| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-human CD3 (clone OKT3) BV785 | BioLegend | Cat# 317329 |
| Anti-human CD3 (clone UCHT1) AF700 | BioLegend | Cat# 300423 |
| Anti-human CD3 (clone UCHT1) PerCP | BioLegend | Cat# 300427 |
| Anti-human Vδ2 (clone B6) BV711 | BioLegend | Cat# 331411 |
| Anti-human CD4 (clone OKT4) BV650 | BioLegend | Cat# 317435 |
| Anti-human CD4 (clone SK3) BUV805 | BD Biosciences | Cat# 612888 |
| Anti-human CD4 (clone RPA-T4) PerCP | BioLegend | Cat# 300527 |
| Anti-human Vα7.2 (clone 3C10) BV605 | BioLegend | Cat# 351719 |
| Anti-human CD45RA (clone HI100) BV785 | BioLegend | Cat# 304139 |
| Anti-human CD103 (clone Ber-ACT8) BV421 | BioLegend | Cat# 350213 |
| Anti-human CD103 (clone Ber-ACT8) APC-Cy7 | BioLegend | Cat# 350227 |
| Anti-human CD103 (clone Ber-ACT8) PE | BioLegend | Cat# 350205 |
| Anti-human γδTCR (clone 11F2) FITC | Miltenyi Biotec | Cat# 130-114-029 |
| Anti-human γδTCR (clone 11F2) VioBlue | Miltenyi Biotec | Cat# 130-113-507 |
| Anti-human γδTCR (clone 5A6.E9) PE | Thermo Fisher Scientific | Cat# MHGD04 |
| Anti-human β7-integrin (clone FIB504) PerCP-Cy5.5 | BioLegend | Cat# 321219 |
| Anti-human CD18 (clone L130) BUV563 | BD Biosciences | Cat# 749441 |
| Anti-human CD18 (clone 7E4) PE | Beckman Coulter | Cat# IM157OU |
| Anti-human CD45 (clone HI30) FITC | BioLegend | Cat# 304038 |
| Anti-human CD69 (clone FN50) PE-Dazzle | BioLegend | Cat# 310941 |
| Anti-human CD69 (clone FN50) BUV395 | BD Biosciences | Cat# 564364 |
| Anti-human CCR7 (clone G043H7) PE Dazzle | BioLegend | Cat# 353235 |
| Anti-human CCR9 (clone L053E8) PE-Cy7 | BioLegend | Cat# 358909 |
| Anti-human CD8 (clone SK1) AF700 | BioLegend | Cat# 344723 |
| Anti-human CD8 (clone SK1) FITC | BioLegend | Cat# 344704 |
| Anti-human CD8 (clone RPA-T8) AF532 | Thermo Fisher Scientific | Cat# 58-0088-42 |
| Anti-human CD161 (clone 191B8) APC | Miltenyi Biotec | Cat# 130-113-591 |
| Anti-human CD161 (clone 191B8) FITC | Miltenyi Biotec | Cat# 130-113-592 |
| Anti-human CD161 (clone 191B8) PE | Miltenyi Biotec | Cat# 130-092-677 |
| Anti-human HLA-A3 (clone GAP.A3) PE | Thermo Fisher Scientific | Cat# 12-5754-41 |
| Anti-human HLA-A2 (clone BB7.2) PE | BioLegend | Cat# 343306 |
| Anti-human CD127 (clone A019D5) BV650 | BioLegend | Cat# 351325 |
| Anti-human CD127 (clone REA614) PE | Miltenyi Biotec | Cat# 130-113-976 |
| Anti-human CD7 (clone M-T701) BB700 | BD Biosciences | Cat# 566489 |
| Anti-human KLRG1 (clone REA261) VioBlue | Miltenyi Biotec | Cat# 130-123-526 |
| Anti-human KLRG1 (clone SA231A2) PE | BioLegend | Cat# 367711 |
| Anti-human CCL4 (clone D21-1351) BV421 | BD Biosciences | Cat# 562900 |
| Anti-human Ki-67 (clone B56) BV480 | BD Biosciences | Cat# 566172 |
| Anti-human Granzyme B (clone GB11) BV510 | BD Biosciences | Cat# 563388 |
| Anti-human TNF-α (clone OKT3) BV650 | BioLegend | Cat# 502935 |
| Anti-human IL-17A (clone BL168) BV711 | BioLegend | Cat# 512327 |
| Anti-human IFN-γ (clone B27) BV750 | BD Biosciences | Cat# 566357 |
| Anti-human IL-2 (clone MQ1-17H12) PE-Dazzle | BioLegend | Cat# 500343 |
| Anti-human Granzyme K (clone GM26E7) PE-Cy7 | BioLegend | Cat# 370515 |
| Anti-human Granzyme K (clone GM26E7) PE | BioLegend | Cat# 370511 |
| Anti-human IL-10 (clone JES3-9D7) APC | BioLegend | Cat# 501409 |
| Anti-human pan Cytokeratin (clone C-11) FITC | GeneTex | Cat# GTX11212 |
| Anti-human Histone H3 (clone 17H2L9) AF488 | Invitogen | Cat# MA702023 |
| Near-IR Live-Dead amine-reactive dye | Thermo Fisher Scientific | Cat# L10119 |
| Zombie Yellow Fixable Viability dye | BioLegend | Cat# 423103 |
| Biological samples | ||
| Leukocyte cones | NHS Blood and Transplant | https://www.nhsbt.nhs.uk |
| Intestinal biopsies (intestinal transplant recipients) | TGU Biobank | http://www.expmedndm.ox.ac.uk/tgu/tgu/home |
| Peripheral blood (intestinal transplant recipients) | TGU Biobank | As above |
| Intestinal biopsies (unaffected control subjects) | TGU Biobank | As above |
| Peripheral blood (unaffected control subjects) | TGU Biobank | As above |
| Chemicals, peptides, and recombinant proteins | ||
| DNase I | Roche/ Merck | Cat# 11284932001 |
| Percoll | GE Healthcare/ Merck | Cat# GE17-0891-01 |
| LymphoPrep | Axis Shield | Cat# 07851 |
| Cytofix/Cytoperm kit | BD Biosciences | Cat# 554714 |
| Cytofix | BD Biosciences | Cat# 554655 |
| DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) | Thermo Fisher Scientific | Cat# D1306 |
| Brillian Stain Buffer Plus | BD Biosciences | Cat# 566385 |
| Critical commercial assays | ||
| Cell Activation cocktail (without Brefeldin A) | Biolegend | Cat# 423301 |
| Brefeldin A | Biolegend | Cat# 420601 |
| Monensin | Biolegend | Cat# 420701 |
| Chromium Single Cell 5′ Library & Gel Bead Kit | 10x Genomics | Cat# PN-1000014 |
| Chromium Single Cell 5′ Library Construction Kit | 10x Genomics | Cat# PN-1000020 |
| Chromium Single Cell V(D)J Enrichment Kit, Human T Cell | 10x Genomics | Cat# PN-1000005 |
| Chromium Single Cell A Chip Kit | 10x Genomics | Cat# PN-1000009 |
| Deposited data | ||
| scRNA-seq (10x genomics) – 1 transplant donor - intestinal tissue resident memory T cells | This paper | GEO: GSE162687 |
| scRNA-seq (Smartseq2) – 2 transplant donors – intestinal tissue resident memory T cells (CD103-/+) | This paper | GEO: GSE162687 |
| scRNA-seq of ileal immune cells | Martin et al., 2019 | https://scdissector.org/martin/ |
| scRNA-seq of murine intestinal tissue resident memory T cells post-LCMV infection | Kurd et al., 2020 | https://immunology.sciencemag.org/content/5/47/eaaz6894 |
| scRNA-seq of colonic CD8+ T cells | Corridoni et al., 2020 | GEO: GSE148837 / GSE148505 |
| Software and algorithms | ||
| Prism Version 8 | GraphPad software | https://www.graphpad.com |
| ZellExplorer | Zellkraftwerk GmbH | http://www.zellkraftwerk.com/products/ |
| FlowJo v9.9.5 & v10.6.1 | FlowJo LLC | https://www.flowjo.com/ |
| Cell Ranger v2.2.0 | 10x Genomics | https://www.10xgenomics.com |
| Seurat v2.3.4 | (Butler et al., 2018); Stuart et al., 2019 | https://satijalab.org/seurat/ |
| Trimmomatic | Bolger et al., 2014 | http://www.usadellab.org/ |
| STAR v2.5.3a | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| Samtools v1.6 | Li et al., 2009 | https://github.com/samtools/samtools |
| featureCounts v1.6.0 | Liao et al., 2014 | http://subread.sourceforge.net |
| Scater v1.10.1 | McCarthy et al., 2017 | https://www.bioconductor.org/packages/release/bioc/html/scater.html |
| Scran v1.12.1 | Lun et al., 2016 | https://bioconductor.org/packages/release/bioc/html/scran.html |
| M3Drop v3.10.4 | Andrews et al., 2019 | https://www.bioconductor.org/packages/release/bioc/html/M3Drop.html |
| SC3 v1.12.0 | Kiselev et al., 2017 | https://bioconductor.org/packages/release/bioc/html/SC3.html |
| DEsingle v1.2.1 | Miao et al., 2018 | https://bioconductor.org/packages/release/bioc/html/DEsingle.html |
| DAVID web tools | Huang et al., 2009 | https://david.ncifcrf.gov/ |
| Gene Set Enrichment Analysis v4.0.3 | Subramanian et al., 2005 | https://www.gsea-msigdb.org/gsea/ |
| Other | ||
| Zellsafe Tissue chips | Zellkraftwerk GmbH | Cat# 28050606/02-010 |
| gentleMACS C Tubes | Miltenyi | Cat# 130-093-237 |
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