Journal: bioRxiv

Article Title: A genome language model for mapping DNA replication origins

doi: 10.64898/2026.01.29.702604

Figure Lengend Snippet: a) Heatmaps of Spearman correlation across combinations of probability- and efficiency-smoothing windows in H1, illustrating genome-wide sensitivity to resolution matching. b) Dependence of the Spearman correlation on smoothing-window size for multiple species/cell types (H1, mESC, and sheep fibroblast), plotted as mean ± standard deviation across autosomes, highlighting cross-species consistency.

Article Snippet: Chicken embryonic fibroblast cells (UMNSAH/DF-1) were purchased from ATCC (ATCC-CRL-3586) and were maintained according to the supplier’s instructions in DMEM (ATCC 30-2002) supplemented with 10% fetal bovine serum (Gibco, 10270-106).

Techniques: Genome Wide, Standard Deviation

Journal: bioRxiv

Article Title: A genome language model for mapping DNA replication origins

doi: 10.64898/2026.01.29.702604

Figure Lengend Snippet: a) Schematic representation of ORILINX training on human origins of replication sequences, followed by applying ORILINX predictions in chicken, sheep and mouse without additional adjustments. b) ROC curves showing the ORILINX model performance in 28,490 SNS-seq chicken embryonic fibroblast cell origins of replication and matched number of random non-origin sequences, resulting in an AUC ROC = 0.92 and AUC PR =0.93. c) Same as in b) but for 79,574 SNS-seq sheep primary fibroblast origins and matched number random non-origin sequences from two replicates, resulting in an AUC ROC = 0.93 and AUC PR = 0.94. d) Same as in b) and c) but for publicly available mouse ESC data of 13,004 SNS-seq origins and matched number of random non-origin sequences, resulting in an AUC ROC = 0.81 and AUC PR = 0.85.

Article Snippet: Chicken embryonic fibroblast cells (UMNSAH/DF-1) were purchased from ATCC (ATCC-CRL-3586) and were maintained according to the supplier’s instructions in DMEM (ATCC 30-2002) supplemented with 10% fetal bovine serum (Gibco, 10270-106).

Techniques:

Journal: bioRxiv

Article Title: A genome language model for mapping DNA replication origins

doi: 10.64898/2026.01.29.702604

Figure Lengend Snippet: AUC ROC and AUC PR curves for individual SNS-seq replicates of the sheep fibroblast cells (see Methods). a) Replicate 1 showed an AUC ROC of 0.93 and AUC PR of 0.94. b) Replicate 2 showed an AUC ROC of 0.94 and AUC PR of 0.95.

Article Snippet: Chicken embryonic fibroblast cells (UMNSAH/DF-1) were purchased from ATCC (ATCC-CRL-3586) and were maintained according to the supplier’s instructions in DMEM (ATCC 30-2002) supplemented with 10% fetal bovine serum (Gibco, 10270-106).

Techniques:

Journal: bioRxiv

Article Title: A genome language model for mapping DNA replication origins

doi: 10.64898/2026.01.29.702604

Figure Lengend Snippet: Correlation analyses for a) sheep primary fibroblast, where Spearman’s ρ = 0.81, p-value ≪ 0.0001, and b) mouse embryonic stem cells (mESC), where Spearman’s ρ = 0.78, p-value ≪ 0.0001. For each species, the left panel shows chromosome 1 profiles comparing ORILINX predicted origin probability (red) with origin efficiency inferred from replication timing data (blue), with both signals smoothed using a 10 Mb moving average window. Spearman correlation coefficients are indicated. The right panel shows the corresponding joint density distributions of origin probability and origin efficiency computed genome-wide.

Article Snippet: Chicken embryonic fibroblast cells (UMNSAH/DF-1) were purchased from ATCC (ATCC-CRL-3586) and were maintained according to the supplier’s instructions in DMEM (ATCC 30-2002) supplemented with 10% fetal bovine serum (Gibco, 10270-106).

Techniques: Genome Wide

Journal: Functional & Integrative Genomics

Article Title: Systematic evaluation of CrRNA design parameters for optimized Cas13d-mediated RNA targeting in chicken cells

doi: 10.1007/s10142-025-01776-x

Figure Lengend Snippet: RfxCas13d-mediated knockdown of DsRed in chicken fibroblast DF1 cells. a Schematic of RfxCas13d-mediated targeted recognition and degradation of DsRed mRNA ( b ) Representative fluorescence microscopy images of RfxCas13d targeting of DsRed using five different crRNA in stable RfxCas13d-expressing DF1 cell line. c DsRed fluorescence knockdown determined by flow cytometry. Data points in the graph are averages of the normalised mean fluorescence intensity from technical triplicates. Error bars show SD

Article Snippet: The chicken fibroblast DF1 cells (American Type Culture Collection number: CRL–12203) were maintained in Dulbecco’s Modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FCS), 2mM L-glutamine, 10mM Hepes, 1.5% (w/v) sodium bicarbonate, 100 U/mL penicillin, and 100 μg/mL of streptomycin.

Techniques: Knockdown, Fluorescence, Microscopy, Expressing, Flow Cytometry

Journal: Functional & Integrative Genomics

Article Title: Systematic evaluation of CrRNA design parameters for optimized Cas13d-mediated RNA targeting in chicken cells

doi: 10.1007/s10142-025-01776-x

Figure Lengend Snippet: Comparison of on-target and collateral effects of RfxCas13d and HfCas13d in chicken cells. a DF1-RfxCas13d and DF1-HfCas13d were each co-transfected with vectors encoding DsRed and five different crRNA (targeting DsRed mRNA) or NT crRNA (negative control). DsRed fluorescence knockdown by different crRNAs was determined by flow cytometry. b DF1-RfxCas13d and DF1-HfCas13d were each co-transfected with vectors encoding GFP and individual crRNA (targeting GFP mRNA) or NT crRNAs (negative). The percentage GFP fluorescence knockdown by different crRNAs was determined by flow cytometry. c Assessment of collateral activity of RfxCas13d and HfCas13d in chicken cells. The corresponding cell lines were transfected with crRNA targeting DsRed, along with expression vectors for DsRed (on-target) and GFP (serves as collateral reporter). Representative microscopy images of both DsRed and GFP fluorescence degradation in DF1-RfxCas13d cells (top panel) compared with DF1-HfCas13d cells (bottom panel). d The percentage DsRed (on-target activity) and GFP (collateral activity) fluorescence knockdown measured by flow cytometry. Values shown as the mean ± Sd. Data points in the graph are averages of the normalised mean fluorescence intensity from technical triplicates

Article Snippet: The chicken fibroblast DF1 cells (American Type Culture Collection number: CRL–12203) were maintained in Dulbecco’s Modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FCS), 2mM L-glutamine, 10mM Hepes, 1.5% (w/v) sodium bicarbonate, 100 U/mL penicillin, and 100 μg/mL of streptomycin.

Techniques: Comparison, Transfection, Negative Control, Fluorescence, Knockdown, Flow Cytometry, Activity Assay, Expressing, Microscopy

Journal: Functional & Integrative Genomics

Article Title: Systematic evaluation of CrRNA design parameters for optimized Cas13d-mediated RNA targeting in chicken cells

doi: 10.1007/s10142-025-01776-x

Figure Lengend Snippet: Transcriptome-wide collateral activity of RfxCas13d and HfCas13d in chicken cell lines. a Venn diagram of overlapping differentially expressed genes (DEGs) upregulated or downregulated. b Volcano plot of the RNA-seq analysis comparing RfxCas13d (left) or HFCas13d (right) DF1 transgenic cells transfected with DsRed and GFP, and either DsRed-crRNA or NT-crRNA. Lines denote a > 1.25-fold change (FC). c Gene ontology (GO) and biological process (BP) term analysis for the DEGs in (b)

Article Snippet: The chicken fibroblast DF1 cells (American Type Culture Collection number: CRL–12203) were maintained in Dulbecco’s Modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FCS), 2mM L-glutamine, 10mM Hepes, 1.5% (w/v) sodium bicarbonate, 100 U/mL penicillin, and 100 μg/mL of streptomycin.

Techniques: Activity Assay, RNA Sequencing, Transgenic Assay, Transfection