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KOLF2.1J iPSC and Differentiated Cell Types

KOLF2.1J is a human induced pluripotent stem cell (iPSC) line that was selected and characterized by the iPSC Neurodegenerative Disease Initiative (iNDI) as a community reference line to support large-scale, collaborative research, with particular emphasis on neurodegenerative disease modeling. The line was generated as a sub-clone of the parental KOLF2-C1 iPSC line, which was originally reprogrammed from fibroblasts obtained from a male donor of European ancestry under informed consent and appropriate ethical approvals. During sub-cloning, a heterozygous 19-bp deletion in ARID2 present in the parental line was corrected, yielding a clonally derived line with a low burden of deleterious variants and no known high-risk alleles for neurodegenerative disease, making it well suited as a neutral genetic background for disease modeling.

KOLF2.1J demonstrates robust and reproducible pluripotency, high genomic stability in culture and after gene editing, efficient CRISPR editing, and reliable tri-lineage differentiation potential, with performance validated across multiple independent laboratories. The KOLF2.1J has been chosen as a high-quality, broadly applicable reference iPSC line suitable for adoption as a common cellular substrate to reduce inter-line variability and facilitate cross-laboratory data integration. To enable widespread use, KOLF2.1J and a growing collection of gene-edited isogenic derivative clones have been made openly available to the research community. More details can be found in Pantazis et al., "A reference human induced pluripotent stem cell line for large-scale collaborative studies", Cell Stem Cell (2022); doi: https://doi.org/10.1016/j.stem.2022.11.004.

Building on this foundation, the present study extends the genomic characterization of KOLF2.1J using long-read and long-range sequencing to generate a complete, telomere-to-telomere reference assembly, together with matched long-read genomic, epigenetic and long- and short-read based expression data from differentiated derivative cell types. This work is described in the accompanying preprint Alvarez Jerez et al., "The complete genome of the KOLF2.1J reference iPSC line", bioRxiv (2026); doi: https://doi.org/10.64898/2026.03.06.710144.

Data available through this dbGaP study include newly generated long-read sequencing data of the parental KOLF2.1J iPSC line and the differentiated cell lines (astrocytes, cortical neurons, NGN2-derived neurons, microglia, and oligodendrocytes) derived from the parental KOLF2.1J, along with corresponding expression data, and the assembled Y chromosome sequence. The assembled Y chromosome will be shared under controlled access for research use only, given the heightened re-identification risk associated with Y chromosome sequence data. The full diploid assembly, excluding the Y chromosome, is available through GenBank under BioProject PRJNA1478016.