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: iScience

Article Title: Genetic dissection of the role of Piga and Pgap2 in the embryonic mouse brain

doi: 10.1016/j.isci.2026.116299

Figure Lengend Snippet: Late onset hypomyelination in Olig2 ; Piga mutant brains (A) Percent genotype ratios of wildtype, Olig2 Cre/wt ; Piga flox/X female and Olig2 Cre/wt ; Piga flox/Y male survival to P21 ( n = 96, Chi-square p = 0.609). Immunostaining of MBP (B–D), CONTACTIN1 (E–G), SOX10 (H–J) and PDGFRα (K–M) in wild type (B, E, H, and K) Olig2 Cre/wt ; Piga flox/X female (C, F, I, and L) and Olig2 Cre/wt ; Piga flox/Y male (D, G, J, and M) animals. MBP and CONTACTIN1 data are from P96 (scale bar, 500 μm) while SOX10 and PDGFRα are from P21 (scale bar, 25 μm) ( n = 4 animals per genotype). Quantification of SOX10 (N, n = 3 animals per genotype, ANOVA p = 0.170), PGDFRα (O, n = 4, ANOVA p = 0.564) positive cells and the PDGFRα/SOX10 ratio (P, n = 3, ANOVA p = 0.430). Data represent individual values and the mean ± s.e.m. White arrows indicate SOX10 and PDGFRα positive cells.

Article Snippet: Mouse: Olig2 -Cre; B6.129- Olig2 tm1.1(cre)Wdr /J , The Jackson Laboratory , RRID:IMSR_JAX:025567.

Techniques: Mutagenesis, Immunostaining