KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
Influenza A virus (A/Puerto Rico/8/34/Mount Sinai(H1N1))	This manuscript	NCBI: txid183764
Influenza A virus (A/Vietnam/1203/2004(H5N1))	This manuscript	NCBI: txid284218
Chemicals, Peptides, and Recombinant Proteins
Lipofectamine 2000	Thermo Fisher Scientific	Cat #: 11668-019
Purified Agar	Oxoid	Cat #: LP0028
SuperScript III One-Step RT-PCR System	Thermo Fisher Scientific	Cat #: 12574018
Superscript III Reverse Transcriptase	Thermo Fisher Scientific	Cat #: 18080044
Trypsin from bovine pancreas, TPCK-treated	SIGMA-ALDRICH	Cat #: T1426-500MG
Critical Commercial Assays
E.Z.N.A Gel Extraction Kit (V-spin)	Omega Bio-Tek	Cat #: D2500-01
KAPA Library Quantification Kit - Illumina GA	Roche	Cat #: KK4824
MiSeq Reagent Kit v3	Illumina	Cat #: MS-102-3001
QIAamp Viral RNA Mini Kit (250)	QIAGEN	Cat #: 52906
TruSeq DNA Library Preparation Kit v2, Set A	Illumina	Cat #: RS-122-2001
TruSeq RNA Sample Prep Kit v2 -Set B	Illumina	Cat #: RS-122-2002
Deposited Data
Illumina deep-sequencing raw data	This manuscript	https://data.mendeley.com/datasets/77x6pyfk79/1 https://data.mendeley.com/datasets/ryr859j6pr/1
Experimental Models: Cell Lines
Dog: MDCK cells	ATCC	Cat #: CCL-34; RRID: CVCL_0422
Human: 293T cells	ATCC	Cat #: CRL-3216; RRID: CVCL_0063
Human: A549 cells	ATCC	Cat #: CCL-185; RRID: CVCL_0023
Experimental Models: Organisms/Strains
Mouse: B6.129S7-Rag1tm1Mom/J	Jackson Laboratories	Cat #: 002216; RRID: IMSR_JAX:002216
Mouse: C57BL/6J	Jackson Laboratories	Cat #: 000664; RRID: IMSR_JAX:000664
Mouse: 129S6/SvEv-Stat1tm1Rds	Taconic	Cat #: 2045-F; RRID: IMSR_TAC:2045
Mouse: 129S6/SvEvTac	Taconic	Cat #: 129SVE-F; RRID: IMSR_TAC:129sve
Chicken: Specific Pathogen Free Fertile Eggs	Charles River	Cat #: 10100329
Oligonucleotides
Barcodes used in the viral library	This manuscript	See Table S1
Primers used in the Illumina deep-sequencing analysis	This manuscript	See Table S2
Recombinant DNA
NS1 sequences used in the library	This manuscript	See Table 1
Software and Algorithms
Barcode Generator 2.8	The Comai Lab	http://comailab.genomecenter.ucdavis.edu/index.php/Barcode_generator
Circos 0.69-4	Krzywinski et al., 2009	http://circos.ca/software/download/circos/
FigTree 1.4.4	The Rambaut Lab	http://tree.bio.ed.ac.uk/software/figtree/
Geneious 9.1.5	Geneious	https://www.geneious.com/
Illumina Basespace	Illumina	https://login.illumina.com/platform-services-manager/?rURL=https://basespace.illumina.com&clientId=basespace&clientVars=aHR0cHM6Ly9iYXNlc3BhY2UuaWxsdW1pbmEuY29tL2Rhc2hib2FyZA&redirectMethod=GET#/
MATLAB 9.7	MathWorks	https://www.mathworks.com/products/matlab.html
MEGA7	Kumar et al., 2016	https://www.megasoftware.net/
MeV	GitHub	https://sourceforge.net/projects/mev-tm4/
Prism 8.2.1	Graphpad	https://www.graphpad.com
RStudio 1.2.5001	Rstudio, Inc.	https://rstudio.com
Other
Customs R scripts to analyze specific datasets of this work	This manuscript	https://data.mendeley.com/datasets/ryr859j6pr/1
R package cluster	CRAN	https://cran.r-project.org/web/packages/cluster/
R package DGCA	CRAN	https://cran.r-project.org/web/packages/DGCA/
R package fpc	CRAN	https://cran.r-project.org/web/packages/fpc/
R package ggplot2	CRAN	https://cran.r-project.org/web/packages/ggplot2/
R package gplots	CRAN	https://cran.r-project.org/web/packages/gplots/
R package igraph	CRAN	https://cran.r-project.org/web/packages/igraph/
R package limma	CRAN	https://cran.r-project.org/src/contrib/Archive/limma/
R package MBA	CRAN	https://cran.r-project.org/web/packages/MBA/
R package msa	BIOINF	http://www.bioinf.jku.at/software/msa/
R package RColorBrewer	CRAN	https://cran.r-project.org/web/packages/RColorBrewer/
R package rgl	CRAN	https://cran.r-project.org/web/packages/rgl/
R package seqinr	CRAN	https://cran.r-project.org/web/packages/seqinr/
R package sna	CRAN	https://cran.r-project.org/web/packages/sna/
R package splines	CRAN	https://cran.r-project.org/src/contrib/Archive/splines/
R package xlsx	CRAN	https://cran.r-project.org/web/packages/xlsx/