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    Supplemental Information: Iscience, Volume 26

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    Ceren Celayir
    This document provides supplemental information for a research article. It includes descriptions of experimental methods and additional data in the form of figures and tables. Figure 1 describes a device used for photostimulation of human retinal organoids. Figures 2-5 show additional experimental results related to the effects of light stimulation on gene expression, miRNA levels, and target genes. Tables 1 and 2 list primer sequences used in quantitative PCR experiments and miRNA assays.

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    Supplemental Information: Iscience, Volume 26

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    Ceren Celayir
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    This document provides supplemental information for a research article. It includes descriptions of experimental methods and additional data in the form of figures and tables. Figure 1 describes a device used for photostimulation of human retinal organoids. Figures 2-5 show additional experimental results related to the effects of light stimulation on gene expression, miRNA levels, and target genes. Tables 1 and 2 list primer sequences used in quantitative PCR experiments and miRNA assays.

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    Celiker et al 2023_Suppl_Light-responsive microRNA molecules in human retinal organoids are differentially regulated by distinct wavelengths of light

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    This document provides supplemental information for a research article. It includes descriptions of experimental methods and additional data in the form of figures and tables. Figure 1 describes a device used for photostimulation of human retinal organoids. Figures 2-5 show additional experimental results related to the effects of light stimulation on gene expression, miRNA levels, and target genes. Tables 1 and 2 list primer sequences used in quantitative PCR experiments and miRNA assays.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    8 views9 pages

    Supplemental Information: Iscience, Volume 26

    Uploaded by

    Ceren Celayir
    This document provides supplemental information for a research article. It includes descriptions of experimental methods and additional data in the form of figures and tables. Figure 1 describes a device used for photostimulation of human retinal organoids. Figures 2-5 show additional experimental results related to the effects of light stimulation on gene expression, miRNA levels, and target genes. Tables 1 and 2 list primer sequences used in quantitative PCR experiments and miRNA assays.

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    © All Rights Reserved
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    Download as pdf or txt
    of 9

    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

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