KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-mouse CD4 BV711 | Biolegend | Cat#100550 |
| Anti-mouse CD45.1 A700 | Biolegend | Cat#110724 |
| Anti-mouse CD45.2 PE | Biolegend | Cat#109807 |
| Anti-mouse CD25 APC | Biolegend | Cat#102012 |
| Anti-mouse CD62L APC-Cy7 | Biolegend | Cat#104428 |
| Anti-mouse CD44 BV605 | Biolegend | Cat#103047 |
| Anti-mouse TCR Va2 APC-Cy7 | Biolegend | Cat#127818 |
| Anti-mouse CD25 PerCP-Cy5.5 | Biolegend | Cat#102030 |
| Anti-mouse CD44 AF430 | Biolegend | Cat#103047 |
| Anti-mouse Thy1.1 PECy7 | Biolegend | Cat#105326 |
| Goat IgG FITC isotype control | Abeam | Cat#37374 |
| Goat anti-human IgA Dylight 650 | Abeam | Cat#98556 |
| Goat anti-human IgG PE | Abeam | Cat#98596 |
| Cell trace violet cell proliferation kit | Invitrogen | Cat#34557 |
| ELISA Goat anti-human kappa IgA | Southern Biotech | Cat# SB 2061-01 |
| ELISA IgA standard | Southern Biotech | Cat# SB 0155K-01 |
| ELISA HRP anti-human IgA | Jackson ImmunoResearch | Cat# 109-035-011 |
| Biological Samples | ||
| Human stool in St. Louis: control, IBS-D, IBD, RA | Collected for this paper | https://research.wustl.edu/core-facilities/biobank-core-digestive-disease-research-core-center/ |
| Human stool in Baltimore, Celiac sprue | Collected by Alessio Fasano | N/A |
| Human stool in Rochester: control and IBS-D | Collected by Purna Kashyap | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Ovalbumin | Sigma | Cat# A5503 |
| N-acetyl-cysteine | Sigma | Cat# A7250 |
| DAPI | Sigma | Cat# D9542 |
| Cholera toxin | Sigma | Cat# C8052 |
| Lysine fixable tetramethylrhodamine labeled 10 kd dextran | Invitrogen | Cat# D1817 |
| Atropine chloride | Sigma | Cat# A0132 |
| Tropicamide | Sigma | Cat# T9778 |
| LPS | Sigma | Cat# L2630 |
| Murine EGF | Shenandoah | Cat# 200–53AF |
| Murine EGFRi (Tryphostin AG 1478) | Sigma | Cat# T4182 |
| Critical Commercial Assays | ||
| SMARTer Stranded Total RNA Sample Prep Kit - Hi Mammalian | Takara | www.takara.com |
| Deposited Data | ||
| Raw and analyzed data (16s rRNA sequencing and RNA seq) | This paper | ENA Accession # PRJEB40130 |
| Experimental Models: Organisms/Strains | ||
| Mouse; C56 BL/6J Foxp3IRES-GFP | Jackson | Cat# 6769 |
| Mouse; OTII | Jackson | Cat# 4149 |
| Mouse; Rag1−/− | Jackson | Cat# 2216 |
| Mouse; C57BL/6J gnotobiotic | Author’s facility | N/A |
| Oligonucleotides | ||
| 16s primer: F-5′-GGTGAATACGTTCCCGG-3′ and R-5′-TACGGCTACCTTGTTACGACTT-3′ | Kostic et al.65 | IDT DNA |
| Software and Algorithms | ||
| UPARSE | Edgar66 | https://www.drive5.com/usearch/manual/uparseotu_algo.html |
| Seqmatch RDP v2.6 | Wang et al.67 | https://rdp.erne.msu.edu/ |
| Phyloseq v1.19.1 | McMurdie and Holmes68 | https://cran.r-project.org/web/packages/gbm/gbm.pdf |
| Vegan | Oksanen et al.69 | https://cran.r-project.org/web/packages/vegan/index.html |
| DESeq2 v1.24 | Love et al.70 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| GBM v2.1.5 | Greenwell et al.71 | https://cran.r-project.org/web/packages/gbm/gbm.pdf |
| pROC v1.10.0 | Robin et al.72 | https://cran.r-project.org/web/packages/pROC/pROC.pdf |
| STAR v2.0.4b | Dobin et al.73 | https://github.com/alexdobin/STAR |
| Sailfish v0.6.3 | Patro et al.74 | http://www.cs.cmu.edu/~ckingsf/software/sailfish/ |
| RSeQC v2.3 | Wang et al.75 | http://rseqc.sourceforge.net/ |
| EdgeR | Robinson et al.,76 McCarthy et al.77 |
https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| GAGE | Luo et al.,91 | https://bioconductor.org/packages/release/bioc/html/gage.html |
| Pathview | Luo and Brouwer78 | https://www.bioconductor.org/packages/release/bioc/vignettes/pathview/inst/doc/pathview.pdf |
| Prism v8 | GraphPad | https://www.graphpad.com/ |
| R v3.6 | The R Foundation | https://www.r-project.org/ |
| QIIME v1.9.1 | Caporaso et al.79 | http://qiime.org |
| Limma | Ritchie et al.80 | https://bioconductor.org/packages/release/bioc/html/limma.html |