Nature - USA (2020-09-24)

2

nature research | reporting summary

October 2018

guts/80819. Source Data for Figures 2j,k and Extended Data Figures 4e, 5, 8b, 9e-f are provided with the paper.

Field-specific reporting

Please select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before making your selection.

Life sciences Behavioural & social sciences Ecological, evolutionary & environmental sciences

For a reference copy of the document with all sections, see nature.com/documents/nr-reporting-summary-flat.pdf

Life sciences study design

All studies must disclose on these points even when the disclosure is negative.

Sample size The study is aimed at the development of a novel bioengineering concept. No specific hypothesis was tested and no sample calculation,

allocation of samples to different groups and randomization was performed. The in vitro modeling of cryptosporidium infection and the

epithelial damage and regeneration were performed as a proof-of-concept of the novel organoid culture system. 2-4 replicates were tested

for each set of experiment, experiments were performed at least twice with similar outcomes.

Data exclusions Exclusion criteria were predetermined to avoid the use of mechanically damaged and other visually defective samples. Total defects rate on

all fabrication steps was less than 10%. Additional details on culture reproducibility are provided in the methods section.

Replication Single cell RNAseq of mini-guts has been done once with n=3 per each condition. Characterization experiments involving assessment of mini-

gut cell type composition via immunofluorescence microscopy/TEM and long-term culture via imaging were reproduced at least twice with

the same results. All other experiments involving functional assays, such as aminopeptidase activity measuremenents, damage/regeneration

and Cryptosporidium infection studies have been reproduced more that two times, with similar outcomes. All experiments were reproducible

as assessed in multiple mini-gut culture microdevices per experiment.

Randomization Mini-gut chips were randomly allocated into the experimental groups.

Blinding All mini-guts sequencing data collection was done blindly. For other assays, investigators were not blinded with respect to the identities of the

samples. However, all experimental and control samples were collected/analyzed at the same time under the same condition, and data

analysis was carried out with the same software settings.

Reporting for specific materials, systems and methods

We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material,

system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.

Materials & experimental systems

n/a Involved in the study

Antibodies

Eukaryotic cell lines

Palaeontology

Animals and other organisms

Human research participants

Clinical data

Methods

n/a Involved in the study

ChIP-seq

Flow cytometry

MRI-based neuroimaging

Antibodies

Antibodies used anti-Lysozyme (Thermo fisher scientific #PA1-29680, clone NA (Polyclonal), dilution 1:50)

anti-Mucin2 (Santa Cruz #sc-15334, clone NA (Polyclonal), lot K0315 no longer available, dilution 1:50)

anti-Chromogranin-A (Santa Cruz #sc-13090, clone NA (Polyclonal),no longer available, dilution 1:50)

anti-E-cadherin (Abcam #ab11512, clone DECMA-1, dilution 1:50)

anti-Sox9 (Abcam #ab185966, clone EPR14335-78, dilution 1:50)

anti-Ki67 (BD Pharmingen #550609, clone B56, dilution 1:50)

anti-GP2 (MBL #D278-3, clone 2F11-C3, dilution 1:50)

anti-L-FABP (Santa Cruz #sc-50380, clone NA (Polyclonal), dilution 1:50)

Anti-EpCAM (Thermo fisher scientific 17-5791-82, clone G8.8, APC conjugated, dilution 1:200)

Anti-ZO-1 (Thermo fisher scientific 33-9100, clone ZO1-1A12, dilution 1:50)

Alexa Fluor 647 goat anti rabbit IgG (Thermo fisher scientific A21245, clone NA (Polyclonal), dilution 1:500)

Alexa Fluor 546 goat anti mouse IgG (Thermo fisher scientific A11030, clone NA (Polyclonal), dilution 1:500)

Alexa Fluor 488 goat anti rat IgG (Thermo fisher scientific A11006, clone NA (Polyclonal), dilution 1:500)

Alexa Fluor 568 donkey anti mouse IgG (Thermo fisher scientific A10037, clone NA (Polyclonal), dilution 1:500)

Alexa Fluor 568 donkey anti rabbit IgG (Thermo fisher scientific A10042, clone NA (Polyclonal), dilution 1:1000)