Overview

This collection contains 44 deeply ingested organoid protocol papers (29 from Round 1 + 15 from Rounds 2-4 gap-filling) spanning foundational hPSC differentiation, adult and patient-derived systems, multi-lineage developmental models, second-wave assay or perturbation workflows, cross-protocol benchmarking, organ+vascular intersections, and pancreatic islet maturation.

What this collection is good for

finding baseline protocols for brain, gastrointestinal, kidney, heart, lung, skin, bone marrow, and gastric organoids
comparing self-organizing versus more directed patterning strategies
identifying when organoid work shifts from derivation into coculture, transplantation, imaging, or screening
choosing between developmental hPSC systems and adult or patient-derived organoid platforms

Major protocol families

Foundational derivation and regional patterning

McCracken 2011
Lancaster 2014
Xia 2014
Takasato 2016
Morizane 2016
Sloan 2018
Broda 2018
Miller 2019
Drakhlis 2021
Vanslambrouck 2023
Ullah 2025

Adult stem and patient-derived platforms

Drost 2016
Broutier 2016
Driehuis 2020
Hendriks 2020
Dekkers 2021

Functional extensions and validation layers

Cattaneo 2019
Puschhof 2021
Co 2021
Watanabe 2022
Kelley 2024
Meng 2025

Multi-lineage and complexity-oriented systems

Koike 2021
Lee 2022
Matkovic Leko 2023
Olijnik 2024
Fitzgerald 2024
Dardano 2025

Brain organoid benchmarking and cross-protocol atlases (Rounds 2-3)

Velasco 2019 — dorsally patterned reproducibility (Nature)
Yoon 2019 — cortical spheroid reliability (Nat Methods, Pasca lab)
Bhaduri 2020 — cell stress and fidelity counterpoint (Nature, Kriegstein lab)
Kanton 2019 — temporal + cross-species scRNA-seq atlas (Nature)
He 2024 — integrated cross-protocol cell atlas, 26 protocols, 1.7M cells (Nature)

Organ+vascular intersections (Round 4)

Wimmer 2019 — standalone blood vessel organoid (Nat Protoc)
Cakir 2019 — ETV2-driven vascularized brain organoid (Nat Methods)
Homan 2019 — flow-enhanced kidney vascularization on chip (Nat Methods)
Wörsdorfer 2019 — MPC-incorporated multi-lineage vascular organoids (Sci Rep)

New organ systems (Rounds 2-3)

Pereira 2021 — sensorimotor organoid with NMJs (spinal cord/neuromuscular, Nat Comms)
Kuwahara 2015 — retinal organoid with ciliary margin niche (Sasai lab, Nat Comms)
Koehler 2017 — inner ear organoid with functional hair cells (Nat Biotech)
van der Valk 2025 — vestibular inner ear organoid protocol (Nat Protoc)
Hogrebe 2021 — planar SC-β cell differentiation (Nat Protoc)
Balboa 2022 — SC-islet functional maturation benchmarking (Nat Biotech)