We applied high-throughput sequencing to investigate the alterations of miRNAs expression in regenerative intestine (3dpeA, 3dpeB, 3dpeC) Vs normal intestine (ControlA, ControlB, ControlC). Overall design: 9 individuals (3 biological replicates×3 sea cucumbers per biological replicate) at 3 days post evisceration (dpe) were used for our experiments (3 biological replicates: 3dpeA, 3dpeB and 3dpeC). 9 non-eviscerated sea cucumbers (3 biological replicates×3 sea cucumbers per biological replicate) served as the control (3 biological replicates: ControlA, ControlB and ControlC).