KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological Samples | ||
| Original TCGA tissue and plasma samples | Indivumed | N/A |
| Healthy plasma samples | Duke Hospital | N/A |
| Critical Commercial Assays | ||
| MagAttract PowerSoil DNA KF Kit | Qiagen | Cat# 27000-4-KF |
| QIAamp UCP Pathogen Mini Kit | Qiagen | Cat# 50214 |
| Deposited Data | ||
| TCGA WGS bam files | GDC API | https://api.gdc.cancer.gov/ |
| TCGA WXS bam files | GDC API | https://api.gdc.cancer.gov/ |
| TCGA sequencing metadata | GDC API | https://api.gdc.cancer.gov/ |
| TCGA sample metadata (biotab) | GDC web portal | https://portal.gdc.cancer.gov/ |
| TCGA patient metadata | PanCanAtlas | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| TCGA clinical data resource outcomes | PanCanAtlas | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| Human and microbe reference genomes | PathSeq bundle | ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/pathseq/ |
| Human and microbe reference genomes | PathSeq bundle | ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/pathseq/ |
| Species and genera designated as commensal or MBI-associated (NHSN Organism List) | (CDC-NHSN, 2019) | https://www.cdc.gov/nhsn/pdfs/pscmanual/pcsmanual_current.pdf (Chapter 4 p.33) |
| Genera designated as common contaminants | (Eisenhofer et al., 2019) | Table 1 |
| Genome for B. vulgatus | GenBank | CP000139.1 |
| Genome for A. junii | GenBank | NZ_CP019041.1 |
| Genome for E. coli | GenBank | U00096.3 |
| Genome for C. provencense | GenBank | NZ_CP024988.1 |
| Genome for F. nucleatum | GenBank | AE009951.2 |
| Pks gene cluster (colibactin) | GenBank | AM229678.1 |
| Greengenes classifier (gg-13-8-99-515-806-nb-classifier.qza) | (DeSantis et al., 2006) | https://docs.qiime2.org/ |
| TCGA mRNA-seq data | PanCanAtlas | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| TCGA miRNA-seq data | PanCanAtlas | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| TCGA RPPA data | PanCanAtlas | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| TCGA DNA Methylation 27K data | PanCanAtlas | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| PARADIGM Pathway inference matrix | PanCanAtlas | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| Gene sets for GSEA (KEGG, GO) | MSigDB v7.1 | https://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp |
| TCMA tissue-resident profiles (COAD, READ, HNSC, ESCA, STAD) | This paper | https://doi.org/10.7924/r4rn36833 |
| 16S sequencing results | This paper | N/A |
| Oligonucleotides | ||
| Primers for 16S analysis FWD:GTGYCAGCMGCCGCGGTAA REV:GGACTACNVGGGTWTCTAAT |
IDT | N/A |
| Software and Algorithms | ||
| GATK 4.0.3 (PathSeq & HaplotypeCaller) | (Kostic et al., 2011; Poplin et al., 2017) | https://github.com/broadinstitute/gatk/ |
| SAMtools 1.9 | (Li et al., 2009) | http://samtools.sourceforge.net/ |
| phyloseq 1.30.0 | (McMurdie and Holmes, 2013) | https://github.com/joey711/phyloseq |
| metacoder 0.3.3 | (Foster et al., 2017) | https://grunwaldlab.github.io/metacoder_documentation/ |
| gffread 0.11.6 | (Pertea and Pertea, 2020) | https://github.com/gpertea/gffread |
| STAR 2.7.3a | (Dobin et al., 2013) | https://github.com/alexdobin/STAR/ |
| subread 1.6.4 | (Liao et al., 2014) | http://subread.sourceforge.net/ |
| deepTools 3.3.0 | (Ramírez et al., 2014) | https://github.com/deeptools/deepTools |
| bedtools 2.29.0 | (Quinlan and Hall, 2010) | https://github.com/arq5x/bedtools2 |
| circos 0.69.8 | (Krzywinski et al., 2009) | http://circos.ca/software/download/ |
| IGV 2.4.14 | (Thorvaldsdottir et al., 2013) | http://software.broadinstitute.org/software/igv/ |
| QIIME2 2019.7 | (Bolyen et al., 2019) | https://qiime2.org/ |
| SparCC | (Friedman and Alm, 2012) | https://bitbucket.org/yonatanf/sparcc/src/default/ |
| MicroPattern | (Ma et al., 2017) | http://www.cuilab.cn/micropattern |
| lifelines 0.23.8 | (Davidson-Pilon et al., 2020) | https://github.com/CamDavidsonPilon/lifelines/tree/0.24.6 |
| GSEA 4.0.3 | (Subramanian et al., 2007) | https://www.gsea-msigdb.org/gsea/ |
| Other | ||
| Patient metadata for TCGA validation samples | This paper | Table S1 |
| Tumor- and normal tissue-associated taxa | This paper | Table S2 |