Journal: iScience

Article Title: Dissecting genotype-specific effects of disease-associated genetic variants

doi: 10.1016/j.isci.2026.116143

Figure Lengend Snippet: Overview of experimental workflow Affinity purification MS were completed on the undifferentiated KOLF2.1J WT cell line. Bulk RNA-seq and ONT long-read WGS + 5 mC methylation analysis was completed on undifferentiated KOLF2.1J clones containing the following rs11610045 genotypes: A|A (WT), G|G (edited), and A|A (reversed). WT and edited (but not reverse edited) clones were differentiated to iPSC-derived cortical neurons and bulk RNA-seq completed. iPSC, induced pluripotent stem cell; sgRNA, single-guide ribonucleic acid; ssODN, single-strand oligodeoxynucleotide; RNP, ribonucleoprotein; HDR enhancer, homology-directed repair enhancer; ONT, Oxford Nanopore Technologies; WGS, whole-genome sequencing.

Article Snippet: The KOLF2.1J iPSC line , was obtained from Jackson laboratory ( https://www.jax.org/jax-mice-and-services/ipsc ).

Techniques: Affinity Purification, RNA Sequencing, Methylation, Clone Assay, Derivative Assay, Sequencing

Journal: iScience

Article Title: Dissecting genotype-specific effects of disease-associated genetic variants

doi: 10.1016/j.isci.2026.116143

Figure Lengend Snippet: Restoring the rs11610045 G|G genotype to A|A also restores gene expression for a subset of genes (A) CRISPR-Cas9 editing of the rs11610045 G|G genotype to A|A restored the expression of 75 genes to WT levels. Green bars represent the log2FC when comparing the edited rs11610045 G|G genotype with that of the A|A genotype (WT) KOLF2.1J cells. Blue bars represent the log2FC when comparing gene expression in the rs11610045 A|A (reversed) with that of the rs11610045 G|G genotype (edit) clones. In all instances, log2FC > 1 and Bonferroni adj. p value <0.05. (B) Expression of CEL , PDGFB , and THBS2 are rs11610045 genotype dependent and have been linked to PD. Boxplots show the median (center line), interquartile range (box), and whiskers extending to 1.5× the interquartile range. Individual data points are overlaid. (C) PDGFB interacts with THBS1 in a protein-protein interaction network (StringDB, high confidence interaction score ≥0.700).

Article Snippet: The KOLF2.1J iPSC line , was obtained from Jackson laboratory ( https://www.jax.org/jax-mice-and-services/ipsc ).

Techniques: Gene Expression, CRISPR, Expressing, Clone Assay

Journal: bioRxiv

Article Title: A Denisovan-derived Alu insertion in OCA2 contributes to pigmentation diversity in present-day Melanesians

doi: 10.64898/2026.03.18.712481

Figure Lengend Snippet: ( A ) Schematic overview of the in vitro experimental design to test the Alu insertion’s functional impact in the human induced pluripotent stem cell (iPSC) line, KOLF2.1J. ( B ) Expression of OCA2 and melanocyte marker genes across seven stages of melanocyte differentiation (days 0, 2, 8, 16, 19, 25, and 30). Each dot represents a technical replicate (heterozygous insertion carriers, red; wildtype, gray). Lines indicate the mean across two replicates at each time point. Two OCA2 amplicons are shown: exon 11-13 and exon 16-18 (exon numbering from RefSeq NM_000275.3 as displayed in the UCSC Genome Browser). ( C ) Representative image illustrating pigmentation differences between wild-type (WT; homozygous reference) and heterozygous (HET; one Alu insertion allele) melanocyte cultures. ( D ) Enrichment of histone marks, H3K4me1 and H3K27ac, at days 19 and 30. “IgG” and “Control” indicate negative controls for the enrichment assay and locus-specific signal, respectively. The locus “Control” is derived from the B2M gene. Fold enrichment values were normalized to 1% of the input control. [Figure created with BioRender]

Article Snippet: We used the human iPSC line KOLF2.1J (The Jackson Laboratory) for all differentiation experiments.

Techniques: In Vitro, Functional Assay, Expressing, Marker, Control, Derivative Assay

Journal: bioRxiv

Article Title: The complete genome of the KOLF2.1J reference iPSC line

doi: 10.64898/2026.03.06.710144

Figure Lengend Snippet: (Left) Oxford Nanopore Technologies (ONT) ultra-long whole genome sequencing (WGS), Pacific Biosciences (PacBio) WGS, and Hi-C data were generated from the KOLF2.1J parental cell line in its iPSC state to generate a custom genome assembly and annotation. The sequencing data was additionally used to catalog structural variants in our line. (Right) KOLF2.1J IPSC was differentiated into multiple cell states: astrocytes, cortical neurons, NGN2 derived neurons, microglia, and oligodendrocytes. We then generated ONT WGS data as well as ONT and PacBio RNA sequencing data to explore methylation and transcript differential expression across cell states and haplotypes. Created with biorender.com

Article Snippet: The iNDI reference parental iPSC KOLF2.1J line was used and obtained from the Jackson Laboratory (Cat# JIPSC001000).

Techniques: Sequencing, Hi-C, Generated, Derivative Assay, RNA Sequencing, Methylation, Quantitative Proteomics

Journal: bioRxiv

Article Title: The complete genome of the KOLF2.1J reference iPSC line

doi: 10.64898/2026.03.06.710144

Figure Lengend Snippet:

Article Snippet: The iNDI reference parental iPSC KOLF2.1J line was used and obtained from the Jackson Laboratory (Cat# JIPSC001000).

Techniques:

Journal: bioRxiv

Article Title: The complete genome of the KOLF2.1J reference iPSC line

doi: 10.64898/2026.03.06.710144

Figure Lengend Snippet: (a) Mapping Reference Panel for KOLF2.1J Reads. (b) KOLF2.1J short read mapping statistics across the reference panel, representing the total aligned, total perfect and total gapless (soft clips included) reads as a fraction of total reads. (c) Insertions Vs Deletions, plot comparing the total number of insertions versus deletions (measured in base pairs) detected for each reference. (d) Mapping quality distribution, displaying the fraction of reads assigned to different MAPQ bins.

Article Snippet: The iNDI reference parental iPSC KOLF2.1J line was used and obtained from the Jackson Laboratory (Cat# JIPSC001000).

Techniques:

Journal: Stem Cell Reports

Article Title: Comparative lipidomics of iPSC-derived microglia protocols reveal lipid droplet and immune differences mediated by media composition

doi: 10.1016/j.stemcr.2025.102779

Figure Lengend Snippet: Omitting B-27 supplement increases TG levels (WTC11 and KOLF2.1J) (A) Representative PCA plot of unbiased lipidomics from one lipidomic run (WTC11). Symbols denote independent cultures with 3 technical replicates each . (B) Total lipid concentration in nmol per 1 × 10 6 cells. One-way ANOVA, Tukey’s multiple comparisons post-hoc test. (C) Lipid class concentration represented as fold change of EB-EB microglia. Two-way ANOVA, Tukey’s multiple comparisons post-hoc test. (B and C) N = 3 independent cultures from WTC11 and KOLF2.1J lines each. Symbols denote different cell lines. ns = non-significant, ∗ p < 0.05, ∗∗∗∗ p < 0.0001. (See also , , and A).

Article Snippet: The KOLF2.1J iPSC lines (male, white) (KOLF2.1J Parental and KOLF2.1J CLYBL 6-TF-iMG) were acquired from Jackson Lab.

Techniques: Concentration Assay