KEY RESOURCES TABLE.

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-Annexin A1	Abcam	Cat# ab214486
anti-BASP1	Abcam	Cat# ab214322
anti-Chromogranin A	Abcam	Cat# ab15160; RRID: AB_301704
anti-CLCA1	Abcam	Cat# ab180851; RRID: AB_2722611
anti-Lysozyme	Agilent	Cat# F037201–1; RRID: AB_578661
anti-Rabbit IgG (secondary, 555)	Thermo Fisher Scientific	Cat# A21428; RRID: AB_2535849
anti-Rabbit IgG (secondary, 647)	Life Technologies	Cat# A21245; RRID: AB_2535813
anti-Villin	Santa Cruz Biotechnology	Cat# sc-58897-AF647; RRID: AB_2304475
Biological Samples
Intestinal organoids from Mouse: Lgr5-DTR-EGFP	This paper	N/A
Intestinal organoids from Mouse: Lgr5-DTR-EGFP/Villin-H2B-mCherry	This paper	N/A
Chemicals, Peptides, and Recombinant Proteins
B27	Thermo Fisher Scientific	Cat# 17504–044
Cell Recovery Solution	Corning	Cat# 354253
CFTRinh-172	Selleck Chemicals	Cat# S7139
Complete crypt culture medium containing EGF, Noggin, and R-Spondin-1 (ENR)	R&D Systems Protocols	https://resources.rndsystems.com/images/site/dw_r-spondinmediumprotocol_34749-web.pdf?v=1
Complete crypt culture medium containing Wnt3a, EGF, Noggin, and R-Spondin-1 (WENR)	Miyoshi and Stappenbeck, 2013	N/A
Diethylaminoethyl (DEAE)-Dextran	Millipore Sigma	SKU- D9885
Forskolin	Selleck Chemicals	Cat# S2449
GdCl3	Millipore Sigma	SKU- G7532
Glutamax	Thermo Fisher Scientific	Cat# 35050–079
GsMTx4	Abcam	Cat# ab141871
Hanks’ Buffer with 20 mM Hepes	AAT Bioquest	Cat# 20011
Matrigel, growth factor reduced, phenol red-free	Corning	Cat# 356231
N-acetyl cysteine 500 mM stock solution	Millipore Sigma	SKU- A7250
N2	Thermo Fisher Scientific	Cat# 17502–048
Noggin	Millipore Sigma	SKU- SRP3227
Ouabain	Tocris	Cat# 1076
Pluronic® F-127	AAT Bioquest	Cat# 20050
Poly(2-hydroxyethyl methacrylate)	Millipore Sigma	SKU- P3932
Primocin	Invivogen	Cat# ant-pm-1
Probenecid	AAT Bioquest	Cat# 20060
Puromycin dihydrochloride	Thermo Fisher Scientific	Cat# A1113803
Recombinant mouse EGF	Thermo Fisher Scientific	Cat# PMG8041
Yoda1	Tocris	Cat# 5586
Critical Commercial Assays
Calcium indicator kit	AAT Bioquest	Cat# 20530
EdU staining kit (AlexaFluor647)	Thermo Fisher Scientific	Cat# C10640
NEBNext Ultra II FS DNA Library Prep kit	NEB	Cat# E7805S
Deposited Data
In vivo reference data for Figure 1D	Haber et al., 2017	GEO: GSE92332
Mouse genome build 38 (GRCm38)	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/
Raw and analyzed single cell RNA-sequencing data	This paper	GEO: GSE164368
Experimental Models: Cell Lines
Human: HEK293T	ATCC	Cat# CRL-3216; RRID: CVCL_0063
Mouse: 293T-HA-RspoI-Fc	Trevigen	Cat# 3710–001-01; RRID: CVCL_RU08
Mouse: L-WRN	ATCC	Cat# CRL-3276; RRID: CVCL_DA06
Experimental Models: Organisms/Strains
Mouse: B6;129S-Gt(ROSA)26Sortm1.1Ksvo/J	Jackson Laboratories	Cat# 023139; RRID:IMSR_JAX:023139
Mouse: B6.Cg-Tg(Vil1-cre)997Gum/J	Jackson Laboratories	Cat# 004586; RRID:IMSR_JAX:004586
Mouse: Lgr5-DTR-EGFP	Tian et al., 2011	N/A
Mouse: Lgr5-DTR-EGFP/Villin-H2B-mCherry	This paper	N/A
Oligonucleotides
RT primers on hydrogel beads: 5’CGATTGATCAACGTAATACGACTCACTATAGGGTGTCGGGTGCAG[bc1,8nt]GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG[bc2,8nt]NNNNNNTTTTTTTTTTTTTTTTTTTV- 3’	This paper; HMS Single Cell Core	N/A
TSO primer: 5’-AAGCAGTGGTATCAACGCAGAGTACATrGrGrG-3’	Datlinger et al., 2019	N/A
Fwd cDNA primer: 5’- CACTATAGGGTGTCGGGTGCAG-3’	This paper; HMS Single Cell Core	N/A
Rev cDNA primer: 5’-AAGCAGTGGTATCAACGCAGAGT-3’	This paper; HMS Single Cell Core	N/A
Ligation Fwd primer: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC	This paper; HMS Single Cell Core	N/A
Ligation Rev primer: 5’- /5AmMC6/GCTCTTCCGATCT -3’	This paper; HMS Single Cell Core	N/A
Indexing primer PCR_p7_r2: 5’-CAAGCAGAAGACGGCATACGAGATGGGTGTCGGGTGCAG-3’	This paper, HMS Single Cell Core	N/A
Indexing primer PCR_p5_r1_ixx: 5’-AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3’	This paper; HMS Single Cell Core	N/A
Recombinant DNA
Plasmid: pLVX-H2B-iRFP670	This paper; Kyogo Kawaguchi	N/A
Software and Algorithms
3D Distance Transform algorithm	Mishchenko, 2015	https://link.springer.com/article/10.1007%2Fs11760-012-0419-9
Exact unbiased inverse of the Anscombe variance-stabilizing transformation – MATLAB implementation	Makitalo and Foi, 2011	https://ieeexplore.ieee.org/document/5721817
Image Denoising by Sparse 3-D Transform-Domain Collaborative Filtering – MATLAB implementation	Dabov et al., 2007	https://ieeexplore.ieee.org/document/4271520
Fiji	Schindelin, J., Arganda-Carreras, I. & Frise, E. et al., 2012	https://imagej.net/Fiji
Imaris 8.4	Oxford Instruments	https://imaris.oxinst.com/support/imaris-release-notes/8-4-0
inDrops pipeline package	Klein et al., 2015; Github	https://github.com/indrops/indrops
Scanpy – Single Cell Analysis in Python	Wolf et al., 2018	https://scanpy.readthedocs.io/en/stable/
Scrublet – Single Cell Removal of Doublets	Wolock et al., 2019	https://github.com/AllonKleinLab/scrublet
Other
Interactive visualization of scRNA-seq data with SPRING - Sandwich and dome data (without stretch signature annotation)	This paper	https://kleintools.hms.harvard.edu/tools/springViewer_1_6_dev.html?datasets/SPRING_private/mouse_intestinal_organoids_21/murine_intestinal_organoid_sandwich_dome_culture_merged_no_stretch_signature/all_cells
Interactive visualization of scRNA-seq data with SPRING - Sandwich and dome data (with stretch signature annotation)	This paper	https://kleintools.hms.harvard.edu/tools/springViewer_1_6_dev.html?datasets/SPRING_private/mouse_intestinal_organoids_21/murine_intestinal_organoid_sandwich_dome_culture_merged/all_cells
Interactive visualization of scRNA-seq data with SPRING - Perturbation data	This paper	https://kleintools.hms.harvard.edu/tools/springViewer_1_6_dev.html?datasets/SPRING_private/mouse_intestinal_organoids_21/murine_intestinal_organoid_inflation_perturbation_expt/all_cells
Jupyter notebooks for scRNA-seq data analysis	This paper	https://github.com/AllonKleinLab/paper-data/tree/master/Tallapragada_Cambra_2021