Journal: bioRxiv

Article Title: The Epigenetic Factor PHF13 Governs Trophoblast Stemness and Differentiation

doi: 10.64898/2026.03.14.711150

Figure Lengend Snippet: PHF13-bound regions at trophoblastic stemness genes, including ELF5 (A), TEAD4 (B), TP63 (C), and TEAD1 (D), and TS-associated genes such as WNT6 (E). Yellow shading denotes signficant PHF13 peaks (A-C, E) in TS-CTB, but not in TS-STB when compared to corresponding IgG controls. In contrast, TEAD1 (D) harbored PHF13 peaks in both TS-CTB and TS-STB. As a positive control, H3K4me3 showed binding in all the five TS-related genes in TS-CTB rather than TS-STB (A-E). The x-axis represents genomic corordinates with exonic and intronic structure, and arrows indicate the direction of transcription. The y-axis represents normalized peak intensity.

Article Snippet: For each reaction, 0.5 μg of antibodies against PHF13 (Sino Biological, #202944-T08), H3K4me3 (EpiCypher, #13-0060), and a control antibody for CUT&RUN (EpiCypher, #13-0042) were used.

Techniques: Positive Control, Binding Assay

Journal: bioRxiv

Article Title: The Epigenetic Factor PHF13 Governs Trophoblast Stemness and Differentiation

doi: 10.64898/2026.03.14.711150

Figure Lengend Snippet: A. PHF13 binds the PENK locus in TS-CTB but not in TS-STB. Yellow shading indicates significant PHF13 peaks relative to IgG controls; no H3K4me3 peaks were detected in these shaded regions in TS-CTB. The x-axis represents genomic corordinates with exonic and intronic structure, and arrows indicate transcription direction. The y-axis represents normalized peak intensity. B. PENK protein is expressed in both TS-CTB and TS-STB, and histone H3 was used as a loading control (n=3).

Article Snippet: For each reaction, 0.5 μg of antibodies against PHF13 (Sino Biological, #202944-T08), H3K4me3 (EpiCypher, #13-0060), and a control antibody for CUT&RUN (EpiCypher, #13-0042) were used.

Techniques: Control

Journal: STAR Protocols

Article Title: Protocol for chromatin immunoprecipitation using isolated antheridia of Marchantia polymorpha

doi: 10.1016/j.xpro.2026.104388

Figure Lengend Snippet: An example of ChIP-qPCR results (A) Tissue expression pattern of alpha-tubulin genes in M. polymorpha . Transcripts per million (TPM) values are log2-transformed after adding a pseudo count of 1 to avoid negative values for expression levels. Raw TPM values are obtained from MarpolBase Expression (MBEX, https://marchantia.info/mbex/ ). (B) Schematic diagrams of genomic regions of Mp TUA5 , Mp TUB4 , and Mp TUA3 . Black closed boxes represent exons. PCR amplicons used for ChIP-qPCR are indicated as short bars with letters, a and b. The DUO1 consensus DNA-binding motif (5′-RRCSGTT-3′) is shown as a blue vertical line. (C) ChIP-qPCR analysis showing the enrichment of MpDUO1 on the TSS of Mp TUA5 and Mp TUB4 . pro Mp DUO1 : mCitrine-NLS plant was used as a negative control. The ChIP DNA was quantified by qPCR, and the DNA enrichment was shown as a percentage of input DNA (%input). Mp TUA3 , whose expression level is very low in antheridia and sperm was used as a negative control. Error bars indicate SD of three biological replicates (n = 3).

Article Snippet: Note: This protocol used the ChIP DNA Clean & Concentrator from ZYMO RESEARCH, following the manufacturer’s instruction ( https://files.zymoresearch.com/protocols/_d5201_d5205_chip_dna_clean_concentrator_kit.pdf ).

Techniques: ChIP-qPCR, Expressing, Transformation Assay, Binding Assay, Negative Control