|
Antibodies
|
| anti-mouse CD45 (Clone ID 30-F11) APC-Cy7 |
BD Pharmingen |
Cat# 557659 |
| anti-mouse CD4 (Clone ID RM4-5) BV421 |
BioLegend |
Cat# 100544 |
| anti-mouse CD4 (Clone ID RM4-5) BB700 |
BD horizon |
Cat# 566407 |
| anti-mouse CD4 (Clone ID RM4-5) A700 |
eBioscience |
Cat# 56-0042-82 |
| anti-mouse TCRβ (Clone ID H57-597) A700 |
BioLegend |
Cat# 109224 |
| anti-mouse TCRβ (Clone ID H57-597) BV605 |
BioLegend |
Cat# 109241 |
| anti-mouse CD8a (Clone ID 53-6.7) BV605 |
BioLegend |
Cat# 100744 |
| anti-mouse CD8a (Clone ID 53-6.7) PerCP-Cy5.5 |
eBioscience |
Cat# 45-0081-82 |
| anti-mouse CD19 (Clone ID 6D5) BV605 |
BioLegend |
Cat# 115540 |
| anti-mouse CD19 (Clone ID 1D3) PerCP-Cy5.5 |
eBioscience |
Cat# 45-0193-82 |
| anti-mouse IL-17A (Clone ID eBio17B7) PE-Cy7 |
eBioscience |
Cat# 25-7177-82 |
| anti-mouse IL-17A (Clone ID TC11-18H10.1) A488 |
BioLegend |
Cat# 506910 |
| anti-mouse IFN-γ (Clone ID XMG1.2) BV421 |
BioLegend |
Cat# 505830 |
| anti-mouse RORγt (Clone ID B2D) APC |
eBioscience |
Cat# 17-6981-82 |
| anti-mouse RORγt (Clone ID B2D) PE |
eBioscience |
Cat# 12-6981-82 |
| anti-mouse FoxP3 (Clone ID FJK-16s) FITC |
eBioscience |
Cat# 11-5773-82 |
| anti-mouse FoxP3 (Clone ID FJK-16s) PE |
eBioscience |
Cat# 12-5773-82 |
| anti-mouse FoxP3 (Clone ID FJK-16s) APC |
eBioscience |
Cat# 17-5773-82 |
| anti-mouse CD62L (Clone ID MEL-14) FITC |
eBioscience |
Cat# 11-0621-85 |
| anti-mouse CD44 (Clone ID IM7) APC |
eBioscience |
Cat# 17-0441-83 |
| anti-mouse CD25 (Clone ID PC61.5) PE-Cy7 |
eBioscience |
Cat# 25-0251-82 |
| anti-mouse CD45RB (Clone ID 16A) PE |
BD Pharmingen |
Cat# 553101 |
| IL-17A-blocking antibody (Clone ID 50104) |
R&D systems |
Cat# MAB421 |
| Isotype control antibody (Clone ID 54447) |
R&D systems |
Cat# MAB006 |
| Purified anti-mouse CD3e (Clone ID 145-2V11) |
Tonbo Biosciences |
Cat# 70-0031-M001 |
|
Bacterial and virus strains
|
|
Citrobacter rodentium (Strain: DBS100) |
ATCC |
Cat# 51459 |
|
Chemicals, peptides, and recombinant proteins
|
| Poly(I:C) potassium salt |
Sigma Aldrich |
Cat# P9582 |
| Poly(I:C) sodium salt |
Sigma Aldrich |
Cat# P1530 |
| Liberase-TM research grade |
Millipore Sigma |
Cat# 5401127011 |
| DNase I |
Millipore Sigma |
Cat# 10104159001 |
| PMA |
Sigma Aldrich |
Cat# P1585 |
| Ionomycin |
Sigma Aldrich |
Cat# 10634 |
| Golgiplug |
BD Biosciences |
Cat# 555029 |
| Metronidazole |
Sigma Aldrich |
Cat# 1442009 |
| MacConkey Agar |
Fisher Scientific |
Cat# B11387
|
| DSS |
TdB labs |
Cat# 9011-18-1 |
| DTT |
Millipore Sigma |
Cat# 10708984001 |
| EDTA 0.5M pH 8.0 |
Corning |
Cat# 46-034-CI |
| FBS |
Hyclone |
Cat# SH30910.03 |
| FBS |
Corning |
Cat# 35-010-CV |
| Percoll |
Sigma Aldrich |
Cat# GE17-0891-01 |
| Bouin’s fixative |
Electron Microscopy Science |
Cat# 15990-01 |
| TCL buffer |
Qiagen |
Cat# 1031576 |
|
Critical commercial assays
|
| Mouse IL-17A enhanced sensitivity flex set |
BD Biosciences |
Cat# 562261 |
| Mouse IFN-γ enhanced sensitivity flex set |
BD Biosciences |
Cat# 562233 |
| Mouse TNF enhanced sensitivity flex set |
BD Biosciences |
Cat# 562336 |
| Mouse IL-6 enhanced sensitivity flex set |
BD Biosciences |
Cat# 562236 |
| Hooke Kit MOG35–55/CFA Emulsion PTX |
Hooke Laboratories |
Cat# EK-2110 |
| RNeasy micro kit |
Qiagen |
Cat# 74004 |
| iScript reverse transcription kit |
Bio-Rad |
Cat# 1708891 |
| iTaq SYBR green mix |
Bio-Rad |
Cat# 1725125 |
| Nextera XT DNA Library preparation kit |
Illumina |
Cat# FC-131-1096 |
| Illumina Tagment DNA Enzyme and Buffer Kit |
Illumina |
Cat# 15027865, Cat# 15027866 |
| MinElute PCR Purification Kit |
Qiagen |
Cat# 28004 |
| PCR purification kit, AMPure XP |
Beckman Coulter |
Cat# A63880 |
| eBioscience Foxp3/Transcription Factor Staining Buffer Kit |
Thermo Fisher Scientific |
Cat# 00-5523-00 |
| LIVE/DEAD Fixable Aqua Dead Cell stain kit |
Thermo Fisher Scientific |
Cat# L34966
|
|
Deposited data
|
| 16s sequencing |
This paper |
Accession# PRJNA694443 |
| ATAC-seq |
This paper |
Accession# GSE165692
|
| RNA-seq |
This paper |
Accession# GSE165693
|
|
Experimental models: Organisms/strains
|
| C57BL/6 specific pathogen-free mice |
Taconic |
Cat# B6 (C57BL/6NTac) |
| C57BL/6 Germ-free mice |
Charles River (maintained in GF isolators at Harvard Medical School) |
Cat# C57BL/6NCrl |
| RAG1-deficient mice |
Jackson Laboratory |
Cat# 002216 |
| CD45.1 B6.SJL congenic mice |
Taconic |
Cat# 4007 (B6.SJL-Ptprca/BoyAiTac) |
| IL-17A-GFP reporter mice |
Jackson Laboratory |
Cat# 018472 |
|
Oligonucleotides
|
| 16S rRNA sequencing V3 and V4 amplicon primers Forward: 5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG-3′, Reverse: 5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC-3′ |
Klindworth et al., 2013
|
N/A |
| 16S Universal primers Forward: 5’-ACTCCTACGGGAGGCAGCAGT-3’, Reverse: 5’-ATTACCGCGGCTGCTGGC-3’ |
This paper |
N/A |
| espB primers Forward: 5’-ATGCCGCAGATGAGACAGTTG-3’, Reverse: 5’-CGTCAGCAGCTTTTCAGCTA-3’ |
Sagaidak et al., 2016
|
N/A |
| Mouse Gapdh qPCR primers Forward: 5’-CATCACTGCCACCCAGAAGACTG-3’, Reverse: 5’-ATGCCAGTGAGCTTCCCGTTCAG-3’ |
Origene |
Cat# MP205604
|
| Mouse Brd4 qPCR primers Forward: 5’-GCCATCTACACTACGAGAGTTGG-3’, Reverse: 5’-ATTCGCTGGTGCTCTCCGACTC-3’ |
Origene |
Cat# MP201449 |
| Mouse Il6ra qPCR primers Forward: 5’-TGCAGTTCCAGCTTCGATACCG-3’, Reverse: 5’-TGCTTCACTCCTCGCAAGGCAT-3’ |
Origene |
Cat# MP206799 |
| Mouse Map4k2 qPCR primers Forward: 5’-GGCTACTCTGAAGCAACAGGAG-3’, Reverse: 5’-GCAGCCATTGAAGACCTTGGAG-3’ |
Origene |
Cat# MP208352 |
| Mouse Smarcd2 qPCR primers Forward: 5’-CTTTCGAGAGGAAGCTGGACCA-3’, Reverse: 5’-GTTCCCGCATTATCTCCATCCG-3’ |
Origene |
Cat# MP220661
|
| Mouse Zbtb7a qPCR primers Forward: 5’-TGCGAGAAGGTGATTCAGGGTG-3’, Reverse: 5’-TTCCGCATGTGCACCTTCAGCT-3’ |
Origene |
Cat# MP218697
|
|
Software and algorithms
|
| EthoVision XT 14 |
Noldus |
https://www.noldus.com
|
| Multiplot studio v1.5.20 |
Genepattern Archive |
http://gparc.org
|
| R v4.0.5 |
R foundation for statistical computing |
https://cran.r-project.org
|
| FlowJo 10 |
BD |
https://www.flowjo.com
|
| Prism 9 |
GraphPad |
https://www.graphpad.com
|
| QIIME2 v2020.02 |
Bolyen et al., 2019
|
https://qiime2.org
|
| Dada2 |
Callahan et al., 2016
|
https://benjjneb.github.io/dada2
|
| NGmerge |
Gaspar, 2018a
|
https://github.com/jsh58/NGmerge
|
| Bowtie2 v2.3.4.3 |
Langmead and Salzberg, 2012
|
http://bowtie-bio.sourceforge.net/bowtie2/
|
| Picard v2.8.0 |
N/A |
https://broadinstitute.github.io/picard/
|
| removeChrom.py |
N/A |
https://github.com/harvardinformatics/ATAC-seq/blob/master/atacseq/removeChrom.py
|
| Samtools v1.9 |
N/A |
http://www.htslib.org
|
| MACS peak caller v2.1.1.20160309 |
Gaspar, 2018b
|
https://pypi.org/project/MACS2/2.1.1.20160309/
|
| ChIPseeker v1.24.0 |
N/A |
https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
|
| Deeptools2 |
Ramírez et al., 2016
|
https://github.com/deeptools/deepTools
|
| clusterProfiler v3.16.0 |
Yu et al., 2012
|
https://guangchuangyu.github.io/software/clusterProfiler/
|
