Proteome and Transcriptome Analysis Data for coelomocytes and membrane fragments of Patiria pectinifera

Proteome analysis was performed on coelomocytes (CCs) and membrane fragments from adult Patiria pectinifera collected in Mutsu Bay. CCs, anucleate cell fragments (AFs), and extracellular vesicles (EVs) were isolated from the coelomic fluid using a stepwise centrifugation protocol. Pellets of CCs, AFs, and EVs collected before (0h) and after (6h) immune stimulation were dissolved in radioimmunoprecipitation assay buffer. Equal amounts of protein (1.5 μg per sample) were subjected to sodium dodecyl sulfate–polyacrylamide gel electrophoresis (n = 4 biological replicates per condition). After electrophoresis, each lane was excised and divided into six sections. Fragments of blank gel were also collected as negative controls. Gel pieces were subjected to in-gel trypsin digestion, and the resulting peptides were analyzed using liquid chromatography–quadrupole time-of-flight mass spectrometry (TripleTOF 5600; SCIEX, Japan). The raw data was converted to mascot generic format (mgf) files using ProteoWizard software (version 3). The mgf files are compiled into zip files for each electrophoresis gel and contain data for eight lanes (six sections each), as well as data for the corresponding blank gel fragment. (gel1 contains data for AF_1 and EV_1–EV_3; gel2 contains data for AF_2–4 and EV_4; gel3 contains data for all CCs.) RNA-seq was performed using coelomocytes collected before (vivo0h) and after (vivo6h) immune stimulation. Coelomocytes pellets were obtained from three independent animals per condition (n = 3), and total RNA was extracted using the NucleoSpin RNA Kit (TAKARA, Japan) according to the manufacturer’s instructions. Libraries were sequenced on a NovaSeq X platform (Illumina) to generate 150 base pair paired-end reads.