected) is 𝑛 base more than known rep_miRSeq in the left side;
R+𝑛 means that the miRNAs_seq (detected) is 𝑛 base more than known rep_miRSeq in the right side;
2ss5TC13TA means 2 substitutin (ss), which are T→C at position 5 and T→A at position 1.
The miRNAs_seq (detected) is exactly the same as known rep_miRSeq; miRNAs_name is the name of representative miRNAs.
Hairpin determination
Definition of MFEI: MFEI = −𝑑𝐺∗100/mirLen/CG%.
Criteria:
(1) free energy (𝑑𝐺 in kCal/mol) ≤−15,
(2) length of hairpin (up and down stem + terminal loop) ≥50,
(3) number of basepairs (bp) in stem region ≥16,
(4) length of terminal loop ≤20,
(5) number of basepairs (bp) in mature or mature * region ≥12,
(6) percentage of small RNA in stem region (pm) ≥80%,
(7) number of allowed errors in mature region ≤7,
(8) number of allowed errors in one bulge in stem ≤12,
(9) number of allowed errors in one bulge in mature region ≤8,
(10) number of allowed biased errors in one bulge in mature region ≤4,
(11) number of allowed biased bulges in mature region ≤2,
(12) MFEI ≥ 0.7.