Source Name	Characteristics[sample_name]	Characteristics[organism]	Characteristics[taxonomy_id]	Characteristics[isolate]	Characteristics[biomaterial_provider]	Characteristics[age]	Characteristics[cell_type]	Characteristics[sex]	Characteristics[tissue]	Comment[BioSample]	Comment[sample_title]	Comment[description]	Protocol REF	Protocol REF	Protocol REF	Extract Name	Material Type	Comment[LIBRARY_LAYOUT]	Comment[LIBRARY_SELECTION]	Comment[LIBRARY_SOURCE]	Comment[LIBRARY_STRATEGY]	Comment[INSTRUMENT_MODEL]	Protocol REF	Assay Name	Comment[SRA_EXPERIMENT]	Comment[SRA_RUN]	Technology Type	Array Data File	Protocol REF	Derived Array Data File	Factor Value[cell_type]	Factor Value[compound]
Rn1474	Rn1474	Homo sapiens	9606	not applicable	Knut Woltjen	not applicable	hiPS cell derived IPCs, no RA	not applicable	not applicable	SAMD00449556	IPC, no RA, 317-12 iPSC derived	hiPSCs (201B7) were gene-edited to create hiPSCs (317-12), which were used in this study. hiPSCs were first treated using an enzymatic method with a 1:1 mixture of TrypLE Select Enzyme and 0.5 mM EDTA/PBS for 5 min and washed with PBS(-). The cells were then detached using a cell scraper, dissociated into single cells by gentle pipetting and seeded onto 24-well plates (CORNING) at a density of 1.3*10^4 cells/cm^2 with 0.5 mL of Stem Fit AK02N supplemented with 10 uM Y-27632 (day -1) and 2.4 uL/mL iMatrix-511 (Nippi). After 24 h (day 0), the cells were cultured with serum-free differentiation medium consisting of DMEM/F12 Glutamax medium (Thermo Fisher Scientific), B27 supplement minus vitamin A (Thermo Fisher Scientific), and 0.5X Penicillin/streptomycin (hereafter called basal medium) supplemented with 5 uM CHIR99021 (Wako), 10 nM RA (SIGMA), 1 ng/mL BMP4 (Peprotech), and 100 ng/mL bFGF (Wako). After another 24 h (day 1), the cells were cultured with 5 uM CHIR99021, 100 ng/mL bFGF, and 1 ng/mL BMP7 (R&D Systems). After a third 24 h (day 2), the medium was switched to basal medium containing 5 uM CHIR99021, 1 ng/mL BMP7, and 10 uM A83-01 (Wako). After a fourth 24 h (day 3), the medium was changed to basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A (R&D Systems), and 30 yM Y-27632 (Wako). After a fifth 24 h (day 4), the cells were washed with PBS (-), treated with Accumax (Innovative Cell Technologies, Inc.), dissociated into single cells by gentle pipetting. On day 4 of PPS induction, the cells were seeded on 96-well U-bottom plates (Sumitomo Bakelite or Thermo Fisher Scientific) at a density of 2.0*10^4 cells/well with basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A and 30 uM Y-27632, to form cellular aggregates and cultured for 48 h. On day 6, the cells were incubated with AK02N minus bFGF medium (Ajinomoto) containing 1 uM CHIR99021, 500 nM Smoothened Agonist (SAG) (Selleck), 10 uM SB431542 (Nakalai tesque) and 10 ng/mL IL-1b (Wako). On day 8, the medium was changed to AK02N minus bFGF medium containing 1 uM CHIR99021, 500 nM/mL SAG and 10 uM SB431542 for 72 h.	P-GEAD-1163	P-GEAD-1164	P-GEAD-1165	Rn1474	total RNA	PAIRED	cDNA_randomPriming	TRANSCRIPTOMIC	RNA_SEQ	Illumina NovaSeq 6000	P-GEAD-1166	Rn1474	DRX342258	DRR356347	sequencing assay	DRR356347	P-GEAD-1167	Rn1474.txt	317-12	none
Rn1473	Rn1473	Homo sapiens	9606	not applicable	Knut Woltjen	not applicable	hiPS cell derived IPCs	not applicable	not applicable	SAMD00449555	IPC, 317-12 iPSC derived	hiPSCs (201B7) were gene-edited to create hiPSCs (317-12), which were used in this study. hiPSCs were first treated using an enzymatic method with a 1:1 mixture of TrypLE Select Enzyme and 0.5 mM EDTA/PBS for 5 min and washed with PBS(-). The cells were then detached using a cell scraper, dissociated into single cells by gentle pipetting and seeded onto 24-well plates (CORNING) at a density of 1.3*10^4 cells/cm^2 with 0.5 mL of Stem Fit AK02N supplemented with 10 uM Y-27632 (day -1) and 2.4 uL/mL iMatrix-511 (Nippi). After 24 h (day 0), the cells were cultured with serum-free differentiation medium consisting of DMEM/F12 Glutamax medium (Thermo Fisher Scientific), B27 supplement minus vitamin A (Thermo Fisher Scientific), and 0.5X Penicillin/streptomycin (hereafter called basal medium) supplemented with 5 uM CHIR99021 (Wako), 10 nM RA (SIGMA), 1 ng/mL BMP4 (Peprotech), and 100 ng/mL bFGF (Wako). After another 24 h (day 1), the cells were cultured with 5 uM CHIR99021, 100 ng/mL bFGF, and 1 ng/mL BMP7 (R&D Systems). After a third 24 h (day 2), the medium was switched to basal medium containing 5 uM CHIR99021, 1 ng/mL BMP7, and 10 uM A83-01 (Wako). After a fourth 24 h (day 3), the medium was changed to basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A (R&D Systems), and 30 yM Y-27632 (Wako). After a fifth 24 h (day 4), the cells were washed with PBS (-), treated with Accumax (Innovative Cell Technologies, Inc.), dissociated into single cells by gentle pipetting. On day 4 of PPS induction, the cells were seeded on 96-well U-bottom plates (Sumitomo Bakelite or Thermo Fisher Scientific) at a density of 2.0*10^4 cells/well with basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A and 30 uM Y-27632, to form cellular aggregates and cultured for 48 h. On day 6, the cells were incubated with AK02N minus bFGF medium (Ajinomoto) containing 1 uM CHIR99021, 0.1 uM RA, 500 nM Smoothened Agonist (SAG) (Selleck), 10 uM SB431542 (Nakalai tesque) and 10 ng/mL IL-1b (Wako). On day 8, the medium was changed to AK02N minus bFGF medium containing 1 uM CHIR99021, 0.1 uM RA, 500 nM/mL SAG and 10 uM SB431542 for 72 h.	P-GEAD-1163	P-GEAD-1164	P-GEAD-1165	Rn1473	total RNA	PAIRED	cDNA_randomPriming	TRANSCRIPTOMIC	RNA_SEQ	Illumina NovaSeq 6000	P-GEAD-1166	Rn1473	DRX342259	DRR356348	sequencing assay	DRR356348	P-GEAD-1167	Rn1473.txt	317-12	retinoic acid
Rn1557	Rn1557	Homo sapiens	9606	not applicable	Kenji Osafune	not applicable	hiPS cell derived IPCs, replicate1	not applicable	not applicable	SAMD00449551	IPC, 17K6 iPSC derived, replicate1	FOXD1 reporter iPSCs (17K6) were generated by gene targeting of iPSCs (201B7) and used in this study. hiPSCs were first treated using an enzymatic method with a 1:1 mixture of TrypLE Select Enzyme and 0.5 mM EDTA/PBS for 5 min and washed with PBS(-). The cells were then detached using a cell scraper, dissociated into single cells by gentle pipetting and seeded onto 24-well plates (CORNING) at a density of 1.3*10^4 cells/cm^2 with 0.5 mL of Stem Fit AK02N supplemented with 10 uM Y-27632 (day -1) and 2.4 uL/mL iMatrix-511 (Nippi). After 24 h (day 0), the cells were cultured with serum-free differentiation medium consisting of DMEM/F12 Glutamax medium (Thermo Fisher Scientific), B27 supplement minus vitamin A (Thermo Fisher Scientific), and 0.5X Penicillin/streptomycin (hereafter called basal medium) supplemented with 5 uM CHIR99021 (Wako), 10 nM RA (SIGMA), 1 ng/mL BMP4 (Peprotech), and 100 ng/mL bFGF (Wako). After another 24 h (day 1), the cells were cultured with 5 uM CHIR99021, 100 ng/mL bFGF, and 1 ng/mL BMP7 (R&D Systems). After a third 24 h (day 2), the medium was switched to basal medium containing 5 uM CHIR99021, 1 ng/mL BMP7, and 10 uM A83-01 (Wako). After a fourth 24 h (day 3), the medium was changed to basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A (R&D Systems), and 30 uM Y-27632 (Wako). After a fifth 24 h (day 4), the cells were washed with PBS (-), treated with Accumax (Innovative Cell Technologies, Inc.), dissociated into single cells by gentle pipetting. On day 4 of PPS induction, the dissociated cells were cryopreserved using STEM-CELLBANKER (ZNQ). The thawed cells were seeded on 96-well U-bottom plates (Sumitomo Bakelite or Thermo Fisher Scientific) at a density of 2.0*10^4 cells/well with basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A and 30 uM Y-27632, to form cellular aggregates and cultured for 48 h. On day 6, the cells were incubated with AK02N minus bFGF medium (Ajinomoto) containing 1 uM CHIR99021, 0.1 uM RA, 500 nM Smoothened Agonist (SAG) (Selleck), 10 uM SB431542 (Nakalai tesque) and 10 ng/mL IL-1b (Wako). On day 8, the medium was changed to AK02N minus bFGF medium containing 1 uM CHIR99021, 0.1 uM RA, 500 nM/mL SAG and 10 uM SB431542 for 72 h.	P-GEAD-1163	P-GEAD-1164	P-GEAD-1165	Rn1557	total RNA	PAIRED	cDNA_randomPriming	TRANSCRIPTOMIC	RNA_SEQ	Illumina NovaSeq 6000	P-GEAD-1166	Rn1557	DRX342260	DRR356349	sequencing assay	DRR356349	P-GEAD-1167	Rn1557.txt	FOXD1 reporter iPSC (17K6)	retinoic acid
Rn1558	Rn1558	Homo sapiens	9606	not applicable	Kenji Osafune	not applicable	hiPS cell derived IPCs, replicate2	not applicable	not applicable	SAMD00449552	IPC, 17K6 iPSC derived, replicate2	FOXD1 reporter iPSCs (17K6) were generated by gene targeting of iPSCs (201B7) and used in this study. hiPSCs were first treated using an enzymatic method with a 1:1 mixture of TrypLE Select Enzyme and 0.5 mM EDTA/PBS for 5 min and washed with PBS(-). The cells were then detached using a cell scraper, dissociated into single cells by gentle pipetting and seeded onto 24-well plates (CORNING) at a density of 1.3*10^4 cells/cm^2 with 0.5 mL of Stem Fit AK02N supplemented with 10 uM Y-27632 (day -1) and 2.4 uL/mL iMatrix-511 (Nippi). After 24 h (day 0), the cells were cultured with serum-free differentiation medium consisting of DMEM/F12 Glutamax medium (Thermo Fisher Scientific), B27 supplement minus vitamin A (Thermo Fisher Scientific), and 0.5X Penicillin/streptomycin (hereafter called basal medium) supplemented with 5 uM CHIR99021 (Wako), 10 nM RA (SIGMA), 1 ng/mL BMP4 (Peprotech), and 100 ng/mL bFGF (Wako). After another 24 h (day 1), the cells were cultured with 5 uM CHIR99021, 100 ng/mL bFGF, and 1 ng/mL BMP7 (R&D Systems). After a third 24 h (day 2), the medium was switched to basal medium containing 5 uM CHIR99021, 1 ng/mL BMP7, and 10 uM A83-01 (Wako). After a fourth 24 h (day 3), the medium was changed to basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A (R&D Systems), and 30 uM Y-27632 (Wako). After a fifth 24 h (day 4), the cells were washed with PBS (-), treated with Accumax (Innovative Cell Technologies, Inc.), dissociated into single cells by gentle pipetting. On day 4 of PPS induction, the dissociated cells were cryopreserved using STEM-CELLBANKER (ZNQ). The thawed cells were seeded on 96-well U-bottom plates (Sumitomo Bakelite or Thermo Fisher Scientific) at a density of 2.0*10^4 cells/well with basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A and 30 uM Y-27632, to form cellular aggregates and cultured for 48 h. On day 6, the cells were incubated with AK02N minus bFGF medium (Ajinomoto) containing 1 uM CHIR99021, 0.1 uM RA, 500 nM Smoothened Agonist (SAG) (Selleck), 10 uM SB431542 (Nakalai tesque) and 10 ng/mL IL-1b (Wako). On day 8, the medium was changed to AK02N minus bFGF medium containing 1 uM CHIR99021, 0.1 uM RA, 500 nM/mL SAG and 10 uM SB431542 for 72 h.	P-GEAD-1163	P-GEAD-1164	P-GEAD-1165	Rn1558	total RNA	PAIRED	cDNA_randomPriming	TRANSCRIPTOMIC	RNA_SEQ	Illumina NovaSeq 6000	P-GEAD-1166	Rn1558	DRX342261	DRR356350	sequencing assay	DRR356350	P-GEAD-1167	Rn1558.txt	FOXD1 reporter iPSC (17K6)	retinoic acid
Rn1559	Rn1559	Homo sapiens	9606	not applicable	Kenji Osafune	not applicable	hiPS cell derived IPCs, no RA, replicate1	not applicable	not applicable	SAMD00449553	IPC, no RA, 17K6 iPSC derived, replicate1	FOXD1 reporter iPSCs (17K6) were generated by gene targeting of iPSCs (201B7) and used in this study. hiPSCs were first treated using an enzymatic method with a 1:1 mixture of TrypLE Select Enzyme and 0.5 mM EDTA/PBS for 5 min and washed with PBS(-). The cells were then detached using a cell scraper, dissociated into single cells by gentle pipetting and seeded onto 24-well plates (CORNING) at a density of 1.3*10^4 cells/cm^2 with 0.5 mL of Stem Fit AK02N supplemented with 10 uM Y-27632 (day -1) and 2.4 uL/mL iMatrix-511 (Nippi). After 24 h (day 0), the cells were cultured with serum-free differentiation medium consisting of DMEM/F12 Glutamax medium (Thermo Fisher Scientific), B27 supplement minus vitamin A (Thermo Fisher Scientific), and 0.5X Penicillin/streptomycin (hereafter called basal medium) supplemented with 5 uM CHIR99021 (Wako), 10 nM RA (SIGMA), 1 ng/mL BMP4 (Peprotech), and 100 ng/mL bFGF (Wako). After another 24 h (day 1), the cells were cultured with 5 uM CHIR99021, 100 ng/mL bFGF, and 1 ng/mL BMP7 (R&D Systems). After a third 24 h (day 2), the medium was switched to basal medium containing 5 uM CHIR99021, 1 ng/mL BMP7, and 10 uM A83-01 (Wako). After a fourth 24 h (day 3), the medium was changed to basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A (R&D Systems), and 30 uM Y-27632 (Wako). After a fifth 24 h (day 4), the cells were washed with PBS (-), treated with Accumax (Innovative Cell Technologies, Inc.), dissociated into single cells by gentle pipetting. On day 4 of PPS induction, the dissociated cells were cryopreserved using STEM-CELLBANKER (ZNQ). The thawed cells were seeded on 96-well U-bottom plates (Sumitomo Bakelite or Thermo Fisher Scientific) at a density of 2.0*10^4 cells/well with basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A and 30 uM Y-27632, to form cellular aggregates and cultured for 48 h. On day 6, the cells were incubated with AK02N minus bFGF medium (Ajinomoto) containing 1 uM CHIR99021, 500 nM Smoothened Agonist (SAG) (Selleck), 10 uM SB431542 (Nakalai tesque) and 10 ng/mL IL-1b (Wako). On day 8, the medium was changed to AK02N minus bFGF medium containing 1 uM CHIR99021, 500 nM/mL SAG and 10 uM SB431542 for 72 h.	P-GEAD-1163	P-GEAD-1164	P-GEAD-1165	Rn1559	total RNA	PAIRED	cDNA_randomPriming	TRANSCRIPTOMIC	RNA_SEQ	Illumina NovaSeq 6000	P-GEAD-1166	Rn1559	DRX342262	DRR356351	sequencing assay	DRR356351	P-GEAD-1167	Rn1559.txt	FOXD1 reporter iPSC (17K6)	none
Rn1560	Rn1560	Homo sapiens	9606	not applicable	Kenji Osafune	not applicable	hiPS cell derived IPCs, no RA, replicate2	not applicable	not applicable	SAMD00449554	IPC, no RA, 17K6 iPSC derived, replicate2	FOXD1 reporter iPSCs (17K6) were generated by gene targeting of iPSCs (201B7) and used in this study. hiPSCs were first treated using an enzymatic method with a 1:1 mixture of TrypLE Select Enzyme and 0.5 mM EDTA/PBS for 5 min and washed with PBS(-). The cells were then detached using a cell scraper, dissociated into single cells by gentle pipetting and seeded onto 24-well plates (CORNING) at a density of 1.3*10^4 cells/cm^2 with 0.5 mL of Stem Fit AK02N supplemented with 10 uM Y-27632 (day -1) and 2.4 uL/mL iMatrix-511 (Nippi). After 24 h (day 0), the cells were cultured with serum-free differentiation medium consisting of DMEM/F12 Glutamax medium (Thermo Fisher Scientific), B27 supplement minus vitamin A (Thermo Fisher Scientific), and 0.5X Penicillin/streptomycin (hereafter called basal medium) supplemented with 5 uM CHIR99021 (Wako), 10 nM RA (SIGMA), 1 ng/mL BMP4 (Peprotech), and 100 ng/mL bFGF (Wako). After another 24 h (day 1), the cells were cultured with 5 uM CHIR99021, 100 ng/mL bFGF, and 1 ng/mL BMP7 (R&D Systems). After a third 24 h (day 2), the medium was switched to basal medium containing 5 uM CHIR99021, 1 ng/mL BMP7, and 10 uM A83-01 (Wako). After a fourth 24 h (day 3), the medium was changed to basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A (R&D Systems), and 30 uM Y-27632 (Wako). After a fifth 24 h (day 4), the cells were washed with PBS (-), treated with Accumax (Innovative Cell Technologies, Inc.), dissociated into single cells by gentle pipetting. On day 4 of PPS induction, the dissociated cells were cryopreserved using STEM-CELLBANKER (ZNQ). The thawed cells were seeded on 96-well U-bottom plates (Sumitomo Bakelite or Thermo Fisher Scientific) at a density of 2.0*10^4 cells/well with basal medium containing 5 uM CHIR99021, 30 ng/mL bFGF, 10 ng/mL activin A and 30 uM Y-27632, to form cellular aggregates and cultured for 48 h. On day 6, the cells were incubated with AK02N minus bFGF medium (Ajinomoto) containing 1 uM CHIR99021, 500 nM Smoothened Agonist (SAG) (Selleck), 10 uM SB431542 (Nakalai tesque) and 10 ng/mL IL-1b (Wako). On day 8, the medium was changed to AK02N minus bFGF medium containing 1 uM CHIR99021, 500 nM/mL SAG and 10 uM SB431542 for 72 h.	P-GEAD-1163	P-GEAD-1164	P-GEAD-1165	Rn1560	total RNA	PAIRED	cDNA_randomPriming	TRANSCRIPTOMIC	RNA_SEQ	Illumina NovaSeq 6000	P-GEAD-1166	Rn1560	DRX342263	DRR356352	sequencing assay	DRR356352	P-GEAD-1167	Rn1560.txt	FOXD1 reporter iPSC (17K6)	none