| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-human CD1a FITC (Clone HI149) | Biolegend | Cat#300104 |
| anti-human CD14 FITC (Clone Tuk4) | LifeTech | Cat#MHCD1401-4 |
| anti-human CD19 FITC (Clone 4G7) | BD | Cat#345776 |
| anti-human CD123 FITC (Clone 6H6) | Biolegend | Cat#306014 |
| anti-human BDCA2 FITC (Clone AC144) | Miltenyi | Cat#130-113-192 |
| anti-human FcER1a FITC (Clone AER-27) | Biolegend | Cat#334608 |
| anti-human CD34 FITC (Clone 581) | Biolegend | Cat#343504 |
| anti-human CD94 FITC (Clone DX22) | Biolegend | Cat#305504 |
| anti-human TCRab FITC (Clone IP26) | Biolegend | Cat#306706 |
| anti-human TCRgd FITC (Clone B1) | Biolegend | Cat#331208 |
| anti-human Eomes FITC (Clone WD1928) | eBioscience | Cat#11-4877-42 |
| anti-human NKG2A (CD159a) APC (Clone Z199) | Beckman Coulter | Cat#60797 |
| anti-human Eomes efluor660 (Clone WD1928) | eBioscience | Cat#50-4877-41 |
| anti-human CD69 AF700 (Clone FN50) | Biolegend | Cat#310992 |
| anti-human CD3 AF700 (Clone UCHT1) | BD | Cat#557943 |
| anti-human CD62L APC-Cy7 (Clone DREG-56) | Biolegend | Cat#304814 |
| anti-human CRTH2 V450 (Clone BM16) | BD | Cat#561661 |
| anti-human CD45 V500 (Clone HI30) | BD | Cat#560777 |
| anti-human CD1a biotin (Clone HI149) | Biolegend | Cat#300112 |
| anti-human CD14 biotin (Clone HCD14) | Biolegend | Cat#325624 |
| anti-human CD19 biotin (Clone HIB19) | Biolegend | Cat#302204 |
| anti-human CD123 biotin (Clone 6H6) | Biolegend | Cat#306004 |
| anti-human BDCA2 biotin (Clone GoH3) | Miltenyi | Cat#130-097-923 |
| anti-human FcER1a biotin (Clone AER-37) | eBioscience | Cat#13-5899-82 |
| anti-human CD34 biotin (Clone 581) | Biolegend | Cat#343524 |
| anti-human CD94 biotin (Clone REA113) | Miltenyi | Cat#130-098-967 |
| anti-human TCRab biotin (Clone IP26) | Biolegend | Cat#306704 |
| anti-human TCRgd biotin (Clone B1) | Biolegend | Cat#331206 |
| Streptavidin BV570 | Biolegend | Cat#405227 |
| anti-human CD90 BV605 (Clone 5E10) | Biolegend | Cat#328128 |
| anti-human CD161 BV605 (Clone HP-3G10) | Biolegend | Cat#339915 |
| anti-human CD45 BV650 (Clone HI30) | Biolegend | Cat#304043 |
| anti-human CD56 BV650 (Clone HCD56) | Biolegend | Cat#318343 |
| anti-human CD56 BV711 (Clone HCD56) | Biolegend | Cat#318336 |
| anti-human CD3 BV785 (Clone OKT3) | Biolegend | Cat#317329 |
| anti-human NKG2A (CD159a) PE (Clone 131411) | R&D | Cat#FAB1059P |
| anti-human ROR-gt PE (Clone AFKJS-9) | eBioscience | Cat#12-6988-82 |
| anti-human HLA-DR PE (Clone L243) | eBioscience | Cat#12-9952-41 |
| anti-human CRTH2 PE-CF594 (Clone BM16) | BD | Cat#563501 |
| anti-human CD161 PE-CF594 (Clone HP-3G10) | Biolegend | Cat#339939 |
| anti-human T-bet PE-CF594 (Clone O4-46) | BD | Cat#562467 |
| anti-human NKp44 PE-Cy5 (Clone Z231) | Beckman Coulter | Cat#A66903 |
| anti-human CD117 PE-Cy5.5 (Clone 95C3) | Beckman Coulter | Cat#A66333 |
| anti-human CD127 PE-Cy7 (Clone R34.34) | Beckman Coulter | Cat#A64618 |
| anti-human CD45 BUV395 (Clone HI30) | BD | Cat#563791 |
| anti-human CD45RA BUV737 (Clone HI100) | BD | Cat#564442 |
| anti-human CD3 BV570 (Clone UTCH1) | Biolegend | Cat#300436 |
| anti-human CD69 BV650 (Clone FN50) | Biolegend | Cat#310934 |
| anti-human CD4 BUV496 (Clone SK3) | BD | Cat#564652 |
| anti-human CD8 BUV805 (Clone SK1) | BD | Cat#612889 |
| Biological samples | ||
| Intestinal biopsies from pediatric IBD and non-IBD patients | Karolinska University Hospital or Sachs’ Children and Youth Hospital | N/A |
| Intestinal specimens from adult IBD and non-IBD patients | Karolinska University Hospital | N/A |
| Peripheral blood from pediatric IBD patients | Karolinska University Hospital | N/A |
| Deposited data | ||
| Count matrix from cell ranger | This paper | GEO Accession Number: GSE169136 |
| R scripts | This paper |
https://github.com/ramvinay/Kokkinou_pIBD https://github.com/jtheorell/Kokkinou_gut_neighbors/ |
| Software and algorithms | ||
| R v.4.1.0 | R Core Team | https://cran.r-project.org/ |
| Cell Ranger v.2.1.1 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software |
| Seurat v.4.1.1 | Butler et al., 201960 | https://github.com/satijalab/seurat/ |
| Harmony v.0.1 | Korsunsky et al., 201961 | https://github.com/immunogenomics/harmony |
| sva v.3.32.1 | Leek et al., 202262 | https://bioconductor.org/packages/release/bioc/html/sva.html |
| Slingshot v.2.2.1 | Street et al., 201863 | https://bioconductor.org/packages/release/bioc/html/slingshot.html |
| WGCNA v.1.70.3 | Langfelder et al., 200823 | https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ |
| SingleCellExperiment | Amezquita et al., 202064 | https://www.bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html |
| DASeq v1.0.0 | Zhao et al., 202138 | https://github.com/KlugerLab/DAseq |
| DepecheR v.1.14.0 | Theorell et al., 201965 | https://www.bioconductor.org/packages/release/bioc/html/DepecheR.html |
| Other | ||
| LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit | Invitrogen | Cat#L34975 |
| LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit | Invitrogen | Cat#L34957 |
| LIVE/DEAD™ Fixable Green Dead Cell Stain Kit | Invitrogen | Cat#L34970 |
| Collagenase II | Sigma-Aldrich | Cat#C6885 |
| DNAse | Sigma-Aldrich | Cat#10104159001 |
| IMDM | Gibco | Cat#12440-053 |
| Foxp3/Transcription Factor Staining Buffer Set | eBioscience | Cat#00-5523-00 |
| Chromium™ Single Cell 3' Library & Gel Bead Kit v2, 16 rxns | 10x Genomics | Cat#PN-120237 |
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