KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological Samples | ||
| Original TCGA tissue | Indivumed | N/A |
| Colon cancer mucosal samples (adenocarcinoma) | Weill Cornell Medicine | N/A |
| Critical Commercial Assays | ||
| Sabouraud dextrose broth | VWR | Cat# 89406–400 |
| Sabouraud 4% dextrose agar | VWR | Cat# EM1.05438.0500 |
| Glycerol monostearate (Alfa Aesar) | Thermo Fisher Scientific | Cat# AA4388330 |
| modified Dixon (mDixon) | ATCC protocol | N/A |
| Deposited Data | ||
| TCGA WGS bam files | GDC API (Legacy) | https://portal.gdc.cancer.gov/legacy-archive |
| TCGA RNA-seq bam files | GDC API | https://api.gdc.cancer.gov/ |
| HCMI RNA-seq 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/ |
| TCGA mRNA-seq data | PanCanAtlas | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| Gene sets for GSEA (KEGG) | MSigDB v7.1 | https://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp |
| TCMA bacterial profiles (COAD, READ, HNSC, ESCA, STAD) | TCMA database | https://doi.org/10.7924/r4rn36833 |
| Software and Algorithms | ||
| GATK 4.2.0 (PathSeq) | (Walker et al., 2018) | https://github.com/broadinstitute/gatk/ |
| TaxaTarget | (Commichaux et al., 2021) | https://github.com/SethCommchaux/taxaTarget |
| SAMtools v1.9, v1.14 | (Li et al., 2009) | http://samtools.sourceforge.net/ |
| Burrows-Wheeler Aligner | (Li and Durbin, 2009) | http://bio-bwa.sourceforge.net/ |
| BEDTools | (Quinlan and Hall, 2010) | https://bedtools.readthedocs.io/ |
| deepTools2 | (Ramirez et al., 2016) | https://deeptools.readthedocs.io/ |
| pyGenomeTracks | (Lopez-Delisle et al., 2021) | https://github.com/deeptools/pyGenomeTracks |
| 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/ |
| STAR 2.7.3a | (Dobin et al., 2013) | https://github.com/alexdobin/STAR/ |
| SparCC | (Friedman and Alm, 2012) | https://bitbucket.org/yonatanf/sparcc/src/default/ |
| 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 | ||
| Decontamination analysis | This paper | Table S1, Related to Figure 1 |
| Fungal composition of TCGA samples | This paper | Table S2, Related to Figures 1–7 |
| False-discovery rate adjustments | This paper | Table S3, Related to Figures 1–7 |