KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PE Mouse Anti-Mouse CD45.2 | BD Biosciences | Cat#560695; RRID:AB_1727493 |
| PE/Cyanine7 anti-mouse TCR β chain Antibody | BioLegend | Cat#109222; RRID:AB_893627 |
| FITC anti-mouse CD4 Antibody | BioLegend | Cat#100510; RRID:AB_312713 |
| PerCP/Cyanine5.5 anti-mouse CD8a Antibody | BioLegend | Cat#100734; RRID:AB_2075239 |
| Chemicals, peptides, and recombinant proteins | ||
| Chloroform | Sigma-Aldrich | Cat#288306 |
| Methanol | Sigma-Aldrich | Cat#322415 |
| Hexane | Sigma-Aldrich | Cat#296090 |
| Diisopropyl ether | Sigma-Aldrich | Cat#673803 |
| Acetic acid | Sigma-Aldrich | Cat#695092 |
| Benzene | Sigma-Aldrich | Cat#401675 |
| Copper (II) sulfate | Sigma-Aldrich | Cat#451657 |
| Phosphoric acid | Sigma-Aldrich | Cat#345245 |
| TLC non-polar lipid mixture A | Cayman Chemical | Cat#29377 |
| TRIzol reagent | ThermoFisher | Cat#15596026 |
| Glycogen | ThermoFisher | Cat#AM9510 |
| Taqman Fast Advanced Master Mix | ThermoFisher | Cat#4444557 |
| RPMI 1640 media | ThermoFisher | Cat#11875093 |
| Fetal bovine serum | R&D Systems | Cat#S11150 |
| Liberase TL | Roche | Cat#5401020001 |
| Deoxyribonuclease I from bovine pancreas | Sigma-Aldrich | Cat#DN25 |
| CompBeads Anti-Rat and Anti-Hamster Ig κ/Negative Control Compensation Particles | BD Biosciences | Cat#552845 |
| CountBright Absolute Counting Beads | ThermoFisher | Cat#C36950 |
| 4% Paraformaldehyde | Fisher Scientific | Cat#AAJ19943K2 |
| ReadyLyse Lysozyme solution | Biosearch Technologies | Cat#R1810M |
| RNAClean XP Beads | Beckman Coulter | Cat#A63987 |
| Critical commercial assays | ||
| SuperScript VILO cDNA Synthesis Kit | ThermoFisher | Cat#11754050 |
| LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit | ThermoFisher | Cat#L10119 |
| AllPrep DNA/RNA FFPE Kit | Qiagen | Cat#80234 |
| Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus | Illumina | Cat#20040529 |
| IDT for Illumina RNA UD Indexes Set A, Ligation | Illumina | Cat#20040553 |
| NextSeq 500/550 High Output Kit v2.5 (150 Cycles) | Illumina | Cat#20024907 |
| MasterPure Yeast DNA Purification Kit | Biosearch Technologies | Cat#MPY80200 |
| PureLink Genomic DNA Mini Kit | Invitrogen | Cat#K182002 |
| DNeasy PowerSoil Pro Kit | Qiagen | Cat#47014 |
| Quick-16S™ NGS Library Prep Kit | Zymo Research | Cat#D6400 |
| NextSeq 1000/2000 P1 Reagents(600cycles) | Illumina | Cat#20075294 |
| Mouse TSLP Quantikine ELISA Kit | R&D Systems | Cat#MTLP00 |
| EasySep Mouse T cell Isolation Kit | Stemcell Technologies | Cat#19851 |
| NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) | Illumina | Cat#20028401 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat#FC-131-1096 |
| Deposited data | ||
| Generated RNA-sequencing data | Gene Expression Omnibus | GEO: GSE240797 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6 WT | Charles River | Strain #556 |
| Mouse: Germ-free C57BL/6 UPenn | University of Pennsylvania | GF-B6 |
| Mouse: Germ-free Swiss-Webster | University of Pennsylvania | GF-SW |
| Mouse: Germ-free C57BL/6 UNC | University of North Carolina-Chapel Hill | UNC GF-B6 |
| Mouse: C57BL/6 Rag2−/− | Jackson Laboratories | Strain #008449 |
| Mouse: C57BL/6 TCRβ−/− | Jackson Laboratories | Strain #002116 |
| Mouse: C57BL/6 Scd1−/− | Jackson Laboratories | Strain #006201 |
| Oligonucleotides | ||
| Taqman Tslp murine assay | ThermoFisher | Mm01157588_m1 |
| Recombinant DNA | ||
| Control-AAV | University of Pennsylvania Vector Core | AAV8.TBG.PI.eGFP.WPRE.bGH |
| TSLP-AAV | University of Pennsylvania Vector Core | AAV8.TBG.PI.mTSLP.IRES.eGFP.WPRE.bGH |
| Software and algorithms | ||
| Adobe Photoshop 2023 | Adobe | https://www.adobe.com/products/photoshop.html |
| FlowJo Software version 10.10 | BD Biosciences | https://www.flowjo.com/solutions/flowjo |
| R statistical computing environment version 4.2 | R | https://www.r-project.org/ |
| RStudio version 2022.02.1 | Posit | https://posit.co/download/rstudio-desktop/ |
| Kallisto pseudoalignment program | Bray et al.71 | https://pachterlab.github.io/kallisto/ |
| R package: edgeR | Robinson et al.72 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| R package: Limma | Ritchie et al.73 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| R package: gprofiler2 | Kolberg et al.74 | https://cran.r-project.org/web/packages/gprofiler2/index.html |
| R package: msigdbr | Liberzon et al.75 | https://cran.r-project.org/web/packages/msigdbr/index.html |
| R package: clusterprofiler | Wu et al.76 | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| QIIME 2 | Boylen et al.77 | https://qiime2.org/ |
| DADA2 | Callahan et al.78 | https://benjjneb.github.io/dada2/ |
| Greengenes reference database | McDonald et al.79 | https://greengenes.secondgenome.com/ |
| ImageJ 1.52q | NIH | N/A |
| Adobe Illustrator 2023 | Adobe | https://www.adobe.com/products/illustrator.html |
| Biorender | Biorender | https://www.biorender.com/ |
| Other | ||
| Thin-Layer Chromatography plate | Sigma-Aldrich | Cat#100390 |
| TissueTube TT05M XT tissue bags | Covaris | Cat#520140 |
| cryoPREP Automated Dry Pulverizer (110V) | Covaris | Cat#CP02 |
| ViiA7 Real-Time PCR | ThermoFisher | Cat#4453536 |
| LSR Fortessa cell analyzer | BD Biosciences | N/A |
| LMD 7000 Laser Capture Microdissection system | Leica Microsystems | LMD7000 |
| Polyethylene naphthalate LCM slides | Leica Microsystems | Cat#11505158 |
| Qubit 2.0 Fluorometer | ThermoFisher | N/A |
| 2100 Bioanalyzer Instrument | Agilent | N/A |
| NextSeq 550 System | Illumina | N/A |
| NextSeq 1000 System | Illumina | N/A |
| NextSeq 2000 System | Illumina | N/A |
| NovaSeq 6000 System | Illumina | N/A |
| 6″ Sterile Standard Foam Swab w/Polystyrene Handle | Puritan | Cat#25-1506 |
| Blood Agar (TSA with Sheep Blood) Medium | Thermo Scientific | Cat#R01200 |
| Eppendorf Safe-Lock Tubes | Eppendorf | Cat#022600044 |
| PowerBead Tubes, Ceramic 1.4 mm | Qiagen | Cat#13113-50 |
| Keyence VHX-6000 digital microscope system | Keyence | VHX-6000 |
| TapeStation 4200 | Agilent | N/A |