Skip to main content
. Author manuscript; available in PMC: 2024 Nov 13.
Published in final edited form as: Cancer Cell. 2023 Oct 19;41(11):1945–1962.e11. doi: 10.1016/j.ccell.2023.09.012

Key Resources Table

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
CD33 antibody BD Biosciences Cat# 740293; RRID:AB_2740032
CD86 (B7-2) antibody BD Biosciences Cat# 564428; RRID:AB_2738804)
CD141 antibody BD Biosciences Cat# 565321; RRID:AB_2739180)
Brilliant Violet 605(TM) anti-human CD11b antibody BioLegend Cat# 301332; RRID:AB_2562021)
Brilliant Violet 711(TM) anti-human Ki-67 antibody BioLegend Cat# 350516; RRID:AB_2563861)
CD152 (CTLA-4) antibody BD Biosciences Cat# 563931; RRID:AB_2738491)
CD3 antibody BD Biosciences Cat# 560835; RRID:AB_2033956)
PE anti-human CD45 antibody BioLegend Cat# 368510; RRID:AB_2566370)
Granzyme B antibody BD Biosciences Cat# 562462; RRID:AB_2737618)
CD11c antibody BD Biosciences Cat# 551077; RRID:AB_394034)
CD4 Monoclonal Antibody (S3.5), PE-Alexa Fluor 700 Thermo Fisher Scientific Cat# MHCD0424; RRID:AB_10372802)
PKR Polyclonal Antibody Thermo Fisher Scientific Cat# PA1-990; RRID:AB_560651)
Mouse Anti-CD69 Monoclonal Antibody BD Biosciences Cat# 555533; RRID:AB_398602)
Alexa Fluor(R) 700 anti-human CD8a antibody BioLegend Cat# 300920; RRID:AB_528885)
APC/Cyanine7 anti-human CD279 (PD-1) antibody BioLegend Cat# 329922; RRID:AB_10933429)
Brilliant Violet 650 anti-IFN-gamma BD Biosciences Cat# 563416
Alexa Fluor 488 anti-Foxp3 Fisher Scientific Cat# 53477642
PE-Cy7 anti-HLA-DR BD Biosciences Cat# 560651
Anti-GammaH2AX antibody EMD Millipore Cat# 05-636
Anti-panCK antibody Novus Biological Cat# NBP2-29429
Alexa Fluor 488-labeled anti-mouse IgG antibody containing DAPI Invitrogen Cat# A21202
Anti-P63 antibody Abcam Cat# AB735
Anti-KI67 antibody Abcam Cat# AB16667
Anti-CK13 antibody Abcam Cat# AB92551
Biological Samples
Human Tumor Sampling - Cytobrush The University of Texas MD Anderson Cancer Center, Houston, TX Protocol 2014-0543
Chemicals, Peptides, and Recombinant Proteins
BBL CultureSwabs BD Biosciences Cat# 220135
Anaerobic Transport Medium Surgery Pack (ATMSP) Anaerobe Systems Cat# AS-914
Cytobrush Plus Endocervical Samplers Cooper Surgical Cat# C0012
BuccalFix Tubes ™ Isohelix Cat# BFX/S1-05-50
Isohelix Swab Pack Isohelix Cat# SK-3S
Stabilization Buffer Isohelix Cat# BFX-25
Serum Blood Collection Tubes Becton Dickinson Cat# 367815
Golgiplug BD Biosciences Cat# 555029
MRS Agar Plates Moltox Cat# 51-40S020.140
TSA Agar Plates (BD BBL™ Trypticase™ Soy Agar with 5% Sheep Blood (BD Trypticase™ Soy Agar II™)) BD Biosciences Cat# 221239
Lactobacillus MRS Dehydrated Culture BD Difco Cat# 288210
HEPES Fisher Bioreagents Cat# BP310100
Proteose Peptone No. 3 Bacto Cat# C838M71
NaCl Fisher Chemical Cat# S271500
D-Glucose Avantor Macron Cat# 491212
Fresh yeast extract Gibco Cat# 18180059
Heat Inactivated Horse Serum Remel Cat# R55075
Corning™ Minimum Essential Medium Eagle (Mod.) 1X (MEM) with Glutamine Corning Cat# 10010CV
Corning® Fetal Bovine Serum (FBS), 500 mL, Regular, USDA Approved Origin Corning Cat# 35010CV
Corning® 100 mL Penicillin-Streptomycin Solution, 100x Corning Cat# 30002CI
Gentra Puregene Yeast/Bact. Kit Qiagen Cat# 158567
Cisplatin (cis-Diammineplatinum(II) dichloride) Sigma-Aldrich Cat# P4394
5-fluoruracil Sigma-Aldrich Cat# F6627
Gemcitabine Selleck Chemical LLC Cat# S1149100MG
CellTiter-Glo and CellTiter-Glo 3D Luminescent Cell Viability Assay Promega Cat# G7572
Cat# G9683
LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit, for 405 nm excitation Thermo Fisher Cat# L34957
Phytohemagglutinin (PHA) Sigma-Aldrich Cat# 11249738001
Corning® 500 mL RPMI 1640 Corning Cat# 10-040-CV
gentamicin antibiotics Lonza Cat# 17518Z
collagenase Sigma-Aldrich Cat# C9407
Hyaluronidase Sigma-Aldrich Cat# H3506
Trypsin-EDTA Gibco cat# 25200056
DNase I Sigma-Aldrich cat# DN25
Red Blood Cell Lysis Buffer Roche Cat# 11814389001
Cultrex BME RGF type 2 Trevigen Cat# 3533-005-02
B27 supplement GIBCO Cat# 175044
nicotinamide Sigma-Aldrich Cat# N0636
n-Acetylcystein Sigma-Aldrich Cat# A9165
ROCK inhibitor Abmole Cat# Y27632
A83-01 Tocris Cat# 2939
Forskolin Bio-Techne Cat# 1099
FGF7 Peprotech Cat# 100-19
FGF10 Peprotech Cat# 100-26
p38 inhibitor SB202190 Sigma-Aldrich Cat# 7067
EGF Peprotech Cat# AF-100-15
Primocin InvivoGen Cat# Ant-pm-1
TrypLE™ Express Enzyme (1X), phenol red Gibco Cat# 12605036
EDTA-containing vacutainers BD Biosciences Cat# 366643
Lymphoprep Stemcell Technologies or Cosmo Bio Usa Cat# 07851 or Cat# AXS1114545
dithiothreitol Invitrogen Cat# P2325
Corning® Phosphate-Buffered Saline, 1X without calcium and magnesium, PH 7.4 ± 0.1 Corning Cat# 21-040-CV
Sodium L-Lactate Sigma-Aldrich Cat# L7022-5g
Sodium D-Lactate Sigma-Aldrich Cat# 71716-5g
D-Lactic Acid TCI America Cat# L02665G
L-Lactic Acid Sigma-Aldrich Cat# L6402-5g
ProLong Gold Antifade Mountant Invitrogen Cat# P36930
Kits
D-/L-Lactic Acid (D-/L-Lactate) (Rapid) Assay Kit Megazyme/Neogen Cat# K-DLATE
ImmunoSEQ human T-cell receptor beta (hsTCRB) Kit, Version 3 Adaptive Biotechnologies Cat# ISK10101
Qiagen Multiplex PCR Kit Qiagen Cat# 206145
NEBNext Ultra II Library Prep Kit for Illumina New England BioLabs Cat# E7645L
Click-iT EdU Alexa Fluor 488 Flow Cytometry Assay Kit Invitrogen Cat# C10425
Megazyme (Neogen) D-/L- Lactic Acid (D-/L-Lactate) (Rapid) Assay Kit Neogen, Megazyme Cat# K-DLATE
Xtreme DNA Isolation Kit Isohelix Cat# XME-50
Deposited Data
16S This paper; SRA BioProject accession numbers: PRJNA989630, PRJNA702617, PRJNA685389
SMS This paper; SRA BioProject accession numbers: PRJNA989630, PRJNA702617, PRJNA685389
L. iners strain assemblies Genome BioSample accession numbers: SAMN27176861, SAMN27176862, SAMN27176863, SAMN27176864
RNA sequencing This paper; NCBI/SRA PRJNA1013527
TCR sequencing This paper; immuneACCESS immuneACCESS: https://doi.org/10.21417/LC2022CIR.
Code for processing TCGA data This paper https://github.com/mda-primetr/Colbert_CancerCell_2023
Experimental Models: Cell Lines
HeLa Sam Mok lab, MD Anderson Cancer Center RRID:CVCL_0030
SiHa ATCC Cat# HTB-35
Ca Ski ATCC Cat# CRM-CRL-1550
Experimental Models: Organisms/Strains
ATCC Lactobacillus iners ATCC ATCC 55195; NCBITaxon:888801
ATCC Lactobacillus crispatus SJ-3C-US ATCC ATCC SJ-3C (PTA-10138);
NCBITaxon:575598
Patient-derived Lactobacillus iners I012T4 This paper, sequences in NCBI Accession # SAMN27176861
Patient-derived Lactobacillus iners IN370 This paper, sequences in NCBI SAMN27176863
Patient-derived Lactobacillus iners IN366 This paper, sequences in NCBI SAMN27176862
Software and Algorithms
ATIMA (Agile Toolkit for Incisive Microbial Analyses) R Studio http://atima.jplab.net/
Galaxy: LEfSe Segata et. al 2010 https://huttenhower.sph.harvard.edu/galaxy/
Other (Resources)
FlowJo FlowJo Software www.flowjo.com
GraphPad Prism GraphPad Software www.graphpad.com
JMP SAS www.jmp.com
Living Image Software IVIS Spectrum - Perkin Elmer Part #128113
FastQC (version 0.11.8) https://www.bioinformatics.babraham.ac.uk/projects/fastqc
FastQ_Screen (version 0.14.0) (Wingett and Andrews 2018) https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen
BBDuk/BBTools (version 20190109) https://jgi.doe.gov/data-and-tools/bbtools
BBMap/BBTools (version 20190109) https://jgi.doe.gov/data-and-tools/bbtools
Bowtie2 (version 2.3.5) (Langmead and Salzberg 2012) https://github.com/BenLangmead/bowtie2
Samtools (version 1.9) (H. Li et al. 2009) https://github.com/samtools
IGGsearch (version 20190921) (Nayfach et al. 2019) https://github.com/snayfach/IGGsearch
MetaPhlAn2 (version 2.0) (mpa_v295_CHOCOPhlAn_201901) (Truong et al. 2015) https://bitbucket.org/biobakery/metaphlan2
MEGAHIT (version 1.2.8) (D. Li et al. 2015) https://github.com/voutcn/megahit
metaSPAdes (version 3.13.1) (Nurk et al. 2017) https://github.com/ablab/spades/releases
MetaBAT2 (version 20191004) (Kang et al. 2019) https://bitbucket.org/berkeleylab/metabat
Prodigal (version 2.6.3) (Hyatt et al. 2010) https://github.com/hyattpd/Prodigal
Diamond (version 0.9.24) (Buchfink, Xie, and Huson 2015) https://github.com/bbuchfink/diamond
KofamScan (version 1.1.0) (Aramaki et al. 2020) https://github.com/takaram/kofam_scan
Subread (version 1.6.3) (Liao, Smyth, and Shi 2014) http://subread.sourceforge.net
DFAST (version 2021.7.12) https://doi.org/10.1093/bioinformatics/btx713 https://dfast.ddbj.nig.ac.jp
MetaCyc (version 25.5) https://doi.org/10.1093/nar/gkx935 https://biocyc.org/download-bundle.shtml
Pathway Tools (version 25.5) https://doi.org/10.1093/bib/bbv079 https://biocyc.org/download-bundle.shtml
FastANI DOI: 10.1038/s41467-018-07641-9 https://github.com/ParBLiSS/FastANI
QIIME2 (version 2020.11) https://www.nature.com/articles/s41587-019-0209-9
DADA2 doi:10.7717/peerj.5364
STAR (v. 2.3.0) DOI: 10.1093/bioinformatics/bts635 http://code.google.com/p/rna-star/
HTSeq (v. 2.0) DOI: 10.1093/bioinformatics/btu638 https://pypi.org/project/HTSeq/
ANNOVAR (v. 20211019) DOI: 10.1093/nar/gkq603 http://www.openbioinformatics.org/annovar/.
RStudio (v. 2023.03.0+386) Posit Team https://posit.co/download/rstudio-desktop/
tidyverse Rstudio doi:10.21105/joss.01686
ggplot2 Rstudio https://ggplot2.tidyverse.org
ggpubr Rstudio https://rpkgs.datanovia.com/ggpubr/
dplyr Rstudio https://CRAN.R-project.org/package=dplyr
ggsignif Rstudio doi:10.31234/osf.io/7awm6
plyr Rstudio https://www.jstatsoft.org/v40/i01/
rstatix Rstudio https://CRAN.R-project.org/package=rstatix
survival Rstudio https://CRAN.R-project.org/package=survival
survminer Rstudio https://CRAN.R-project.org/package=survminer
broom Rstudio https://CRAN.R-project.org/package=broom
lmerTest Rstudio https://doi.org/10.18637/jss.v082.i13
sjPlot Rstudio https://CRAN.R-project.org/package=sjPlot
sjmisc Rstudio https://doi.org/10.21105/joss.00754
tidyr Rstudio https://CRAN.R-project.org/package=tidyr
purrr Rstudio https://CRAN.R-project.org/package=purrr
mclust Rstudio https://doi.org/10.32614/RJ-2016-021
circlize Rstudio https://cran.r-project.org/web/packages/circlize/index.html
ComplexHeatmap Rstudio doi:10.1093/bioinformatics/btw313