Table 3 Summary of characterization tests performed on HLA-iPSC lines#1 and #2

Morphology

Phase-contrast imaging

Typical primed pluripotent human stem cell morphology

Figure 2C, Top

Karyotype

G-banding

46, XX

Figure 2C, Bottom

Pluripotency status

Quantitative analysis (Flow cytometry, RT-qPCR)

Flow Cytometry: 98% OCT4, 96% NANOG, 99% SOX2

RT-qPCR: positive expression for OCT4, NANOG, SOX2, LIN28

Figure 2D, 2E

Qualitative analysis (Immunocytochemistry)

Positive for the pluripotency markers: OCT4, NANOG, and SOX2

Figure 2F

Genetic identity

STR profiling

24 loci tested, all matched between donor EPCs and derived iPSC lines

Additional file 4: Fig. S2A

Verification of the absence of episomal vectors

PCR analysis

The five episomal DNA plasmids were undetected after 12 passages

Additional file 4: Fig. S2B

Mycoplasma testing

RT-qPCR

Negative

Additional file 4: Fig. S2C

Multilineage differentiation potential

Directed differentiation

RT-qPCR measurement of expression levels of ectoderm (PAX6 and NESTIN), mesoderm (BRACHYURY and CDX2), and endoderm (SOX17 and GATA4). Immunocytochemistry: Positive for NESTIN, BRACHYURY, and SOX17

Figure 3A, 3B

HLA typing

WGS

Homozygous at class I loci A, B, C, and class II loci DQB1 and DRB1, with only DPB1 being heterozygous

Figure 1

SV analysis

WGS; Manta + Delly + SURVIVOR

No SVs in iPSC#2; one tandem duplication in iPSC#1

Additional file 5: Fig. S3

SNP analysis

WGS; GATK, Mutect2

No high-impact SNP acquired during cell line establishment; SNPs in genetic background of the donor classified as benign

Additional file 8: Table S3

Table 4