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. 2021 Jun 16;10:e66954. doi: 10.7554/eLife.66954

Key resources table.

Reagent type
(species)
or resource		 Designation Source or reference Identifiers Additional information
Biological sample (Marsupenaeus japonicus) Hemocytes NA NA Hemocytes from hemolymph from 20 g of kuruma shrimp
Sequence-based reagent 1st PCR primer Macosko et al., 2015 DOI: 10.1016/j.cell.2015.05.002 AAGCAGTGGTATCAACGCAGAGT
Sequence-based reagent P5 universal primer Illumina, Inc NA AATGATACGGCGACCACCGAGATCTACACGCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGT*A*C
Sequence-based reagent i7 index primer Illumina, Inc NA N703: CAAGCAGAAGACGGCATACGAGATTTCTGCCTGTCTCGTGGGCTCGG
N704: CAAGCAGAAGACGGCATACGAGATGCTCAGGAGTCTCGTGGGCTCGG
N705: CAAGCAGAAGACGGCATACGAGATAGGAGTCCGTCTCGTGGGCTCGG
Sequence-based reagent Custom sequence primer Macosko et al., 2015 DOI: 10.1016/j.cell.2015.05.002 GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC
Sequence-based reagent EF-1α Koiwai et al., 2019 DOI:10.1007/s12562-019-01311-5 sequence accession number: AB458256 For: ATTGCCACACCGCTCACA
Rev: TCGATCTTGGTCAGCAGTTCA
Sequence-based reagent HemTGase Yeh et al., 2006 DOI: 10.1016/j.bbapap.2006.04.005 sequence accession number: DQ436474 For: GAGTCAGAAGTCGCCGAGTGT
Rev: TGGCTCAGCAGGTCGTTTAA
Sequence-based reagent Penaeidin An et al., 2016 DOI: 10.1016/j.dci.2016.02.001 sequence accession number: KU057370 For: TTAGCCTTACTCTGTCAAGTGTACGCC
Rev: AACCTGAAGTTCCGTAGGAGCCA
Sequence-based reagent Crustin Hipolito et al., 2014 DOI: 10.1016/j.dci.2014.06.001 sequence accession number: AB121740 For: AACTACTGCTGCGAAAGGTCTCA
Rev: GGCAGTCCAGTGGCTTGGTA
Sequence-based reagent Stylicin Liu et al., 2015 DOI: 10.1016/j.fsi.2015.09.044 sequence accession number: KR063277 For: GGCTCTTCCTTTTCACCTG
Rev: GTCGGGCATTCTTCATCC
Sequence-based reagent proPO Koiwai et al., 2019 DOI: 10.1007/s12562-019-01311-5 sequence accession number: AB073223 For: CCGAGTTTTGTGGAGGTGTT
Rev: GAGAACTCCAGTCCGTGCTC
Sequence-based reagent SOD Hung et al., 2014 DOI: 10.1016/j.fsi.2014.07.030 sequence accession number: AB908996 For: GCCGACACTTCCGACATCA
Rev: TTTTGCTTCCGGGTTGGA
Sequence-based reagent C-lysozyme Hikima et al., 2003 DOI:10.1016/s0378-1119(03)00761-3 For: ATTACGGCCGCTCTGAGGTGC
Rev: CCAGCAATCGGCCATGTAGC
Sequence-based reagent VRP Elbahnaswy et al., 2017 DOI: 10.1016/j.fsi.2017.09.045 sequence accession number: LC179543 For: CTACGGTCGCTACCTTCGTTTG
Rev: TCAACAACGCTTCTGAACTTATTCC
Commercial assay or kit TRI REAGENT Molecular Research Center, Inc TR118 NA
Commercial assay or kit Direct-zol RNA MiniPrep Zymo Research R2050 NA
Commercial assay or kit Dynabeads Oligo(dT)25 Thermo Fisher Scientific DB61002 NA
Commercial assay or kit Direct RNA Sequencing kit Oxford Nanopore Technologies SQK-RNA002 kit NA
Commercial assay or kit MinION Flow Cell Oxford Nanopore Technologies Flow Cell R9.4.1 NA
Commercial assay or kit Negative Photoresist Nippon Kayaku Co., Ltd. SU-8 3050 NA
Commercial assay or kit Polydimethylsiloxane sylgard 184 Dow Corning Corp. SYLGARD 184
Silicone Elastomer Kit		 NA
Commercial assay or kit Barcoded Bead SeqB ChemGenes Corporation MACOSKO-2011–10 NA
Commercial assay or kit Maxima H Minus Reverse Transcriptase Thermo Fisher Scientific EP0751 NA
Commercial assay or kit Exonuclease I New England Biolabs M0293S NA
Commercial assay or kit KAPA HiFi HotStart ReadyMix Roche Ltd. KK2601 NA
Commercial assay or kit KAPA HiFi DNA polymerase Roche Ltd. KK2103 NA
Commercial assay or kit Agencourt AMPure XP beads Beckman Coulter A63882 NA
Commercial assay or kit DNA Clean and Concentrator Kit Zymo Research D4013 NA
Commercial assay or kit Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 NA
Commercial assay or kit High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Scientific 4368814 NA
Commercial assay or kit KOD SYBR qPCR TOYOBO Co. Ltd. QKD-201 NA
Cell staining solution May-Grünwald‘s eosin methylene blue solution modified Merck KGaA 101424 NA
Cell staining solution Giemsa’s Azure Eosin Methylene Blue solution Merck KGaA 109204 NA
Software, algorithm Guppy v3.6.1 Oxford Nanopore Technologies NA https://community.nanoporetech.com/
Software, algorithm MinKNOW v3.6.5 Oxford Nanopore Technologies NA https://community.nanoporetech.com/
Software, algorithm TALC v1.01 Broseus et al., 2020a, Broseus et al., 2020b DOI: 10.1093/bioinformatics/btaa634 https://gitlab.igh.cnrs.fr/lbroseus/TALC
Software, algorithm rnaSPAdes v3.14.1 Bushmanova et al., 2019a, Bushmanova et al., 2019b DOI: 10.1093/gigascience/giz100 https://cab.spbu.ru/software/rnaspades/
Software, algorithm Trinity 2.10.0 Grabherr et al., 2011, Grabherr et al., 2018 DOI: 10.1038/nbt.1883 https://github.com/trinityrnaseq/trinityrnaseq/wiki
Software, algorithm EvidentialGene v2022.01.20 Gilbert, 2019 NA http://arthropods.eugenes.org/EvidentialGene/
Software, algorithm BUSCO v5.0.0 Seppey et al., 1962 DOI: 10.1007/978-1-4939-9173-0_14 https://busco.ezlab.org/
Software, algorithm Blast+ v2.2.31 Altschul et al., 1990;
Camacho et al., 2009 		DOI: 10.1016/s0022-2836(05)80360-2
DOI: 10.1186/1471-2105-10-421 		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Software, algorithm Drop-seq tools v2.3.0 McCarroll Lab Wysoker et al., 2020 NA https://github.com/broadinstitute/Drop-seq
Software, algorithm Picard Toolkit Broad Institute Picard Toolkit, 2019 NA http://broadinstitute.github.io/picard/
Software, algorithm STAR v2.7.8a Dobin et al., 2013; Dobin et al., 2021 DOI:
10.1093/bioinformatics/bts635 		https://github.com/alexdobin/STAR
Software, algorithm Surat v4.0.1 Butler et al., 2018; Stuart et al., 2019 DOI: 10.1038/nbt.4096
DOI: 10.1016/j.cell.2019.05.031 		https://satijalab.org/seurat/
Software, algorithm Monocle 3 v0.2.3.0 Trapnell et al., 2014, Trapnell et al., 2021 DOI: 10.1038/nbt.2859 https://github.com/cole-trapnell-lab/monocle3