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. Author manuscript; available in PMC: 2023 Oct 10.
Published in final edited form as: Cancer Cell. 2022 Oct 10;40(10):1240–1253.e5. doi: 10.1016/j.ccell.2022.09.009

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit monoclonal anti-CA19-9 clone CA19.9/1390R Novus Cat#NBP2-54585APC
Biological samples
Fresh human tumor samples This paper See deposited data section
Chemicals, peptides, and recombinant proteins
Collagenase Gibco Cat#17100-017
DNaseI Sigma Cat#DN25
Hyalaronidase Sigma Cat#H3506
ACK lysing buffer Gibco Cat#A10492-01
Critical commercial assays
Qiagen blood and cell culture DNA mini kit Qiagen 13323
QIAamp Fast DNA Tissue Kit Qiagen 51404
RNeasy Mini Kit Qiagen 74104
High Sensitivity dsDNA kit Invitrogen Q32851
RNA High Sensitivity kit Invitrogen Q32852
Deposited data
Genomic data This paper dbGaP: phs003035.v1
Processed data This paper https://github.com/sjdlabgroup/SAHMI
scPDA1 scRNA-seq counts data Peng et al., 2019 GSA: CRA001160
scPDA2 scRNA-seq counts data Steele et al., 2020 dbGaP: phs002071
TCGA microbiome genus level summarized read counts Poore et al., 2020 ftp://ftp.microbio.me/pub/cancer_microbiome_analysis/
16S rDNA-seq of pancreatic tumors Nejman et al., 2020 DOI: 10.1126/science.aay9189
TCGA PAAD normalized bulk RNA-seq and clinical data Raphael et al., 2017 https://tcga-data.nci.nih.gov/docs/publications/
ICGC pancreatic cancer normalized bulk RNA-seq and clinical data Hudson et al., 2010 https://dcc.icgc.org/repositories
CPTAC3 pancreatic cancer normalized bulk RNA-seq and clinical data Cao et al., 2021 dbGaP: phs001287.v1.p1
scRNA-seq of normal pancreas tissue Baron et al., 2016 GEO: GSE84133
Software and algorithm
SAHMI (v1.0) This paper, and Ghaddar et al. 2022 https://github.com/sjdlabgroup/SAHMI DOI: 10.5281/zenodo.7017103
R (v3.6.1) R CRAN https://www.r-project.org/
Kraken2Uniq (v2) Wood et al., 2019 https://github.com/DerrickWood/kraken2
STAR (v2.7.3) Dobin et al., 2013 https://github.com/alexdobin/STAR
Salmon (v1.9.0) Patro et al., 2017 https://github.com/COMBINE-lab/salmon
Seurat Stuart et al., 2019 https://cran.r-project.org/web/packages/Seurat/index.html
Tidyverse (v1.3.2) R CRAN https://www.tidyverse.org/
clusterProfiler Yu et al., 2016 https://guangchuangyu.github.io/software/clusterProfiler/
ReactomePA Yu et al., 2016 https://yulab-smu.top/biomedical-knowledge-mining-book/reactomepa.html
Survminer R CRAN https://github.com/kassambara/survminer
RTCGA Bioconductor https://www.bioconductor.org/packages/release/bioc/html/RTCGA.html