Antibodies |
Bacterial and Virus Strains |
Cowpea mosaic virus |
Dr. Dinesh Kumar, UC Davis |
N/A |
Biological Samples |
|
|
NATtrol Respiratory Validation Panel (RVP) (Qualitative) |
ZeptoMetrix Corporation |
NATRVP-3 |
Chemicals, Peptides, and Recombinant Proteins |
Pyridine |
FISHER SCIENTIFIC |
AC131780500 |
Octanoic acid |
Sigma |
C2875–10ML |
Hexanoic acid |
Sigma |
53745–2.5G |
Decanoic acid |
Sigma |
C1875–100G |
N,N-diethyl-m-toluamide (DEET) |
Fisher Scientific |
AC114571000 |
Tangeretin |
Fisher Scientific |
505943 |
Nobiletin (Hexamethoxyflavone) |
Fisher Scientific |
505360 |
Phthalate |
Sigma |
90677–100ML |
Diethylene glycol |
Sigma |
03128–5ML-F |
Omethoate |
Sigma |
36181–100MG |
Critical Commercial Assays |
The Ovation RNA-Seq System V2 |
NuGEN |
7102–32 |
PowerWater® DNA kit |
Qiagen-Mo Bio |
14900–100-NF |
PowerWater® RNA kit |
Qiagen-Mo Bio |
14700–100-NF |
REPLI-g Single Cell Kit |
Qiagen |
150343; 150345 |
HyperPlus library kit |
Roche-Kapa Biosystems |
KK8514 |
Deposited Data |
Raw sequencing reads for DNA and RNA |
This study |
NCBI Bioproject PRJNA421162 |
Co-assembled contigs for DNA and RNA |
This study |
NCBI Bioproject PRJNA421162 |
Experimental Models: Cell Lines |
Experimental Models: Organisms/Strains |
Oligonucleotides |
Recombinant DNA |
Software and Algorithms |
Moves App |
ProtoGeo Oy |
N/A |
R analysis script |
This study |
Data File 1 |
PAVA |
PMID: 21937731 |
https://www.ncbi.nlm.nih.gov/pubmed/21937731 |
Rstudio |
https://www.rstudio.com |
https://www.rstudio.com |
Bioconductor package |
https://www.bioconductor.org/ |
https://www.bioconductor.org/ |
DESeq2 |
PMID: 25516281 |
https://genomebiology.biomedcentral.com/articles/10.1186/s13059–014-0550–8 |
phyloseq |
PMID: 23630581 |
https://www.ncbi.nlm.nih.gov/pubmed/23630581 |
reshape2 |
https://www.rdocumentation.org/packages/reshape2/versions/1.4.3 |
https://www.rdocumentation.org/packages/reshape2/versions/1.4.3 |
ggplot2 |
https://github.com/hadley/ggplot2-book |
https://github.com/hadley/ggplot2-book |
edgeR |
PMID: 19910308 |
https://www.ncbi.nlm.nih.gov/pubmed/19910308 |
NMF |
PMID: 20598126 |
https://www.ncbi.nlm.nih.gov/pubmed/20598126 |
RcolorBrewer |
https://cran.r-project.org/web/packages/RColorBrewer/index.html |
https://cran.r-project.org/web/packages/RColorBrewer/index.html |
vegan |
https://cran.r-project.org/web/packages/vegan/index.html |
https://cran.r-project.org/web/packages/vegan/index.html |
factoextra |
https://cran.r-project.org/web/packages/factoextra/index.html |
https://cran.r-project.org/web/packages/factoextra/index.html |
glmnet |
PMID: 20808728 |
https://www.ncbi.nlm.nih.gov/pubmed/20808728 |
e1071 |
https://cran.r-project.org/web/packages/e1071/index.html |
https://cran.r-project.org/web/packages/e1071/index.html |
relaimpo |
https://cran.r-project.org/web/packages/relaimpo/index.html |
https://cran.r-project.org/web/packages/relaimpo/index.html |
ade4 |
https://www.jstatsoft.org/article/view/v022i04 |
https://www.jstatsoft.org/article/view/v022i04 |
ViromeScan |
PMID: 29492895 |
https://www.ncbi.nlm.nih.gov/m/pubmed/29492895/ |
PubChem |
PMID: 15879180 |
https://pubchem.ncbi.nlm.nih.gov |
phyloT |
PMID: 27095192 |
https://phylot.biobyte.de |
iTOL |
PMID: 27095192 |
https://itol.embl.de |
megahit |
PMID: 25609793 |
https://github.com/voutcn/megahit |
bbtools |
https://jgi.doe.gov/data-and-tools/bbtools/ |
https://jgi.doe.gov/data-and-tools/bbtools/ |
Bwa-mem |
https://arxiv.org/abs/1303.3997 |
http://bio-bwa.sourceforge.net |
Gephi |
https://www.aaai.org/ocs/index.php/ICWSM/09/paper/view/154 |
https://gephi.org |
XCalibur |
Thermo-Fisher Scientific |
https://www.thermofisher.com/order/catalog/product/OPTON-30487 |
SIMCA |
Umetric |
https://umetrics.com/products/simca |
Other |
ODP2 HP-4B (LC column) |
Shodex |
F009121 |
OPD2 HPG-4A (LC guard column) |
Shodex |
G207063 |
Information and statistics on classified contigs of Rotifer and Apicomplexa |
This Study |
Data File 2 |
MicroPEM Personal Aerosol Exposure Monitor v3.2A |
RTI International |
N/A |
Teflo Air Sampling Filters |
PALL Life Science |
R2P1025 |
Polyethersulfone Membrane Filters |
STERLITECH Corporation |
PES0825100 |
The TSI Mass Flowmeter |
TSI Inc |
Model 4143 D |
Bioanalyzer |
Agilent |
G2939BA |
Illumina HiSeq 4000 platform |
Illumina Inc. |
https://www.illumina.com/systems/sequencing-platforms/hiseq-3000–4000.html |
Molecular Sieve Adsorben Sigma 20304 |
Sigma-Aldrich Corp., St. Louis, MO USA |
https://www.sigmaaldrich.com/catalog/product/supelco/20304?lang=en®ion=US |
Structural database of allergenic proteins (SDAP) |
PMID: 12520022 |
http://fermi.utmb.edu |
Protein Family database (Pfam) |
PMID: 26673716 |
https://pfam.xfam.org |
Gene Ontology database (GO) |
PMID: 10802651 |
http://www.geneontology.org |
Cluster of orthologous groups database (COG) |
PMID: 10592175 |
https://www.ncbi.nlm.nih.gov/COG/ |
Metlin database |
PMID: 16404815 |
https://metlin.scripps.edu/landing_page.php?pgcontent=mainPage |