chicken embryonic fibroblast cells  (ATCC)

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: Frontiers in Physiology

Article Title: Dual roles of syndecan-4 in regulating chicken fibrosis in vitro

doi: 10.3389/fphys.2026.1782914

Figure Lengend Snippet: Overexpression of SDC4 in SL-29 chicken fibroblast cells. (A) Chicken embryonic SL-29 fibroblasts were transiently transfected with HA-tagged SDC4, fixed with 4% PFA, stained with mouse α-HA (left) and rabbit α-SDC4 (middle) followed by goat anti-mouse Alexa Fluor 488 and goat anti-rabbit Alexa Fluor 546 before fluorescence microscopy analyses. NucBlue was used to stain nuclei (blue). The inserts represent a higher magnification of the framed areas. Arrows indicate focal adhesions. Scalebar 50 µm. (B) SL-29 cells were transiently transfected with SDC4 (n = 6), or HA-SDC4 (n = 3) plasmids. Lipofectamine only was used as control (Ctrl). Bars show the relative mRNA gene expression in transfected cells compared with the mean average of Ctrl cells (n = 6). The bars are presented as ± SEM. Asterisks denote significant differences between Ctrl and transfected cells, statistics assessed using unpaired t-test with Welch correction (ns > 0.05; *p ≤ 0.05; **p ≤ 0.01). (C) A representative western blot showing the level of SDC4 after transient transfection of the chicken fibroblasts. Cells treated as in B were subjected to western blotting using antibodies against HA tag adding a molecular size increase around nine amino acid (top) or only the cytoplasmic part of SDC4 (middle panel). The lowermost panel shows total protein. (D) Quantification of the levels of the 15 and 20 kDa SDC4 fragments, normalized to total protein level. The bars represent n = 8 in one technical replicate for SDC4 and Ctrl, and n = 4 in one technical replicate for HA-SDC4. The bars are presented as ± SEM. Asterisks denote significant differences between Ctrl and transfected cells, statistics assessed using unpaired Mann-Whitney non-parametric t-test (ns > 0.05; **p ≤ 0.01; ***p ≤ 0.001).

Article Snippet: The embryonic chicken fibroblast cell line SL-29 was purchased from ATCC (#CRL 1590, Manassas, VA).

Techniques: Over Expression, Transfection, Staining, Fluorescence, Microscopy, Control, Gene Expression, Western Blot, MANN-WHITNEY

Journal: Frontiers in Physiology

Article Title: Dual roles of syndecan-4 in regulating chicken fibrosis in vitro

doi: 10.3389/fphys.2026.1782914

Figure Lengend Snippet: Effect of SDC4 overexpression on fibrosis markers in chicken fibroblasts SL-29. Protein expression of (A) pro-collagen I beta chain (250 kDa) and alpha chain (100 kDa), (B) pro-collagen III (250 kDa) and collagen I (100 kDa), (C) MMP-2 and (D) MMP-9 in SDC4 transfected SL-29 cells. GAPDH was used as a reference protein. The bars represent n = 3 in one technical replicate. Gene expression (n = 6 in technical triplicates) of (E) COL1A1, COL3A1, MMP2, MMP9, (F) TGFβ and IL1β in SDC4 transfected SL-29 cells. The bars are presented as ± SEM. Asterisks denote significant differences between Ctrl (lipofectamine only) and transfected cells, statistics assessed using unpaired t-test with Welch correction and Mann-Whitney U (ns > 0.05; *p ≤ 0.05; **p ≤ 0.001).

Article Snippet: The embryonic chicken fibroblast cell line SL-29 was purchased from ATCC (#CRL 1590, Manassas, VA).

Techniques: Over Expression, Expressing, Transfection, Gene Expression, MANN-WHITNEY

Journal: Frontiers in Physiology

Article Title: Dual roles of syndecan-4 in regulating chicken fibrosis in vitro

doi: 10.3389/fphys.2026.1782914

Figure Lengend Snippet: Effect of SDC4 overexpression on signaling pathways chicken fibroblasts. Protein expression analysis following SDC4 overexpression in SL-29 chicken fibroblasts. Detected proteins include (A) phosphorylated p38 at Thr186/Tyr182 and total p38, (B) phosphorylated Akt at Ser473 (pSer473- Akt) and total Akt, (C) phosphorylated ribosomal protein S6 at Ser240/244 (pSer240/244-S6) and total ribosomal protein S6, and (D) non-phosphorylated (active) β-catenin at Ser33/37 and Thr41 and total β-catenin. The ratio of phosphorylated to total or active to total protein was calculated for each protein, illustrating the impact of SDC4 overexpression. As a control (ctrl) was used treatment with lipofectamine only. GAPDH was used as a reference protein. The bars are presented as ± SEM from n = 3-6 in one technical replicate. Asterisks denote significant differences between Ctrl and transfected cells, statistics assessed using either unpaired t-test with Welch correction or Mann-Whitney U test (ns > 0.05; *p ≤ 0.05; **p ≤ 0.01).

Article Snippet: The embryonic chicken fibroblast cell line SL-29 was purchased from ATCC (#CRL 1590, Manassas, VA).

Techniques: Over Expression, Protein-Protein interactions, Expressing, Control, Transfection, MANN-WHITNEY

Journal: Frontiers in Physiology

Article Title: Dual roles of syndecan-4 in regulating chicken fibrosis in vitro

doi: 10.3389/fphys.2026.1782914

Figure Lengend Snippet: Effect of blocking peptides on the gene expression of the various SDCs. Effect of BP1-5 on the levels of SDC1-4 expression in SDC4 transfected chicken fibroblasts SL-29 showing no significant differences compared to control (Ctrl). All results were compared to the appropriate solvent for each blocking peptide. Gene expression was measured in three biological replicates, each performed in technical triplicates, and statistical significance was calculated using one-way ANOVA with Welch and Brown-Forsythe corrections. The bars are presented as ± SEM.

Article Snippet: The embryonic chicken fibroblast cell line SL-29 was purchased from ATCC (#CRL 1590, Manassas, VA).

Techniques: Blocking Assay, Gene Expression, Expressing, Transfection, Control, Solvent

Journal: Frontiers in Physiology

Article Title: Dual roles of syndecan-4 in regulating chicken fibrosis in vitro

doi: 10.3389/fphys.2026.1782914

Figure Lengend Snippet: Effect of blocking peptides on the gene expression of fibrosis markers. Effect of BP1-5 on TGFB1, COL1A1, COL3A1, MMP9, MMP2, IL1B, ACTA2, DCN gene expression levels in SDC4 transfected chicken fibroblasts SL-29. All results were compared to the appropriate solvent for each blocking peptide. Gene expression was measured in three biological replicates, each performed in technical triplicates, and statistical significance was calculated using one-way ANOVA with Welch and Brown-Forsythe corrections. The bars are presented as ± SEM.

Article Snippet: The embryonic chicken fibroblast cell line SL-29 was purchased from ATCC (#CRL 1590, Manassas, VA).

Techniques: Blocking Assay, Gene Expression, Transfection, Solvent

Journal: Frontiers in Physiology

Article Title: Dual roles of syndecan-4 in regulating chicken fibrosis in vitro

doi: 10.3389/fphys.2026.1782914

Figure Lengend Snippet: Effect of TGF-β1 on different gene and protein expression levels. Chicken fibroblasts were treated with TGF-β1 for 24 h. The gene expression levels were assessed for (A) syndecans (SDC1-4) and various fibrotic markers, including (B) COL1A1, (C) COL3A1, (D) MMP2, and (E) MMP9. Additionally, cytokines such as (F) TGFB1 and (G) IL1B were measured, and the expression of (H) ACTA2, a myofibroblast marker, and (I) DCN, a small leucine-rich proteoglycan. Results are expressed as fold change relative to the control (Ctrl; SL-29 cells treated with the solvent of TGF-β1). Gene expression (n = 7, in technical triplicates) was calculated by an unpaired t-test with Welch’s correction. ns > 0.05; *p ≤ 0.05; **p ≤ 0.01. The bars are presented as ± SEM. (J) Immunoblotting analysis of the 20 kDa SDC4 fragment following 24-h treatment with TGF-β1, compared to control (Ctrl) conditions. Quantification (N = 3 in one technical replicate) is presented as the mean, normalized to total protein, and expressed as a percentage relative to the control.

Article Snippet: The embryonic chicken fibroblast cell line SL-29 was purchased from ATCC (#CRL 1590, Manassas, VA).

Techniques: Expressing, Gene Expression, Marker, Control, Solvent, Western Blot