| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Human/mouse gremlin antibody | R&D | Cat#AF956 |
| Recombinant Anti-CD34 antibody [EP373Y] | Abcam | Cat#ab81289 |
| Recombinant Anti-CD146 antibody [EPR3208] | Abcam | Cat#ab75769 |
| Anti-alpha smooth muscle Actin antibody | Abcam | Cat#ab5694 |
| Recombinant Anti-Periostin antibody [EPR20806] | Abcam | Cat#ab227049 |
| E-Cadherin (24E10) Rabbit mAb | Cell Signaling Technology | Cat#3195 |
| Purified Rat Anti-Mouse Ly-6G Clone 1A8 | BD Biosciences | Cat#551459 |
| Recombinant Anti-CD4 antibody [EPR19514] | Abcam | Cat#ab183685 |
| CD8α (D4W2Z) XP Rabbit mAb | Cell Signaling Technology | Cat#98941 |
| Anti-CD68 antibody | Abcam | Cat#ab125212 |
| FoxP3 (D6O8R) Rabbit mAb | Cell Signaling Technology | Cat#126553 |
| Ki-67 (D3B5) Rabbit mAb | Cell Signaling Technology | Cat#CS12202S |
| Human/Mouse Active Caspase-3 Antibody | R&D Systems | Cat#AF835 |
| L/D Fixable Green dye | Thermofisher | L34969 |
| Pacific Blue anti-mouse Ly-6A/E (Sca-1) Antibody (4 in 200 uL) | BioLegend | 108119 |
| APC-secondary antibody (10 uL in 1 million cells) | RND | F0108 |
| CD31/cy7 (1 in 200 uL) | eBioscience | 25-0311-82 |
| CD45/cy7 (0.25 in 200 uL) | PharminGen | 561868 |
| Ephb2 primary (0.5 ug/10uL in 1 million cells) | RND | AF467 |
| EpCAM (1 in 200uL) | BD Biosciences | 740281 |
| Fc Block | BD Biosciences | 553141 |
| anti-mouse Ly6a-APC | eBioscience | #17-5981-81 |
| Biological Samples | ||
| Human colorectal polyps and tumors from the S:CORT cohort | S:CORT | N/A |
| Human colorectal tumors from the Oxford BRC Cancer cohort | Oxford BRC Cancer cohort | N/A |
| Human colitis tissue samples from the Oxford GI Biobank | Oxford GI Biobank | N/A |
| Human colorectal polyps from the Oxford GI Biobank | Oxford GI Biobank | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Tamoxifen | Sigma-Aldrich | Cat# T5648 |
| Neutral buffered formalin | Merck | Cat# HT501128-4L |
| Diethyl pyrocarbonate (DEPC) | Merck | Cat# D5758-100ML |
| Diphtheria Toxin (DT) | Merck | Cat # 322326-1mg |
| IFN-γ recombinant mouse protein | Peprotech | Cat # 315-05 |
| IFN-γ recombinant mouse protein | R&D Systems | Cat # 485-MI |
| TGFβ recombinant mouse protein | R&D Systems | Cat # 7666-MB |
| Critical Commercial Assays | ||
| High Pure FFPE RNA Isolation kit | Roche Life Sciences | Cat#06650775001 |
| RNeasy Micro kit | Qiagen | Cat#74004 |
| DNA-free™ DNA Removal Kit | ThermoFisher | Cat#AM1906 |
| Qubit RNA HS Assay Kit | ThermoFisher | Cat#Q32855 |
| Qubit RNA BR Assay Kit | ThermoFisher | Cat#Q10211 |
| QuantSeq 3′ mRNA-Seq Library Prep Kit FWD | Lexogen | Cat#015.96 |
| High Sensitivity D1000 ScreenTape devices | Agilent | Cat#5067-5584 |
| RNAscope Multiplex Fluorescent Detection Kit v2 | Bio-techne | Cat#323110 |
| ISH probe: Mm-Anxa1 | ACD Bio (Bio-techne) | Cat#509291 |
| ISH probe: Hs-ANXA1 | ACD Bio (Bio-techne) | Cat#465319 |
| ISH probe: Mm-Ly6a-C2 | ACD Bio (Bio-techne) | Cat#427571-C2 |
| ISH probe: Hs-PLAUR | ACD Bio (Bio-techne) | Cat#542701 |
| ISH probe: Mm-Clu-C3 | ACD Bio (Bio-techne) | Cat#427891-C3 |
| ISH probe: Hs-CLU | ACD Bio (Bio-techne) | Cat#606241 |
| Deposited Data | ||
| RNA-seq data from the Lgr5DTR;ApcMin mouse experiment | This paper | ArrayExpress: E-MTAB-10470. |
| RNA-seq data from treated intestinal organoids | This paper | ArrayExpress: E-MTAB-11769 ArrayExpress: E-MTAB-11784 |
| Experimental Models: Cell Lines | ||
| villinCreER; KrasG12D/+; Trp53fl/flRosa26N1icd/+ (KPN organoids) | Jackstadt et al., (2019) | N/A |
| villinCreER; KrasG12D/+; Trp53fl/fl (KP organoids) | Jackstadt et al., (2019) | N/A |
| villinCreER; Apcfl/fl; KrasG12D/+; Trp53fl/flTgfbrIfl/fl (AKPT organoids) | Jackstadt et al., (2019) | N/A |
| wild-type C57BL/6J (WT organoids) | This study | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: villinCreER; KrasG12D/+; Trp53fl/flRosa26N1icd/+ (KPN) | Jackstadt et al., (2019) | N/A |
| Mouse: villinCreER; KrasG12D/+; Trp53fl/fl(KP) | Jackstadt et al., (2019) | N/A |
| Mouse: villinCreER; Apcfl/fl; KrasG12D/+;Trp53fl/flTgfbrIfl/fl (AKPT) | Jackstadt et al., (2019) | N/A |
| C57BL/6J-ApcMin/J | The Jackson Laboratory | Stock No: 002020 |
| villinCreER, Tg(Vil-cre/ERT2)23Sy | el Marjou et al., 2004 | N/A |
| Apc (floxed), Apctm1Tno | Shibata and Toyoma (1997) | N/A |
| Rosa26-Notch1 ICD, Gt(ROSA)26Sortm1(Notch1)Dam | Murtaugh et al. (2003) | N/A |
| p53 (floxed), Trp53tm1Brn | (Marino et al., 2000) | N/A |
| Kras (G12D); Krastm4Tyj | Jackson et al. (2001) | N/A |
| Tgfbr1 (floxed), tm1Kar | Larsson et al. (2001) | N/A |
| BrafLSL-V600E/+ | Mercer et al. (2005) | N/A |
| Lgr5tm2(DTR/EGFP)Fjs | Tian et al. (2011) | N/A |
| Software and Algorithms | ||
| ISCindex | This paper | https://doi.org/10.5281/zenodo.6473396 |
| ImageJ | Schneider et al. (2012) | https://ImageJ.nih.gov/ij/ |
| QuPath | Bankhead et al. (2017) | https://qupath.github.io |
| HALO Image analysis software | Indica labs | https://indicalab.com/halo/ |
| BWA-MEM | Li (2013) | http://bio-bwa.sourceforge.net |
| BBTools ver. 38.46 | Bushnell (2014) | sourceforge.net/projects/bbmap/ |
| STAR ver. 2.7.0f | Dobin et al. (2013) | https://github.com/alexdobin/STAR/releases/tag/2.7.0f |
| featureCounts ver. 1.6.4 | Liao et al. (2014) | http://subread.sourceforge.net |
| FastQC version 0.11.8 | http://www.bioinformatics.babraham.ac.uk/projects/fastqc | |
| Trim Galore version 0.6.4. | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | |
| HISAT2 version 2.1.0 | Kim et al., 2019, Koppens et al., 2021 | http://daehwankimlab.github.io/hisat2/ |
| affy package v1.56.0 | Gautier et al. (2004) | http://daehwankimlab.github.io/hisat2/ |
| SingleR | Aran et al. (2019) | https://bioconductor.org/packages/release/bioc/html/SingleR.html |
| scran | Lun et al. (2016) | https://bioconductor.org/packages/release/bioc/html/scran.html |
| Seurat | Satija et al. (2015) | https://satijalab.org/seurat/ |
| GSVA ver 1.38.2 | Hänzelmann et al. (2013) | https://bioconductor.org/packages/release/bioc/html/GSVA.html |
| EdgeR ver. 3.32.1 | Robinson (2010) | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| Limma ver 3.46.0 | Ritchie et al. (2015) | https://bioconductor.org/packages/release/bioc/html/limma.html |
| SIFT | Ng and Henikoff (2003) | https://sift.bii.a-star.edu.sg |
| PolyPhen | Ramensky et al. (2002) | http://genetics.bwh.harvard.edu/pph/ |
| copynumber | Nilsen et al. (2012) | https://bioconductor.org/packages/release/bioc/html/copynumber.html |
| TCGAbiolinks 2.18.0 | https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html | |
| survival 3.2-7 | https://cran.r-project.org/web/packages/survival/index.html | |
| Other | ||
| TCGA RNA-seq, mutation, and copy number alteration data from colon and rectal adenocarcinomas (TCGA-COADREAD) | GDC data portal | https://gdc.cancer.gov/ |
| Human colon single cell RNA sequencing data | Lee et al. (2020) | GEO: GSE132257 GEO: GSE144735 |
| Gene expression microarray data from colorectal tumors | Jorissen et al. (2009) | GEO: GSE14333 |
| Gene expression microarray data from colon cancers | Marisa et al. (2013) | GEO: GSE39582 |
| Single cell RNA-seq data from mouse small intestinal organoids grown in Matrigel or on collagen | Ramadan et al. (2021) | https://github.com/davidhuels/collagen_matrigel_project |
| RNA-seq data from mouse epithelial cells grown in Matrigel or Type I collagen | Yui et al. (2018) | ArrayExpress: E-MTAB-5247 |
| RNA-seq data from mouse small intestinal organoids grown in Matrigel or on Type I collagen | Ramadan et al. (2021) | ArrayExpress: E-MTAB-10082 |
| Gene expression microarray data from multiple random non-adjacent biopsies of colon tumors | Ubink et al. (2017) | GEO: GSE85043 |
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