7.1 sequence analysis software Search Results


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ATCC cell lines raw 264 7 atcc cat
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MedChemExpress hy 18983 hek293 freestyle medium invitrogen cat
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Thermo Fisher n a qpcr data
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ATCC ev70 prototype strain j670
FIG. 1. Host range of <t>EV70-Rmk14</t> and EV70-Dne in cultured cells. One-step growth analysis of viruses was performed in human (HeLa), monkey (LLC-MK2), and murine (L, L-hDAF) cell lines with EV70-Rmk14 (top) or EV70-Dne (bottom) virus at an MOI of 5. Infections were halted at different times postinfection, and virus titers were determined by plaque assay.
Ev70 Prototype Strain J670, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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TargetMol dmso
( A ) Surface electrostatic potentials of predicted crystal structure of human TDP1/Lawsone complex. Red depicts a positive partial charge on the surface, blue depicts negative partial charge and gray shows neutral/lipophilic areas. ( B ) Docking model of Lawsone bind to TDP1 and Lawsone. Dotted yellow line: hydrogen bond, Dotted green line: Pi bond. Blue: N atom, Red: O atom, White: H atom, Green: protein skeleton, Gold: compound skeleton. ( C ) Representative graphs showing measurement of fluorescence development over time. The slope of the initial linear phase is a representation of the TDP1 activity assay. ( D ) Dose–response analysis of Lawsone <t>and</t> <t>SPI-112.</t> The activity of TDP1 was treated with purified TDP1 enzyme 3.125, 6.25, 12.5, 25, 50, 100, 200 μM. Data are mean ± SD from three biological replicates. IC 50 values were calculated using log(inhibitor) compared with normalized response (variable slope), using the program Prism, and are given in graphs. ( E ) Quantification of γ-H2AvD staining intensity in nuclear of body-wall muscles at third instar larvae of Wild-type . Quantification at least five animals of each sample/experiment, five experiments. Data are mean ± SD. Two-tailed, unpaired t test. *** P = 0.0007 CPT versus CPT + Lawsone, *** P = 0.0003 CPT versus CPT + SPI-112. ( F ) Bioanalyzer quantitation of CCTG repeat lengths at 15-days-old Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds. Tissue from three animals per sample. ( G ) Bioanalyzer quantitation of CCTG repeat lengths across 15-days-old different genotypes with treatment of different compounds. Tissue from three animals per sample. ( H ) Quantification of ( F , G ) from three biological replicates. Data are mean ± SD. One-way ANOVA *** P = 0.0002 <t>DMSO</t> versus CPT, * P = 0.00286 DMSO versus Amikacin, *** P = 0.0010 DMSO versus Lawsone, ** P = 0.0011 DMSO versus SPI-112, ** P = 0.0024 Lawsone versus Lawsone ( TOP1 RI ), ** P = 0.0099 SPI-112 versus SPI-112 ( TOP1 RI ). .
Dmso, supplied by TargetMol, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ATCC cell lines raw264 7 atcc tib 71 hek293t cells atcc crl 11268 thp1 cells atcc tib 202 hl60 cells atcc ccl
( A ) Surface electrostatic potentials of predicted crystal structure of human TDP1/Lawsone complex. Red depicts a positive partial charge on the surface, blue depicts negative partial charge and gray shows neutral/lipophilic areas. ( B ) Docking model of Lawsone bind to TDP1 and Lawsone. Dotted yellow line: hydrogen bond, Dotted green line: Pi bond. Blue: N atom, Red: O atom, White: H atom, Green: protein skeleton, Gold: compound skeleton. ( C ) Representative graphs showing measurement of fluorescence development over time. The slope of the initial linear phase is a representation of the TDP1 activity assay. ( D ) Dose–response analysis of Lawsone <t>and</t> <t>SPI-112.</t> The activity of TDP1 was treated with purified TDP1 enzyme 3.125, 6.25, 12.5, 25, 50, 100, 200 μM. Data are mean ± SD from three biological replicates. IC 50 values were calculated using log(inhibitor) compared with normalized response (variable slope), using the program Prism, and are given in graphs. ( E ) Quantification of γ-H2AvD staining intensity in nuclear of body-wall muscles at third instar larvae of Wild-type . Quantification at least five animals of each sample/experiment, five experiments. Data are mean ± SD. Two-tailed, unpaired t test. *** P = 0.0007 CPT versus CPT + Lawsone, *** P = 0.0003 CPT versus CPT + SPI-112. ( F ) Bioanalyzer quantitation of CCTG repeat lengths at 15-days-old Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds. Tissue from three animals per sample. ( G ) Bioanalyzer quantitation of CCTG repeat lengths across 15-days-old different genotypes with treatment of different compounds. Tissue from three animals per sample. ( H ) Quantification of ( F , G ) from three biological replicates. Data are mean ± SD. One-way ANOVA *** P = 0.0002 <t>DMSO</t> versus CPT, * P = 0.00286 DMSO versus Amikacin, *** P = 0.0010 DMSO versus Lawsone, ** P = 0.0011 DMSO versus SPI-112, ** P = 0.0024 Lawsone versus Lawsone ( TOP1 RI ), ** P = 0.0099 SPI-112 versus SPI-112 ( TOP1 RI ). .
Cell Lines Raw264 7 Atcc Tib 71 Hek293t Cells Atcc Crl 11268 Thp1 Cells Atcc Tib 202 Hl60 Cells Atcc Ccl, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Cell Signaling Technology Inc anti phosphorylated thr71 atf2
(A) Concordance between discrete/continuous single-cell GGCs and continuous 10-cell GGCs for two example gene pairs. Simulated 10-cell GGCs shown as 2D contour density (in gray) are computed using the single-cell data only (see STAR methods). See also Figure S3A and S3B. (B) Within each treatment condition, scGGC networks are assembled based on individual gene-gene correlations (i.e., edges in the network) computed using the “discovery” 10-cell data set passing the FDR<0.2 cutoff. Thickness of edges indicate the extent of replication in additional validation experiments. Genes and edges discussed in the text are highlighted in color. Note that nodes are fixed in the same relative position for each network. See also Figure S3C. (C) The four dscGGC hubs with the largest number of partner genes identified in the IL-10 vs. CNT comparison, which were then combined to form the <t>ATF2</t> extended module. The Spearman correlation coefficients between the hub gene (e.g. ATF2 in the first panel) and partner genes are shown for the IL-10 and CNT conditions as boxplots (see STAR methods). For each hub gene and its associated gene module, dscGGC is shown for the discovery experiment (Exp. 1), and the two validation experiments (Exp. 2 and Exp. 3). P values from the bootstrap procedure testing the significance of the aggregate dscGGC of the gene module are shown (see STAR Methods). See also Figure S3D,E.
Anti Phosphorylated Thr71 Atf2, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ATCC raw264 7 murine macrophage cell line

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ATCC human sk mel 24 cells
Key Resources Table
Human Sk Mel 24 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Technelysium ltd chromaspro software
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ATCC generation anti cd97 car t cells

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Image Search Results


FIG. 1. Host range of EV70-Rmk14 and EV70-Dne in cultured cells. One-step growth analysis of viruses was performed in human (HeLa), monkey (LLC-MK2), and murine (L, L-hDAF) cell lines with EV70-Rmk14 (top) or EV70-Dne (bottom) virus at an MOI of 5. Infections were halted at different times postinfection, and virus titers were determined by plaque assay.

Journal: Journal of Virology

Article Title: Enterovirus 70 Receptor Utilization Is Controlled by Capsid Residues That Also Regulate Host Range and Cytopathogenicity

doi: 10.1128/jvi.01569-06

Figure Lengend Snippet: FIG. 1. Host range of EV70-Rmk14 and EV70-Dne in cultured cells. One-step growth analysis of viruses was performed in human (HeLa), monkey (LLC-MK2), and murine (L, L-hDAF) cell lines with EV70-Rmk14 (top) or EV70-Dne (bottom) virus at an MOI of 5. Infections were halted at different times postinfection, and virus titers were determined by plaque assay.

Article Snippet: EV70 prototype strain J670/71 was obtained from the American Type Culture Collection (Manassas, VA) and propagated in rhesus monkey kidney LLC-MK2 cells at 37°C.

Techniques: Cell Culture, Virus, Plaque Assay

FIG. 2. Host range in cell lines derived from human eye and brain. One-step growth analysis of viruses was performed using EV70-Rmk14 (top) or EV70-Dne (bottom) virus to infect (MOI 5) the following eye and brain derived cell lines: HeLa, T98, LLCMK2, U373MG, 15C4, SY5Y, or HCE. Infections were halted at different times postin- fection, and virus titers were determined by plaque assay.

Journal: Journal of Virology

Article Title: Enterovirus 70 Receptor Utilization Is Controlled by Capsid Residues That Also Regulate Host Range and Cytopathogenicity

doi: 10.1128/jvi.01569-06

Figure Lengend Snippet: FIG. 2. Host range in cell lines derived from human eye and brain. One-step growth analysis of viruses was performed using EV70-Rmk14 (top) or EV70-Dne (bottom) virus to infect (MOI 5) the following eye and brain derived cell lines: HeLa, T98, LLCMK2, U373MG, 15C4, SY5Y, or HCE. Infections were halted at different times postin- fection, and virus titers were determined by plaque assay.

Article Snippet: EV70 prototype strain J670/71 was obtained from the American Type Culture Collection (Manassas, VA) and propagated in rhesus monkey kidney LLC-MK2 cells at 37°C.

Techniques: Derivative Assay, Virus, Plaque Assay

FIG. 3. Effect on viral replication of enzyme or antibody treatment of cultured cells. HeLa cells were incubated with one of the following as indicated along the x axis: phosphate-buffered saline (PBS [mock treated]), neuraminidase, PI-PLC, or antibodies specific for hapten or the SCR1 or SCR2 domains of the human DAF molecule. Cells were washed and infected with EV70-Rmk14 or EV70-Dne at an MOI of 3. At 24 h postinfection, the total RNA was isolated from infected cells and transferred onto a nitrocellulose membrane for slot blot analysis. Positive-strand viral replication was assessed by hybridization with a radiolabeled negative-strand EV70 RNA probe. The amount of hy- bridized probe was determined with a PhosphorImager and Image- Quant software and reported as the optical density. The data were normalized to the mock (PBS)-treated sample (PBS treatment 100% replication).

Journal: Journal of Virology

Article Title: Enterovirus 70 Receptor Utilization Is Controlled by Capsid Residues That Also Regulate Host Range and Cytopathogenicity

doi: 10.1128/jvi.01569-06

Figure Lengend Snippet: FIG. 3. Effect on viral replication of enzyme or antibody treatment of cultured cells. HeLa cells were incubated with one of the following as indicated along the x axis: phosphate-buffered saline (PBS [mock treated]), neuraminidase, PI-PLC, or antibodies specific for hapten or the SCR1 or SCR2 domains of the human DAF molecule. Cells were washed and infected with EV70-Rmk14 or EV70-Dne at an MOI of 3. At 24 h postinfection, the total RNA was isolated from infected cells and transferred onto a nitrocellulose membrane for slot blot analysis. Positive-strand viral replication was assessed by hybridization with a radiolabeled negative-strand EV70 RNA probe. The amount of hy- bridized probe was determined with a PhosphorImager and Image- Quant software and reported as the optical density. The data were normalized to the mock (PBS)-treated sample (PBS treatment 100% replication).

Article Snippet: EV70 prototype strain J670/71 was obtained from the American Type Culture Collection (Manassas, VA) and propagated in rhesus monkey kidney LLC-MK2 cells at 37°C.

Techniques: Cell Culture, Incubation, Saline, Infection, Isolation, Membrane, Dot Blot, Hybridization, Software

FIG. 4. Role of amino acid differences between EV70-Rmk and EV70-Dne viruses in replication in HeLa cells. One-step growth anal- ysis was performed with mutants of EV70-Dne harboring single amino acid substitutions to the EV70-Rmk14 sequence. HeLa cells were infected at an MOI of 5, infections were halted at different times postinfection, and virus titers were determined by plaque assay. (A) Growth analysis of viruses DDDDD (EV70-Dne encoding amino acids K14, M238, L133, P178, and D226), DRRRR (K14K, I238, F133, R178, N226), RDRRR (E14, M238, F133, R178, and N226), RRDRR (E14, I238, L133, R178, and N226), RRRDR (R14, I238, F133, P178, and N226), and RRRRR (EV70-Rmk, E14, I283, F133, R178, and N226). (B) Growth analysis of viruses DDDDD (see above), RDDDD (E14, M238, L133, P178, and D226), DRDDD (K14, I238, L133, P178, and D226), DDRDD (K14, M238, F133, P178, and D226), DDDRD (K14, M238, L133, R178, and D226), and DDDDR (K14, M238, L133, P178, and N226).

Journal: Journal of Virology

Article Title: Enterovirus 70 Receptor Utilization Is Controlled by Capsid Residues That Also Regulate Host Range and Cytopathogenicity

doi: 10.1128/jvi.01569-06

Figure Lengend Snippet: FIG. 4. Role of amino acid differences between EV70-Rmk and EV70-Dne viruses in replication in HeLa cells. One-step growth anal- ysis was performed with mutants of EV70-Dne harboring single amino acid substitutions to the EV70-Rmk14 sequence. HeLa cells were infected at an MOI of 5, infections were halted at different times postinfection, and virus titers were determined by plaque assay. (A) Growth analysis of viruses DDDDD (EV70-Dne encoding amino acids K14, M238, L133, P178, and D226), DRRRR (K14K, I238, F133, R178, N226), RDRRR (E14, M238, F133, R178, and N226), RRDRR (E14, I238, L133, R178, and N226), RRRDR (R14, I238, F133, P178, and N226), and RRRRR (EV70-Rmk, E14, I283, F133, R178, and N226). (B) Growth analysis of viruses DDDDD (see above), RDDDD (E14, M238, L133, P178, and D226), DRDDD (K14, I238, L133, P178, and D226), DDRDD (K14, M238, F133, P178, and D226), DDDRD (K14, M238, L133, R178, and D226), and DDDDR (K14, M238, L133, P178, and N226).

Article Snippet: EV70 prototype strain J670/71 was obtained from the American Type Culture Collection (Manassas, VA) and propagated in rhesus monkey kidney LLC-MK2 cells at 37°C.

Techniques: Sequencing, Infection, Virus, Plaque Assay

FIG. 5. Role of amino acid differences between EV70-Rmk and EV70-Dne viruses in hDAF usage. One-step growth analysis was per- formed using mutants of EV70-Dne virus (described in the legend to Fig. 4). L-hDAF cells were infected at an MOI of 5, infections were halted at different times postinfection, and virus titers were deter- mined by plaque assay.

Journal: Journal of Virology

Article Title: Enterovirus 70 Receptor Utilization Is Controlled by Capsid Residues That Also Regulate Host Range and Cytopathogenicity

doi: 10.1128/jvi.01569-06

Figure Lengend Snippet: FIG. 5. Role of amino acid differences between EV70-Rmk and EV70-Dne viruses in hDAF usage. One-step growth analysis was per- formed using mutants of EV70-Dne virus (described in the legend to Fig. 4). L-hDAF cells were infected at an MOI of 5, infections were halted at different times postinfection, and virus titers were deter- mined by plaque assay.

Article Snippet: EV70 prototype strain J670/71 was obtained from the American Type Culture Collection (Manassas, VA) and propagated in rhesus monkey kidney LLC-MK2 cells at 37°C.

Techniques: Virus, Infection, Plaque Assay

FIG. 6. Role of amino acid differences between EV70-Rmk and EV70-Dne viruses in cell killing. HeLa cells were infected at an MOI of 3, using EV70-Dne (DDDDD), EV70-Rmk14 (RRRRR), or mu- tant viruses described in the legend to Fig. 4. Infections were halted at different times postinfection, and cells were pelleted by low-speed centrifugation, resuspended in PBS with trypan blue dye, and exam- ined by light microscopy. The percent viability was determined by dividing the number of cells that excluded dye by the number of cells examined.

Journal: Journal of Virology

Article Title: Enterovirus 70 Receptor Utilization Is Controlled by Capsid Residues That Also Regulate Host Range and Cytopathogenicity

doi: 10.1128/jvi.01569-06

Figure Lengend Snippet: FIG. 6. Role of amino acid differences between EV70-Rmk and EV70-Dne viruses in cell killing. HeLa cells were infected at an MOI of 3, using EV70-Dne (DDDDD), EV70-Rmk14 (RRRRR), or mu- tant viruses described in the legend to Fig. 4. Infections were halted at different times postinfection, and cells were pelleted by low-speed centrifugation, resuspended in PBS with trypan blue dye, and exam- ined by light microscopy. The percent viability was determined by dividing the number of cells that excluded dye by the number of cells examined.

Article Snippet: EV70 prototype strain J670/71 was obtained from the American Type Culture Collection (Manassas, VA) and propagated in rhesus monkey kidney LLC-MK2 cells at 37°C.

Techniques: Infection, Centrifugation, Light Microscopy

FIG. 7. Predicted location in the viral capsid of EV70 amino acids that influence host range and cell killing. The known crystallographic structure of BEV-1 was used to predict the locations in the viral capsid of amino acid residues that differ between EV70-Rmk14 and EV70-Dne. Capsid protomer proteins are color coded, with VP1 blue, VP2 yellow, and VP3 red. VP4 is omitted for clarity. Amino acid changes are enumerated in white. (A) Exterior view of a pentamer, comprising five copies each of VP1, VP2, VP3, and VP4 (not shown), revealing the locations of four of the five strain-specific amino acid changes: in the VP1 DE loop, amino acid 133 of EV70 VP1 (F1133L, BEV 1128 in figure), and three in the canyon, including 238 of EV70 VP3 (I3238M, BEV 3240), 178 of EV70 VP1 (R1178P, BEV 1151), and 226 of EV70 VP1 (N1226D, BEV 1219). Residues on only one protomer are labeled. (B) Closer exterior view of canyon and fivefold axis of symmetry. Amino acid changes in all five protomers are labeled.

Journal: Journal of Virology

Article Title: Enterovirus 70 Receptor Utilization Is Controlled by Capsid Residues That Also Regulate Host Range and Cytopathogenicity

doi: 10.1128/jvi.01569-06

Figure Lengend Snippet: FIG. 7. Predicted location in the viral capsid of EV70 amino acids that influence host range and cell killing. The known crystallographic structure of BEV-1 was used to predict the locations in the viral capsid of amino acid residues that differ between EV70-Rmk14 and EV70-Dne. Capsid protomer proteins are color coded, with VP1 blue, VP2 yellow, and VP3 red. VP4 is omitted for clarity. Amino acid changes are enumerated in white. (A) Exterior view of a pentamer, comprising five copies each of VP1, VP2, VP3, and VP4 (not shown), revealing the locations of four of the five strain-specific amino acid changes: in the VP1 DE loop, amino acid 133 of EV70 VP1 (F1133L, BEV 1128 in figure), and three in the canyon, including 238 of EV70 VP3 (I3238M, BEV 3240), 178 of EV70 VP1 (R1178P, BEV 1151), and 226 of EV70 VP1 (N1226D, BEV 1219). Residues on only one protomer are labeled. (B) Closer exterior view of canyon and fivefold axis of symmetry. Amino acid changes in all five protomers are labeled.

Article Snippet: EV70 prototype strain J670/71 was obtained from the American Type Culture Collection (Manassas, VA) and propagated in rhesus monkey kidney LLC-MK2 cells at 37°C.

Techniques: Labeling

( A ) Surface electrostatic potentials of predicted crystal structure of human TDP1/Lawsone complex. Red depicts a positive partial charge on the surface, blue depicts negative partial charge and gray shows neutral/lipophilic areas. ( B ) Docking model of Lawsone bind to TDP1 and Lawsone. Dotted yellow line: hydrogen bond, Dotted green line: Pi bond. Blue: N atom, Red: O atom, White: H atom, Green: protein skeleton, Gold: compound skeleton. ( C ) Representative graphs showing measurement of fluorescence development over time. The slope of the initial linear phase is a representation of the TDP1 activity assay. ( D ) Dose–response analysis of Lawsone and SPI-112. The activity of TDP1 was treated with purified TDP1 enzyme 3.125, 6.25, 12.5, 25, 50, 100, 200 μM. Data are mean ± SD from three biological replicates. IC 50 values were calculated using log(inhibitor) compared with normalized response (variable slope), using the program Prism, and are given in graphs. ( E ) Quantification of γ-H2AvD staining intensity in nuclear of body-wall muscles at third instar larvae of Wild-type . Quantification at least five animals of each sample/experiment, five experiments. Data are mean ± SD. Two-tailed, unpaired t test. *** P = 0.0007 CPT versus CPT + Lawsone, *** P = 0.0003 CPT versus CPT + SPI-112. ( F ) Bioanalyzer quantitation of CCTG repeat lengths at 15-days-old Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds. Tissue from three animals per sample. ( G ) Bioanalyzer quantitation of CCTG repeat lengths across 15-days-old different genotypes with treatment of different compounds. Tissue from three animals per sample. ( H ) Quantification of ( F , G ) from three biological replicates. Data are mean ± SD. One-way ANOVA *** P = 0.0002 DMSO versus CPT, * P = 0.00286 DMSO versus Amikacin, *** P = 0.0010 DMSO versus Lawsone, ** P = 0.0011 DMSO versus SPI-112, ** P = 0.0024 Lawsone versus Lawsone ( TOP1 RI ), ** P = 0.0099 SPI-112 versus SPI-112 ( TOP1 RI ). .

Journal: EMBO Molecular Medicine

Article Title: Modulating CCTG repeat expansion toxicity in DM2 Drosophila model through TDP1 inhibition

doi: 10.1038/s44321-025-00217-3

Figure Lengend Snippet: ( A ) Surface electrostatic potentials of predicted crystal structure of human TDP1/Lawsone complex. Red depicts a positive partial charge on the surface, blue depicts negative partial charge and gray shows neutral/lipophilic areas. ( B ) Docking model of Lawsone bind to TDP1 and Lawsone. Dotted yellow line: hydrogen bond, Dotted green line: Pi bond. Blue: N atom, Red: O atom, White: H atom, Green: protein skeleton, Gold: compound skeleton. ( C ) Representative graphs showing measurement of fluorescence development over time. The slope of the initial linear phase is a representation of the TDP1 activity assay. ( D ) Dose–response analysis of Lawsone and SPI-112. The activity of TDP1 was treated with purified TDP1 enzyme 3.125, 6.25, 12.5, 25, 50, 100, 200 μM. Data are mean ± SD from three biological replicates. IC 50 values were calculated using log(inhibitor) compared with normalized response (variable slope), using the program Prism, and are given in graphs. ( E ) Quantification of γ-H2AvD staining intensity in nuclear of body-wall muscles at third instar larvae of Wild-type . Quantification at least five animals of each sample/experiment, five experiments. Data are mean ± SD. Two-tailed, unpaired t test. *** P = 0.0007 CPT versus CPT + Lawsone, *** P = 0.0003 CPT versus CPT + SPI-112. ( F ) Bioanalyzer quantitation of CCTG repeat lengths at 15-days-old Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds. Tissue from three animals per sample. ( G ) Bioanalyzer quantitation of CCTG repeat lengths across 15-days-old different genotypes with treatment of different compounds. Tissue from three animals per sample. ( H ) Quantification of ( F , G ) from three biological replicates. Data are mean ± SD. One-way ANOVA *** P = 0.0002 DMSO versus CPT, * P = 0.00286 DMSO versus Amikacin, *** P = 0.0010 DMSO versus Lawsone, ** P = 0.0011 DMSO versus SPI-112, ** P = 0.0024 Lawsone versus Lawsone ( TOP1 RI ), ** P = 0.0099 SPI-112 versus SPI-112 ( TOP1 RI ). .

Article Snippet: The compounds utilized in this study are as follows: 2160 compounds from the JHCCL, Lawsone (MCE), SPI-112 (MCE), Camptothecin (CPT, TargetMol), Amikacin (TargetMol), and DMSO (TargetMol).

Techniques: Docking Assay, Fluorescence, Activity Assay, Analysis, Purification, Staining, Muscles, Two Tailed Test, Quantitation Assay, Tissue, Immunofluorescence

( A – C ) The average counts per 30 min in Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds from 15-days-old to the 25-days-old. Fifteen animals per sample. ( C ) Quantification from five biological replicates. Data are mean ± SD. One-way ANOVA. *** P = 0.005 DMSO versus Lawsone, ** P = 0.0014 DMSO versus SPI-112. ( D , E ) Representative images of paraffin-embedded adult thoraces showing IFMs of Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at 15-days-old. Scale bars 100 μm. ( E ) Quantification of at least ten independent thoraces of each sample/experiment, three experiments. Data are mean ± SD. One-way ANOVA. * P = 0.00148 DMSO versus CPT, ** P = 0.0023 DMSO versus Lawsone, ** P = 0.0018 DMSO versus SPI-112. ( F , G ) Representative images of the compound eyes of Gmr-Gal4 > UAS-(CCTG) 720 with the treatment of different compounds at 15-days-old. Top, LM images. Middle and Bottom, SEM images. Scale bars 20 μm. ( G ) Quantification of at least sixty independent eyes of each sample/experiment, three experiments. Data are mean ± SD. One-way ANOVA. **** P < 0.0001 DMSO versus Amikacin, **** P < 0.0001 DMSO versus Lawsone, **** P < 0.0001 DMSO versus SPI-112. ( H , I ) Representative IF images of thoracic muscle fibers of Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at 15-days-old. White arrows, action blobs. Scale bars 5 μm. ( I ) Quantification of at least ten animals of each sample/experiment, three experiments. Data are mean ± SD. One-way ANOVA. *** P = 0.0006 DMSO versus CPT, ** P = 0.0078 DMSO versus Amikacin, *** P = 0.0006 DMSO versus Lawsone, **** P < 0.0001 DMSO versus SPI-112. ( J , K ) Representative Confocal images of CCUG-repeat foci with (CAGG) 5 probe of Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at body-wall muscles of third instar larvae. Scale bars 5 μm. ( K ) Quantification of at least ten animals of each sample/experiment, three experiments. Data are mean ± SD. One-way ANOVA. **** P < 0.0001. ( L ) Representative gel image of endogenous Zasp52 exon 7 with RT-PCR in Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at 15-days-old. Tissue from ten animals per sample/experiment, 5 experiments. Lower panel, quantification of Zasp52 exon 7 inclusion. Data are mean ± SD. One-way ANOVA. * P = 0.0217 DMSO versus CPT, ** P = 0.0022 DMSO versus Lawsone, * P = 0.0404 DMSO versus SPI-112. ( M ) Representative gel image of endogenous Fhos exon 10 with RT-PCR in Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at 15-days-old. Tissue from ten animals per sample/experiment, five experiments. Lower panel, quantification of Fhos exon 10 inclusion. Data are mean ± SD. One-way ANOVA. ** P = 0.0061 DMSO versus CPT, * P = 0.0470 DMSO versus Amikacin, * P = 0.0249 DMSO versus Lawsone, ** P = 0.0012 DMSO versus SPI-112. .

Journal: EMBO Molecular Medicine

Article Title: Modulating CCTG repeat expansion toxicity in DM2 Drosophila model through TDP1 inhibition

doi: 10.1038/s44321-025-00217-3

Figure Lengend Snippet: ( A – C ) The average counts per 30 min in Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds from 15-days-old to the 25-days-old. Fifteen animals per sample. ( C ) Quantification from five biological replicates. Data are mean ± SD. One-way ANOVA. *** P = 0.005 DMSO versus Lawsone, ** P = 0.0014 DMSO versus SPI-112. ( D , E ) Representative images of paraffin-embedded adult thoraces showing IFMs of Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at 15-days-old. Scale bars 100 μm. ( E ) Quantification of at least ten independent thoraces of each sample/experiment, three experiments. Data are mean ± SD. One-way ANOVA. * P = 0.00148 DMSO versus CPT, ** P = 0.0023 DMSO versus Lawsone, ** P = 0.0018 DMSO versus SPI-112. ( F , G ) Representative images of the compound eyes of Gmr-Gal4 > UAS-(CCTG) 720 with the treatment of different compounds at 15-days-old. Top, LM images. Middle and Bottom, SEM images. Scale bars 20 μm. ( G ) Quantification of at least sixty independent eyes of each sample/experiment, three experiments. Data are mean ± SD. One-way ANOVA. **** P < 0.0001 DMSO versus Amikacin, **** P < 0.0001 DMSO versus Lawsone, **** P < 0.0001 DMSO versus SPI-112. ( H , I ) Representative IF images of thoracic muscle fibers of Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at 15-days-old. White arrows, action blobs. Scale bars 5 μm. ( I ) Quantification of at least ten animals of each sample/experiment, three experiments. Data are mean ± SD. One-way ANOVA. *** P = 0.0006 DMSO versus CPT, ** P = 0.0078 DMSO versus Amikacin, *** P = 0.0006 DMSO versus Lawsone, **** P < 0.0001 DMSO versus SPI-112. ( J , K ) Representative Confocal images of CCUG-repeat foci with (CAGG) 5 probe of Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at body-wall muscles of third instar larvae. Scale bars 5 μm. ( K ) Quantification of at least ten animals of each sample/experiment, three experiments. Data are mean ± SD. One-way ANOVA. **** P < 0.0001. ( L ) Representative gel image of endogenous Zasp52 exon 7 with RT-PCR in Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at 15-days-old. Tissue from ten animals per sample/experiment, 5 experiments. Lower panel, quantification of Zasp52 exon 7 inclusion. Data are mean ± SD. One-way ANOVA. * P = 0.0217 DMSO versus CPT, ** P = 0.0022 DMSO versus Lawsone, * P = 0.0404 DMSO versus SPI-112. ( M ) Representative gel image of endogenous Fhos exon 10 with RT-PCR in Mef2-Gal4 > UAS-(CCTG) 720 with treatment of different compounds at 15-days-old. Tissue from ten animals per sample/experiment, five experiments. Lower panel, quantification of Fhos exon 10 inclusion. Data are mean ± SD. One-way ANOVA. ** P = 0.0061 DMSO versus CPT, * P = 0.0470 DMSO versus Amikacin, * P = 0.0249 DMSO versus Lawsone, ** P = 0.0012 DMSO versus SPI-112. .

Article Snippet: The compounds utilized in this study are as follows: 2160 compounds from the JHCCL, Lawsone (MCE), SPI-112 (MCE), Camptothecin (CPT, TargetMol), Amikacin (TargetMol), and DMSO (TargetMol).

Techniques: Confocal, Muscles, Reverse Transcription Polymerase Chain Reaction, Tissue, Immunofluorescence, In Situ Hybridization

( A , B ) Representative capillary electropherograms across different genotypes at 60-days-old. Tissue from three animals. ( B ) Quantification of mean length of CTG repeats from five biological replicates. Data are mean ± SD. Two-tailed, unpaired t test. * P = 0. 0103, ** P = 0. 0054. ( C , D ) Representative gel image of PCR across different genotypes Hek293 cell line following 7 days of treatment from bioanalyzer. ( D ) Quantification of mean length of CTG/CCTG repeats from three biological replicates. Data are mean ± SD. Two-tailed, unpaired t test. * P = 0.0324 (CTG) 400 cell line, * P = 0.0341 (CCTG) 400 cell line. ( E , F ) Representative gel image of DM1 patient-derived lymphocytes following 15 days treatment of different compounds from bioanalyzer. ( F ) Quantification of ( E ) from three biological replicates. Data are mean ± SD. One-way ANOVA. ** P = 0.0082 DMSO versus Lawsone, *** P = 0.001 DMSO versus SPI-112.

Journal: EMBO Molecular Medicine

Article Title: Modulating CCTG repeat expansion toxicity in DM2 Drosophila model through TDP1 inhibition

doi: 10.1038/s44321-025-00217-3

Figure Lengend Snippet: ( A , B ) Representative capillary electropherograms across different genotypes at 60-days-old. Tissue from three animals. ( B ) Quantification of mean length of CTG repeats from five biological replicates. Data are mean ± SD. Two-tailed, unpaired t test. * P = 0. 0103, ** P = 0. 0054. ( C , D ) Representative gel image of PCR across different genotypes Hek293 cell line following 7 days of treatment from bioanalyzer. ( D ) Quantification of mean length of CTG/CCTG repeats from three biological replicates. Data are mean ± SD. Two-tailed, unpaired t test. * P = 0.0324 (CTG) 400 cell line, * P = 0.0341 (CCTG) 400 cell line. ( E , F ) Representative gel image of DM1 patient-derived lymphocytes following 15 days treatment of different compounds from bioanalyzer. ( F ) Quantification of ( E ) from three biological replicates. Data are mean ± SD. One-way ANOVA. ** P = 0.0082 DMSO versus Lawsone, *** P = 0.001 DMSO versus SPI-112.

Article Snippet: The compounds utilized in this study are as follows: 2160 compounds from the JHCCL, Lawsone (MCE), SPI-112 (MCE), Camptothecin (CPT, TargetMol), Amikacin (TargetMol), and DMSO (TargetMol).

Techniques: Tissue, Two Tailed Test, Derivative Assay, Polymerase Chain Reaction, Knockdown

Reagents and tools table

Journal: EMBO Molecular Medicine

Article Title: Modulating CCTG repeat expansion toxicity in DM2 Drosophila model through TDP1 inhibition

doi: 10.1038/s44321-025-00217-3

Figure Lengend Snippet: Reagents and tools table

Article Snippet: The compounds utilized in this study are as follows: 2160 compounds from the JHCCL, Lawsone (MCE), SPI-112 (MCE), Camptothecin (CPT, TargetMol), Amikacin (TargetMol), and DMSO (TargetMol).

Techniques: Drosophila, Control, Recombinant, Sequencing, Sensitivity, DNA Extraction, Software, Activity Assay

(A) Concordance between discrete/continuous single-cell GGCs and continuous 10-cell GGCs for two example gene pairs. Simulated 10-cell GGCs shown as 2D contour density (in gray) are computed using the single-cell data only (see STAR methods). See also Figure S3A and S3B. (B) Within each treatment condition, scGGC networks are assembled based on individual gene-gene correlations (i.e., edges in the network) computed using the “discovery” 10-cell data set passing the FDR<0.2 cutoff. Thickness of edges indicate the extent of replication in additional validation experiments. Genes and edges discussed in the text are highlighted in color. Note that nodes are fixed in the same relative position for each network. See also Figure S3C. (C) The four dscGGC hubs with the largest number of partner genes identified in the IL-10 vs. CNT comparison, which were then combined to form the ATF2 extended module. The Spearman correlation coefficients between the hub gene (e.g. ATF2 in the first panel) and partner genes are shown for the IL-10 and CNT conditions as boxplots (see STAR methods). For each hub gene and its associated gene module, dscGGC is shown for the discovery experiment (Exp. 1), and the two validation experiments (Exp. 2 and Exp. 3). P values from the bootstrap procedure testing the significance of the aggregate dscGGC of the gene module are shown (see STAR Methods). See also Figure S3D,E.

Journal: Cell systems

Article Title: Environment tunes propagation of cell-to-cell variation in the human macrophage gene network

doi: 10.1016/j.cels.2017.03.002

Figure Lengend Snippet: (A) Concordance between discrete/continuous single-cell GGCs and continuous 10-cell GGCs for two example gene pairs. Simulated 10-cell GGCs shown as 2D contour density (in gray) are computed using the single-cell data only (see STAR methods). See also Figure S3A and S3B. (B) Within each treatment condition, scGGC networks are assembled based on individual gene-gene correlations (i.e., edges in the network) computed using the “discovery” 10-cell data set passing the FDR<0.2 cutoff. Thickness of edges indicate the extent of replication in additional validation experiments. Genes and edges discussed in the text are highlighted in color. Note that nodes are fixed in the same relative position for each network. See also Figure S3C. (C) The four dscGGC hubs with the largest number of partner genes identified in the IL-10 vs. CNT comparison, which were then combined to form the ATF2 extended module. The Spearman correlation coefficients between the hub gene (e.g. ATF2 in the first panel) and partner genes are shown for the IL-10 and CNT conditions as boxplots (see STAR methods). For each hub gene and its associated gene module, dscGGC is shown for the discovery experiment (Exp. 1), and the two validation experiments (Exp. 2 and Exp. 3). P values from the bootstrap procedure testing the significance of the aggregate dscGGC of the gene module are shown (see STAR Methods). See also Figure S3D,E.

Article Snippet: After adding an 2x volume of staining buffer and centrifugation, cells were then resuspended in staining buffer containing Human Trustain FcX (Biolegend) to block non-specific antibody binding, and stained for 1hr at room temperature using anti-phosphorylated Thr71 ATF2 (Cell Signaling Technology, clone 11G2) and anti-phosphorylated Tyr 705 STAT3 (BD Biosciences, clone 4/P-STAT3).

Techniques: Biomarker Discovery, Comparison

(A and B) ATF2 ChIP-qPCR data (expressed as percent of input or fold enrichment, respectively) was performed to evaluate binding of ATF2 to select H3K27ac peak regions near ATF2 dscGGC extended module genes in CNT and IL-10 environments. Data are obtained from three independent ChIP experiments using cells from three distinct donors for 14 target and 4 background regions. P values are based on F-test comparing two nested linear models after accounting for donor and target region effects (see STAR Methods). (C) pATF2 and pSTAT3 induction dynamics following IL-10 treatment. Representative of two independent experiments. Plot shows mean ± standard deviation (SD) of replicate samples from one experiment. See also Figure S4D,E. (D) pATF2 induction at two hours following IL-10 treatment from 7 independent experiments using cells from 4 different donors is shown (paired data from each experiment is connected by a line). P value was obtained from paired t test. (E and F) Nuclear pATF2 staining 24 hours post IL-10 treatment measured using confocal imaging. Each dot in (F) corresponds to the level of pATF2 staining intensity in a single nuclei after normalization by nuclear size delineated by DAPI co-staining. Multiple fields of view are combined; data shown are from one experiment, and are representative of two experiments utilizing cells from different donors. P value shown in (F) was obtained from Student’s t-test. (G) pATF2 and pSTAT3 induction dynamics after IL-10 treatment in the absence/presence of an IL-10 receptor-blocking antibody. Points represent data from three independent experiments, measured at 1hr, 2hr, or both timepoints. Values shown correspond to changes in MFI relative to the non-treated cells (baseline).

Journal: Cell systems

Article Title: Environment tunes propagation of cell-to-cell variation in the human macrophage gene network

doi: 10.1016/j.cels.2017.03.002

Figure Lengend Snippet: (A and B) ATF2 ChIP-qPCR data (expressed as percent of input or fold enrichment, respectively) was performed to evaluate binding of ATF2 to select H3K27ac peak regions near ATF2 dscGGC extended module genes in CNT and IL-10 environments. Data are obtained from three independent ChIP experiments using cells from three distinct donors for 14 target and 4 background regions. P values are based on F-test comparing two nested linear models after accounting for donor and target region effects (see STAR Methods). (C) pATF2 and pSTAT3 induction dynamics following IL-10 treatment. Representative of two independent experiments. Plot shows mean ± standard deviation (SD) of replicate samples from one experiment. See also Figure S4D,E. (D) pATF2 induction at two hours following IL-10 treatment from 7 independent experiments using cells from 4 different donors is shown (paired data from each experiment is connected by a line). P value was obtained from paired t test. (E and F) Nuclear pATF2 staining 24 hours post IL-10 treatment measured using confocal imaging. Each dot in (F) corresponds to the level of pATF2 staining intensity in a single nuclei after normalization by nuclear size delineated by DAPI co-staining. Multiple fields of view are combined; data shown are from one experiment, and are representative of two experiments utilizing cells from different donors. P value shown in (F) was obtained from Student’s t-test. (G) pATF2 and pSTAT3 induction dynamics after IL-10 treatment in the absence/presence of an IL-10 receptor-blocking antibody. Points represent data from three independent experiments, measured at 1hr, 2hr, or both timepoints. Values shown correspond to changes in MFI relative to the non-treated cells (baseline).

Article Snippet: After adding an 2x volume of staining buffer and centrifugation, cells were then resuspended in staining buffer containing Human Trustain FcX (Biolegend) to block non-specific antibody binding, and stained for 1hr at room temperature using anti-phosphorylated Thr71 ATF2 (Cell Signaling Technology, clone 11G2) and anti-phosphorylated Tyr 705 STAT3 (BD Biosciences, clone 4/P-STAT3).

Techniques: ChIP-qPCR, Binding Assay, Standard Deviation, Staining, Imaging, Blocking Assay

Systematic identification of the extended  ATF2  dscGGC module.

Journal: Cell systems

Article Title: Environment tunes propagation of cell-to-cell variation in the human macrophage gene network

doi: 10.1016/j.cels.2017.03.002

Figure Lengend Snippet: Systematic identification of the extended ATF2 dscGGC module.

Article Snippet: After adding an 2x volume of staining buffer and centrifugation, cells were then resuspended in staining buffer containing Human Trustain FcX (Biolegend) to block non-specific antibody binding, and stained for 1hr at room temperature using anti-phosphorylated Thr71 ATF2 (Cell Signaling Technology, clone 11G2) and anti-phosphorylated Tyr 705 STAT3 (BD Biosciences, clone 4/P-STAT3).

Techniques: Construct, Binding Assay, Activity Assay, ChIP-qPCR

KEY RESOURCES TABLE

Journal: Cell systems

Article Title: Environment tunes propagation of cell-to-cell variation in the human macrophage gene network

doi: 10.1016/j.cels.2017.03.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: After adding an 2x volume of staining buffer and centrifugation, cells were then resuspended in staining buffer containing Human Trustain FcX (Biolegend) to block non-specific antibody binding, and stained for 1hr at room temperature using anti-phosphorylated Thr71 ATF2 (Cell Signaling Technology, clone 11G2) and anti-phosphorylated Tyr 705 STAT3 (BD Biosciences, clone 4/P-STAT3).

Techniques: Blocking Assay, Purification, Recombinant, Staining, Isolation, High Throughput Screening Assay, Sequencing, Software

Journal: Cell Reports

Article Title: Propionic Acid Promotes the Virulent Phenotype of Crohn’s Disease-Associated Adherent-Invasive Escherichia coli

doi: 10.1016/j.celrep.2020.01.078

Figure Lengend Snippet:

Article Snippet: RAW264.7 murine macrophage cell line , American Type Culture Collection (ATCC) , ATCC TIB71.

Techniques: Virus, Recombinant, Modification, Saline, SYBR Green Assay, Sequencing, Software, Membrane

Key Resources Table

Journal: Molecular cell

Article Title: Dietary supplement chondroitin-4-sulfate exhibits oncogene-specific pro-tumor effects on BRAF V600E melanoma cells

doi: 10.1016/j.molcel.2018.02.010

Figure Lengend Snippet: Key Resources Table

Article Snippet: Human: SK-MEL-24 cells , ATCC , Cat# HTB-71; RRID: CVCL_0599.

Techniques: Virus, Recombinant, RNA Extraction, Transfection, SYBR Green Assay, Protease Inhibitor, Enzyme-linked Immunosorbent Assay, Malachite Green Assay, Activity Assay, shRNA, Sequencing, Mutagenesis, CRISPR, Plasmid Preparation, Software, Expressing

Journal: Cell Reports Medicine

Article Title: CD97 maintains tumorigenicity of glioblastoma stem cells via mTORC2 signaling and is targeted by CAR Th9 cells

doi: 10.1016/j.xcrm.2024.101844

Figure Lengend Snippet:

Article Snippet: Murine CD3 + T cells were purified from C57BL/6J mice splenocytes using the EasySep Mouse T cell Isolation Kit (STEMCELL Technologies Inc.) and stimulated on plates coated with 2 μg/mL mCD3ε (BD Pharmingen) and 2 μg/mL mCD28 mAbs (Biolegend) for 48 h. The stimulated T cell population underwent lentiviral transduction to express a second-generation anti-CD97 CAR T cells were expanded in complete medium RPMI-1640 (ATCC), 10% FBS (Hyclone), 1% Penicillin-Streptomycin (Gibco) with hIL-2 (10 ng/mL; PeproTech.) changing medium every 2 days.

Techniques: Produced, Virus, Plasmid Preparation, Recombinant, Purification, Cell Culture, Cell Isolation, Reporter Gene Assay, cDNA Synthesis, Apoptosis Assay, Cytotoxicity Assay, Gene Expression, shRNA, Sequencing, Amplification, Software, Microscopy, Western Blot