Journal: American Journal of Translational Research

Article Title: TRF-20-M0NK5Y93 suppresses the metastasis of colon cancer cells by impairing the epithelial-to-mesenchymal transition through targeting Claudin-1

doi:

Figure Lengend Snippet: Primer sequences for qRT-PCR

Article Snippet: When the cells reached 70-80% confluence, the cells were ready for transfection. tRF-20-M0NK5Y93 inhibitor (5’-ACCCACAAUCCCCAGCUCCG-3’) and negative control (NC-inhibitor, 5’-UUCUCCGAACGAGUCACGUTT-3’) were purchased from GenePharma (Shanghai, China).

Techniques: Sequencing

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Aberrant regulation of synovial T cell activation by soluble costimulatory molecules in rheumatoid arthritis.

doi: 10.4049/jimmunol.177.12.8844

Figure Lengend Snippet: FIGURE 2. Induction of the expression of costimulatory molecules by cytokines. A, Mononuclear cell specimens of healthy volunteers were in- cubated with the indicated recombinant human cytokines at the indicated concentrations for 12 h. CD4 T cells or CD14 monocytes were purified from the resulting cell preparations for real-time PCR analysis. B, The resulting cell preparations treated with the indicated cytokines at a con- centration of 25 ng/ml were analyzed for the surface expression of the indicated costimulatory molecules by flow cytometry. CTLA-4 was ana- lyzed by both surface and intracellular expression. Open contours represent untreated cell preparations. Shaded contours indicate the expression profile of cells treated with the indicated cytokines. The data are representative of three independent experiments with separate specimens.

Article Snippet: Induction of the expression of costimulatory molecules PBMCs from healthy individuals were cultured in 24-well plates at 1 million cells/ml in RPMI 1640 medium containing 10% FBS in the presence or absence of a panel of recombinant human cytokines (i.e., IFN- , IL-10, or TNF- ; R&D Systems), respectively, at the indicated concentrations.

Techniques: Expressing, Recombinant, Real-time Polymerase Chain Reaction, Cytometry

Journal: EMBO Molecular Medicine

Article Title: An immunohistochemical atlas of necroptotic pathway expression

doi: 10.1038/s44321-024-00074-6

Figure Lengend Snippet: Reagents and tools table

Article Snippet: For experiments in Fig. , co-housed 8-week-old female C57BL/6J wild-type mice were administered either 300 μg/kg TNF (R&D Systems Cat#410-MT/CF Lot CS152103 ) in endotoxin-free DPBS or endotoxin-free DPBS alone (Merck Cat# TMS-012-A) via bolus tail vein injection.

Techniques: Derivative Assay, Polymer, Plasmid Preparation, Blocking Assay, Membrane, Staining, RNA HS Assay, dsDNA Assay, Protease Inhibitor, Software, Imaging, Enzyme-linked Immunosorbent Assay

Journal: iScience

Article Title: Human SKI component SKIV2L regulates telomeric DNA-RNA hybrids and prevents telomere fragility

doi: 10.1016/j.isci.2024.111096

Figure Lengend Snippet:

Article Snippet: Mouse monoclonal anti-TRF1 , Santa Cruz Biotechnology , Catsc-56807; RRID: AB_793407.

Techniques: Virus, Recombinant, Protease Inhibitor, Reverse Transcription, Blocking Assay, Mass Spectrometry, SYBR Green Assay, Flow Cytometry, Imaging, Mutagenesis, Cell Cycle Assay, shRNA, Software

Journal: eLife

Article Title: Transferrin receptor 1-mediated iron uptake regulates bone mass in mice via osteoclast mitochondria and cytoskeleton

doi: 10.7554/eLife.73539

Figure Lengend Snippet: ( A ) Detection of mRNA expression of genes involved in iron uptake and export pathways in bone marrow monocytes (BMM), mononuclear pre-osteoclasts (pOC), and mature osteoclasts (OC) by real-time quantitative PCR. Tfrc encodes Tfr1; Slc11a1 encodes Dmt1 (divalent metal ion transporter 1); Slc39a14 encodes Zip14; Slc46a1 encodes heme transporter Hcp1; Flvcr2 encodes Flvcr2 heme transporter 2. ( B ) Measurement of 59 Fe-labeled transferrin (Tf- 59 Fe) uptake in control (con) and Tfr1 myeloid conditional knockout (Tfr1 ΔLysM ) osteoclasts by a gamma counter. ( C ) Measurement of intracellular total iron by a colorimetric iron assay kit in control and Tfr1-deficient osteoclast lineage cells. The data are presented as mean ± SD. n=3. * p<0.05, ** p<0.01, and *** p<0.001 vs BMM ( A ) and vs control OC ( C ) by one-way ANOVA and Student’s t-test. Figure 1—source data 1. Tfr1 is a major transferrin transporter and regulates cellular iron homeostasis in osteoclasts.

Article Snippet: Commercial assay or kit , Tfrc , Thermo-Fisher Scientific , Mm00441941_m1 , qPCR primer.

Techniques: Expressing, Real-time Polymerase Chain Reaction, Labeling, Control, Knock-Out, Iron Assay

Journal: eLife

Article Title: Transferrin receptor 1-mediated iron uptake regulates bone mass in mice via osteoclast mitochondria and cytoskeleton

doi: 10.7554/eLife.73539

Figure Lengend Snippet: ( A ) TRAP staining (scale bar = 10 μm) and quantification of numbers of total and spreading osteoclasts (OCs) cultured on plastic 24-well dishes. n=6. ( B ) Quantitative PCR detection of the mRNA expression of Tfr1 and osteoclast marker genes relative to the mitochondrial gene Mrps2. Tfrc , encoding Tfr1; Acp5 , encoding TRAP; Ctsk , encoding Cathepsin K; Nfatc1 , encoding NFATc1; Dcstamp , encoding DC-Stamp. n=3. ( C ) The protein level of Tfr1 and osteoclast markers, NFATc1 and Cathepsin K (Ctsk), in bone marrow monocytes ( m ), mono-nuclear pre-osteoclasts ( p ), and mature osteoclasts ( c ) was detected by western blotting and quantified by densitometry using the NIH ImageJ software. Tubulin served as loading control. n=3. ( D ) The actin filaments and nuclear were stained by Alexa-488 conjugated Phalloidin and Hoechst 33258, respectively, in osteoclasts cultured on glass coverslips (scale bar = 10 μm). The number of osteoclasts with different nuclei and the percentage of spreading osteoclasts with the peripheral distributed podosome-belt were counted. n=3–4. ( E ) The actin filaments and nuclear were stained by Alexa-488 conjugated Phalloidin and Hoechst 33342, respectively, in osteoclasts cultured on cortical bovine bone slices (scale bar = 10 μm). The total number of osteoclasts and the number of osteoclasts with actin-ring were counted, and the percentage of active osteoclasts per bone slices was calculated. n=3. ( F ) Resorption pits were stained by horseradish peroxidase conjugated wheat-germ agglutinin (scale bar = 20 μm). The percentage of resorbed area per bone slice was calculated using the NIH ImageJ software. The data are presented as mean ± SD. n=3. * p<0.05; ** p<0.01; *** p<0.001;**** p<0.0001 vs control (f/f;+/+) by one-way ANOVA and Student’s t-test. Figure 4—source data 1. Deletion of Tfr1 in osteoclast myeloid precursors has no effects on osteoclast differentiation but attenuates cytoskeleton organization and bone resorption in mature osteoclasts cultured from female mice. Figure 4—source data 2. Immunoblotting for .

Article Snippet: Commercial assay or kit , Tfrc , Thermo-Fisher Scientific , Mm00441941_m1 , qPCR primer.

Techniques: Staining, Cell Culture, Real-time Polymerase Chain Reaction, Expressing, Marker, Western Blot, Software, Control

Journal: eLife

Article Title: Transferrin receptor 1-mediated iron uptake regulates bone mass in mice via osteoclast mitochondria and cytoskeleton

doi: 10.7554/eLife.73539

Figure Lengend Snippet: Quantitative PCR detection of the mRNA levels of Tfrc , Fpn , and mt-Co1 in vehicle ( v ), estrogen ( E2 ), and androgen ( T ) treated control (con) and Tfr1 ΔLysM osteoclast lineage cells. The data are presented as mean ± SD. n=3. * p<0.05; ** p<0.01; *** p<0.001, **** p<0.0001 vs vehicle or control analyzed by one-way ANOVA. Figure 2—figure supplement 8—source data 1. Estrogen but not androgen synergistically with Tfr1-deficiency inhibits the mRNA expression of mitochondrial cytochrome c oxidase subunit I in osteoclast lineage cells.

Article Snippet: Commercial assay or kit , Tfrc , Thermo-Fisher Scientific , Mm00441941_m1 , qPCR primer.

Techniques: Real-time Polymerase Chain Reaction, Control, Expressing

Journal: eLife

Article Title: Transferrin receptor 1-mediated iron uptake regulates bone mass in mice via osteoclast mitochondria and cytoskeleton

doi: 10.7554/eLife.73539

Figure Lengend Snippet:

Article Snippet: Commercial assay or kit , Tfrc , Thermo-Fisher Scientific , Mm00441941_m1 , qPCR primer.

Techniques: Cell Culture, Blocking Assay, Staining, Protease Inhibitor, Western Blot, Membrane, Reverse Transcription, Enzyme-linked Immunosorbent Assay, Iron Assay, Fluorescence, Recombinant, Transfection, Real-time Polymerase Chain Reaction

Journal: EMBO Reports

Article Title: Human PC4 supports telomere stability and viability in cells utilizing the alternative lengthening of telomeres mechanism

doi: 10.1038/s44319-024-00295-3

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Primary antibodies were: a rabbit polyclonal anti-PC4 (same as above, 1:5000 dilution), a rabbit polyclonal anti-RPA32 pSer33 (same as above, 1:2000 dilution), a rabbit polyclonal anti-RPA32 (Bethyl Laboratories, A300-244A; 1:2000 dilution), a mouse monoclonal anti-beta Actin (Abcam, ab8224; 1:5000 dilution), a rabbit polyclonal anti-PML (same as above, 1:1000 dilution), a rabbit polyclonal anti-TRF2 (Novus Biologicals, NB110-57130; 1:1000 dilution), a rabbit monoclonal anti-Vinculin (Cell Signaling Technology, #13901; 1:1000 dilution), a rabbit polyclonal anti-Bloom (Bethyl Laboratories, A300-110A; 1:1000 dilution), a rabbit polyclonal anti-ATRX (Bethyl Laboratories, A301-045A; 1:1000 dilution), a rabbit polyclonal anti-RNA PolII (Bethyl Laboratories, A300-653A; 1:2000 dilution), a rabbit polyclonal anti-phospho RNA PolII (S2) (Bethyl Laboratories, A300-654A; 1:10000 dilution), a rabbit polyclonal anti-phospho RNA PolII (S5) (Bethyl Laboratories, A300-655A; 1:10000 dilution), and a goat polyclonal anti-Helic2 (Santa Cruz Biotechnology, SC-68563; 1:1000 dilution).

Techniques: In Vitro, Recombinant, shRNA, Control, Plasmid Preparation, Sequencing, Negative Control, Magnetic Beads, Protease Inhibitor, Blocking Assay, Software, Microscopy

Journal: Cell

Article Title: Stabilization of Reversed Replication Forks by Telomerase Drives Telomere Catastrophe

doi: 10.1016/j.cell.2017.11.047

Figure Lengend Snippet:

Article Snippet: Rabbit monoclonal anti-TRF2 , Cell Signaling Technology , Cat#13136.

Techniques: Plasmid Preparation, Recombinant, Protease Inhibitor, In Situ, DNA Extraction, Mutagenesis, cDNA Synthesis, RNAscope, SYBR Green Assay, Control, Software