Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-human ST6GALNAC1 | Sigma | Cat# HPA014975; RRID: AB 1857529 |
| Rabbit monoclonal recombinant anti-human MUC2 | Abcam | Cat# ab133555 |
| Rabbit monoclonal anti-HSP90 | Ceii Signaling Technology | Cat# 4877; RRID: AB 2233307 |
| Mouse monoclonal anti-human Sialyl Tn (S-Tn) [BRST3, B72.3] | BioLegend | Cat# 915206; RRID: AB 2616965 |
| Goat polyclonal anti-human EGFR | R&D | Cat# AF231; RRID: AB 355220 |
| Rabbit monoclonal anti-HA-tag | Ceii Signaling Technology | Cat# 3724; RRID: AB 1549585 |
| Rabbit monoclonal anti-GAPDH | Ceii Signaling Technology | Cat# 2118; RRID: AB 561053 |
| Rabbit polyclonal anti-H3K27ac | Abcam | Cat# ab4729; RRID: AB 2118291 |
| Rabbit monoclonal anti-H3K9ac | Ceii Signaling Technology | Cat# 9649; RRID: AB 823528 |
| Rabbit monoclonal anti-histone H3 | Ceii Signaling Technology | Cat# 4499; RRID: AB 10544537 |
| Mouse monoclonal anti-MUC2 | Santa Cruz Biotechnology | Cat# sc-515032; RRID: AB 2815005 |
| Mouse monoclonal anti-HA epitope tag | Covance | Cat# MMS-101P; RRID: AB 2314672 |
| Rabbit monoclonal recombinant anti-GM130 | Abcam | Cat# ab52649; RRID: AB 880266 |
| Rabbit polyclonal anti-MUC2 | GeneTex | Cat# GTX100664; RRID:AB 1950958 |
| Mouse monoclonal anti-Sialyl Tn | Abcam | Cat# ab115957; RRID: AB 10901541 |
| Rabbit polyclonal anti-CD45 | Abcam | Cat# ab10558; RRID: AB 442810 |
| Rabbit polyclonal anti-REG3G | Abgent | Cat# AP5606c; RRID: AB 10817069 |
| Goat polyclonal anti-rabbit IgG (H+L) highly crossadsorbed Alexa Fluor Plus 647 | Thermo Fisher Scientific | Cat# A32733; RRID: AB 2633282 |
| Goat polyclonal anti-mouse IgG (H+L) highly crossadsorbed Alexa Fluor Plus 647 | Thermo Fisher Scientific | Cat# A32728; RRID: AB 2633277 |
| Goat polyclonal anti-rabbit IgG (H+L) highly crossadsorbed Alexa Fluor Plus 555 | Thermo Fisher Scientific | Cat# A32732; RRID: AB 2633281 |
| Goat recombinant polyclonal anti-mouse IgG (H+L) Superclonal™ Alexa Fluor 555 | Thermo Fisher Scientific | Cat# A28180; RRID: AB 2536164 |
| Goat recombinant polyclonal anti-rabbit IgG (H+L) Superclonal™ Alexa Fluor 488 | Thermo Fisher Scientific | Cat# A27034; RRID: AB 2536097 |
| Goat polyclonal anti-mouse IgG (H+L) highly crossadsorbed Alexa Fluor Plus 488 | Thermo Fisher Scientific | Cat# A32723; RRID: AB 2633275 |
| Mouse monoclonal Ultra-LEAF™ purified anti-human CD3 | BioLegend | Cat# 300334; RRID: AB 2616670 |
| Mouse monoclonal LEAF™ purified anti-human CD28 | BioLegend | Cat# 302914; RRID: AB 314316 |
| Human IgG recombinant monoclonal human EGFR (Research Grade Cetuximab Biosimilar) Alexa Fluor® 488-conjugated | R&D | Cat# FAB9577G-100 |
| Mouse anti-mouse-IgG-control-human | Santa Cruz Biotechnology | Cat# sc-2025; RRID: AB 737182 |
| Mouse monoclonal FITC anti-human CD57 | BioLegend | Cat# 322306; RRID: AB 535992 |
| Mouse monoclonal Brilliant Violet 421™ anti-human CD197 (CCR7) | BioLegend | Cat# 353208; RRID: AB 11203894 |
| Mouse monoclonal PerCP/Cyanine5.5 anti-human CD4 | BioLegend | Cat# 344608; RRID: AB 1953236 |
| Mouse monoclonal PE/Cyanine7 anti-human CD45RA | BioLegend | Cat# 304126; RRID: AB 10708879 |
| Armenian hamster monoclonal APC antimouse/rat/human CD27 | BioLegend | Cat# 124212; RRID: AB 2073425 |
| Mouse monoclonal Brilliant Violet 605™ anti-human CD8a | BioLegend | Cat# 301040; RRID: AB 2563185 |
| Mouse monoclonal PE anti-human CD28 | BioLegend | Cat# 302940; RRID: AB 2564147 |
| Mouse monoclonal Brilliant Violet 605™ anti-human CD3 | BioLegend | Cat# 317321; RRID: AB 11126166 |
| Mouse monoclonal Alexa Fluor® 488 antimouse/rat/human FOXP3 | BioLegend | Cat# 320012; RRID: AB 439748 |
| Mouse monoclonal PE anti-human CD25 | BioLegend | Cat# 302606; RRID: AB 314276 |
| Mouse monoclonal APC anti-human CD127 (IL-7Ra) | BioLegend | Cat# 351316; RRID: AB 10900804 |
| Mouse monoclonal PE/Cyanine7 anti-human CD194 (CCR4) | BioLegend | Cat# 359410; RRID: AB 2562431 |
| Mouse monoclonal Pacific Blue™ anti-human CD45RO | BioLegend | Cat# 304216; RRID: AB 493659 |
| Mouse monoclonal PE anti-human CD24 | BioLegend | Cat# 311106; RRID: AB 314855 |
| Mouse BV786 anti-Human IgM | BD Biosciences | Cat# 740998; RRID: AB 2740621 |
| Mouse monoclonal PE-Cy™5 anti-human CD20 | BD Biosciences | Cat# 561761; RRID: AB 10898182 |
| Mouse monoclonal FITC anti-human CD19 | BD Biosciences | Cat# 555412; RRID: AB 395812 |
| Mouse monoclonal PerCP anti-human CD27 | BioLegend | Cat# 302817; RRID: AB 893294 |
| Mouse monoclonal APC anti-human CD38 | BioLegend | Cat# 356606; RRID: AB 2561902 |
| Mouse monoclonal Brilliant Violet 421™ anti-human CD3 | BioLegend | Cat# 344834; RRID: AB 2565675 |
| Mouse monoclonal Brilliant Violet 510™ anti-human IgD | BioLegend | Cat# 348220; RRID: AB 2561945 |
| Mouse monoclonal PE anti-human CD56 (NCAM) | BioLegend | Cat# 362507; RRID: AB 2563924 |
| Mouse monoclonal APC anti-human CD16 | BioLegend | Cat# 302011; RRID: AB 314211 |
| Mouse monoclonal FITC eBioscience™ anti-human CD14 | Thermo Fisher Scientific | Cat# 11–0149-42; RRID: AB 10597597 |
| Mouse monoclonal Brilliant Violet 421™ anti-human HLA-DR | BioLegend | Cat# 307636; RRID: AB 2561831 |
| Mouse monoclonal PE/Cyanine7 anti-human CD11c | BioLegend | Cat# 371507; RRID: AB 2650779 |
| Mouse monoclonal PerCP anti-human CD19 | BioLegend | Cat# 302228; RRID: AB 893272 |
| Rat monoclonal Brilliant Violet 605™ anti-mouse/human CD44 | BioLegend | Cat# 103047; RRID: AB 2562451 |
| Mouse monoclonal Alexa Fluor® 700 anti-human CD3 | BioLegend | Cat# 344821; RRID: AB 2563419 |
| Mouse monoclonal PerCP anti-human CD8a | BioLegend | Cat# 300922; RRID: AB 1575072 |
| Mouse monoclonal APC anti-human CD4 | BioLegend | Cat# 300552; RRID: AB 2564153 |
| Mouse monoclonal Brilliant Violet 510™ anti-human CD183 (CXCR3) | BioLegend | Cat# 353725; RRID: AB 2562066 |
| Mouse monoclonal Brilliant Violet 421™ anti-human CD184 (CXCR4) | BioLegend | Cat# 306517; RRID: AB 10901163 |
| Mouse monoclonal FITC anti-human CD196 (CCR6) | BioLegend | Cat# 353411; RRID: AB 10915473 |
| Mouse monoclonal PE/Cyanine7 anti-human CD194 (CCR4) | BioLegend | Cat# 359409; RRID: AB 2562430 |
| Armenian hamster monoclonal PE anti-human CCR10 | BioLegend | Cat# 341503; RRID: AB 1595542 |
| Mouse monoclonal FITC anti-human CD8a | BioLegend | Cat# 300906; RRID: AB 314110 |
| Mouse monoclonal APC anti-human CD69 | BioLegend | Cat# 310910; RRID: AB 314845 |
| Rat monoclonal Brilliant Violet 711 ™ anti-mouse CD45 | BioLegend | Cat# 103147; RRID: AB 2564383 |
| Armenian hamster monoclonal FITC anti-mouse TCR p chain | BioLegend | Cat# 109206; RRID: AB 313429 |
| Rat monoclonal PerCP/Cyanine5.5 anti-mouse CD4 | BioLegend | Cat# 100434; RRID: AB 893324 |
| Armenian hamster monoclonal Alexa Fluor® 647 antimouse TCR y/6 | BioLegend | Cat# 118133; RRID: AB 2566406 |
| Syrian hamster monoclonal Alexa Fluor® 700 antimouse CD3e | Biolegend | Cat# 152316; RRID: AB 2632713 |
| Rat monoclonal PE anti-mouse CD8a | BD Biosciences | Cat# 553033; RRID: AB 394571 |
| Mouse monoclonal PE-Cyanine7 eBioscience™ antihuman CD8b | Thermo Fisher Scientific | Cat# 25–5273-41; RRID: AB 11217487 |
| Rat monoclonal Brilliant Violet 510™ anti-mouse/human CD45R/B220 | BioLegend | Cat# 103248; RRID: AB 2561394 |
| Rat monoclonal FITC anti-mouse CD8a | BioLegend | Cat# 100706; RRID: AB 312745 |
| Rat monoclonal PerCP anti-mouse/human CD44 | BioLegend | Cat# 103035; RRID: AB 10639933 |
| Rat monoclonal APC anti-mouse CD62L | BioLegend | Cat# 104412; RRID: AB 313099 |
| Rat monoclonal PE anti-mouse CD4 | BioLegend | Cat# 100407; RRID: AB 312692 |
| Mouse monoclonal PE-Cy™7 anti-mouse NK-1.1 | BD Biosciences | Cat# 552878; RRID: AB 394507 |
| Mouse monoclonal BV650 anti-mouse NK-1.1 | BD Biosciences | Cat# 564143; RRID: AB 2738617 |
| Rat monoclonal EOMES (Dan11 mag), eFluor 450, eBioscience™ | Thermo Fisher Scientific | Cat# 48–4875-82; RRID: AB 2574062 |
| Rat monoclonal Alexa Fluor® 488 anti-mouse CD3 | BioLegend | Cat# 100212; RRID: AB 493530 |
| Rat monoclonal Alexa Fluor® 488 anti-mouse CD19 | BioLegend | Cat# 115524; RRID: AB 493339 |
| Rat monoclonal Alexa Fluor® 488 anti-mouse Ter119 | BioLegend | Cat# 116215; RRID: AB 493402 |
| Rat monoclonal Alexa Fluor® 488 anti-mouse Gr-1 | BioLegend | Cat# 108419; RRID: AB 493480 |
| Rat monoclonal Alexa Fluor® 488 anti-mouse CD11 b | BioLegend | Cat# 101219; RRID: AB 493545 |
| Hamster monoclonal Alexa Fluor® 488 anti-mouse CD11c | BioLegend | Cat# 117313; RRID: AB 492849 |
| Hamster monoclonal Alexa Fluor® 488 anti-mouse FceRIa | BioLegend | Cat# 134329; RRID: AB 2687238 |
| Mouse monoclonal BUV395 anti-mouse CD45.2 | BD Biosciences | Cat# 565448; RRID: AB 2738867 |
| Rat monoclonal BUV737 anti-mouse CD335 (NKp46) | BD Biosciences | Cat# 612805; RRID: AB 2870131 |
| Mouse monoclonal Alexa Fluor® 647 anti-T-bet | BD Biosciences | Cat# 561267; RRID: AB 10564093 |
| Armenian hamster monoclonal PE anti-mouse CD196 (CCR6) | BioLegend | Cat# 129804; RRID: AB 1279137 |
| Mouse monoclonal PE-CF594 anti-mouse RORYt | BD Biosciences | Cat# 562684; RRID: AB 2651150 |
| Rat monoclonal PE/Cyanine7 anti-mouse CD127 (IL-7Ra) | BioLegend | Cat# 135014; RRID: AB 1937265 |
| Rat monoclonal Brilliant Violet 421 ™ anti-mouse Ly-6C | BioLegend | Cat# 128031; RRID: AB 2562177 |
| Rat monoclonal anti-CD11 b mouse | BD Biosciences | Cat# 553310; RRID: AB 394774 |
| Rat monoclonal PerCP/Cyanine5.5 anti-mouse I-A/I-E | BioLegend | Cat# 107625; RRID: AB 2191072 |
| Rat monoclonal Alexa Fluor® 647 anti-mouse F4/80 | BioLegend | Cat# 123121; RRID: AB 893492 |
| Rat monoclonal PE anti-mouse Ly-6G | BioLegend | Cat# 127608; RRID: AB 1186099 |
| Armenian hamster monoclonal PE/Cyanine7 anti-mouse CD11c | BioLegend | Cat# 117318; RRID: AB 493568 |
| Rat monoclonal V450 anti-mouse Foxp3 | BD Biosciences | Cat# 561293; RRID: AB 10611728 |
| Rat monoclonal APC-R700 anti-mouse CD25 | BD Biosciences | Cat# 565134; RRID: AB 2744344 |
| Bacterial and virus strains | ||
| Stellar™ Competent Cells | Takara | Cat# 636766 |
| One Shot™ Stbl3™ Chemically Competent E. coli | ThermoFisher Scientific |
Cat# C737303 |
| BL21(DE3) Competent Cells | ThermoFisher Scientific |
Cat# EC0114 |
| Sendai virus (from Cytotune 2.0 kit) | ThermoFisher Scientific |
Cat# A16517 |
| Biological samples | ||
| Healthy human PBMCs | This study | NIH biood bank |
| Patient and family PBMCs (Pt 1) | This study | Marmara University School of Medicine |
| Patient and family PBMCs (Pt 2) | This study | Schneider Children’s Medical Center of Israel |
| Human Colon Total RNA | Zyagen | Cat# HR-311 |
| Human Small Intestine Total RNA | Zyagen | Cat# HR-306 |
| Human Spleen Paraffin Sections | Zyagen | Cat# HP-701 |
| Human Thymus Paraffin Sections | Zyagen | Cat# HP-702 |
| Human Lung Paraffin Sections | Zyagen | Cat# HP-601 |
| Human Colon Paraffin Sections | Zyagen | Cat# HP-311 |
| Human Salivary Gland Paraffin Sections | Zyagen | Cat# HP-317 |
| Human Lung Total Protein | zyagen | Cat# HT-601 |
| Human Rectum Total Protein | zyagen | Cat# HT-312 |
| Human Small Intestine Total Protein | zyagen | Cat# HT-306 |
| Human Spleen Total Protein | zyagen | Cat# HT-701 |
| Human Stomach Total Protein | zyagen | Cat# HT-302 |
| Human Liver Total Protein | zyagen | Cat# HT-314 |
| Human Brain Total Protein | zyagen | Cat# HT-201 |
| Human Esophagus Whole Tissue Lysate | novusbio | Cat# NB820–59214 |
| Human Kidney Total Protein | zyagen | Cat# HT-901 |
| Human Small Intestine, Duodenum Paraffin Sections | zyagen | Cat# HP-307 |
| Human Small Intestine, Ileum Paraffin Sections | zyagen | Cat# HP-309 |
| Human Esophagus Paraffin Sections | zyagen | Cat# HP-301 |
| Human Stomach Paraffin Sections | zyagen | Cat# HP-302 |
| Human Multi-tissue Tissue MicroArray | novusbio | Cat# NBP2–78067 |
| Chemicals, peptides, and recombinant proteins | ||
| HILIC amphion | Welch | Lot# 7301.26 |
| Sera-Mag SpeedBeads | GE Healthcare | Cat# 45152101010250 Cat# 65152105050250 |
| Corning® Matrigel® Growth Factor Reduced (GFR) Basement Membrane Matrix, LDEV-free, 10 mL | Corning Life Science | Cat# 354230 |
| CryoStor® CS10 Freeze Media | Biolifesolutions | Cat# 210374 |
| A 83–01 | Cayman | Cat# 9001799 |
| DBZ | Cayman | Cat# 14627 |
| STEMdiff™ Intestinal Organoid Growth Medium | Stemcell | Cat# 05145 |
| IntestiCult™ Organoid Growth Medium (Mouse) | Stemcell | Cat# 06005 |
| mEGF | PeproTech | Cat# 315–09 |
| mWnt3a | PeproTech | Cat# 315–20 |
| Essential 8™ Medium | ThermoFisher Scientific |
Cat# A1517001 |
| Opti-MEM™ I Reduced Serum Medium | ThermoFisher Scientific |
Cat# 31985062 |
| Guanidine hydrochloride | Sigma | Cat# G3272–25G |
| Iodoacetamide | Sigma | Cat# I1149–5G |
| Dextran Sulfate Sodium Salt | MPbio | Cat# SKU 0216011050 |
| BsmBI-v2 | NEB | Cat# R0739S |
| STEMdiff™ Intestinal Organoid Kit | Stemceii | Cat# 05140 |
| T4 Polynucleotide Kinase | NEB | Cat# M0201s |
| T4 DNA Ligase | NEB | Cat# M0202L |
| Human TruStain FcX™ (Fc Receptor Blocking Solution) | Bioiegend | Cat# 422301 |
| Protein Deglycosylation Mix II | NEB | Cat# P6044S |
| a2–3,6,8,9 Neuraminidase A | NEB | Cat# P0722S |
| PNGase F (Glycerol-free), Recombinant | NEB | Cat# P0709S |
| O-Glycosidase | NEB | Cat# P0733S |
| Recombinant Human ST6GALNAC1 Protein | R&D | Cat# 9154-GI-020 |
| Manganese(II) chloride | Sigma | Cat# 244589–10G |
| Asialofetuin from fetal calf serum | Sigma | Cat# A4781–50MG |
| CMP-Cy5-Sialic Acid | R&D | Cat# ES302–050 |
| Corning® Matrigel® Growth Factor Reduced (GFR) Basement Membrane Matrix, LDEV-free, 10 mL | Corning Life Science | Cat# 354230 |
| TrypLE™ Express Enzyme (1X), no phenol red | Thermo Fisher Scientific | Cat# 12604013 |
| BSA | Sigma | Cat# A7030 |
| EDTA | Thermo Fisher Scientific | Cat# AM9261 |
| StcE | From Dr. Bertozzi’s lab | N/A |
| OgpA | From Dr. Lawrence Tabak’s lab, NIDCR | N/A |
| polybrene | Sigma-Aldrich | Cat# TR-1003 |
| Blasticidin S HCl | Thermo Fisher Scientific | Cat# A1113903 |
| Puromycin | Thermo Fisher Scientific | Cat# A1113803 |
| SCF | R&D | Cat# 7466-SC |
| StemSpan™SFEM II medium | StemCell | Cat# 09605 |
| IL-3 | R&D | Cat# 203-IL |
| EPO | R&D | Cat# 287-TC |
| IGF-1 | R&D | Cat# 201-G1 |
| Dexamethasone | Sigma | Cat# D4902 |
| holo-transferrin | Sigma | Cat# I0665 |
| IWP2 | Sigma | Cat# I0536 |
| DAPT | Sigma | Cat# D5942 |
| Y27632 | Cayman | Cat# 10005583 |
| DAPI Fluoromount-G | SouthernBiotech | Cat# 0100–20 |
| GalNAcEXO | From Dr. Lawrence Tabak’s lab, NIDCR | N/A |
| Dithiothreitol | Sigma | Cat# 10197777001 |
| Trifluoroacetic acid (TFA) | Sigma | Cat# I6508–1L |
| Urea | Sigma | Cat# U0631–1 KG |
| Formic acid | Thermo Fisher Scientific | Cat# A117–50 |
| Trypsin | Promega | Cat# V5111 |
| Tris-(2-Carboxyethyl)phosphine, Hydrochloride (TCEP) | Thermo Fisher Scientific | Cat# I2556 |
| Acetonitrile (ACN) | Thermo Fisher Scientific | Cat# A9554 |
| Guanidine hydrochloride solution | Sigma | Cat# SRE0066– 100ML |
| carbenoxolone (CBX) | Selleckchem | Cat# S4368 |
| Ampicillin sodium salt | Sigma | Cat# A9518 |
| Metronidazole | Sigma | Cat# M3761 |
| Vancomycin hydrochloride from Streptomyces orientalis | Sigma | Cat# V2002 |
| Neomycin trisulfate salt hydrate | Sigma | Cat# N1876 |
| Liberase | Sigma | Cat# 5401020001 |
| DNase I | Sigma | Cat# 4716728001 |
| Collagenase D | Sigma | Cat# 11088858001 |
| phenol-chloroform-isoamyl alcohol (25:24:1) | Sigma | Cat# P2069–100ML |
| SCFA standards | Protein Characterization Core, NCI |
N/A |
| Percoll Plus | GE Healthcare | Cat# 17544501 |
| Monensin Solution | Biolegend | Cat# 420701 |
| EcoR I-HF | NEB | Cat# R3101L |
| MluI-HF | NEB | Cat# R3198S |
| Lipo3000 transfection reagent | ThermoFisher Scientific |
Cat# L3000075 |
| Sodium Pyruvate (100 mM) | ThermoFisher Scientific |
Cat# 11360070 |
| Percoll | Sigma | Cat# GE17–0891-01 |
| UEA 1 fluorescin | Vector Laboratories | Cat# FL-1061 |
| Cy5-Peanut agglutinin (PNA) | Vectorlabs | Cat# CL-1075–1 |
| Fixable Viability Dye eFluor™ 780 | Thermo Fisher Scientific | Cat# 65–0865-18 |
| β-mercaptoethanol | Gibco | Cat# 21985 |
| L-Glutamine | Gibco | Cat# 25030 |
| NEAA | Gibco | Cat# 11140 |
| Penicillin and streptomycin | Gibco | Cat# 15140 |
| Critical commercial assays | ||
| TMT10plex™ Isobaric Labeling Reagent Set | ThermoFisher Scientific |
Cat# 90110 |
| Pierce BCA Protein Assay Kit | ThermoFisher Scientific |
Cat# 23225 |
| XBridge Peptide BEH C18 Column, 300Ä, 3.5 μm, 1 mm × 150 mm | Waters | Cat# SKU: 186003606 |
| Histone Deacetylase (HDAC) Activity Assay Kit (Fluorometric) (ab156064) | Abcam | Cat# ab156064 |
| Human Pan T cell isolation kit | Miltenyi | Cat# 130–096-535 |
| Dynabeads™ Human T-Activator CD3/CD28 for T Cell Expansion and Activation | Thermo Fisher Scientific | Cat#11131D |
| Dynabeads™ Protein G for Immunoprecipitation | ThermoFisher Scientific |
Cat# 10004D |
| Lenti-X™ Concentrator | Takara | Cat# 631231 |
| PrimeScript™ RT Reagent Kit (Perfect Real Time) | Takara | Cat# RR037A |
| In-Fusion® HD Cloning Kit | Takara | Cat# 639650 |
| Lipofectamine™ 3000 Transfection Reagent | ThermoFisher Scientific |
Cat# L3000075 |
| NuPAGE™ 4–12% Bis-Tris Protein Gels, 1.5 mm, 15-well | ThermoFisher Scientific |
Cat# NP0336B0X |
| NuPAGE™ 3 to 8%, Tris-Acetate, 1.5 mm, Mini Protein Gel, 15-well | ThermoFisher Scientific |
Cat# EA03785BOX |
| Foxp3 / Transcription Factor Staining Buffer Set | Thermo Fisher Scientific, | Cat# 00–5523-00 |
| BCA protein assay kit | Thermo Fisher Scientific, | Cat# 23225 |
| Sialyltransferase Activity Kit | R&D | Cat# EA002 |
| In-Fusion® HD Cloning Plus CE kit | Iakara | Cat# 638919 |
| Anti-Adherence Rinsing solution | Stemceii | Cat# 07010 |
| ATAC-Seq Kit | Active motif | Cat# 53150 |
| LabSafe GEL Blue | G-biosciences | Cat# 786–35 |
| C18 cartridge | Seq-Pak C18 | Cat# WAI054955 |
| Sera-Mag SpeedBeads with a hydrophilic surface | GE Healthcare | Cat# 45152101010250 |
| Sera-Mag SpeedBeads with a hydrophobic surface | GE Healthcare | Cat# 65152105050250 |
| Halt™ Protease Inhibitor Cocktail, EDTA-Free | Thermo Fisher Scientific | Cat# 78439 |
| Halt™ PhosphataseInhibitor Cocktail | Thermo Fisher Scientific | Cat# 78427 |
| EndoTrap red | Biovendor | Cat# LEI0001 |
| ToxinSensor™ Chromogenic LAL Endotoxin Assay Kit | Genescript | Cat# L00350 |
| DNeasy Blood & Tissue Kit | Qiagen | Cat# 69506 |
| Cytotune 2.0 kit | ThermoFisher Scientific |
Cat# A16517 |
| Deposited data | ||
| Site-specific N-glycoproteome MS raw and searched data | This paper | https://www.ebi.ac.uk/pride/archiveidentifierPXD028239 |
| mRNA-seq and ATAC-seq data | This paper | GEO ID: GSE183821 |
| whole exome sequencing (WES) (Pt 1) | This paper | dbGaP ID: phs002598.v1.p1 |
| Experimental models: Celi lines | ||
| HI-29 | AICC | Cat# HTB-38 |
| LS 180 | AICC | Cat# CL-187 |
| Lenti-X™ 293T Cells | Iakara | Cat# 632180 |
| HEK293I | AICC | Cat# CRL-3216 |
| Experimental models: Organisms/strains | ||
| Mouse: Myd88flox/flox | The Jackson Laboratory | Cat# 008888 |
| Mouse: Vil1cre | The Jackson Laboratory | Cat# 21504 |
| Mouse: Tlr4−/− | The Jackson Laboratory | Cat# 29015 |
| Mouse: St6 (St6galnac1R319Q) | This paper | N/A |
| Oligonucleotides | ||
| A full list is provided in Table S3 | ||
| Recombinant DNA | ||
| pLV-EFIa-IRES-Puro | Hayer et al., 2016 | Addgene, Cat# 85132 |
| psPAX2 | A gift from Didier Trono | Addgene, Cat# 12260 |
| pMD2.G | A gift from Didier Trono | Addgene, Cat# 12259 |
| lentiGuide-Puro | Sanjana et al., 2014 | Addgene, Cat# 52963 |
| lentiCas9-Blast | Sanjana et al., 2014 | Addgene, Cat# 52962 |
| lentiCRISPRv2 | Sanjana et al., 2014 | Addgene, Cat# 52961 |
| pLV-EF1a-2a-tEGFR | This paper | N/A |
| Software and algorithms | ||
| ImageJ | Schneider et al., 2012 | https://imagej.nih.gov/ij/ |
| Graphpad Prism | https://www.graphpad.com/scientific-software/prism | version 9.0 |
| QIIME2 | Bolyen et al., 2019 | version 2019.10 |
| DADA2 method | Callahan et al., 2016 | https://benjjneb.github.io/dada2/ |
| Thermo Xcalibur software | https://www.thermofisher.com/order/catalog/product/0PT0N-30965 | Cat# 0PT0N-30965 |
| HOMER | http://homer.ucsd.edu/homer/interactions/ | version 4.11.1 |
| Python | https://www.python.org/ | Version 3.6–3.8 |
| Macs | https://pypi.org/project/MACS/ | version 1.4.3 |
| Bedtools | https://bedtools.readthedocs.io/en/latest/ | version 2.30.0 |
| HTSeq | https://pypi.org/project/HTSeq/ | version 0.11.4 |
| DESeq2 | version 1.30.1 | |
| RStudio | https://www.rstudio.com/ | version 1.4.1106 |
| R | https://www.r-project.org | version 4.0.4 |
| RColorBrewer | http://colorbrewer2.org/ | version 1.1–2 |
| Samtools | http://www.htslib.org/ | version 1.12 |
| Deeptools | https://deeptools.readthedocs.io/en/develop/ | version 3.5.0 |
| Enrichr | Kuleshov at el., 2016 | https://maayanlab.cloud/Enrichr/ |
| FastQC | https://www.bioinformatics.babraham.ac.uk | version 0.11.9 |
| Bowtie | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | version 1.3.0 |
| IGV | https://software.broadinstitute.org/software/igv/ | version 2.10.0 |
| Benchling algorithm | https://www.benchling.com/crispr/ | https://www.benchling.com |
| PyMOL | https://pymol.org/2/ | version 2.3.1 |
| I-TASSER | Roy et al., 2010 | https://zhanggroup.org/I-TASSER/ |
| pFind3.0 | Chi et al., 2018 | https://github.com/pFindStudio/pFind3 |
| FlowJo | https://www.flowjo.com/ | version 10.6.2 |
| GlycoBinder | Fang et al., 2020 | https://github.com/IvanSilbern/GlycoBinder |
| IPA | https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/ | version 01–20-04 |
| Imaris | https://imaris.oxinst.com/ | version 9.8.1 |
| Snapgene | https://www.snapgene.com/ | version 6.0 |
| Cytoscape | https://cytoscape.org/ | version 3.8.2 |
| Other | ||
| Agilent 1100 series HPLC | Agilent Technologies | https://www.agilent.com/en/products/liquid-chromatography |
| Orbitrap Fusion™ Lumos™ Tribrid™ Mass Spectrometer | ThermoFisher Scientific |
https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMBHQ |
| Fluorescent imager Azure 500 | Azure biosystems | https://www.azurebiosystems.com/imaging-systems/azure-500/ |