Single hemocytes were analyzed through the microfluidics-based Drop-seq, mRNA sequencing for the preparation of de novo assembled gene sets, in silico analysis workflow, and morphology-based cell …
Distribution and the median of the number of transcripts (unique molecular identifiers [UMIs]) (A), genes (B), and percentage of mitochondrial UMIs (C) detected per cell. Uniform manifold …
Excel sheets pertaining to UMIs, genes , mitochondrial UMIs detected per hemocyte used for Figure 2A-C.
Uniform manifold approximation and projection plot of SCTransform batch corrected and integrated of hemocytes from individual shrimps (D).
Excel sheets pertaining to UMIs, genes , mitochondrial UMIs detected per hemocyte on individual shrimp used for Figure 2—figure supplement 1A-C.
Dot plot representing the average expression of KOGs (A) and GOs (B) per cluster. Color gradient of dots represents the expression level, while the size represents the percentage of cells expressing …
Heat map profile of the marker in each cluster (A). Color gradient represents the expression level of each single cell. The numbers in parentheses represent the number of genes estimated as markers …
Percentage of each cell cycle on clusters (A). Uniform manifold approximation and projection plot of cell cycles of hemocytes from three shrimps (n = 2566) (B). Visualization of clusters onto the …
Source data of the percentage of each cell state per cluster used for Figure 5A.
Batch effect was removed, and there were no differences between individuals.
Dot plot representing the average expression of G2/M and S phase-related genes per cluster. Color gradient of the dot represents the expression level, while the size represents the percentage of …
Color gradient of the dot represents the expression level, while the size represents the percentage of cells expressing any gene per cluster. Detailed blast results are listed in Supplementary file 4.
Dot plots profiling of cell growth-related genes in each cluster (A). Color gradient of the dot represents the expression level, while the size represents the percentage of cells expressing any gene …
Dot plot representing the average expression of each immune-related gene per cluster (A). Color gradient of the dot represents the expression level, while the size represents the percentage of cells …
Color gradient of the dot represents the expression level, while the size represents the percentage of cells expressing any gene per cluster. The details of the identified genes are listed in Supplem…
Color gradient of the dot represents the expression level, while the size represents the percentage of cells expressing any gene per cluster. The details of identified genes are listed in Supplementa…
Color gradient of the dot represents the expression level, while the size represents the percentage of cells expressing any gene per cluster. The details of the identified genes are listed in Supplem…
Color gradient of the dot represents the expression level, while the size represents the percentage of cells expressing any gene per cluster. The details of the identified genes are listed in Supplem…
Color gradient of the dot represents the expression level, while the size represents the percentage of cells expressing any gene per cluster. The details of the identified genes are listed in Supplem…
Color gradient of the dot represents the expression level, while the size represents the percentage of cells expressing any gene per cluster. The details of the identified genes are listed in Supplem…
(A) Differential interference contrast (DIC) image of unsorted total hemocytes. (B) Dye-stained total hemocytes. (C) DIC imaging and dye staining of region 1 (R1)-sorted hemocytes. (D) DIC imaging …
Source data for CT values of each gene used for Figure 9F.
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 |
Table representing blastx researching of assembled genes against penaeid shrimp's proteins.
Table representing predicted marker genes per cluster.
Table representing blastx researching of assembled genes against Drosophila cell cycle markers.
Table representing blastx researching of assembled genes against Drosophila cell-type markers.