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: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: Tail tip fibroblasts from non-sibling Diversity Outbred mice were cultured on gelatin-coated plates and reprogrammed by lentiviral transduction of a doxycycline-inducible mouse OKSM cassette. Twenty-four hours after transduction, virus-containing medium was replaced with mESM + 2i/LIF supplemented with doxycycline to induce expression of the reprogramming factors. Emerging iPSC colonies were pooled and expanded as polyclonal lines. After three passages, lines were cryopreserved at P3. One vial per line was subsequently expanded to P5 for quality control screening and genotyping. Finalized lines were banked with associated metadata in The Jackson Laboratory Biobank (see Supplemental Table 1).

Article Snippet: Supplemental Table 1 delineates the iPSC lines with associated metadata (including source fibroblast line IDs and source animal IDs) and bankstock information that can be used to obtain lines from The Jackson Laboratory.

Techniques: Cell Culture, Transduction, Virus, Expressing, Control

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: (A) Founder haplotype frequencies across chromosomes were estimated from GigaMUGA genotypes. Contributions from each of the eight DO founder strains are shown for chromosomes 1–19 and X. Deviations from the expected 0.125 founder contribution are summarized in Supplemental Table 2. (B) Pairwise kinship coefficients were calculated from GigaMUGA-derived genotypes to assess relatedness among iPSC lines. Eight pairs of lines showed high kinship (kin_raw > 0.4; highlighted in green and arrows), and one member of each pair was flagged in the final panel . All remaining line pairs showed kinship values consistent with non-sibling Diversity Outbred mice.

Article Snippet: Supplemental Table 1 delineates the iPSC lines with associated metadata (including source fibroblast line IDs and source animal IDs) and bankstock information that can be used to obtain lines from The Jackson Laboratory.

Techniques: Derivative Assay

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: (A) Example of growth profiling of male and female DO iPSC lines. Cells were cultured for 96 hours and cell counts were used to calculate doubling time. Lines were assayed across multiple experimental batches. Representative colony morphologies are shown, including flattened morphology observed in some lines (e.g., line 5387, XX, 72 hours). (B) Embryoid body (EB) formation from 12 randomly selected iPSC lines. All lines formed EBs, with variation in EB morphology, some smooth and spherical and some rough and irregular, depending on the line. (C) Gene expression analysis before and after EB differentiation. RNA was collected from undifferentiated iPSCs and from EBs. Expression of pluripotency markers and early lineage markers representing ectoderm, mesoderm, and endoderm was quantified. Undifferentiated lines showed high pluripotency marker expression and low lineage marker expression, whereas EBs showed reduced pluripotency marker expression and increased lineage marker expression.

Article Snippet: Supplemental Table 1 delineates the iPSC lines with associated metadata (including source fibroblast line IDs and source animal IDs) and bankstock information that can be used to obtain lines from The Jackson Laboratory.

Techniques: Cell Culture, Gene Expression, Expressing, Marker

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: (A) Gene expression of core pluripotency genes and early lineage markers in 218 DO iPSC lines. (B) Variance component analysis showing contributing factors to the variance in gene expression. Genotype is represented by the top 10 principal components informed by genotype probabilities.

Article Snippet: Supplemental Table 1 delineates the iPSC lines with associated metadata (including source fibroblast line IDs and source animal IDs) and bankstock information that can be used to obtain lines from The Jackson Laboratory.

Techniques: Gene Expression

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: Quantile–quantile (Q–Q) plots of per-sample chromosome expression scores (median gene-level z-scores) were generated for each chromosome using the data from 218 DO iPSC lines. Observed values were statistically compared to the expected normal distribution. Deviation from the diagonal reflects broad chromosome-scale expression shifts. (A, B) Two examples are shown, one for a chromosome without gains or losses (Chromosome 2, A) and one for which there were frequent copy number gains (Chromosome 11, B). (C) To provide an overview for all chromosomes, the chromosome Z score was plotted for each iPSC line. Potential copy number gains were observed for Chromosomes 1, 6, 8, 11, 12, 13, and 14. Potential copy number losses were found for Chromosomes 7, 12, and 19.

Article Snippet: Supplemental Table 1 delineates the iPSC lines with associated metadata (including source fibroblast line IDs and source animal IDs) and bankstock information that can be used to obtain lines from The Jackson Laboratory.

Techniques: Expressing, Generated

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: Tail tip fibroblasts from non-sibling Diversity Outbred mice were cultured on gelatin-coated plates and reprogrammed by lentiviral transduction of a doxycycline-inducible mouse OKSM cassette. Twenty-four hours after transduction, virus-containing medium was replaced with mESM + 2i/LIF supplemented with doxycycline to induce expression of the reprogramming factors. Emerging iPSC colonies were pooled and expanded as polyclonal lines. After three passages, lines were cryopreserved at P3. One vial per line was subsequently expanded to P5 for quality control screening and genotyping. Finalized lines were banked with associated metadata in The Jackson Laboratory Biobank (see Supplemental Table 1).

Article Snippet: The remaining 296 polyclonal iPSC lines were frozen at P3, genotyped, and expanded to P5-P6 for QC and biobanking at The Jackson Laboratory ( , Supplemental Table 1).

Techniques: Cell Culture, Transduction, Virus, Expressing, Control

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: (A) Founder haplotype frequencies across chromosomes were estimated from GigaMUGA genotypes. Contributions from each of the eight DO founder strains are shown for chromosomes 1–19 and X. Deviations from the expected 0.125 founder contribution are summarized in Supplemental Table 2. (B) Pairwise kinship coefficients were calculated from GigaMUGA-derived genotypes to assess relatedness among iPSC lines. Eight pairs of lines showed high kinship (kin_raw > 0.4; highlighted in green and arrows), and one member of each pair was flagged in the final panel . All remaining line pairs showed kinship values consistent with non-sibling Diversity Outbred mice.

Article Snippet: The remaining 296 polyclonal iPSC lines were frozen at P3, genotyped, and expanded to P5-P6 for QC and biobanking at The Jackson Laboratory ( , Supplemental Table 1).

Techniques: Derivative Assay

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: (A) Histogram of kinship values estimated from genotype probabilities across the full DO iPSC panel. Each bar represents the frequency of pairwise comparisons between distinct lines. Most comparisons are tightly centered around K ≈ 0.15 (median = 0.151; mean = 0.154), consistent with the expected relatedness structure of a multiparent Diversity Outbred population. Ninety-five percent of pairs fall below K = 0.171 and 99% below K = 0.230. A small number of pairs are in the extreme upper tail (K > 0.50), approaching the diagonal kinship value expected for genetically identical samples. (B, C) Minor allele frequency (MAF) and heterozygosity (H) were evaluated in the DO iPSC panel and across all measures the population structure of this panel is comparable to a similarly sized genetic mapping cohort of non-sibling DO mice with median MAF = 0.278, mean expected heterozygosity = 0.367 and mean observed = 0.364

Article Snippet: The remaining 296 polyclonal iPSC lines were frozen at P3, genotyped, and expanded to P5-P6 for QC and biobanking at The Jackson Laboratory ( , Supplemental Table 1).

Techniques:

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: (A) Example of growth profiling of male and female DO iPSC lines. Cells were cultured for 96 hours and cell counts were used to calculate doubling time. Lines were assayed across multiple experimental batches. Representative colony morphologies are shown, including flattened morphology observed in some lines (e.g., line 5387, XX, 72 hours). (B) Embryoid body (EB) formation from 12 randomly selected iPSC lines. All lines formed EBs, with variation in EB morphology, some smooth and spherical and some rough and irregular, depending on the line. (C) Gene expression analysis before and after EB differentiation. RNA was collected from undifferentiated iPSCs and from EBs. Expression of pluripotency markers and early lineage markers representing ectoderm, mesoderm, and endoderm was quantified. Undifferentiated lines showed high pluripotency marker expression and low lineage marker expression, whereas EBs showed reduced pluripotency marker expression and increased lineage marker expression.

Article Snippet: The remaining 296 polyclonal iPSC lines were frozen at P3, genotyped, and expanded to P5-P6 for QC and biobanking at The Jackson Laboratory ( , Supplemental Table 1).

Techniques: Cell Culture, Gene Expression, Expressing, Marker

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: (A) Gene expression of core pluripotency genes and early lineage markers in 218 DO iPSC lines. (B) Variance component analysis showing contributing factors to the variance in gene expression. Genotype is represented by the top 10 principal components informed by genotype probabilities.

Article Snippet: The remaining 296 polyclonal iPSC lines were frozen at P3, genotyped, and expanded to P5-P6 for QC and biobanking at The Jackson Laboratory ( , Supplemental Table 1).

Techniques: Gene Expression

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: Quantile–quantile (Q–Q) plots of per-sample chromosome expression scores (median gene-level z-scores) were generated for each chromosome using the data from 218 DO iPSC lines. Observed values were statistically compared to the expected normal distribution. Deviation from the diagonal reflects broad chromosome-scale expression shifts. (A, B) Two examples are shown, one for a chromosome without gains or losses (Chromosome 2, A) and one for which there were frequent copy number gains (Chromosome 11, B). (C) To provide an overview for all chromosomes, the chromosome Z score was plotted for each iPSC line. Potential copy number gains were observed for Chromosomes 1, 6, 8, 11, 12, 13, and 14. Potential copy number losses were found for Chromosomes 7, 12, and 19.

Article Snippet: The remaining 296 polyclonal iPSC lines were frozen at P3, genotyped, and expanded to P5-P6 for QC and biobanking at The Jackson Laboratory ( , Supplemental Table 1).

Techniques: Expressing, Generated

Journal: bioRxiv

Article Title: Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

doi: 10.64898/2026.05.02.722403

Figure Lengend Snippet: (A) Genomic locations of DO iPSC eQTLs (LOD > 7.78). Red arrow denotes chromosome 15 eQTL hotspot with over 600 distant target genes. (B) Distant eQTL hotspots, where distant is defined as eQTL greater than 2Mbp from its target gene. Asterisks denote hotspots shared with published DO ESC transcriptomics. (C) Heat map of mediation analysis identifying Lifr as the strongest mediator for the chromosome 15 hotspot. Potential mediators were identified using the change in LOD score and the associated adjusted pvalues for each mediator-target interaction are represented by color. (D) Haplotype effect at the local eQTL for Lifr showing a 3:5 split, with more recently wild-derived strains grouping separately from the classic inbred strains. (E) Heatmap of the haplotype effects at the 696 distant eQTL within the chromosome 15 hotspot showing a 3:5 split between the wild-derived and classic inbred strains.

Article Snippet: The remaining 296 polyclonal iPSC lines were frozen at P3, genotyped, and expanded to P5-P6 for QC and biobanking at The Jackson Laboratory ( , Supplemental Table 1).

Techniques: Transcriptomics, Derivative Assay