Journal: bioRxiv

Article Title: Engineering a pacemaker-driven human mini-heart guided by spatial and single cell multi-omics of sinoatrial node development

doi: 10.64898/2026.05.07.723626

Figure Lengend Snippet: a, Schematic of zebrafish drug treatment experiments. b, Representative bright-field images of zebrafish larvae at 54 hpf. Scale bar=100 µm. c, Representative fluorescence images of zebrafish /larvae at 54 hpf treated with 5 µM Afatinib, 5 uM BAY-593 (YAPi) or vehicle control. Scale bar=100 µm. d, e, Quantification of the number of ISL1/2 + cells (c) and ISL1/2 + area in zebrafish larvae treated with 5 uM Afatinib, 5 uM BAY-593 or vehicle control. Data are shown as mean ± SEM; *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001. For each experiment, N = 25 larvae. For each drug-treated set there was a consistent loss of Isl1-staining; 3 larvae from each set were randomly chosen for quantification, carried out by a blinded investigator.

Article Snippet: At 54 hpf larvae were fixed in 2% PFA for 2 hours at room temperature, washed extensively in PBS with 0.3% TritonX-100 (PBX), incubated in blocking buffer (BB: PBX, 0.5% BSA, 10% goat serum) for 2 hours at room temperature, incubated overnight at 4°C in BB containing 1/50 dilution of mouse anti-ISL1/2 antibody (Iowa Developmental Studies Hybridoma Bank #39.4D5), washed extensively with PBX, incubated at room temperature for 2 hours in BB with a 1/200 dilution of goat anti-mouse IgG2b Alexa Fluor568 (Invitrogen #A-21144), washed extensively with PBX, and mounted in 1:1 PBS:glycerol for imaging on a Zeiss LSM800 confocal microscope.

Techniques: Fluorescence, Control, Staining

Journal: bioRxiv

Article Title: Generation of human hindlimb/genital tubercle progenitors from pluripotent stem cells

doi: 10.64898/2026.04.14.718471

Figure Lengend Snippet: (A) Schematics showing the location and signalling requirements of NMP and pLPM progenitors in the mouse E8.5 embryo (left) and the treatment conditions used to induce NMPs and pLPM cells from hPSCs (right). (B) RT-qPCR-based expression analysis of key NMP and pLPM markers after 3 days of iPSC differentiation toward NMPs in the presence and absence of BMP4 ( n = 3 independent experiments). Relative expression levels to iPSCs were normalised to GAPDH gene expression (* p<0.05, ** p<0.01, *** p<0.001, mean ±SD) (paired, two-tailed t -test). (C) Immunofluorescence analysis of the expression of TBXT and ISL1 on day 3 of differentiation. Scale bars represent 100 µm. Image analysis of the percentage of nuclei positive for TBXT and ISL1 protein expression is also shown. Graph shows mean values ( n = 3 independent experiments) (* p<0.05, ** p<0.01, *** p<0.001, mean ±SD) (unpaired t -test with Welch’s correction). (D) Heatmap of differentially expressed genes showing key NMP and pLPM/HGTp markers from bulk RNA-seq analysis on day 3. Expression values are shown as Z-scores across samples. (E) Heatmap of differentially expressed genes showing KEGG signalling components on day 3. Expression values are shown as Z-scores across samples.

Article Snippet: Following primary antibodies were used; TBXT (Abcam, ab209665, 1:1000), ISL1 (DSHB, 39.4D5, 1:200), HAND1 (R&D Systems, AF3168, 1:100), PITX1 (Novus Bio, NBP1-88644, 1:500), HOXC9 (Abcam, ab50839, 1:200), KDR (R&D Systems, AF357, 1:1000), TP63 (Abcam, ab124762, 1:200).

Techniques: Quantitative RT-PCR, Expressing, Gene Expression, Two Tailed Test, Immunofluorescence, RNA Sequencing

Journal: bioRxiv

Article Title: Generation of human hindlimb/genital tubercle progenitors from pluripotent stem cells

doi: 10.64898/2026.04.14.718471

Figure Lengend Snippet: (A) UMAP visualisation of sc-RNA seq data from late RA treated cells collected on day 10 of differentiation. Cells were divided into 3 clusters indicated by different colours. Below: Bar graph showing the percentage of total cells per cluster. (B) Stacked violin plots showing the expression (log-normalized) of key lineage markers enriched across identified cell clusters. (C) Dot plot showing the proportion of cells per cluster expressing the indicated marker genes. The colour bar indicates the average log-normalized expression values. (D, E) Feature UMAPs showing the expression of representative marker genes (log-normalized). (F) UMAP showing the proportions of ISL+/TBX5+/TBX4+ cells across the identified cell clusters. Below: Bar graph showing the percentage of cells per cluster calculated for each cluster. (G) Dot plot showing the percentage expression of key surface ectoderm markers for each cell cluster. The colour bar indicates the average log-normalized expression values. (H) Immunofluorescence analysis of the expression of TP63 and ISL1 on day 10 HGTps. Sequential z-stacks are shown (z=1 bottom, z=20 top). Scale bars represent 100 µm.

Article Snippet: Following primary antibodies were used; TBXT (Abcam, ab209665, 1:1000), ISL1 (DSHB, 39.4D5, 1:200), HAND1 (R&D Systems, AF3168, 1:100), PITX1 (Novus Bio, NBP1-88644, 1:500), HOXC9 (Abcam, ab50839, 1:200), KDR (R&D Systems, AF357, 1:1000), TP63 (Abcam, ab124762, 1:200).

Techniques: RNA Sequencing, Expressing, Marker, Immunofluorescence

Journal: bioRxiv

Article Title: Dyrk1a gene dosage controls bipolar cell development and retinal connectivity

doi: 10.64898/2026.03.15.710015

Figure Lengend Snippet: (A – C) Representative coronal sections taken from the retina of Lhx2-Cre (A), Lhx2-Cre:Dyrk1a +/f (B) and Lhx2-Cre:Dyrk1a f/f (C) at E14.5 to illustrate the presence of Isl1/2 + neurons and cleaved Caspase3 + apoptotic cells (A – C, arrowheads in inset images). (D – F) Representative coronal sections taken from the retina of Lhx2-Cre (D), Lhx2-Cre:Dyrk1a +/f (E) and Lhx2-Cre:Dyrk1a f/f (D) at P0 to illustrate the presence of Isl1/2 + neurons and cleaved Caspase3 + apoptotic cells (D – F, arrowheads in inset images). (G – H) Quantitative analysis of Lhx2-Cre ( n = 5), Lhx2-Cre:Dyrk1a +/f ( n = 5) and Lhx2-Cre:Dyrk1a f/f ( n = 5) animals at E14.5 (G) and P0 (H) demonstrates a significant reduction in the number of amacrine and RGCs in the retinas of homozygous animals at both ages. (I – J) Quantitative analysis of Lhx2-Cre ( n = 5), Lhx2-Cre:Dyrk1a +/f ( n = 5) and Lhx2-Cre:Dyrk1a f/f ( n = 5) mice at E14.5 (I) and P0 (J) demonstrates a significant increase the number of apoptotic cells in the retinas of Lhx2-Cre:Dyrk1a f/f animals at both ages. All data represents the mean ± SEM values. Statistical differences were calculated using one-way ANOVA followed by a Tukey’s multiple comparison test. p-values are denoted as follows: *p ≤ 0.05, **p ≤ 0.01 and ****p ≤ 0.0001. Scale bars: (A – F) 100 μm. Abbreviations: Casp3, cleaved Caspase3; CM, ciliary margin; D, dorsal; LE, lens; NR, neural retina; RPE, retinal pigment epithelium; V, ventral.

Article Snippet: The following primary antibodies and dilutions were used in this study: Calbindin (1:300, Sigma-Aldrich, #C9848); Calretinin (1:1000, Swant, #CG1); cleaved Caspase3 (Asp175) (1:500, Cell Signalling, #9661S); chAT (1:100, Millipore, #AB144P); Chx10 (1:50, SCBT, #SC365519); Dyrk1a (1:100, Novus, #NBP1-84032); Isl1/2 (recognises both Isl1 and Isl2 proteins) (1:500; DSHB, #39.4D5); M-opsin (1:500, Proteintech, #30975-1-AP); Pax6 (1:100, DSHB, #Pax6); Pikachurin (1:200, Proteintech, #14578-1-AP); Rhodopsin (1:500, Millipore, #MABN15); S-opsin (1:500, Proteintech, #24660-1-AP); TH (1:300, Millipore, #AB152); vGlut1 (1:2000, Millipore, #AB5905).

Techniques: Comparison