KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD57 Monoclonal Antibody (TB01 (TBO1)), FITC | eBioscience | Cat# 11–0577-42, RRID:AB_1311193 |
| F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, PE | eBioscience | Cat# 12–4010-82, RRID:AB_11063706 |
| IgM Monoclonal Antibody (eB121–15F9), FITC | eBioscience | Cat# 11–5890-81, RRID:AB_465291 |
| Streptavidin PE Conjugate | eBioscience | Cat# 12–4317-87 |
| Biological Samples | ||
| Cholera Toxin Subunit B (CtxB) (Recombinant), Alexa Fluor 488 Conjugate | Invitrogen | Cat# C34775 |
| Lectin GS-II From Griffonia simplicifolia, Alexa Fluor 488 Conjugate | Invitrogen | Cat# L21415 |
| ABA (Agaricus bisporus)-FITC (fluorescein isothiocyanate) | J-Chemical | Cat# 10601C |
| ConA (Canavalia ensiformis)-Biotin | J-Chemical | Cat# 03102C |
| DBA (Dolichos biflorus)-FITC | J-Chemical | Cat# 42204C |
| DSA (Datura stramonium)-FITC/Biotin | J-Chemical | Cat# 31211C |
| ECA (Erythrina cristagalli)-FITC | J-Chemical | Cat# 12204C |
| LCA (Lens culinaris)-Biotin | J-Chemical | Cat# 41213C |
| Lotus (Lotus tetragonolobus)-FITC | J-Chemical | Cat# 52500C |
| MAM (Maackia amurensis)-FITC | J-Chemical | Cat# 92600C |
| PHA-E4 (Phaseolus vulgaris)-FITC | J-Chemical | Cat# 81503C |
| PHA-L4 (Phaseolus vulgaris)-FITC | J-Chemical | Cat# 61210C |
| PNA (Arachis hypogaea)-FITC | J-Chemical | Cat# 61213C |
| SBA (Glycine max)-FITC | J-Chemical | Cat# 71600C |
| SSA (Sambucus sieboldiana)-Biotin | J-Chemical | Cat# 51213C |
| UEA-I (Ulex europaeus)-FITC | J-Chemical | Cat# 21503C |
| WGA (Triticum vulgaris)-FITC | J-Chemical | Cat# 02101C |
| Lycopersicon Esculentum (Tomato) Lectin (LEL, TL), DyLight 488 | Vector Laboratories | Cat# DL-1174, RRID:AB_2336404 |
| Wisteria Floribunda Lectin (WFA, WFL), Fluorescein | Vector Laboratories | Cat# FL-1351, RRID:AB_2336875 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Certified Fetal Bovine Serum (FBS) | Biological Industries | Cat# 04–001-1ACS |
| DMEM, high glucose | Biological Industries | Cat# 01–052-1A |
| Kifunensine | Cayman Chemical | Cat#10009437 |
| Opti-MEM Reduced Serum Medium | Gibco | Cat# 31985062 |
| Lipofectamine™ 2000 Transfection Reagent | Invitrogen | Cat# 11668–019 |
| Hygromycin B Gold | Invitrogen | Cat# ant-hg-5 |
| Puromycin | Invitrogen | Cat# ant-pr-5 |
| Blasticidin | Invitrogen | Cat# ant-bl-5 |
| PEI MAX - Transfection Grade Linear Polyethylenimine Hydrochloride (MW 40,000) | Polysciences | Cat# 24765 |
| D-PBS | Sangon Biotech | Cat# E607009–0500 |
| Trypsin-EDTA Solution, With Phenol Red | Sangon Biotech | Cat# E607002–0100 |
| Critical Commercial Assays | ||
| SV Total RNA Isolation System | Promega | Cat# Z3100 |
| Hyaluronan Quantikine ELISA Kit | R&D Systems | Cat# DHYAL0 |
| SanPrep Column DNA Gel Extraction Kit | Sangon Biotech | Cat# B518131 |
| SanPrep Column PCR Product Purification Kit | Sangon Biotech | Cat# B518141 |
| SanPrep Column Plasmid Mini-Preps Kit | Sangon Biotech | Cat# B518191 |
| PrimeSTAR® GXL DNA Polymerase | Takara | Cat# R050A |
| DNA Ligation Kit <Mighty Mix> | Takara | Cat# 6023 |
| PrimeScript™ RT Master Mix (Perfect Real Time) | Takara | Cat# RR036A |
| TB Green® Premix Ex Taq™ II (Tli RNaseH Plus), Bulk | Takara | Cat# RR820L |
| EcoRI | Takara | Cat# 1040S |
| NotI | Takara | Cat# 1166S |
| XhoI | Takara | Cat# 1094A |
| In-Fusion HD Cloning Kit | Takara | Cat# 639649 |
| FastDigest BpiI (IIs class) | Thermo Fisher Scientific | Cat# FD1014 |
| KOD FX Neo | TOYOBO | Cat# KFX-201 |
| Deposited Data | ||
| RNA seq of HEK293 cells | This study | SRA: SRR12213061; SRR12213062; SRR12213063 |
| RNA seq of T-KO cells | This study | SRA: SRR12213058; SRR12213059; SRR12213060 |
| RNA seq of QT-KO cells | This study | SRA: SRR12213055; SRR12213056; SRR12213057 |
| Glycomics MS raw data | This study | https://glycopost.gly cosmos.org (ID: GPST000125) |
| RNA seq of 288 colon primary tumor samples and 304 normal colon tissue samples | Chang et al., 2019/ UCSC Xena platform | https://xenabrowser. net/ |
| Experimental Models: Cell Lines | ||
| HEK293 cells (parental HEK293) | Jin et al., 2018 | N/A |
| HEK293 FF6 cells | Hirata et al., 2015 | N/A |
| DPM1-KO cells | This paper | N/A |
| STT3A-KO cells | Toshihiko Kitajima et., 2018 | STT3A-knockout cell lines |
| STT3B-KO cells | Toshihiko Kitajima et., 2019 | STT3B-knockout cell lines |
| MOGS-KO cells | Liu et al., 2018 | MOGS-KO cells |
| GANAB-KO cells | Liu et al., 2018 | GANAB-KO cells |
| CANX-KO cells | Liu et al., 2018 | CANX-KO cells |
| CALR-KO cells | Liu et al., 2018 | CALR-KO cells |
| CANX&CALR-KO cells | Liu et al., 2018 | CANX/CALR double-KO |
| MAN1A1-KO cells | Jin et al., 2018 | A1-KO24 |
| MAN1A2-KO cells | Jin et al., 2018 | A2-KO37 |
| MAN1A1&A2-KO cells | Jin et al., 2018 | D-KO35 |
| T-KO (MAN1A1&A2&B1) cells | Jin et al., 2018 | T-KO |
| MAN1A1&A2&C1-KO cells | Jin et al., 2018 | N/A |
| MAN1A1&A2&B1&C1-KO cells | Ren et al., 2019 | QD-KO |
| QT-KO (MAN1A1&A2&B1&C1&MGAT1) cells | Ren et al., 2019 | QT-KO |
| MAN2A1-KO cells | This study | N/A |
| MAN2A2-KO cells | This study | N/A |
| MAN2A1&A2-KO cells | This study | N/A |
| MGAT1-KO cells | This study | N/A |
| MGAT2-KO cells | This study | N/A |
| MGAT3-KO cells | This study | N/A |
| MGAT4A-KO cells | This study | N/A |
| MGAT4B-KO cells | This study | N/A |
| MGAT4A&4B-KO cells | This study | N/A |
| MGAT5-KO cells | This study | N/A |
| MGAT5B-KO cells | This study | N/A |
| MGAT5&5B-KO cells | This study | N/A |
| FUT8-KO cells | This study | N/A |
| MGAT4A&4B&3&5&FUT8-KO cells | This study | N/A |
| B4GALT1-KO cells | This study | N/A |
| B4GALT2-KO cells | This study | N/A |
| B4GALT3-KO cells | This study | N/A |
| B3GNT8-KO cells | This study | N/A |
| ST6GAL1-KO cells | This study | N/A |
| B4GALNT3&4-KO cells | This study | N/A |
| CHST8&9-KO cells | This study | N/A |
| B4GALNT2-KO cells | This study | N/A |
| SLC35A1-KO cells | This study | N/A |
| SLC35A2-KO cells | This study | N/A |
| SLC35C1-KO cells | This study | N/A |
| B3GNT5-KO | This study | N/A |
| Oligonucleotides | ||
| qPCR Primers for the HPRT gene: 5′-TGGCGTCGTGATTAGTGATG-3′ 5′-TCCAGCAGGTCAGCAAAGAA-3′ |
Liu et al., 2018 | N/A |
| qPCR Primers for the CERS1 gene: 5′-TCCATCTACGCTACGCTATACA-3′ 5′-GCACAAGGATGCCCACATTG-3′ |
PrimerBank | 11641421a2 |
| qPCR Primers for the HAS2 gene: 5′-CTCTTTTGGACTGTATGGTGCC-3′ 5′-AGGGTAGGTTAGCCTTTTCACA-3′ |
PrimerBank | 169791020c1 |
| qPCR Primers for the RENBP gene: 5′-CTGCTCCGTCATTGCATTCG-3′ 5′-AGGGCAACAATAGGAACTTGTC-3′ |
PrimerBank | 213417819c3 |
| sgRNA sequence of KO cells | This study | Table SX |
| DNA and Plasmids | ||
| pME-hyg | Ohishi et al., 2003 | pMEhyg |
| pME-hyg-B3GAT1 | This study | N/A |
| pME-hyg-GCNT2 | Thermo Fisher Scientific | Cat# A11613 |
| pME-hyg-ST8SIA2 | Thermo Fisher Scientific | Cat# A11613 |
| pME-hyg-ST8SIA4 | Thermo Fisher Scientific | Cat# A11613 |
| pME-hyg-B3GAT1 | This study | N/A |
| pME-hyg-ST8SIA2 | This study | N/A |
| pME-hyg-ST8SIA4 | This study | N/A |
| pME-hyg-GCNT2 | This study | N/A |
| pME-puro | Ohishi et al., 2003 | pMEpuro |
| pME-puro-ST8SIA1 | Tashima et al,. 2006 | N/A |
| pME-puro-ST8SIA1 | This study | N/A |
| pX330-mEGFP | Hirata et al., 2015 | N/A |
| Software and Algorithms | ||
| FlowJo software | https://www.flowjo.com/ | Version 7.6 |
| R | https://www.r-project.org/ | Version 3.6.2 |
| HISAT2 | http://ccb.jhu.edu/software/hisat2/manual.shtml | Version 2.1.0 |
| SAMtools | http://samtools.sourceforge.net/ | Version 1.9 |
| Stringtie | http://ccb.jhu.edu/software/stringtie/ | Version 1.3.5 |
| BD Accuri C6 software | http://www.bdbiosciences.com/accuri/ | Version 1.0.264.21 |
| Bio-Rad S3e cell Sorter & ProSort Software | https://www.bio-rad.com/ | Version 1.4 |
| Inkscape | https://inkscape.org/ | Version 0.92.5 |
| Other | ||
| MicroAmp™ Fast Optical 96-Well Reaction Plate with Barcode, 0.1 mL | Applied Biosystems | 4346906 |
| StepOnePlus Real-Time PCR system | Applied Biosystems | 4376692 |
| Flow Cytometry | BD biosciences | C6 |
| Cell sorter | Bio-Rad | S3e |
| T100 Thermal Cycler | Bio-Rad | T100 |
| iMark Microplate Absorbance Reader | Bio-Rad | N/A |
| PNGaseF | Promega | Cat#V4831 |
| Sep-Pak Vac C18 1cc, 100mg | Waters | WAT023590 |
| Sep-Pak Plus Light tC18 | Waters | WAT036805 |
| Supelclean ENVI-Carb spe | Spelco | 57109-U |
| LTQ XL, Orbitrap Discovery | Thermo Fisher Scientific | |
| Iodomethane | Sigma-Aldrich | 289566–100G |
| Sodium hydroxide solution, 50% w/w | Fisher | SS254–1 |
| Anyhydrous DMSO | Sigma-Aldrich | |
| Oligosaccharides Kit | Supelco | 47265 |
| Dowex® 50WX8 hydrogen form 100–200 mesh | Sigma-Aldrich | 217506–500G |
| Sodium borohydride | Sigma-Aldrich | 213462–25G |
| Xcalibur software | Thermo Fisher Scientific | Ver 3.0.63 |