iScience, Volume 26

Supplemental information

Light-responsive microRNA molecules in human

retinal organoids are differentially regulated
by distinct wavelengths of light
Canan Celiker, Kamila Weissova, Katerina Amruz Cerna, Jan Oppelt, Birthe
Dorgau, Francisco Molina Gambin, Jana Sebestikova, Majlinda Lako, Evelyne
Sernagor, Petra Liskova, and Tomas Barta
Supplementary Figure 1: Description of Cell LighteR – a device for photostimulation of human
retinal organoids, related to STAR Methods. A) The Cell LighteR with LED modules. B) Schematic
illustration of the cross-section of a single well in the 96-well plate LED module. C) Emission
wavelengths of individual LED channels. D) Schematic illustration of Cell LighteR. E) Luminous
intensities of individual LED channels. F) Temperature change (ΔT) in a well during photostimulation
using different light intensities relative to dark well, as determined by ultra-thin digital sensor (Dallas
Instrument). G) Expression of BIM and PUMA genes upon 3 hours of photostimulation using different
light intensities, as determined by RT-qPCR.
Supplementary Figure 2: Light stimulation does not upregulate genes involved in apoptosis, DNA
damage and oxidative stress, related to Figure 3. A) Expression of BIM, BAX, BCL2, PUMA, and
TP53 upon 1h and 3h of photo stimulation, as determined by RT-qPCR (n = 3). B) Expression of DUOX1
and GSS upon 1h and 3h of photo stimulation, as determined by RT-qPCR (n = 3). Incubation of retinal
organoids in the presence of 100 µM H2O2 for 3 hours represents a positive control.

Supplementary Figure 3: Number of miRNA reads in each NGS sample, related to STAR
Methods.
Supplementary Figure 4: Expression of selected mir-124 family and mir-216 family target genes,
related to Figure 3. Organoids were photostimulated for 3 hours using white light at 100 lx and
expression of mir-124 family (A) and mir-216 family (B) target genes was assessed using RT-qPCR
approach (n = 3).
Supplementary Figure 5: Characterization of hiPS cell line Neo5 using flowcytometry analysis of
SOX2 and OCT3/4 expression, related to STAR Methods.

Supplementary Table S1: List of the primer sequences used for SYBR-green RT-qPCR, related to
STAR Methods.

Gene Name Gene Sequence (5’-3’)

OPN1SW forward ATACCGCAGCGAGTCCTATAC

OPN1SW reverse GATCCTACCATCACAACCAC

OPN1MW forward CATCTTTGGTTGGAGCAGGTACT

OPN1MW reverse TCTCTGCCTTCTGGGTGGAT

OPN1LW forward GCCTACTTTGCCAAAAGTGC

OPN1LW reverse GATGAGACCTCCGTTTTGGA

RHODOPSIN forward TTTGGAGGGCTTCTTTGCCA

RHODOPSIN reverse CCTCGGGGATGTACCTGGAC

PUMA forward ACGACCTCAACGCACAGTACGA

PUMA reverse CCTAATTGGGCTCCATCTCGGG

BIM forward TTCTGAGTGTGACCGAGAAGG

BIM reverse TGCCTTCAGGATTACCTTGTG

BAX forward TGATGGACGGGTCCGGG

BAX reverse GCAATCATCCTCTGCAGCTC

BCL2 forward CCCGCGACTCCTGATTCATT

BCL2 reverse AGTCTACTTCCTCTGTGATGTTGT

TP53 forward TTCACCCTTCAGATCCGTGG

TP53 reverse AGTCTGAGTCAGGCCCTTCT

GAPDH forward TGCACCACCAACTGCTTAGC

 GAPDH reverse GGCATGGACTGTGGTCATGAG

DUOX1 forward AGGCACCGGACGAGAGAG

DUOX1 reverse CAAAATGGAGACCCTGCGGC

GSS forward CCAAGACCGAAGGCTGTTTGTG

GSS reverse TGTGACCTCTCCAGCAGTAGAC

CSGALNACT1 forward TTGACCCAGAGGAGCAATGA

CSGALNACT1 reverse ACAGCAAGAGGGGACCTGG

LMAN2L forward CGAAGCCCTACCAGGGTGTG

LMAN2L reverse TGCATATCTGGGGTAAGGCG

FAM89A forward GCTCCGCAAAGAGATGGTTG

FAM89A reverse TCCAGAGCGTAAGTGCAGTC

GRIN2A forward GAGCCTCCGGCTGGGATAG

GRIN2A reverse ACTGACGGTCCCTGTAGCC

SDR16C5 forward TCCTTGACTGTCCAGATGAGC

SDR16C5 reverse TTGCACAGTAATCTGCCAGC

NNT forward CCTCCCGGCCCAGTGATT

NNT reverse AGACCCTTACAGGACCCCAA

Supplementary Table S2: List of the miRNA primers/probes used for TaqMan® MicroRNA Assay,
related to STAR Methods.

Assay Name Assay ID Catalog Number #

RNU6B 001093 4440887
mmu-miR-96 000186 4427975
hsa-miR-182 002334 4427975
hsa-miR-183 002269 4427975
hsa-miR-204 000508 4427975
hsa-miR-211 000514 4427975
hsa-miR-196a 241070_mat 4427975
hsa-miR-205 000509 4427975
hsa-miR-145 000467 4427975
hsa-miR-214 002306 4427975