rabbit anti gfp living colors  (TaKaRa)

Journal: EMBO Reports

Article Title: PIWI proximity proteome reveals Set1-mediated piRNA biogenesis for transposon silencing at telomeres

doi: 10.1038/s44319-026-00901-6

Figure Lengend Snippet: ( A ) Immunoprecipitation of GFP or GFP-Set1 proteins from ovaries using anti-GFP antibody (GFP-IP) after crosslinking treatment. Tubulin serves as a loading control. ( B ) Proportion (%) of miRNA and piRNA in ovarian small RNAs. miRNA: reads mapping to miRNA precursors. piRNA: 23–29-nt reads (excluding rRNA, tRNA, snoRNA, snRNA, and miRNA mappers), or 23–29-nt reads mapping to TE consensus sequences. Control: single replicate of gfp -GLKD and GFP-Set1 WT -rescue conditions. set1 -GLKD: biological duplicate of set1 -GLKD condition. Bars: mean values, dots: individual values from biological replicates ( n = 2). ( C ) Fold changes (FC) of piRNA levels in set1 -GLKD compared to the control condition (RPM/RPM). Dots: individual TE families. TEs having few mappers (RPM < 5) were excluded. ( D ) Track view of piRNAs mapping to HTT family members. ( E ) Bar graph showing mean FC of TE-mapping piRNA levels in the mutants compared to the controls (RPM/RPM). Public data: panx KO from GSE71374 , rhi KO from GSE126578 . Dots: individual FC values from biological replicates ( n = 2). .

Article Snippet: Rabbit anti-GFP Living Colors , Clontech , 632592.

Techniques: Immunoprecipitation, Control

Journal: EMBO Reports

Article Title: PIWI proximity proteome reveals Set1-mediated piRNA biogenesis for transposon silencing at telomeres

doi: 10.1038/s44319-026-00901-6

Figure Lengend Snippet: ( A ) Immunoprecipitation of GFP-Set1 proteins from ovaries using anti-GFP antibody (GFP-IP) without crosslinking treatment. W/o: sibling control without GFP-Set1 expression. Tubulin serves as a loading control. ( B ) Ping-pong signature analysis on piRNAs mapping to telomeric TE families. Z10 scores (reflecting 10-nt overlap frequency within piRNA groups) were highlighted. Values are means of biological replicates ( n = 2). ( C ) Bar graph showing mean fold change (FC) of piRNA abundance in mutants relative to their respective controls. Raw data from GSE126578 and GSE55824 were re-analyzed using the same pipeline. GSE126578 includes biological replicates ( n = 2), and individual values are shown as dots.

Article Snippet: Rabbit anti-GFP Living Colors , Clontech , 632592.

Techniques: Immunoprecipitation, Control, Expressing, Analysis

Journal: EMBO Reports

Article Title: PIWI proximity proteome reveals Set1-mediated piRNA biogenesis for transposon silencing at telomeres

doi: 10.1038/s44319-026-00901-6

Figure Lengend Snippet: ( A ) Venn diagram showing overlap of Set1-binding peak-associated genes and TEs between biological replicates ( n = 2). Peak called by MACS2 comparing GFP-Set1 WT and GFP, or GFP-Set1 E1613K and GFP ( p < 0.01, Poisson test). ( B ) Track view for CUT&Tag signals of GFP proteins (green) and H3K4me3 (black) on TE consensus sequences. ORFs were predicted by ORF Finder. ( C ) Alignment of HeT-A{}6278 with GFP-Set1 E1613K binding signals to HeT-A consensus sequence. ( D ) Track view for anti-GFP CUT&Tag signals at 42AB locus (partial). Blue and red: piRNAs mapped to the plus and minus strands, respectively.

Article Snippet: Rabbit anti-GFP Living Colors , Clontech , 632592.

Techniques: Binding Assay, Sequencing

Journal: EMBO Reports

Article Title: PIWI proximity proteome reveals Set1-mediated piRNA biogenesis for transposon silencing at telomeres

doi: 10.1038/s44319-026-00901-6

Figure Lengend Snippet: ( A ) Venn diagram for genes and TEs having GFP-Set1 WT - or GFP-Set1 E1613K -binding peaks. Peaks called by MACS2 ( p < 0.01, estimated by Poisson distribution model). ( B ) Scatter plot comparing fold differences of CUT&Tag signals (GFP-Set1 - GFP) on genes and TEs identified by peak calling. Mean values of biological replicates ( n = 2). Signals on exons of genes and TEs were counted. r : Pearson correlation coefficient. ( C ) Heatmap shows GFP-Set1 enrichment within genes expressed in ovaries ( n = 8196, genes analyzed in Fig. ). Log2 FC of mean CPM + 1 pseudocount (GFP-Set1/GFP). Gene bodies were scaled to 5 kb. ( D ) Track view on aub gene showing signals from anti-GFP (green) or anti-H3K4me3 (black) CUT&Tag. Mean CPM of biological replicates ( n = 2). ( E ) Heatmap shows GFP-Set1 localization on TE consensus sequences. >3 kb TE families were selected. Log2 FC of mean CPM + 1 pseudocount (GFP-Set1/GFP). ( F ) Track view on HeT-A consensus sequence showing signals from anti-GFP (green) or anti-H3K4me3 (black) CUT&Tag. ( G ) Track view at the subtelomeric cluster 3 locus. Blue and red: piRNAs mapping to genomic plus and minus strands, respectively. .

Article Snippet: Rabbit anti-GFP Living Colors , Clontech , 632592.

Techniques: Binding Assay, Sequencing

Journal: EMBO Reports

Article Title: PIWI proximity proteome reveals Set1-mediated piRNA biogenesis for transposon silencing at telomeres

doi: 10.1038/s44319-026-00901-6

Figure Lengend Snippet: ( A ) Track view at subtelomeric cluster 3 or 38C locus. Light green: signals from anti-Rhi CUT&Tag. Dark green: GFP-Set1-EK signals in set1 -GLKD (anti-GFP CUT&Tag). Blue and red: piRNAs mapped to genomic plus and minus strands, respectively. Mean CPM from biological replicates ( n = 2). ( B ) Quantification of anti-Rhi CUT&Tag signals. Bars: mean FPKM (fragments per kilobase per million mapped reads), dots: individual FPKM, from biological replicates ( n = 2). ( C ) Working model. Set1 interacting with HTT sequences cooperates with Piwi for piRNA cluster formation in subtelomeric regions. Set1 provides target templates for Piwi-piRNA complexes and/or precursor transcripts for piRNA production. Fragmented HeT-A 3’UTR retaining antisense TSS plays a crucial role in the latter process. Cooperation between Set1 and Piwi promotes H3K9me3 deposition and Rhi accumulation. Once this piRNA cluster status is established, Set1 and Piwi become dispensable. Similar mechanisms operate in the silencing of stand-alone TEs. Germline cells lacking the noncanonical functions of Set1 not only fail to establish piRNA clusters at subtelomeric loci but also exhibit aberrant Rhi distribution and piRNA overproduction at certain loci. .

Article Snippet: Rabbit anti-GFP Living Colors , Clontech , 632592.

Techniques:

Journal: EMBO Reports

Article Title: PIWI proximity proteome reveals Set1-mediated piRNA biogenesis for transposon silencing at telomeres

doi: 10.1038/s44319-026-00901-6

Figure Lengend Snippet: ( A ) Track view at 42AB or 20A locus. Light green: signals from anti-Rhi CUT&Tag. Dark green: GFP-Set1-EK signals (anti-GFP CUT&Tag). Blue and red: piRNAs mapped to genomic plus and minus strands, respectively. ( B ) Quantification of anti-Rhi CUT&Tag signals. Bars: mean FPKM, dots: individual FPKM, from biological replicates ( n = 2). Analyzed regions within 42AB are indicated in ( A ). ( C ) Track view in the subtelomeric region on chromosome 2R. ( D ) Track view at subtelomeric cluster 3 showing H3K9me3 signal (mean CPM from biological replicates ( n = 2)). embKD: knockdown at embryonic stages. Raw data: GSE83238 .

Article Snippet: Rabbit anti-GFP Living Colors , Clontech , 632592.

Techniques: Knockdown

Journal: EMBO Reports

Article Title: PIWI proximity proteome reveals Set1-mediated piRNA biogenesis for transposon silencing at telomeres

doi: 10.1038/s44319-026-00901-6

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Rabbit anti-GFP Living Colors , Clontech , 632592.

Techniques: Drosophila, shRNA, Recombinant, Sequencing, Plasmid Preparation, Protease Inhibitor, Mass Spectrometry, Membrane, Reverse Transcription, SYBR Green Assay, Multiplex Assay, Purification, Staining, Gel Extraction, Cloning, Cross-linking Immunoprecipitation, Qubit, Software, Imaging, Confocal, Microscopy, Real-time Polymerase Chain Reaction

Journal: bioRxiv

Article Title: IRES-mediated translation of Δ160p53 regulates p53 functions and fine-tunes cancer homeostasis

doi: 10.64898/2026.08.21.744132

Figure Lengend Snippet: (A) Western blot analysis of cell extracts from H1299 transfected with pcDNA and Δ133p53, and treated with 5-fluorouracil (5-FU; 20 µM) and thapsigargin (0.1 µM) for 16 h, probed with BiP antibody, p53 polyclonal antibody, and β-actin antibody. (B) Partial sequence of p53 transcript variants 5,6 and 7, which are known to produce Δ133p53, and the putative IRES sequence was marked. (C) Schematic representation of bicistronic plasmids; H1299 cells were transfected with the plasmids along with pRL-TK. At 48 h post-transfection, relative luciferase activity was calculated in the presence of different IRES sequences and the control sequence (null). (D) Schematic representation of the peGFPΔEMCVI3Δ160p53 construct; western blot analysis of cell extracts from H1299 cells transfected with pcDNA (negative control), Δ160p53 (positive control), and peGFPΔEMCVI3Δ160p53, probed with p53 polyclonal antibody, β-actin antibody, and green fluorescence protein (GFP) antibody. (E) Splicing assay: Semiquantitative polymerase chain reaction (PCR) analysis using two sets of primers (P1/P2 and P3/P4), RNA isolated from pRI3F-transfected (Lanes 2–7) and untransfected (Lane 1) H1299 cells. Lanes 2 and 5 show the reverse transcriptase negative control, and lanes 4 and 7 show the PCR product amplified from the pRI3F bicistronic plasmid (Positive control). (F) Cryptic promoter activity assay: pGL3-basic (Promoter-less luciferase vector as negative control), PG13 (p53 binding sites containing luciferase plasmid as positive control), and IRES-pGL3 plasmids were transfected into H1299 cells along with pRL-TK, and relative luciferase activity was measured. (G) Real-time PCR of Fluc mRNA in H1299 cells transfected with pGL3-basic, PG13, and IRES-pGL3 plasmids. Error bars indicate standard deviation (SD). All experiments were performed in three biological replicates (n = 3). The criterion for significance was determined using a two-tailed Student’s t-test (**P ≤ 0.01 or ***P ≤ 0.001).

Article Snippet: Rabbit anti-GFP-Tag antibody (Abclonal, Cat. No. AE011) and β-actin antibodies (Sigma) were horseradish peroxidase-conjugated, and no secondary antibodies were required for detection.

Techniques: Western Blot, Transfection, Sequencing, Luciferase, Activity Assay, Control, Construct, Negative Control, Positive Control, Fluorescence, Splicing Assay, Polymerase Chain Reaction, Isolation, Reverse Transcription, Amplification, Plasmid Preparation, Binding Assay, Real-time Polymerase Chain Reaction, Standard Deviation, Two Tailed Test