Journal: Biosensors & bioelectronics

Article Title: Microarray method to monitor 40 intestinal bacterial species in the study of azo dye reduction

doi: 10.1016/j.bios.2004.04.011

Figure Lengend Snippet: Bacteria and the probe numbers in the microarray

Article Snippet: Anaerobic bacteria were cultured at 35 °C in either prereduced anaerobically sterilized (PRAS) Brain Heart Infusion (BIH) broth supplemented with vitamin K and hemin (Remel, Lenexa, KS, USA), inoculated under an oxygen-free cannula using 85% nitrogen, 10% hydrogen and 5% carbon dioxide, or on PRAS brucella blood agar plates supplemented with vitamin K and hemin (Remel). table ft1 table-wrap mode="anchored" t5 caption a7 Number Bacterial species and strain Probe number 1 B. thetaiotaomicron ATCC 29148 1, 2, 3 2 B. vulgatus ATCC 8482 4, 5, 6 3 B. fragilis ATCC 23745 7, 8, 9 4 B. distasonis ATCC 8503 10, 11, 12 5 C. clostridioforme ATCC 29084 13, 14, 15 6 C. leptum ATCC 29065 16, 17, 18 7 F. prausnitzii ATCC 27768 19, 20, 21 8 P. productus ATCC 27340 22, 23, 24 9 R. obeum ATCC 29174 25, 26, 27 10 R. bromii ATCC 27255 28, 29, 30 11 R. callidus ATCC 27760 31, 32, 33 12 R. albus ATCC 27210 34, 35, 36 13 B. longum ATCC 15707 37, 38, 39 14 B. adolescentis ATCC 15703 40, 41, 42 15 B. infantis ATCC 15697 43, 44, 45 16 E. biforme ATCC 27806 46, 47, 48 17 E. aerofaciens ATCC 25986 49, 50, 51 18 L. acidophilus ATCC 4356 52, 53, 54 19 E. coli ATCC 25922 55, 56, 57 20 E. faecium ATCC 19434 58, 59, 60 21 B. uniformis ATCC 8492 61, 62, 63 22 B. ovatus ATCC 8483 64, 65, 66 23 B. caccae ATCC 43185 67, 68, 69 24 C. perfringens ATCC 13124 70, 71, 72 25 C. butyricum ATCC 19398 73, 74, 75 26 C. ramosum ATCC 25582 76, 77, 78 27 C. difficile ATCC 9689 79, 80, 81 28 C. indolis ATCC 25771 82, 83, 84 29 F. russii ATCC 25533 85, 86, 87 30 F. nucleatum ATCC 25586 88, 89, 90 31 B. catenulatum ATCC 27539 91, 92, 93 32 B. angulatum ATCC 27535 94, 95, 96 33 E. rectale ATCC 33656 97, 98, 99 34 E. eligens ATCC 27750 100, 101, 102 35 E. limosum ATCC 8486 103, 104, 105 36 E. lentum ATCC 25553 106, 107, 108 37 L. fermentum ATCC 9338 109, 110, 111 38 E. faecalis ATCC 27274 112, 113, 114 39 P. magnus ATCC 14955 115, 116, 117 40 R. gnavus ATCC 291492 118, 119, 120 Open in a separate window Bacteria and the probe numbers in the microarray

Techniques: Bacteria

Journal: Biosensors & bioelectronics

Article Title: Microarray method to monitor 40 intestinal bacterial species in the study of azo dye reduction

doi: 10.1016/j.bios.2004.04.011

Figure Lengend Snippet: Microarray test results read from

Article Snippet: Anaerobic bacteria were cultured at 35 °C in either prereduced anaerobically sterilized (PRAS) Brain Heart Infusion (BIH) broth supplemented with vitamin K and hemin (Remel, Lenexa, KS, USA), inoculated under an oxygen-free cannula using 85% nitrogen, 10% hydrogen and 5% carbon dioxide, or on PRAS brucella blood agar plates supplemented with vitamin K and hemin (Remel). table ft1 table-wrap mode="anchored" t5 caption a7 Number Bacterial species and strain Probe number 1 B. thetaiotaomicron ATCC 29148 1, 2, 3 2 B. vulgatus ATCC 8482 4, 5, 6 3 B. fragilis ATCC 23745 7, 8, 9 4 B. distasonis ATCC 8503 10, 11, 12 5 C. clostridioforme ATCC 29084 13, 14, 15 6 C. leptum ATCC 29065 16, 17, 18 7 F. prausnitzii ATCC 27768 19, 20, 21 8 P. productus ATCC 27340 22, 23, 24 9 R. obeum ATCC 29174 25, 26, 27 10 R. bromii ATCC 27255 28, 29, 30 11 R. callidus ATCC 27760 31, 32, 33 12 R. albus ATCC 27210 34, 35, 36 13 B. longum ATCC 15707 37, 38, 39 14 B. adolescentis ATCC 15703 40, 41, 42 15 B. infantis ATCC 15697 43, 44, 45 16 E. biforme ATCC 27806 46, 47, 48 17 E. aerofaciens ATCC 25986 49, 50, 51 18 L. acidophilus ATCC 4356 52, 53, 54 19 E. coli ATCC 25922 55, 56, 57 20 E. faecium ATCC 19434 58, 59, 60 21 B. uniformis ATCC 8492 61, 62, 63 22 B. ovatus ATCC 8483 64, 65, 66 23 B. caccae ATCC 43185 67, 68, 69 24 C. perfringens ATCC 13124 70, 71, 72 25 C. butyricum ATCC 19398 73, 74, 75 26 C. ramosum ATCC 25582 76, 77, 78 27 C. difficile ATCC 9689 79, 80, 81 28 C. indolis ATCC 25771 82, 83, 84 29 F. russii ATCC 25533 85, 86, 87 30 F. nucleatum ATCC 25586 88, 89, 90 31 B. catenulatum ATCC 27539 91, 92, 93 32 B. angulatum ATCC 27535 94, 95, 96 33 E. rectale ATCC 33656 97, 98, 99 34 E. eligens ATCC 27750 100, 101, 102 35 E. limosum ATCC 8486 103, 104, 105 36 E. lentum ATCC 25553 106, 107, 108 37 L. fermentum ATCC 9338 109, 110, 111 38 E. faecalis ATCC 27274 112, 113, 114 39 P. magnus ATCC 14955 115, 116, 117 40 R. gnavus ATCC 291492 118, 119, 120 Open in a separate window Bacteria and the probe numbers in the microarray

Techniques: Microarray

Journal: Biosensors & bioelectronics

Article Title: Microarray method to monitor 40 intestinal bacterial species in the study of azo dye reduction

doi: 10.1016/j.bios.2004.04.011

Figure Lengend Snippet: Azo dye (Direct Blue 15) reduction activity of 17 bacterial species in pure culture

Article Snippet: Anaerobic bacteria were cultured at 35 °C in either prereduced anaerobically sterilized (PRAS) Brain Heart Infusion (BIH) broth supplemented with vitamin K and hemin (Remel, Lenexa, KS, USA), inoculated under an oxygen-free cannula using 85% nitrogen, 10% hydrogen and 5% carbon dioxide, or on PRAS brucella blood agar plates supplemented with vitamin K and hemin (Remel). table ft1 table-wrap mode="anchored" t5 caption a7 Number Bacterial species and strain Probe number 1 B. thetaiotaomicron ATCC 29148 1, 2, 3 2 B. vulgatus ATCC 8482 4, 5, 6 3 B. fragilis ATCC 23745 7, 8, 9 4 B. distasonis ATCC 8503 10, 11, 12 5 C. clostridioforme ATCC 29084 13, 14, 15 6 C. leptum ATCC 29065 16, 17, 18 7 F. prausnitzii ATCC 27768 19, 20, 21 8 P. productus ATCC 27340 22, 23, 24 9 R. obeum ATCC 29174 25, 26, 27 10 R. bromii ATCC 27255 28, 29, 30 11 R. callidus ATCC 27760 31, 32, 33 12 R. albus ATCC 27210 34, 35, 36 13 B. longum ATCC 15707 37, 38, 39 14 B. adolescentis ATCC 15703 40, 41, 42 15 B. infantis ATCC 15697 43, 44, 45 16 E. biforme ATCC 27806 46, 47, 48 17 E. aerofaciens ATCC 25986 49, 50, 51 18 L. acidophilus ATCC 4356 52, 53, 54 19 E. coli ATCC 25922 55, 56, 57 20 E. faecium ATCC 19434 58, 59, 60 21 B. uniformis ATCC 8492 61, 62, 63 22 B. ovatus ATCC 8483 64, 65, 66 23 B. caccae ATCC 43185 67, 68, 69 24 C. perfringens ATCC 13124 70, 71, 72 25 C. butyricum ATCC 19398 73, 74, 75 26 C. ramosum ATCC 25582 76, 77, 78 27 C. difficile ATCC 9689 79, 80, 81 28 C. indolis ATCC 25771 82, 83, 84 29 F. russii ATCC 25533 85, 86, 87 30 F. nucleatum ATCC 25586 88, 89, 90 31 B. catenulatum ATCC 27539 91, 92, 93 32 B. angulatum ATCC 27535 94, 95, 96 33 E. rectale ATCC 33656 97, 98, 99 34 E. eligens ATCC 27750 100, 101, 102 35 E. limosum ATCC 8486 103, 104, 105 36 E. lentum ATCC 25553 106, 107, 108 37 L. fermentum ATCC 9338 109, 110, 111 38 E. faecalis ATCC 27274 112, 113, 114 39 P. magnus ATCC 14955 115, 116, 117 40 R. gnavus ATCC 291492 118, 119, 120 Open in a separate window Bacteria and the probe numbers in the microarray

Techniques: Activity Assay

Journal: Nature Communications

Article Title: Crucial roles of RSK in cell motility by catalysing serine phosphorylation of EphA2

doi: 10.1038/ncomms8679

Figure Lengend Snippet: ( a ) Whole-cell lysates from HeLa cells treated with TNF-α (20 ng ml −1 ) for 10, 20 and 60 min were separated by Zn 2+ -Phos-tag SDS–PAGE and immunoblotted with anti-EphA2 and EGFR antibodies. ( b ) Whole-cell lysates from HeLa cells treated with TNF-α for 20 min were separated by Zn 2+ -Phos-tag SDS–PAGE and immunoblotted with anti-EphA2, pS-EphA2 and pY-EphA2. ( c ) Whole-cell lysates from HeLa cells treated with ephrin-A1 (100 ng ml −1 ) for 10 min or TNF-α for 20 min were separated by normal SDS–PAGE and immunoblotted with anti-pS-EphA2, pY-EphA2, EphA2 and α-tubulin antibodies. ( d ) HeLa cells were stimulated with TNF-α for the indicated periods. Whole-cell lysates were electrophoresed and probed with primary antibodies against pS-EphA2, pY-EphA2, EphA2, pT-EGFR, pS-EGFR, EGFR and α-tubulin. ( e ) HeLa cells were stimulated with TNF-α for 20 and 60 min. After fixation and permeabilization, cells were immunofluorescently stained with pS-EphA2, EphA2 or EGFR (clone LA1). Scale bar, 20 μm. Shown are representative images from three independent experiments.

Article Snippet: Antibodies against total EphA2 (C-20; sc-924), RSK1 (C-21; sc-231), RSK2 (C-19; sc-1430), EGFR (1005; sc-03), TAK1 (M-579; sc-7162), β-actin (I-19; sc-1616) and α-tubulin (B-7; sc-5286) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).

Techniques: SDS Page, Staining

Journal: Nature Communications

Article Title: Crucial roles of RSK in cell motility by catalysing serine phosphorylation of EphA2

doi: 10.1038/ncomms8679

Figure Lengend Snippet: ( a , b ) HeLa ( a ) or T98G ( b left) cells were pre-treated with LY294002 (10 μM) or MK-2206 (10 μM) for 30 min and then stimulated with TNF-α for 20 min. T98G cells were starved using FCS-free medium for 24 h, treated with LY294002 for 30 min and then treated with 10% FCS for 10 min ( b , right). ( c ) MDA-MB-231 and Panc-1 cells were treated with LY294002 for 30 min. ( d ) HeLa cells stably transfected shRNA expression vectors against luciferase and TAK1 were stimulated with TNF-α for 20 min. ( e ) HeLa cells were transfected with siRNAs against TAK1 or negative control. At 72 h post transfection, cells were treated with TNF-α for 20 min. Whole-cell lysates were immunoblotted with anti-pS-EphA2, EphA2, pAKT, pRSK, RSK1, RSK2, TAK1, β-actin and α-tubulin antibodies.

Article Snippet: Antibodies against total EphA2 (C-20; sc-924), RSK1 (C-21; sc-231), RSK2 (C-19; sc-1430), EGFR (1005; sc-03), TAK1 (M-579; sc-7162), β-actin (I-19; sc-1616) and α-tubulin (B-7; sc-5286) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).

Techniques: Stable Transfection, Transfection, shRNA, Expressing, Luciferase, Negative Control

Journal: Nature Communications

Article Title: Crucial roles of RSK in cell motility by catalysing serine phosphorylation of EphA2

doi: 10.1038/ncomms8679

Figure Lengend Snippet: ( a ) HeLa cells were stimulated with TNF-α for the indicated periods. Whole-cell lysates were immunoblotted with anti-pS-EphA2, EphA2, pRSK, RSK1, RSK2 and α-tubulin antibodies. ( b , c ) Whole-cell lysates from HeLa cells pre-treated with LY294002 (10 μM), SB203580 (10 μM), U0126 (5 μM) or BI-D1870 (10 μM) for 30 min and then stimulated with TNF-α for 20 min were separated by Zn 2+ -Phos-tag SDS–PAGE and immunoblotted with anti-EphA2 and pS-EphA2 antibodies ( b ), or by normal SDS–PAGE and immunoblotted with anti-pS-EphA2, EphA2, pT-EGFR, pS-EGFR, EGFR, pRSK, RSK1, RSK2 and α-tubulin antibodies ( c ). ( d ) HeLa cells were pre-treated with LY294002 or BI-D1870 for 30 min and then stimulated with NaCl (0.3 M), TPA (100 ng ml −1 ) or EGF (10 ng ml −1 ) for 10 min. Whole-cell lysates were immunoblotted with primary antibodies against pS-EphA2, EphA2, pRSK, RSK1, RSK2, pAKT and α-tubulin. ( e ) T98G and U-87 MG cells starved in FCS-free medium for 24 h were treated with LY294002, MK-2206, U0126 and BI-D1870 for 30 min and then stimulated with 10% FCS for 10 min. Whole-cell lysates were immunoblotted with primary antibodies against pS-EphA2, EphA2, pRSK, RSK1, RSK2, pAKT, pERK and α-tubulin.

Article Snippet: Antibodies against total EphA2 (C-20; sc-924), RSK1 (C-21; sc-231), RSK2 (C-19; sc-1430), EGFR (1005; sc-03), TAK1 (M-579; sc-7162), β-actin (I-19; sc-1616) and α-tubulin (B-7; sc-5286) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).

Techniques: SDS Page

Journal: Nature Communications

Article Title: Crucial roles of RSK in cell motility by catalysing serine phosphorylation of EphA2

doi: 10.1038/ncomms8679

Figure Lengend Snippet: ( a , b ) HEK293 cells were transfected with expression vectors for EphA2, RSK1 and its substitution mutants. At 24 h post transfection, whole-cell lysates were immunoblotted with anti-pS-EphA2, pY-EphA2, EphA2, pRSK, RSK1 and α-tubulin antibodies. ( c ) HeLa cells were transfected with siRNAs against RSK1, RSK2 or negative control. At 72 h post transfection, cells were stimulated with TNF-α for 20 min. Whole-cell lysates were immunoblotted with primary antibodies against pS-EphA2, EphA2, pRSK, RSK1, RSK2 and α-tubulin. ( d ) Recombinant human GST-EphA2 was incubated with recombinant human active GST-RSK1 or RSK2 in the absence or presence of BI-D1870 (0.1 μM) at 30 °C for 30 min. The reaction mixtures were analysed by immunoblotting with anti-pS-EphA2, EphA2, RSK1 and RSK2 antibodies.

Article Snippet: Antibodies against total EphA2 (C-20; sc-924), RSK1 (C-21; sc-231), RSK2 (C-19; sc-1430), EGFR (1005; sc-03), TAK1 (M-579; sc-7162), β-actin (I-19; sc-1616) and α-tubulin (B-7; sc-5286) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).

Techniques: Transfection, Expressing, Negative Control, Recombinant, Incubation, Western Blot

Journal: Nature Communications

Article Title: Crucial roles of RSK in cell motility by catalysing serine phosphorylation of EphA2

doi: 10.1038/ncomms8679

Figure Lengend Snippet: ( a ) Whole-cell lysates from HeLa cells treated with TNF-α for 20 min or untreated MDA-MB-231 cells were separated by Zn 2+ -Phos-tag SDS–PAGE and immunoblotted with anti-EphA2 antibody. ( b – f ) MDA-MB-231 cells were pre-treated with BI-D1870 (10 μM) for 30 min and then scratched with a pipette tip. After 48 h of incubation, whole-cell lysates were immunoblotted with primary antibodies against pS-EphA2, EphA2 and β-actin ( b ) Migrated cells were counted manually under a microscope ( c ) Data are the means±s.d. of at least three fields. Similar results were obtained in at least three independent experiments. * P <0.05 by Student's t -test. At the same time, the migration border cells were immunofluorescently stained with anti-pS-EphA2 or EphA2 antibodies ( d , e ) and cells harbouring lamellipodia were counted manually under a microscope ( f ) Scale bar, 20 μm. Data are the means±s.d. of at least three fields. Similar results were obtained in at least three independent experiments. * P <0.05 by Student's t -test. ( g , h ) MDA-MB-231 cells were transfected with siRNA against EphA2 or negative control and EphA2 mutation-expression plasmids. The immunoblotting results from whole-cell lysates with anti-pS-EphA2, EphA2 and β-actin antibodies are shown in g and the results of scratch assay are shown in h . Data are the means±s.d. of at least three fields. Similar results were obtained in at least three independent experiments. * P <0.05 by analysis of variance followed by Tukey–Kramer HSD test.

Article Snippet: Antibodies against total EphA2 (C-20; sc-924), RSK1 (C-21; sc-231), RSK2 (C-19; sc-1430), EGFR (1005; sc-03), TAK1 (M-579; sc-7162), β-actin (I-19; sc-1616) and α-tubulin (B-7; sc-5286) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).

Techniques: SDS Page, Transferring, Incubation, Microscopy, Migration, Staining, Transfection, Negative Control, Mutagenesis, Expressing, Western Blot, Wound Healing Assay

Journal: Nature Communications

Article Title: Crucial roles of RSK in cell motility by catalysing serine phosphorylation of EphA2

doi: 10.1038/ncomms8679

Figure Lengend Snippet: ( a ) Human melanoma cells (A2058, SK-MEL-28, A375, UACC62, UACC257 and SK-MEL-2), ( b ) DLD-1 colon cancer cells and ( c ) lung adenocarcinoma cells (PC-9, HCC827, HCC4006, NCI-H1650, H2228 and A549) were treated with vemurafenib (1 μM), BI-D1870 (10 μM), gefitinib (1 μM), crizotinib (10 μM) or U0126 (5 μM) for 30–60 min. Whole-cell lysates were immunoblotted with primary antibodies against pS-EphA2, EphA2, pRSK, RSK1, RSK2, pY-EGFR, EGFR, β-actin and α-tubulin.

Article Snippet: Antibodies against total EphA2 (C-20; sc-924), RSK1 (C-21; sc-231), RSK2 (C-19; sc-1430), EGFR (1005; sc-03), TAK1 (M-579; sc-7162), β-actin (I-19; sc-1616) and α-tubulin (B-7; sc-5286) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).

Techniques:

Journal: Nature Communications

Article Title: Crucial roles of RSK in cell motility by catalysing serine phosphorylation of EphA2

doi: 10.1038/ncomms8679

Figure Lengend Snippet: ( a ) A multi-cancer tissue microarray, including 1,010 cores from 13 organ cancer tissues, was adopted for immunohistochemical staining using primary antibodies against pS-EphA2 and pRSK. Typical staining images of lung cancer tissues, including adenocarcinoma (AD) and squamous cell carcinoma (SCC), at low- and high-power magnifications are shown. Scale bar, 20 μm. ( b ) Typical immunohistochemical staining of pS-EphA2 and pRSK in EGFR -mutated (exon 19 deletion) lung adenocarcinoma tissues are shown. Scale bar, 20 μm. ( c – f ) Postoperative overall Kaplan–Meier survival curves of all the lung cancer patients ( c , d ) or smoking patients ( e , f ) were compared according to pRSK negativity or positivity ( c , e ) or pS-EphA2/pRSK double positivity ( d , f ) P values were calculated by the log-rank tests.

Article Snippet: Antibodies against total EphA2 (C-20; sc-924), RSK1 (C-21; sc-231), RSK2 (C-19; sc-1430), EGFR (1005; sc-03), TAK1 (M-579; sc-7162), β-actin (I-19; sc-1616) and α-tubulin (B-7; sc-5286) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).

Techniques: Microarray, Immunohistochemical staining, Staining

Journal: Oncotarget

Article Title: The deubiquitinase USP54 is overexpressed in colorectal cancer stem cells and promotes intestinal tumorigenesis

doi: 10.18632/oncotarget.12769

Figure Lengend Snippet: A. Analysis of USP54 expression from microarray data (GEO accession number GSE27605). High, high Lgr5 or EphB2 receptor expression levels; Med, medium EphB2 receptor expression levels; Low, low Lgr5 or EphB2 receptor expression levels. B. qRT-PCR analysis of USP54 expression in two different colorectal carcinoma xenografts (SP5 and SP9), two-tailed Student's t-test (***, P < 0.001). C. Anchorage-independent growth of control (pLKO.1) and USP54-depleted HCT116 cells (shUSP54.854 and shUSP54.856), two-tailed Student's t-test (**, P < 0.01; ***, P < 0.001). RFU, relative fluorescence units. D. qRT-PCR analysis of USP54 expression in HCT116 cells transduced with control (pLKO.1) or USP54 -specific shRNAs (shUSP54.854 and shUSP54.856). Statistical significance was assessed by two-tailed Student's t-test (***, P < 0.001). E. MTT proliferation analysis of wild-type and USP54-deficient HCT116 cells, Mann Whitney-Wilcoxon test (**, P < 0.01). F. Average area of invasion of HCT116 cells transduced with empty vector (pLKO.1) or USP54 -specific shRNAs (shUSP54.854 and shUSP54.856). Mann Whitney-Wilcoxon test was used to analyze statistical significance (*, P < 0.05; **, P < 0.01). G. Tumor xenograft model performed with subcutaneously injected control and USP54-depleted HCT116 cells. Data are presented as mean ± SEM and statistical significance was assessed by using a non-parametric Mann Whitney-Wilcoxon test (*, P < 0.05).

Article Snippet: Then, qRT-PCR was performed using TaqMan ® gene expression assay for murine samples ( Usp54 , Mm00513373_m1) or Power SYBR ® Green PCR Master Mix for human cells (Life Technologies), using an Applied Biosystems 7300HT Real-Time PCR System.

Techniques: Expressing, Microarray, Quantitative RT-PCR, Two Tailed Test, Control, Fluorescence, Transduction, MANN-WHITNEY, Plasmid Preparation, Injection

Journal: Oncotarget

Article Title: The deubiquitinase USP54 is overexpressed in colorectal cancer stem cells and promotes intestinal tumorigenesis

doi: 10.18632/oncotarget.12769

Figure Lengend Snippet: A. , B. Kaplan-Meier survival curves for wild-type and Usp54-deficient males (A) and females (B). C. TaqMan-based qRT-PCR analysis of Usp54 in MEFs and liver tissues from Usp54 +/+ and Usp54 KF/KF mice. Data are represented as relative quantification, RQ ± SEM, two-tailed Student's t-test (**, P < 0.01). D. Body weight curves of Usp54 +/+ and Usp54 KF/KF female mice kept on standard diet. E. Body weight curves of Usp54 +/+ and Usp54 KF/KF female mice kept on high-fat diet and a representative image of females of each genotype at the end of the experiment. F. Total weight gain in the same animals. G. Percentage of gonadal and subscapular fat mass with respect to total body weight of the same animals. H. Mean adipocyte area in gonadal and skin fat. I. Representative histological images. Scale bar: 20 μm (gonadal fat) and 200 μm (skin fat). J. Average thickness of the subcutaneous fat deposits for each genotype. Statistical significance was assessed by a non-parametric Mann Whitney-Wilcoxon test (*, P < 0.05; **, P < 0.01; ***, P < 0.001).

Article Snippet: Then, qRT-PCR was performed using TaqMan ® gene expression assay for murine samples ( Usp54 , Mm00513373_m1) or Power SYBR ® Green PCR Master Mix for human cells (Life Technologies), using an Applied Biosystems 7300HT Real-Time PCR System.

Techniques: Quantitative RT-PCR, Quantitative Proteomics, Two Tailed Test, MANN-WHITNEY

Journal: Oncotarget

Article Title: The deubiquitinase USP54 is overexpressed in colorectal cancer stem cells and promotes intestinal tumorigenesis

doi: 10.18632/oncotarget.12769

Figure Lengend Snippet: A. Schematic representation of azoxymethane-induced colon tumor protocol. B. Percentage of animals with the indicated histological alterations. L-Dys, light dysplasia; S-Dys, severe dysplasia; Adeno, adenocarcinomas; Inf. Adeno., infiltrating adenocarcinomas. C. Percentage of infiltrating and mucosal tumors within all carcinomas of each genotype and representative histological images. Scale bar: 500 μm. D. Average number of adenocarcinomas per mouse. E. Length of the colon at the end of the experiment. F. Analysis of USP54 expression from 32 colorectal cancer patient samples, comprising pairs of tumor and matched normal mucosa (GEO accession GDS2947). G. Kaplan-Meier survival plot for 269 patients with intestinal cancer grouped as a function of quantile expressions of USP54 . Statistical significance was assessed by a non-parametric Mann Whitney-Wilcoxon test (*, P < 0.05; **, P < 0.01).

Article Snippet: Then, qRT-PCR was performed using TaqMan ® gene expression assay for murine samples ( Usp54 , Mm00513373_m1) or Power SYBR ® Green PCR Master Mix for human cells (Life Technologies), using an Applied Biosystems 7300HT Real-Time PCR System.

Techniques: Expressing, MANN-WHITNEY

Journal: Oncotarget

Article Title: The deubiquitinase USP54 is overexpressed in colorectal cancer stem cells and promotes intestinal tumorigenesis

doi: 10.18632/oncotarget.12769

Figure Lengend Snippet: A. TaqMan-based qRT-PCR analysis of Usp54 expression in B16F10 cells transduced with the indicated Usp54-specific shRNA or the empty lentiviral vector (pLKO.1) as a control. Data are represented as relative quantification, RQ ± SEM, two-tailed Student's t-test (***, P < 0.001). B. Number of metastases bigger than 200 μm in diameter. Statistical significance was assessed using a non-parametric Mann Whitney-Wilcoxon test (*, P < 0.05; ***, P < 0.001). C. Representative images of lungs and histological analysis for each condition. Scale bar: 200 μm.

Article Snippet: Then, qRT-PCR was performed using TaqMan ® gene expression assay for murine samples ( Usp54 , Mm00513373_m1) or Power SYBR ® Green PCR Master Mix for human cells (Life Technologies), using an Applied Biosystems 7300HT Real-Time PCR System.

Techniques: Quantitative RT-PCR, Expressing, Transduction, shRNA, Plasmid Preparation, Control, Quantitative Proteomics, Two Tailed Test, MANN-WHITNEY

Journal: Oncotarget

Article Title: The deubiquitinase USP54 is overexpressed in colorectal cancer stem cells and promotes intestinal tumorigenesis

doi: 10.18632/oncotarget.12769

Figure Lengend Snippet: Summary of USP54 genetic alterations found in human cancer. ACC, Adrenocortical Carcinoma; Adeno, Adenocarcinoma; CCLE, Cancer Cell Line Encyclopedia; chRCC, Kidney Chromophobe; CS, Carcinosarcoma; DESM, Desmoplastic Melanoma; MPNST, Malignant Peripheral Nerve Sheath Tumor; NEPC, Neuroendocrine Prostate Cancer; PAAC, Acinar Cell Carcinoma of the Pancreas; SC, Small Cell; Sq and Squ, Squamous Cell Carcinoma; ucs, Uterine Carcinosarcoma. Data were obtained from cBioportal ( http://cbioportal.org ).

Article Snippet: Then, qRT-PCR was performed using TaqMan ® gene expression assay for murine samples ( Usp54 , Mm00513373_m1) or Power SYBR ® Green PCR Master Mix for human cells (Life Technologies), using an Applied Biosystems 7300HT Real-Time PCR System.

Techniques:

Journal: The Journal of Experimental Medicine

Article Title: Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1 –transformed acute lymphoblastic leukemia cells

doi: 10.1084/jem.20062662

Figure Lengend Snippet: BCR-ABL1–mediated up-regulation of AID involves repression of ID2, a negative regulator of AID. Two Ph + ALL cell lines (BV173 and SUP-B15) were incubated in the presence or absence of 10 μmol/l STI571 for 16 h and subjected to microarray analysis using the Affymetrix U133A 2.0 platform as described in Materials and methods (A). mRNA levels of ID2 were compared with those of AID and its positive regulators E2A and PAX5. As controls, known STI571-inducible genes ( IGKC , RAG1 , RAG2 , and BACH2 ) are shown. (B) The two Ph + ALL cell lines were cultured for 48 h in the presence or absence of STI571, and protein levels of ID2 (top) and AID (bottom) were measured by flow cytometry. (C) To test the functional relevance of BCR-ABL1–mediated down-regulation of ID2 in Ph + ALL cells, the effect of ID2 overexpression on AID mRNA levels was measured in Ph + ALL cells. Therefore, the two Ph + ALL cell lines were stably transduced with a vector encoding only GFP (left) or both GFP and ID2 (right). Overexpression of ID2 was monitored together with mRNA levels of AID. GAPDH mRNA levels were used for normalization of cDNA amounts.

Article Snippet: For analysis of AID and ID2 expression by flow cytometry, antibodies against ID2 (rabbit anti–human ID2 IgG; C-20; Santa Cruz Biotechnology, Inc.) and AID (mouse anti–human AID IgG1; L7E7; Cell Signaling Technology) were used together with secondary antibodies (goat anti–rabbit IgG Cy2 and goat anti–mouse IgG Cy3; Jackson ImmunoResearch Laboratories).

Techniques: Incubation, Microarray, Cell Culture, Flow Cytometry, Functional Assay, Over Expression, Stable Transfection, Transduction, Plasmid Preparation

Journal: PLoS ONE

Article Title: Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling

doi: 10.1371/journal.pone.0040321

Figure Lengend Snippet: (A) Relative vs. absolute gene expression profiling. Conventional methods compare differences in gene expression between samples within an individual experiment, and result in relative values only (left). In Gene Expression Commons, raw microarray data is individually normalized against a large-scale common reference, then mapped onto the probeset meta profile. This strategy enables profiling of absolute expression levels of all genes on the microarray (right). (B) Relationship between the size of the common reference and the accuracy of the probeset dynamic range estimation. The result of one out of five experiments is shown. The Y-axis represents % probesets with false estimation of dynamic range in mean ± S.E.M (n = 10). (C) The dynamic range versus the mean of each probeset in Affymetrix Mouse 430 2.0 (n = 11,939) (left) and Affymetrix Human U133 Plus 2 (n = 25,229) (right) presented by a density plot and histograms. (D) Graphical representation of probeset meta profile. The Y-axis represents expression intensity without units in log2 scale. The distribution of expression levels is displayed by a histogram (right side of the axis). The high/low threshold computed is shown by a solid bar, and the distribution of percentiles in either the high or low expression range is indicated by a gradation of color, displayed as highest (+100%) in dark red, threshold (0%) in white, lowest (−100%) in dark blue (left side of the axis). Four diverse distributions of probesets for four different genes (Aak1, Rbx1, Hif1a and Ikzf1) (left), and diverse distribution of four probesets of one gene (Il16) (right) are shown.

Article Snippet: We downloaded 11,939 Affymetrix Mouse Genome 430 2.0 and 25,299 Affymetrix Human Genome U133 Plus 2.0 gene expression microarray data from the NCBI Gene Expression Omnibus (GEO) public repository .

Techniques: Expressing, Microarray

Journal: PLoS ONE

Article Title: Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling

doi: 10.1371/journal.pone.0040321

Figure Lengend Snippet: Size of universal reference and probeset dynamic-range estimation Affymetrix Human U133 Plus 2 (54677 probesets).

Article Snippet: We downloaded 11,939 Affymetrix Mouse Genome 430 2.0 and 25,299 Affymetrix Human Genome U133 Plus 2.0 gene expression microarray data from the NCBI Gene Expression Omnibus (GEO) public repository .

Techniques: