mouse anti atf3  (Santa Cruz Biotechnology)

Journal: Cell Genomics

Article Title: Sequential activation of transcription factors promotes liver regeneration through specific and developmental enhancers

doi: 10.1016/j.xgen.2025.100887

Figure Lengend Snippet: Time point-specific TF motif patterns during liver regeneration (A) Differential TF binding sites at each time point identified by HINT-ATAC footprinting. Each point represents a TF; only those with expression >1 TPM in at least one condition and significant change in activity ( p < 0.05) are labeled. Circle color reflects log2FC of the TF-encoding gene. (Below) ATAC-seq profiles for two example TF footprints at 24 h post PHx (CTRL vs. REG). (B) Expression of Fos , Jun , Egr1 , Atf3 , Nrf2 , Cebpb , Cebpa , and Dbp over time in CTRL (gray) and REG (red). Significance: ∗∗ p adjusted < 0.01, ∗ p adjusted < 0.05 (DESeq2, pairwise comparison vs. control, Wald test, assuming negative binomial distribution). (C) Top 10 enriched TF motifs in de novo , increasing, or decreasing promoters (left) and enhancers (right), identified using AME with the HOCOMOCO v11 database (Mann-Whitney U test, p adjusted < 0.05). Scaled enrichment E-scores are shown. †Includes all family members. See also .

Article Snippet: Plasmid: Atf3 ( NM_007498 ) Mouse Tagged ORF Clone , Origene , MR201634.

Techniques: Binding Assay, Footprinting, Expressing, Activity Assay, Labeling, Comparison, Control, MANN-WHITNEY

Journal: Cell Genomics

Article Title: Sequential activation of transcription factors promotes liver regeneration through specific and developmental enhancers

doi: 10.1016/j.xgen.2025.100887

Figure Lengend Snippet: Early regeneration GRN (A) GRN with edges colored by TF-target Pearson’s correlation coefficient (blue, ≥0.8; gray, ≤ −0.8). While most correlations are positive, negative interactions are predicted for some TFs. (B) GRN at 6 h: Nodes are colored by target gene normalized expression and edges by RRE classification at 6 h. (C) GRN at 24 h: same as (B), but for 24 h. (D) GRN at 48 h: same as (B), but for 48 h. (E) Number and type of RREs with ATF3 motifs (left axis) and Atf3 expression in Z scores (right axis) (REG in red, CTRL in gray). (F) Expression of predicted target genes linked to ATF3 motif-containing RREs. Each column is one condition (average across replicates), gene expression as Z scores. (G) Number of RREs containing TF motif pairs. (H) Expression of predicted target genes associated with RREs with co-localization of the NRF2 and FOXM1 motifs. Each column is one condition (average across replicates), gene expression as Z scores. See also .

Article Snippet: Plasmid: Atf3 ( NM_007498 ) Mouse Tagged ORF Clone , Origene , MR201634.

Techniques: Expressing, Gene Expression

Journal: Cell Genomics

Article Title: Sequential activation of transcription factors promotes liver regeneration through specific and developmental enhancers

doi: 10.1016/j.xgen.2025.100887

Figure Lengend Snippet: ATF3 and NRF2 bind to de novo and increasing RREs to activate the expression of regeneration-associated genes (A) Representative ATF3 immunostaining images in control and regenerating livers at 6 h post surgery. No positive nuclei observed in controls. (B) Proportion of de novo and increasing RREs overlapping ATF3 ChIP-seq peaks at each time point. Fisher’s exact test (∗∗∗ p adjusted < 0.001). (C) Genome browser screenshot of the Hcar2 locus at 6h. Promoter shows ATF3 binding and is linked to an ATF3-bound de novo enhancer. (D) Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway analysis of target genes from ATF3-bound de novo and increasing RREs ( p adjusted < 0.05). (E) UMAP of cells from quiescent (PHx0) and regenerating (PHx24–PHx48) livers, colored by condition (left) or annotated cell type (right). (F) Feature plot of Atf3 expression at PHx0 and PHx24–PHx48. (G) Proportion of increasing RREs overlapping NRF2 ChIP-seq peaks at each time point. Fisher’s exact test (∗∗∗ p adjusted < 0.001). (H) Genome browser views of Hmox1 and Aldh1a7 loci at 48 h. Both promoters show NRF2 binding and are linked to NRF2-bound increasing enhancers. (I) Relative luciferase activity of candidate enhancers co-transfected with ATF3 or NRF2 vectors, or alone (−), in hepatocyte cultures. One-way ANOVA with Tukey’s HSD ( p < 0.05). See also .

Article Snippet: Plasmid: Atf3 ( NM_007498 ) Mouse Tagged ORF Clone , Origene , MR201634.

Techniques: Expressing, Immunostaining, Control, ChIP-sequencing, Binding Assay, Luciferase, Activity Assay, Transfection

Journal: Investigative ophthalmology & visual science

Article Title: De-Differentiation of Corneal Epithelial Cells Into Functional Limbal Epithelial Stem Cells After the Ablation of Innate Stem Cells.

doi: 10.1167/iovs.65.13.32

Figure Lengend Snippet: FIGURE 2. The regeneration of LESCs at the limbus after innate stem cells ablation. (A) Immunostaining of potential LESCs markers (CK14, deltaN-p63, p75NTR, CD63, TSPAN7, IFITM3, ATF3, and ApoE), Cx43 and CECs marker CK12 in frozen sections of normal cornea. (B-D) Immunostaining of Cx43, ApoE, and CK12 in frozen sections of normal cornea and LESCs-ablation cornea at indicated days after the limbal epithelial removal. The limbus was shown. (E) The percentage of ApoE+ cells at the limbus, and MFI (limbal basal cells)/MFI (peripheral basal cells) of Cx43 and CK12 were determined to indicate the recovery of LESCs. N, normal cornea. Scale bars = 50 μm. Note that the limbus is localized based on the location of iris and ciliary body in the bright field and the expressions of LESC markers.

Article Snippet: The following primary antibodies were used: rabbit anti-CK12 monoclonal antibody (Abcam, ab185627; 1:400), rabbit anti-CK7 monoclonal antibody (Abcam, ab181598; 1:400), rabbit anti-connexin 43 (Cx43) monoclonal antibody (CST, #3512; 1:80), rabbit anti-ApoE monoclonal antibody (Abcam, ab183596; 1:400), rabbit anti-CK14 monoclonal antibody (Abcam, ab119695; 1:200), rabbit anti-deltaN-p63 polyclonal antibody (BioLegend, 619002; 1:400), rabbit anti-p75NTR monoclonal antibody (CST, #8238; 1:800), rabbit anti-CD63 polyclonal antibody (Bioworld, BS72936; 1:400), rabbit anti-TSPAN7 polyclonal antibody (Proteintech, 18695-1-AP; 1:100), rabbit anti-IFITM3 monoclonal antibody (CST, #59212; 1:100), mouse anti-ATF3 monoclonal antibody (Santa Cruz, sc-518032; 1:100), rabbit anti-YAP monoclonal antibody (CST, #14074; 1:100), rabbit anti-active-YAP (non-phosphorylated YAP) monoclonal antibody (Abcam, ab205270; 1:200), rabbit anti-Ki67 monoclonal antibody (CST, #9129; 1:100), rabbit anti-p-Histone H3-Ser10 (pH3) monoclonal antibody (CST, #53348; 1:100), and mouse antiCK15 monoclonal antibody (Santa Cruz, sc-47697; 1:200).

Techniques: Immunostaining, Marker