Multi-omic data of mdfi knockout grass carp (Ctenopharyngodon idella): ATAC-seq and RNA-seq

This study investigates the role of mdfi in regulating grass carp (Ctenopharyngodon idella) muscle growth using CRISPR/Cas9, RNA-seq, and ATAC-seq. We aim to elucidate how mdfi knockout remodels epigenetic landscapes and transcriptional programs to drive hyperplastic growth.Total RNA was extracted using TRIzol reagent (ThermoFisher, USA). RNA quality was assessed with Qubit 3.0 (ThermoFisher, USA) and an Agilent 5300 Fragment Analyzer (Agilent, USA). Only samples with RIN>7.0 were used for library preparation. Following polyadenylated mRNA enrichment with oligo(dT) magnetic beads, the isolated mRNA was fragmented, utilized for strand-specific cDNA synthesis, and then processed through end-repair, A-tailing, and adapter ligation to construct the final sequencing libraries. Strand‑specific libraries were sequenced on an Illumina NovaSeq™ 6000 platform (LC Bio Technology Co., Ltd., China) in 150-bp paired-end (PE150) mode.Raw reads were quality‑filtered with Fastp (version 0.20.0) to remove adapters and low‑quality bases (Q-value ≤ 20).Cells isolated from muscle tissue were counted using Countstar Rigel S2 (Shanghai Ruiyu, China). Nuclei were collected after lysing the required number of cells for 5 min, then resuspended in a transposition reaction system containing Tn5 transposase. Following incubation and DNA purification, the products were amplified and specific indices were introduced. The PCR program was: 72°C for 3 min; pre‑denaturation at 98°C for 1 min; denaturation at 98°C for 10 s, annealing at 60°C for 25 s, and extension at 72°C for 25 s for a total of 13–15 cycles; final extension at 72°C for 5 min. Library fragments of 200–700 bp were selected using magnetic beads. Library concentration was measured with Qubit (ThermoFisher, USA), and fragment integrity was assessed with Bioanalyzer 5400 (Agilent, USA). Paired‑end 150‑bp sequencing was performed on the Illumina NovaSeq X Plus platform.