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STAR+METHODS

KEY RESOURCES TABLE

REAGENT or RESOURCE

SOURCE

IDENTIFIER

Mouse monoclonal anti-CNG Channel

GeneTex

Cat#GTX79456; RRID: AB_11167547

Rabbit polyclonal anti-CONE ARRESTIN

Merck Millipore

Cat#AB15282; RRID: AB_1163387

Goat polyclonal anti-NRL

R&D systems

Cat#FNK-AF2945; RRID: AB_2155098

Rabbit polyclonal anti-RECOVERIN

ProteinTech

Cat#10073-1-AP; RRID: AB_2178005

Antibodies

Mouse monoclonal anti-RHODOPSIN

Sigma Aldrich

Cat#O4886; RRID: AB_260838

Goat anti-rabbit Alexa- 488

Thermo Fisher Scientific

Cat#A11034

Goat anti-mouse Alexa- 488

Thermo Fisher Scientific

Cat#A11029

Goat anti-mouse Alexa- 594

Thermo Fisher Scientific

Cat#A11032

Donkey anti-goat Alexa- 594

Thermo Fisher Scientific

Cat#A11058

Doxycycline

TAKARA

Cat#631311

9-cis-Retinal

Cayman

Cat#21692

N-acetylcysteine

Wako

Cat#015-05132

Z-VAD-FMK

Peptide Institute

Cat#3188-v

miRNeasy Mini Kit (50)

QUIAGEN

Cat#217004

SuperScript VILO MasterMix

Thermo Fisher Scientific

Cat#11755050

TaqMan Gene expression Master Mix

Thermo Fisher Scientific

Cat#4369016

Lipofectamine LTX Reagent

Thermo Fisher Scientific

Cat#15338100

Pluronic F-127

Sigma-Aldrich

Cat#P2443

Fluo-8 AM

AAT Bioquest

Cat#21080

8-Br-cGMP

Sigma-Aldrich

Cat#B1381

This paper, deposited at NBDC/GEA

J-DS000586

Chemicals, peptides, and recombinant proteins

Critical commercial assays

Deposited data

Single-cell RNA sequencing data

Experimental models: Cell lines

Human iPSCs

RIKEN BioResource Research Center

HPS1042

HPS1749

HPS0063

Human ESCs

WiCell

H9

Kim et al., 2015

Addgene; Plasmid #80474

Recombinant DNA

KW110_PB_TA_ERN (Ef1a_rtTA_neo) vector

RESOURCE AVAILABILITY

Lead contact

Further information and requests for resources and reagents should be directed to and will be fulfilled by

the lead contact, Haruhisa Inoue (haruhisa.inoue@riken.jp).

Materials availability

Antibodies, and other reagents used in this study were commercially available, and company and catalog

numbers were provided in supplemental information. Plasmids generated on this study are available from

the corresponding author on request.

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Data and code availability

Single-cell RNA sequencing data have been deposited at National Bioscience Database Center (NBDC)

and Genomic Expression Archive (GEA) under application number J-DS000586 (https://biosciencedbc.

jp/en/).

This study did not generate novel computer code/ software.

Any additional information required to reanalyze the data reported in this paper is available from the

lead contact upon request.

EXPERIMENTAL MODEL AND SUBJECT DETAILS

iPS and ES cell lines and maintenance

The use of iPSCs and ESCs was approved by the Ethics Committees of RIKEN BioResource Research Center

and department of Medicine and Graduate School of Medicine of Kyoto University. The data on human

iPSCs and ESCs used in the present study are shown in Table S1. Human iPSCs were maintained on laminin

(iMatrix-511; TAKARA, Kusatsu, Japan) in StemFit AK02N medium (Ajinomoto, Tokyo, Japan) at 37
C in a

standard 5% CO2 incubator, according to a published protocol (Nakagawa et al., 2015), with slight modifications. Passages were performed every seventh day. Prior to passaging, culture plates were coated with

laminin in phosphate buffered saline (PBS) at 37
C for at least one hour. iPSC colonies were treated with

TrypLE Select Enzyme (Thermo Fisher Scientific, Waltham, MA) at 37
C for four minutes (min) and dissociated into single cells by gentle pipetting. The dissociated iPSCs were suspended in StemFit medium and

counted with Countess II Automated Cell Counter (Thermo Fisher Scientific). The single-cell iPSC suspension was plated at a density of 13,000 cells per well and cultured in StemFit medium with 10 mM Y-27632

Rock inhibitor (Nacalai-Tesque, Kyoto, Japan). The medium was changed to StemFit without Y-27632 on

the following day and then further changed every other day. ESCs were cultured as well as iPSCs.

METHOD DETAILS

Preparation of a piggyBac vector and introduction into iPSCs

Polycistronic vectors were generated, containing murine cytomegalovirus (mCMV) promoter, CRX and

NEUROD1 under control of the tetracycline operator rtTA and neomycin resistance gene with the

KW110_PB_TA_ERN (Ef1a_rtTA_neo) vector backbone (Kim et al., 2015). The plasmid was gifted from Knut

Woltjen (Addgene plasmid # 80474). For transfection purpose, iPSCs were seeded on laminin coated 6-well

plates at a density of 13,000 cells per well. The cells were grown for three days and transfected with 1.75 mg

of DNA using Lipofectamine LTX Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. The following day, culture medium was changed to StemFit medium. After clone selection using

neomycin (G418 Sulfate; Sigma-Aldrich, St. Louis, MO), stable iPSC and ESC clones were established.

Photoreceptor-like cell differentiation from human iPSCs

For differentiation toward photoreceptor-like cells, we used differentiation media based on the previous reports (Kuwahara et al, 2015), containing DMEM/F12 - Glutamax (Thermo Fisher Scientific), 1% N2 supplement

(Thermo Fisher Scientific), 10% Fetal Bovine Serum (FBS; Thermo Fisher Scientific), 0.5 mM RA (Sigma-Aldrich),

and 0.1 mM taurine (Sigma-Aldrich). CRX and NEUROD1 introduced iPSCs were dissociated with TrypLE

Select and plated on laminin-coated 6-well plates at a density of 150,000 cells per well, with the medium containing 10 mM Y-27632. At this point, 1 mg/ml doxycycline (TAKARA) was added to the medium until three days

before any analysis. After overnight incubation, the medium was changed to fresh medium without Y-27632,

and half of the medium was changed every 2-3 days. ESCs were differentiated as well as iPSCs.

For the formation of 3D structure, iPSCs were dissociated into single cells in TrypLE select and re-aggregated using low-cell adhesion 96-well plates with V-bottomed conical wells (Sumilon PrimeSurface plate;

Sumitomo Bakelite, Tokyo, Japan) in differentiation medium (12,000 cells per well, 100 ml) supplemented

with 20 mM Y-27632 under 5% CO2 at 37
C (defined as day 0). On culture day 3, 50 mL medium was added

to the culture. From day 5, half of the medium was changed every 2-3 days.

Reverse transcription quantitative polymerase chain reaction (RT-qPCR)

Total RNAs were extracted using RNeasy PlusMini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. RNA yields and quality were checked with a NanoDrop spectrophotometer (Thermo

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Fisher Scientific). Complementary DNA (cDNA) was synthesized from 2 mg of mRNA using SuperScript

VILO MasterMix (Thermo Fisher Scientific) following the manufacturer’s recommendations. Synthesized

cDNA was diluted at 1/9 in DNase-free water before performing quantitative PCR. qPCR analysis was performed on QuantStudioTM 12K Flex Real-Time PCR System (Thermo Fisher Scientific) with custom

TaqMan Array 96-Well Fast plates and TaqMan Gene expression Master Mix (Thermo Fisher Scientific)

according to the manufacturer’s instructions. All primers and Minor Groove Binder (MGB) probes labeled

with fluorescein (FAM) for amplification were purchased from Thermo Fischer Scientific (Table S2). Results

were normalized against glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and quantification of

gene expression was based on the Delta Delta Ct Method in three independent biological experiments.

Immunocytochemistry (ICC)

Cells were fixed in 4% paraformaldehyde (PFA) for 15 min at room temperature, washed with PBS and permeabilized in PBS containing 0.2% Triton X-100 for 30 min at room temperature, and incubated with block

reagent (Block Ace; Yukijirushi, Tokyo, Japan). After incubation with primary antibodies overnight at 4
C,

cells were washed three times with PBS and incubated with appropriate secondary antibodies for one hour

at room temperature. Cell images were acquired with FLUOVIEW FV3000 (Olympus Life Science, Tokyo,

Japan) or IN Cell Analyzer 6000 (GE Healthcare, Chicago, IL). The numbers of cells were quantified with

IN Cell Analyzer 6000 and IN CELL Developer toolbox software 1.9. The primary antibodies used in this

assay were listed in Table S3.

The immunostaining procedure for the 3D structure was performed by the following steps. Aggregates

were fixed with 4% PFA for 15 min at room temperature and incubated in 30% sucrose in PBS overnight

at 4
C for cryo-protection. The fixed aggregates were embedded in OCT compound (Sakura Finetek,

Tokyo, Japan) and stored at -80
C. Cryo-sections of 12 mm thickness were made with a Cryostat (Leica, Wetzlar, Germany). Samples were permeabilized with 0.3% Triton X-100 in PBS-T (PBS with 0.1% Tween 20) for

15 min and incubated with block buffer for one hour at room temperature. They were incubated with primary antibodies dilated in blocking buffer at 4
C overnight, followed by incubation with secondary antibodies conjugated with Alexa 488, 594 and DAPI at room temperature for one hour.

Single-cell RNA sequencing

Two dimensional iPRCs on day 28 were collected with Accumax Cell/Tissue Dissociation Solution (Lagen

Laboratories, Rochester, MI) at 37
C for 10 min. The dissociated cells were suspended in PBS containing

10 mM Y-27632 and 0.1% BSA, which was then immediately followed by a library preparation targeting single

cells using the Chromium Next GEM Single Cell 30 Reagent Kits v3.1 (103Genomics, CA) according to the

manufacturer’s instructions. Six thousand cells were analyzed, and the library was sequenced on NovaSeq

6000 (Illumina, San Diego, CA). Cell-specific FASTQ files were generated by deconvolution of UMIs and cell

barcodes using bcl2fastq 2.20.0.422 (Illumina). Alignment to the human reference genome GRCh38 and UMI

counting were conducted by Cell Ranger v6.1.1 pipeline (103Genomics). Data analysis including t-distributed Stochastic Neighbor Embedding (tSNE) were implemented in the Seurat package v3.2.3.

Calcium imaging

For functional analysis, iPRCs on day 21 were collected using Accumax Cell/Tissue Dissociatetion Solution

at 37
C for five min and dissociated into single cells by gentle pipetting. The dissociated cells were suspended in the differentiation medium with 10 mM Y-27632, counted and plated on laminin-coated m-dish

(ibidi, GmbH, Gra¨felfing, Germany) at a density of 200,000 cells in 100 mL per dish. The medium was

changed to differentiation medium without Y-27632 on the following day and doxycycline was removed

on day 25.

After PBS wash, iPRCs on day 28 were exposed to differentiation medium containing 0.05 % Pluronic F-127

(Sigma-Aldrich) and 5 mm Fluo-8 AM (AAT Bioquest, Sunnyvale, CA) at 37
C for 30 min. Cells were washed

with PBS three times and changed to Neurobasal Minus Phenol Red (Thermo Fisher Scientific). Fluorescence intensity of iPRCs was monitored using Nikon A1R MP microscopy (Nikon, Tokyo, Japan). As control,

the medium without cGMP analogue was applied and the trace of fluorescence was recorded. For each

measurement, 30-second baseline activity was recorded before cGMP analogue (8-Br-cGMP; Sigma-Aldrich) was added at a final concentration of 100 mM. Fluorescence change was analyzed with NIS-Elements

AR Analysis software using the formula of Df / f, where f was the average cellular fluorescence during baseline activity and Df was the change from baseline fluorescence.

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Light-induced cell death analysis

Differentiated cells were replated into laminin-coated 24-well plates at a density of 50,000 cells per well on

day 14. After overnight incubation, the medium was changed to fresh medium without Y-27632. Half of the

medium was changed every 2-3 days and doxycycline was removed on day 25. On day 27, the medium was

changed to DMEM/F12, no phenol red (Thermo Fisher Scientific) supplemented with 1% N2 supplement,

0.5 mM RA, 0.1 mM taurine to prevent nutrients from degrading. To activate the phototransduction

cascade, 9-cis-Retinal vitamin A analog (Cayman Chemical, Michigan, CA) was added to the media four

hours before light exposure (final concentration: 10 mM). After iPRCs were treated with N-acetylcysteine

(NAC) (Wako, Osaka, Japan) or 25mM Z-VAD-FMK (Peptide Institute、Osaka, Japan) or vehicle (phenol

free DMEM), the cells were incubated for 1 hour. The cells were then exposed to 10,000 lux white LED light

under 5% CO2 at 37
C for 24 hours. Dark control cells were all from the same stock and were cultured simultaneously in another incubator. We confirmed that medium temperature did not affect the cell viability by

thermometer measurements. Following light exposure, cells were fixed in 4% PFA for immunostaining.

QUANTIFICATION AND STATISTICAL ANALYSIS

We conducted the experiments with biological triplicates and data are expressed as mean G standard error of mean (SEM). Results were analyzed using one-way analysis of variance (ANOVA) followed by Dunnett’s post hoc test or unpaired t-test to determine statistical significances of the data. All analyses were

performed using statistical software (SPSS Statistics 19; SPSS, Inc., Chicago, IL), and statistical significance

was defined as p < 0.05.

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iScience 25, 103987, April 15, 2022

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