KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological Samples | ||
| Human PBMCs | Consented Donors | N/A |
| NASA Twin Study Unsorted PBMCs | Consented Donors | N/A |
| NASA Twin Study Lymphocyte Depleted Cells | Consented Donors | N/A |
| NASA Twin Study CD8 CD4, CD14 and CD19 Cells | Consented Donors | N/A |
| Mouse Blood | C57BL/6J Wt female | N/A |
| Mouse Plasma | C57BL/6J Wt female | N/A |
| Mouse Liver | C57BL/6J Wt female | N/A |
| Mouse Heart | C57BL/6J Wt female | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| RLT+ Buffer | QIAGEN | Cat# 1053393 |
| Triton X-100 | Sigma | Cat# X100 |
| TRIzol | ThermoFisher | Cat# 15596026 |
| Ficoll-Paque | VWR | Cat# 95038-168 |
| 1x Phosphate Buffered Saline (pH 7.4) | Thermofisher Scientific | Cat# 10010023 |
| EGM-2 Endothelial Cell Growth Medium-2 Bullet-Kit | Lonza | Cat# CC-3162 |
| EGM Endothelial Cell Growth Medium Bullet-Kit | Lonza | Cat# CC-3124 |
| Rat tail Collagen Type 1 | BD Biosciences | Cat# 354236 |
| Matrigel Matrix | BD Biosciences | Cat# 356230 |
| Phorbol-12-myristate-13-acetate: PMA | Millipore | Cat# 524400 |
| 5-(4,6-Dichlorotriazinyl) Aminofluorescein (DTAF) | Thermofisher Scientific | Cat# D-16 |
| MP Biomedicals Trypsin-EDTA Solution | Thermofisher Scientific | Cat# ICN1689149 |
| Critical Commercial Assays | ||
| miRNeasy serum/plasma kit | QIAGEN | Cat# 217184 |
| miRNeasy mini kit | QIAGEN | Cat# 217004 |
| Allprep kit | QIAGEN | Cat# 80204 |
| miRCURY LNA RT kit | QIAGEN | Cat# 339340 |
| QX200 ddPCR Evagreen Supermix | BioRad | Cat# 1864034 |
| miRNA primers | QIAGEN | Listed under “Oligonucleotides” |
| NEBNext® Multiplex Small RNA Library Prep Set for Illumina® | NEB | NEB# E7560 |
| NEBNext® Multiplex Oligos for Illumina® Dual Index Primers | NEB | NEB# E7600, NEB# E7780 |
| Index primers | NEB | NEB# E7560 |
| iSCRIPT™ cDNA synthesis kit | Bio-Rad | Cat# 1708890 |
| iQ™ SYBR® Green Supermix | Bio-Rad | Cat# 170-8880 |
| TruSeq Small RNA Sample Prep Kits | Illumina | RS-200-0012 |
| Rhapsody AbSeq reagent pack | BD Biosciences | Cat# 633771 |
| Rhapsody Human Immune Response panel | BD Biosciences | Cat# 633750 |
| Rhapsody custom gene panel (See Table S3) | BD Biosciences | Cat# 633743 |
| Human Single cell multiplexing kit | BD Biosciences | Cat# 633781 |
| SureCell ATAC-seq Library Prep Kit | Bio-Rad | Cat# 17004620 |
| SureCell ddSEQ Index Kit | Bio-Rad | Cat# 12009360 |
| Deposited Data | ||
| MirGeneDB sequences | (Fromm et al., 2020) | https://mirgenedb.org/ |
| miRNA-seq for mice data | NASA GeneLab (https://genelab.nasa.gov/) | GLDS-334, GLDS-335, GLDS-336, GLDS-337 |
| NASA Twin Study miRNA-seq results | This paper | N/A |
| miRNA ddPCR raw data | This paper | LSDA (NASA) |
| NASA Twin Study BD Rhapsody Data | This paper and Getz et al. (2020) | N/A |
| NASA Twin Study scATAC Data | This paper | N/A |
| Experimental Models: Cell Lines | ||
| Human: HUVECs | Lonza | Cat# CC-2519 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | Jackson Labs, Sacramento, CA | (IMSR Cat# JAX:000664, RRID:IMSR_JAX:000664) |
| Mouse: C57BL/6J | Jackson Laboratory Maine, | (IMSR Cat# JAX:000664, RRID:IMSR_JAX:000664) |
| Rat: Wistar | Charles River Laboratories, Wilmington, MA | (RGD Cat# 2312511, RRID:RGD_2312511) |
| Mouse: BALB/cAnNTac | Taconic | (IMSR Cat# TAC:balb, RRID:IMSR_TAC:balb) |
| Oligonucleotides | ||
| hsa-miR-17-5p miRCURY LNA miRNA PCR Assay: MIMAT0000070: 5′CAAAGUGCUUACAGUGCAGGUAG | QIAGEN | Cat# YP02119304 |
| hsa-miR-146a-5p miRCURY LNA miRNA PCR Assay: MIMAT0000449: 5′UGAGAACUGAAUUCCAUGGGUU | QIAGEN | Cat# YP00204688 |
| hsa-miR-223-3p miRCURY LNA miRNA PCR Assay: MIMAT0000280: 5′UGUCAGUUUGUCAAAUACCCCA | QIAGEN | Cat# YP00205986 |
| hsa-let-7a-5p miRCURY LNA miRNA PCR Assay: MIMAT0000062: 5′UGAGGUAGUAGGUUGUAUAGUU | QIAGEN | Cat# YP00205727 |
| hsa-mir-92a-3p miRCURY LNA miRNA PCR Assay: MIMAT0000092: 5′UAUUGCACUUGUCCCGGCCUGU | QIAGEN | Cat# YP00204258 |
| hsa-miR-24-3p miRCURY LNA miRNA PCR Assay: MIMAT0000080: 5′UGGCUCAGUUCAGCAGGAACAG | QIAGEN | Cat# YP00204260 |
| hsa-miR-125b-5p miRCURY LNA miRNA PCR Assay: MIMAT0000423: 5′UCCCUGAGACCCUAACUUGUGA | QIAGEN | Cat# YP00205713 |
| hsa-miR-16-5p miRCURY LNA miRNA PCR Assay: MIMAT0000069: 5′UAGCAGCACGUAAAUAUUGGCG | QIAGEN | Cat# YP00205702 |
| hsa-miR-26a-5p miRCURY LNA miRNA PCR Assay: MIMAT0000082: 5′UUCAAGUAAUCCAGGAUAGGCU | QIAGEN | Cat# YP00206023 |
| hsa-miR-145-5p miRCURY LNA miRNA PCR Assay: MIMAT0000437: 5′GUCCAGUUUUCCCAGGAAUCCCU | QIAGEN | Cat# YP00204483 |
| mmu-miR-217-5p miRCURY LNA miRNA PCR Assay: MIMAT0000679: 5′UACUGCAUCAGGAACUGACUGGA | QIAGEN | Cat# YP00205070 |
| hsa-miR-34a-5p miRCURY LNA miRNA PCR Assay: MIMAT0000255: 5′UGGCAGUGUCUUAGCUGGUUGU | QIAGEN | Cat# YP00204486 |
| hsa-miR-21-5p miRCURY LNA miRNA PCR Assay: MIMAT0000076: 5′UAGCUUAUCAGACUGAUGUUGA | QIAGEN | Cat# YP00204230 |
| mmu-miR-25-5p miRCURY LNA miRNA PCR Assay: MIMAT0017049: 5′AGGCGGAGACUUGGGCAAUUGC | QIAGEN | Cat# YP02118413 |
| hsa-let-7c-5p miRCURY LNA miRNA PCR Assay: MIMAT0000064: 5′UGAGGUAGUAGGUUGUAUGGUU | QIAGEN | Cat# YP00204767 |
| Software and Algorithms | ||
| miRTrace | (Kang et al., 2018) | https://github.com/friedlanderlab/mirtrace |
| miRDeep2 | (Friedländer et al., 2012) | https://www.mdc-berlin.de/content/mirdeep2-documentation; RRID:SCR_010829 |
| Cytoscape | (Shannon et al., 2003) | https://cytoscape.org; RRID:SCR_003032 |
| ClueGo/CluePedia | (Bindea et al., 2013) | http://www.ici.upmc.fr/cluego/; RRID:SCR_005748 |
| DIANA microT-CDS tool | (Paraskevopoulou et al., 2013; Reczko et al., 2012) | http://carolina.imis.athena-innovation.gr/dianatools/web/index.php; RRID:SCR_016510 |
| miRNet 2.0 | (Chang et al., 2020) | https://www.mirnet.ca/ |
| Rtsne v0.15 | (van der Maaten and Hinton, 2008) | https://github.com/jkrijthe/Rtsne; RRID:SCR_016342 |
| corrplot v0.84 | n/a | https://github.com/taiyun/corrplot |
| ggplot2 v3.3.1 | (Wickham, 2016) | https://ggplot2.tidyverse.org; RRID:SCR_014601 |
| pheatmap V1.0.12 | Kolde Rpheatmap: Pretty heatmaps software; 2015 | https://cran.r-project.org/web/packages/pheatmap/index.html; RRID:SCR_016418 |
| ACGT101-miR | LC Sciences | N/A |
| miRBase 22.0 | (Kozomara et al., 2019) | http://www.mirbase.org/; RRID:SCR_003152 |
| RBiomirGS V0.2.12 R package | (Zhang and Storey, 2018) | https://github.com/jzhangc/git_RBiomirGS |
| GO Mouse Genome Informatics (MGI) | (Smith and Eppig, 2009) | http://www.informatics.jax.org/; RRID:SCR_006489 |
| R package version 3.6.1 | https://www.r-project.org/; RRID:SCR_001905 | |
| QuantaSoft V1.7.4.0917 | Bio-Rad Laboratories | https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10047467.pdf |
| OriginPro 2015 | OriginLab Corporation | https://www.originlab.com; RRID:SCR_014212 |
| R package version 4.0.2 (for single cell analysis) | https://www.r-project.org/; RRID:SCR_001905 | |
| Seurat 3.2.0 | (Stuart et al., 2019) | https://github.com/satijalab/seurat; RRID:SCR_007322 |
| MAST | (Finak et al., 2015) | https://www.bioconductor.org/packages/release/bioc/html/MAST.html; RRID:SCR_016340 |
| multiMiR | (Ru et al., 2014) | https://www.bioconductor.org/packages/release/bioc/html/multiMiR.html |
| SnapTools 1.4.1 | (Fang et al., 2020) | https://github.com/r3fang/SnapTools; RRID:SCR_018097 |
| SnapATAC | (Fang et al., 2020) | https://github.com/r3fang/SnapATAC |
| Rmagic 2.0.3 | (van Dijk et al., 2018) | https://github.com/KrishnaswamyLab/MAGIC |
| Patchwork 1.0.1 | https://github.com/thomasp85/patchwork; RRID:SCR_000072 | |
| Other | ||
| QX200 Automated Droplet Generator | BioRad | Cat# 1864101 |
| QX200 Droplet Reader | BioRad | Cat# 1864003 |
| Illumina Hiseq 2500 | LC Sciences | N/A |
| ABI 7500 Real-Time PCR | Applied Biosystems | N/A |
| NovaSeq 6000 | Illumina | N/A |
| BD Rhapsody | BD Biosciences | Cat# 633701 |
| ddSEQ Single-Cell Isolator | Bio-Rad | Cat# 12004366 |
| BioAnalyzer | Agilent | Cat# D1000 HS |
| Simplified 5-ion GCR Simulation: Protons at 1000 MeV, 28Si at 600 MeV/n, 4He at 250 MeV/n, 16O at 350 MeV/n, 56Fe at 600 MeV/n, and protons at 250 MeV | Brookhaven National Lab - NSRL | N/A |
| Simulated SPE: Protons at 50MeV to 150MeV | Brookhaven National Lab - NSRL | N/A |
| Gamma: 137Cs source (5 Gy) | Brookhaven National Lab – NSRL | N/A |
| 56Fe Irradiation: 600 MeV/n | Brookhaven National Lab – NSRL | N/A |