Journal: Analytical biochemistry

Article Title: Stain-Free total-protein normalization enhances the reproducibility of Western blot data

doi: 10.1016/j.ab.2022.114840

Figure Lengend Snippet: (A–C) BEAS-2B cells were transfected with dsiRNA control vs. dsiRNA targeting an E3 ligase that degrades FoxP1 protein. Lysates (20 μg) were electrophoresed using 10% Stain-Free gels and transferred onto PVDF membranes. A Stain-Free image was captured, the membranes cut horizontally at 65KD and 50KD, and the respective pieces immunoblotted for FoxP1, β-Tubulin, and Actin. The experiment was repeated 3 times, >2 weeks apart. (D) FoxP1 protein levels with standard deviations when normalized to β-Tubulin, Actin, or the Stain-Free signal. (E) The statistical significance and mean difference in FoxP1 protein levels in dsi control vs. dsi E3 ligase when normalized to β-Tubulin, Actin, or the Stain-Free signal. (F) Levels of Actin or β-Tubulin normalized to Stain-Free signal in dsi control vs. dsi E3 ligase.

Article Snippet: Antibodies and reagents β-Tubulin antibody was obtained from Cell Signaling (cat # 2146S, used at 1:2000 dilution), Actin and GAPDH antibodies were obtained from Proteintech (cat # 60000-IG and 10494-1-AP, both used at 1:4000 dilution), and FoxP1 antibody was obtained from Santa Cruz (cat# sc-398811, used at 1:1000 dilution).

Techniques: Transfection, Control, Staining

Journal: Analytical biochemistry

Article Title: Stain-Free total-protein normalization enhances the reproducibility of Western blot data

doi: 10.1016/j.ab.2022.114840

Figure Lengend Snippet: The estimated total number of samples needed to detect a 15%, 20%, and 30% difference in FoxP1 protein levels by immunoblot using standard deviations assessed in Fig. 3E and assuming a two-sided p < 0.05 and 90% power.

Article Snippet: Antibodies and reagents β-Tubulin antibody was obtained from Cell Signaling (cat # 2146S, used at 1:2000 dilution), Actin and GAPDH antibodies were obtained from Proteintech (cat # 60000-IG and 10494-1-AP, both used at 1:4000 dilution), and FoxP1 antibody was obtained from Santa Cruz (cat# sc-398811, used at 1:1000 dilution).

Techniques: Western Blot

Journal: Journal of neurochemistry

Article Title: FoxP1 promotes midbrain identity in embryonic stem cell-derived dopamine neurons by regulating Pitx3.

doi: 10.1111/j.1471-4159.2010.06650.x

Figure Lengend Snippet: Fig. 3 FoxP1 regulates Pitx3 promoter activity. (a) Schematic repre- sentation of the mouse Pitx3 promoter indicating the position of putative FoxP1 binding sites and the sequences of the mouse putative FoxP1 binding sites. (b) P19 cells were transiently cotransfected with a 3.2-kb Pitx3 promoter–reporter gene construct and increasing amounts of either control (pPyCAG-IP) or full-length FoxP1 expression vector. (c) Schematic representation of the different promoter–reporter gene deletion constructs used. (d) The promoter–reporter gene dele-

Article Snippet: Fragmented chromatin (140 lg, 300–1000 bp) was subjected to immunoprecipitation with specific antibodies: anti-H3-carboxy terminal (Abcam), anti-dimethyl-H3K4 (Upstate Biotechnology, Lake Placid, NY, USA), anti-trimethylH3K27 (Upstate), FoxP1 (AVIVA Systems Biology, San Diego, CA, USA) and anti-b-catenin (Sigma).

Techniques: Activity Assay, Binding Assay, Construct, Control, Expressing, Plasmid Preparation

Journal: Journal of neurochemistry

Article Title: FoxP1 promotes midbrain identity in embryonic stem cell-derived dopamine neurons by regulating Pitx3.

doi: 10.1111/j.1471-4159.2010.06650.x

Figure Lengend Snippet: Fig. 4 FoxP1 binds to the Pitx3 promoter. (a) Sequences of the oli- gonucleotide probes used in in vitro binding assays. (b) In vitro binding and supershift assays performed with nuclear extracts prepared from either Ptg or Ptg–FoxP1 ES cells. Wilt-type and mutant probes were used in binding reactions. Unlabelled cold competitor, as well as specific antibody to FoxP1 (a-FoxP1), were used for DNA competition and antibody supershift. Data are representative of three independent experiments. (c) Diagram illustrating the position of primer pairs (ar- rows), within the Pitx3 promoter, used for ChIP analysis. Primers

Article Snippet: Fragmented chromatin (140 lg, 300–1000 bp) was subjected to immunoprecipitation with specific antibodies: anti-H3-carboxy terminal (Abcam), anti-dimethyl-H3K4 (Upstate Biotechnology, Lake Placid, NY, USA), anti-trimethylH3K27 (Upstate), FoxP1 (AVIVA Systems Biology, San Diego, CA, USA) and anti-b-catenin (Sigma).

Techniques: In Vitro, Binding Assay, Mutagenesis

Journal: Journal of Clinical Medicine

Article Title: Examining the Potential Link Between Forkhead Box P1 and Severity and Social Impairment in Children with Autism Spectrum Disorder

doi: 10.3390/jcm14207132

Figure Lengend Snippet: Median FOXP1 (pg/mL) levels in ASD and control groups.

Article Snippet: The plasma levels of FOXP1 were evaluated using commercially available sandwich ELISA kits (Cusabio Biotech Co. Ltd., Wuhan, China, Cat# E15456h), according to the manufacturer’s instruction.

Techniques: Control

Journal: Journal of Clinical Medicine

Article Title: Examining the Potential Link Between Forkhead Box P1 and Severity and Social Impairment in Children with Autism Spectrum Disorder

doi: 10.3390/jcm14207132

Figure Lengend Snippet: Correlation between FOXP1 protein (pg/mL) and CARS in ASD group.

Article Snippet: The plasma levels of FOXP1 were evaluated using commercially available sandwich ELISA kits (Cusabio Biotech Co. Ltd., Wuhan, China, Cat# E15456h), according to the manufacturer’s instruction.

Techniques:

Journal: Journal of Clinical Medicine

Article Title: Examining the Potential Link Between Forkhead Box P1 and Severity and Social Impairment in Children with Autism Spectrum Disorder

doi: 10.3390/jcm14207132

Figure Lengend Snippet: Correlation between FOXP1 protein (pg/mL) and SRS in ASD group.

Article Snippet: The plasma levels of FOXP1 were evaluated using commercially available sandwich ELISA kits (Cusabio Biotech Co. Ltd., Wuhan, China, Cat# E15456h), according to the manufacturer’s instruction.

Techniques:

Journal: Journal of Clinical Medicine

Article Title: Examining the Potential Link Between Forkhead Box P1 and Severity and Social Impairment in Children with Autism Spectrum Disorder

doi: 10.3390/jcm14207132

Figure Lengend Snippet: Correlation between FOXP1 protein (pg/mL) and age in ASD group.

Article Snippet: The plasma levels of FOXP1 were evaluated using commercially available sandwich ELISA kits (Cusabio Biotech Co. Ltd., Wuhan, China, Cat# E15456h), according to the manufacturer’s instruction.

Techniques:

Journal: Nature

Article Title: Epigenetic memory of colitis promotes tumour growth

doi: 10.1038/s41586-026-10258-4

Figure Lengend Snippet: a , Schematic for derivation of de novo motifs from footprinting data. b , Left, mean accessibility change over control for all de novo and known motifs. Right, sequence information content of de novo derived AP-1 composite motifs. c , Top, FOX/AP-1 composite motif accessibility change over control through colitis progression. Mean across n = 9 control, 4 acute, 5 chronic and 5 recovered mice. Bottom, predicted effect of motif presence on footprint scores. The x axis represents distance from motif, the y axis represents size of footprint and colour indicates predicted change of footprint score when motif is added. d , Disruption of cobinding with AP-1 for select TF families following 24 h of AP-1 inhibition. e , Cobinding of select TF families at IBD-specific AP-1 footprints in human organoids. f , Comparison of cobinding scores between mouse and human organoids. g , Schematic for quantification of in vitro binding capability. h , Example locus assayed by the in vitro binding assay. Top, seq2PRINT footprint scores from control and colitis-recovered mice. Bottom, in vitro TF binding score at the same sequence. i , In vitro binding scores for AP-1 and FOX TFs alone and in combination. The y axis represents the binding score at the AP-1 motif normalized to the FOS–JUN heterodimer alone. Error bars represent s.e.m. across all tested loci ( n = 29 sequences for AP-1 alone, n = 34 sequences for FOX/AP-1). j , AlphaFold3 predicted structure for FOXP1, composite motif DNA and FOS–JUN dimer (left) or JUN alone (right). All error bars represent s.e.m. Significance values are from two-sided t -tests unless otherwise indicated. For box and whisker plots, the centre line represents median, the box upper and lower quartiles and the whiskers 1.5× IQR. Panels d and e created in BioRender; Nagaraja, S. https://biorender.com/or0ceke (2026).

Article Snippet: In vitro footprinting was performed as described in ref. with the following modifications: briefly, selected sequences (25 ng per reaction) were incubated with various combinations of recombinant JUN (Active Motif, 31116), FOS (OriGene, TP760257), FOXP1 (OriGene, TP313862) and FOXA1 protein (OriGene, TP306045), along with tagmentation buffer (20 mM Tris, 10 mM MgCl 2 and 20% dimethylformamide) and water in a 22.5-μl total volume at room temperature for 1 h. Then, 0.15 μl of preassembled Tn5 (seqWell, Tagify) was combined with 2.35 μl of dilution buffer (50 mM Tris, 100 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 0.1% NP-40 and 50% glycerol), and subsequently added to samples (resulting in final TF concentrations of 300 nM each).

Techniques: Footprinting, Control, Sequencing, Derivative Assay, Disruption, Inhibition, Comparison, In Vitro, Binding Assay, Whisker Assay

Journal: Nature

Article Title: Epigenetic memory of colitis promotes tumour growth

doi: 10.1038/s41586-026-10258-4

Figure Lengend Snippet: a, Gene expression of FOX family transcription factors in all stem cells in primary tissue (n = 23 mice). b, Multi-scale footprinting at sample genomic loci. Top, expanded copy of multiscale plot below. The X-axis represents distance in base pairs from the AP-1 motif center and the Y-axis represents radius of footprint being evaluated. The color represents -log10(p-value) from a one-sided binomial test of the predicted footprint at given radius and genomic position. For all in vitro binding scores, a 14 bp footprint radius was used. c, Genomic tracks of in vivo tissue footprint score (top), Tn5 insertions relative to naked DNA alone (middle), and in vitro binding score for given TF combinations. d, All loci and combinations of TFs tested by in vitro binding assay. Columns are positions relative to AP-1 motif site center and rows are each individual genomic locus. Color represents in vitro binding score calculation of -log10(p-value) at 14 bp radius. e, Average in vitro binding scores across all loci in panel (d). f, AlphaFold predicted structures for Fos-Jun dimer, composite motif and either Foxa1, Foxn2 or Foxj2. g, UniProt domain annotation for FOX TFs with black boxes indicating regions predicted to interact with Fos/Jun heterodimer. Numbers indicate amino acid positions. DBD = DNA binding domain, ZF = Zinc finger, LZ = Leucine zipper. h, Predicted interactions with Foxp1 and Jun alone. All error bars are s.e.m.

Article Snippet: In vitro footprinting was performed as described in ref. with the following modifications: briefly, selected sequences (25 ng per reaction) were incubated with various combinations of recombinant JUN (Active Motif, 31116), FOS (OriGene, TP760257), FOXP1 (OriGene, TP313862) and FOXA1 protein (OriGene, TP306045), along with tagmentation buffer (20 mM Tris, 10 mM MgCl 2 and 20% dimethylformamide) and water in a 22.5-μl total volume at room temperature for 1 h. Then, 0.15 μl of preassembled Tn5 (seqWell, Tagify) was combined with 2.35 μl of dilution buffer (50 mM Tris, 100 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 0.1% NP-40 and 50% glycerol), and subsequently added to samples (resulting in final TF concentrations of 300 nM each).

Techniques: Gene Expression, Footprinting, In Vitro, Binding Assay, In Vivo