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: Stem cell research & therapy

Article Title: Extracellular vesicles derived from human umbilical cord mesenchymal stem cells alleviate osteoarthritis of the knee in mice model by interacting with METTL3 to reduce m6A of NLRP3 in macrophage.

doi: 10.1186/s13287-022-03005-9

Figure Lengend Snippet: Fig. 2 HucMSCs-EVs alleviate knee osteoarthritis in DMM-induced OA mice model. A. Safranin O and Fast Green staining of knee sections and micro-CT analysis of knee joint in mice with DMM-induced OA. Expression levels of COL2A1, Aggrecan, ADAMTS5, and MMP13 were determined by immunofluorescence staining. Scale bar = 400 μm for Safranin O and Fast Green staining; Scale bar = 1 mm for Micro-CT; Scale bar = 100 μm for immunofluorescence staining. B. OARIS scores of knee sections in each group (n = 10). C. Osteophyte score of each group (n = 10). D. Quantification of mean fluorescence intensity of COL2A1, Aggrecan, ADAMTS5, and MMP13 in each group (n = 10). E. Levels of IL-1β, IL-18, and TNF-α in mice knee tissue as determined by ELISA (n = 3). Data are presented as mean ± SD. ns, no significance; *p < 0.05; **p < 0.01; ***p < 0.001

Article Snippet: Primary antibodies used in this experiment included antibodies against COL2A1 (1:2000, Abcam, ab188570), antibodies against Aggrecan (1:2000, Proteintech, 13,880–1-AP), antibodies against ADAMTS5 (1:2000, Abcam, ab182795), antibodies against MMP13 (1:2000, Proteintech, 18,165–1-AP), antibodies against CD9 (1:2000; Abcam; ab223052), antibodies against CD63 (1:2000; Abcam; ab134045), antibodies against Alix (1:1500; Proteintech; 12,422–1-AP), antibodies against TSG101 (1:2000; Proteintech; 14,497–1-AP), antibodies against Calnexin (1:2000; Proteintech; 10,427–2- AP), antibodies against Tubulin (1:2000; Proteintech; 10,094–1-AP), antibodies against Ago2 (1:2000; Abcam; ab186733), antibodies against NLRP3 (1:1000, Adipogen, AG-20B-0014), antibodies against METTL3 (1:2000, Proteintech; 15,073–1-AP), antibodies against IL-1β (1:1000, R&D Systems, AF-401-NA), antibodies against Ubiquitin (1:1000, Santa Cruz, sc-8017), and antibodies against caspase-1 (1:1000, Abcam, ab108362). miRNA target prediction analysis TargetScan (http:// www. targe tscan. org/ vert 80/), GeneCards (https:// www. genec ards. org/), and miRWalk (http:// mirwa lk. umm. uni- heide lberg. de/) were used to predict the miRNA of target genes of interest, and the target miRNA was determined by the intersection of prediction results. miRNA microarray assay Suri Medicine Company conducted miRNA arrays on hucMSCs-EVs (Nanjing, China).

Techniques: Staining, Micro-CT, Expressing, Immunofluorescence, Fluorescence, Enzyme-linked Immunosorbent Assay

Journal: Stem cell research & therapy

Article Title: Extracellular vesicles derived from human umbilical cord mesenchymal stem cells alleviate osteoarthritis of the knee in mice model by interacting with METTL3 to reduce m6A of NLRP3 in macrophage.

doi: 10.1186/s13287-022-03005-9

Figure Lengend Snippet: Fig. 3 The protection effect of knee OA by hucMSCs-EVs was abolished in NLRP3−/− mice. A. Safranin O and Fast Green staining of knee sections and micro-CT analysis of knee joint in NLRP3−/− mice with DMM-induced OA. Expression levels of COL2A1, Aggrecan, ADAMTS5, and MMP13 were determined by immunofluorescence staining. Scale bar = 400 μm for Safranin O and Fast Green staining; Scale bar = 1 mm for Micro-CT; Scale bar = 100 μm for immunofluorescence staining. B. OARIS scores of knee sections in each group (n = 10). C. Osteophyte score of each group (n = 10). D. Quantification of mean fluorescence intensity of COL2A1, Aggrecan, ADAMTS5, and MMP13 in each group (n = 10). E. Levels of IL-1β, IL-18, and TNF-α in mice knee tissue as determined by ELISA (n = 3). Data are presented as mean ± SD. ns, no significance; *p < 0.05; **p < 0.01; ***p < 0.001

Article Snippet: Primary antibodies used in this experiment included antibodies against COL2A1 (1:2000, Abcam, ab188570), antibodies against Aggrecan (1:2000, Proteintech, 13,880–1-AP), antibodies against ADAMTS5 (1:2000, Abcam, ab182795), antibodies against MMP13 (1:2000, Proteintech, 18,165–1-AP), antibodies against CD9 (1:2000; Abcam; ab223052), antibodies against CD63 (1:2000; Abcam; ab134045), antibodies against Alix (1:1500; Proteintech; 12,422–1-AP), antibodies against TSG101 (1:2000; Proteintech; 14,497–1-AP), antibodies against Calnexin (1:2000; Proteintech; 10,427–2- AP), antibodies against Tubulin (1:2000; Proteintech; 10,094–1-AP), antibodies against Ago2 (1:2000; Abcam; ab186733), antibodies against NLRP3 (1:1000, Adipogen, AG-20B-0014), antibodies against METTL3 (1:2000, Proteintech; 15,073–1-AP), antibodies against IL-1β (1:1000, R&D Systems, AF-401-NA), antibodies against Ubiquitin (1:1000, Santa Cruz, sc-8017), and antibodies against caspase-1 (1:1000, Abcam, ab108362). miRNA target prediction analysis TargetScan (http:// www. targe tscan. org/ vert 80/), GeneCards (https:// www. genec ards. org/), and miRWalk (http:// mirwa lk. umm. uni- heide lberg. de/) were used to predict the miRNA of target genes of interest, and the target miRNA was determined by the intersection of prediction results. miRNA microarray assay Suri Medicine Company conducted miRNA arrays on hucMSCs-EVs (Nanjing, China).

Techniques: Staining, Micro-CT, Expressing, Immunofluorescence, Fluorescence, Enzyme-linked Immunosorbent Assay

Journal: Stem cell research & therapy

Article Title: Extracellular vesicles derived from human umbilical cord mesenchymal stem cells alleviate osteoarthritis of the knee in mice model by interacting with METTL3 to reduce m6A of NLRP3 in macrophage.

doi: 10.1186/s13287-022-03005-9

Figure Lengend Snippet: Fig. 8 miR-1208 alleviates knee osteoarthritis and decreases the cartilage degradation in vivo. A. Safranin O and Fast Green, Micro-CT, and immunofluorescence staining of each group of mice knee section. B. OARIS scores of knee sections in each group (n = 10). C. Osteophyte score of each group (n = 10). D. Quantification of mean fluorescence intensity of COL2A1, Aggrecan, ADAMTS5, and MMP13 in each group (n = 10)

Article Snippet: Primary antibodies used in this experiment included antibodies against COL2A1 (1:2000, Abcam, ab188570), antibodies against Aggrecan (1:2000, Proteintech, 13,880–1-AP), antibodies against ADAMTS5 (1:2000, Abcam, ab182795), antibodies against MMP13 (1:2000, Proteintech, 18,165–1-AP), antibodies against CD9 (1:2000; Abcam; ab223052), antibodies against CD63 (1:2000; Abcam; ab134045), antibodies against Alix (1:1500; Proteintech; 12,422–1-AP), antibodies against TSG101 (1:2000; Proteintech; 14,497–1-AP), antibodies against Calnexin (1:2000; Proteintech; 10,427–2- AP), antibodies against Tubulin (1:2000; Proteintech; 10,094–1-AP), antibodies against Ago2 (1:2000; Abcam; ab186733), antibodies against NLRP3 (1:1000, Adipogen, AG-20B-0014), antibodies against METTL3 (1:2000, Proteintech; 15,073–1-AP), antibodies against IL-1β (1:1000, R&D Systems, AF-401-NA), antibodies against Ubiquitin (1:1000, Santa Cruz, sc-8017), and antibodies against caspase-1 (1:1000, Abcam, ab108362). miRNA target prediction analysis TargetScan (http:// www. targe tscan. org/ vert 80/), GeneCards (https:// www. genec ards. org/), and miRWalk (http:// mirwa lk. umm. uni- heide lberg. de/) were used to predict the miRNA of target genes of interest, and the target miRNA was determined by the intersection of prediction results. miRNA microarray assay Suri Medicine Company conducted miRNA arrays on hucMSCs-EVs (Nanjing, China).

Techniques: In Vivo, Micro-CT, Immunofluorescence, Staining, Fluorescence

Journal: Cell Death & Disease

Article Title: Long non-coding RNAs in ischemic stroke

doi: 10.1038/s41419-018-0282-x

Figure Lengend Snippet: The timeline of lncRNA discovery

Article Snippet: FosDT expression in rats was highly upregulated during the acute period after focal ischemia in MCAO rats using arraystar lncRNA expression microarrays (about 13 folds of control).

Techniques:

Journal: Cell Death & Disease

Article Title: Long non-coding RNAs in ischemic stroke

doi: 10.1038/s41419-018-0282-x

Figure Lengend Snippet: 1. Chromosome modification. The lncRNA Xist scaffolds and recruits different kinds of regulatory proteins, such as SMRT/HDAC1-associated repressor protein (SHARP), binds to chromatin by scaffold attachment factor A (SAFA), and promotes histone deacetylation on X chromosomes. Xist also recruits PRCs and triggers methylation of lysine H3K9 and H3k27. 2. Modulating splicing. lncRNA binds to pre-mRNA and blocks the binding of spliceosome to target sequence, results in the formation of splicing variants. 3. Source of miRNA. Many lncRNA genes contain embedded miRNA sequence in its introns or exons, which harbors miRNAs. 4. CeRNA to miRNAs. Some lncRNAs contain complementary binding sites to certain miRNA, which soak up the target miRNA and result in the reduction of miRNA functions in cells. 5. Binding to mRNA and affect its stability or translation

Article Snippet: FosDT expression in rats was highly upregulated during the acute period after focal ischemia in MCAO rats using arraystar lncRNA expression microarrays (about 13 folds of control).

Techniques: Modification, Methylation, Binding Assay, Sequencing

Journal: eLife

Article Title: Mechanically transduced immunosorbent assay to measure protein-protein interactions

doi: 10.7554/eLife.67525

Figure Lengend Snippet:

Article Snippet: Antibody , Anti-GST (rabbit polyclonal) , Epicypher , 13–0022 , (1:1000).

Techniques: Recombinant, Plasmid Preparation, Software, Avidin-Biotin Assay, Peptide Microarray

Journal: eLife

Article Title: GIV/Girdin, a non-receptor modulator for Gαi/s, regulates spatiotemporal signaling during sperm capacitation and is required for male fertility

doi: 10.7554/elife.69160

Figure Lengend Snippet: Figure 1. GIV (CCDC88A) is highly expressed in spermatocytes in testis and localizes to the acrosomal cap. (A) Bar graph displays the relative fluorescence unit (RFU) of endogenous full-length GIV protein in immunoblots of organ lysates published previously using three independent anti-GIV antibodies raised against different epitopes of GIV (Anai et al., 2005). (Figure 1—source data 1)(B) RNA expression in the single-cell-type clusters identified in the human testis visualized by a UMAP plot (inset) and a bar plot. The bar plot shows RNA expression (pTPM) in each cell-type cluster.

Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Rabbit polyclonal anti- GIV (Girdin) (T- 13) Santa Cruz Biotechnology sc- 133371 Antibody Rabbit monoclonal diagnostic grade anti- Girdin/GIV antibody Custom; Sprint Bioscience SP173 Validated in prior publication Ghosh et al., 2016 Antibody Rabbit polyclonal anti- GIV (Girdin) (CC- Ab) Millipore Sigma ABT80 Antibody Rabbit polyclonal anti- GIV pS1675 Ab Custom, from 21t Century Biosciences n/a Validated in prior publication Bhandari et al., 2015 Antibody Rabbit polyclonal anti- GIV pS1689 Ab Custom, from 21st Century Biosciences n/a Validated in prior publication LópezSánchez et al., 2013 Antibody Rabbit monoclonal anti- GIV pY1764 Ab Custom, Spring Biosciences Inc n/a Validated in prior publications Midde et al., 2015; Lin et al., 2011; Midde et al., 2018; Dunkel et al., 2016 Antibody Rabbit monoclonal antipT308 AKT Cell Signaling Technology D9E Antibody Mouse monoclonal anti- total AKT Cell Signaling Technology 40D4 Antibody Mouse anti- sp56 Thermo Fisher Scientific (Waltham, MA) MA1- 10866 Antibody Mouse anti- human hexokinase 1/2 monoclonal antibody R&D Systems, (Minneapolis, MN) MAB8179 Antibody Rabbit anti- phospho- PKA substrate (RRXS*/T*)100G7E Cell Signaling Technology 9624 Antibody Goat anti- rabbit IgG, Alexa Fluor 594 conjugated ThermoFisher Scientific A11072 For immunofluorescence (IF) Antibody Goat anti- mouse IgG, Alexa Fluor 488 conjugated ThermoFisher Scientific A11017 For immunofluorescence (IF) Antibody IRDye 800CW goat antimouse IgG secondary (1:10,000) LI- COR Biosciences 926- 32210 For immunoblotting Antibody IRDye 680RD goat anti- rabbit IgG secondary (1:10,000) LI- COR Biosciences 926- 68071 For immunoblotting Reynoso, Castillo, Katkar et al. eLife 2021;10:e69160.

Techniques: Fluorescence, Western Blot, RNA Expression

Journal: eLife

Article Title: GIV/Girdin, a non-receptor modulator for Gαi/s, regulates spatiotemporal signaling during sperm capacitation and is required for male fertility

doi: 10.7554/elife.69160

Figure Lengend Snippet: Figure 2. Transcripts of CCDC88A (GIV) are downregulated in infertile male testis and semen. (A) Schematic displays the approach used to search NCBI GEO database for testis and sperm transcriptomic datasets suitable to study correlations between the abundance of CCDC88A transcripts and male fertility. (B–E) Whisker plots show the relative abundance of CCDC88A (expressed as Log2 normalized expression; see Materials and methods for different normalization approaches used for microarray and RNA-seq datasets) in sperm or testis samples (as annotated using schematics) in samples

Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Rabbit polyclonal anti- GIV (Girdin) (T- 13) Santa Cruz Biotechnology sc- 133371 Antibody Rabbit monoclonal diagnostic grade anti- Girdin/GIV antibody Custom; Sprint Bioscience SP173 Validated in prior publication Ghosh et al., 2016 Antibody Rabbit polyclonal anti- GIV (Girdin) (CC- Ab) Millipore Sigma ABT80 Antibody Rabbit polyclonal anti- GIV pS1675 Ab Custom, from 21t Century Biosciences n/a Validated in prior publication Bhandari et al., 2015 Antibody Rabbit polyclonal anti- GIV pS1689 Ab Custom, from 21st Century Biosciences n/a Validated in prior publication LópezSánchez et al., 2013 Antibody Rabbit monoclonal anti- GIV pY1764 Ab Custom, Spring Biosciences Inc n/a Validated in prior publications Midde et al., 2015; Lin et al., 2011; Midde et al., 2018; Dunkel et al., 2016 Antibody Rabbit monoclonal antipT308 AKT Cell Signaling Technology D9E Antibody Mouse monoclonal anti- total AKT Cell Signaling Technology 40D4 Antibody Mouse anti- sp56 Thermo Fisher Scientific (Waltham, MA) MA1- 10866 Antibody Mouse anti- human hexokinase 1/2 monoclonal antibody R&D Systems, (Minneapolis, MN) MAB8179 Antibody Rabbit anti- phospho- PKA substrate (RRXS*/T*)100G7E Cell Signaling Technology 9624 Antibody Goat anti- rabbit IgG, Alexa Fluor 594 conjugated ThermoFisher Scientific A11072 For immunofluorescence (IF) Antibody Goat anti- mouse IgG, Alexa Fluor 488 conjugated ThermoFisher Scientific A11017 For immunofluorescence (IF) Antibody IRDye 800CW goat antimouse IgG secondary (1:10,000) LI- COR Biosciences 926- 32210 For immunoblotting Antibody IRDye 680RD goat anti- rabbit IgG secondary (1:10,000) LI- COR Biosciences 926- 68071 For immunoblotting Reynoso, Castillo, Katkar et al. eLife 2021;10:e69160.

Techniques: Whisker Assay, Expressing, Microarray, RNA Sequencing

Journal: eLife

Article Title: GIV/Girdin, a non-receptor modulator for Gαi/s, regulates spatiotemporal signaling during sperm capacitation and is required for male fertility

doi: 10.7554/elife.69160

Figure Lengend Snippet: Figure 8. Summary and working model: spatiotemporally segregated roles of GIV/Girdin during sperm capacitation. Schematic summarizes the key findings in this work and places them in the context of existing literature. GIV is likely to primarily function during capacitation of sperm, during which it fulfills two key roles as a signal transducer in a spatiotemporally segregated manner. The first role (right, top) is in the head of the sperm, where GIV’s GEM motif inhibits the AC→cAMP pathway and prevents acrosomal reaction. The second role (right, bottom) is in the mid-piece and tail region of the sperm, which involves tyrosine phosphorylation of GIV, which

Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Rabbit polyclonal anti- GIV (Girdin) (T- 13) Santa Cruz Biotechnology sc- 133371 Antibody Rabbit monoclonal diagnostic grade anti- Girdin/GIV antibody Custom; Sprint Bioscience SP173 Validated in prior publication Ghosh et al., 2016 Antibody Rabbit polyclonal anti- GIV (Girdin) (CC- Ab) Millipore Sigma ABT80 Antibody Rabbit polyclonal anti- GIV pS1675 Ab Custom, from 21t Century Biosciences n/a Validated in prior publication Bhandari et al., 2015 Antibody Rabbit polyclonal anti- GIV pS1689 Ab Custom, from 21st Century Biosciences n/a Validated in prior publication LópezSánchez et al., 2013 Antibody Rabbit monoclonal anti- GIV pY1764 Ab Custom, Spring Biosciences Inc n/a Validated in prior publications Midde et al., 2015; Lin et al., 2011; Midde et al., 2018; Dunkel et al., 2016 Antibody Rabbit monoclonal antipT308 AKT Cell Signaling Technology D9E Antibody Mouse monoclonal anti- total AKT Cell Signaling Technology 40D4 Antibody Mouse anti- sp56 Thermo Fisher Scientific (Waltham, MA) MA1- 10866 Antibody Mouse anti- human hexokinase 1/2 monoclonal antibody R&D Systems, (Minneapolis, MN) MAB8179 Antibody Rabbit anti- phospho- PKA substrate (RRXS*/T*)100G7E Cell Signaling Technology 9624 Antibody Goat anti- rabbit IgG, Alexa Fluor 594 conjugated ThermoFisher Scientific A11072 For immunofluorescence (IF) Antibody Goat anti- mouse IgG, Alexa Fluor 488 conjugated ThermoFisher Scientific A11017 For immunofluorescence (IF) Antibody IRDye 800CW goat antimouse IgG secondary (1:10,000) LI- COR Biosciences 926- 32210 For immunoblotting Antibody IRDye 680RD goat anti- rabbit IgG secondary (1:10,000) LI- COR Biosciences 926- 68071 For immunoblotting Reynoso, Castillo, Katkar et al. eLife 2021;10:e69160.

Techniques: Phospho-proteomics

Journal: The Journal of comparative neurology

Article Title: Expression profile analysis of vulnerable CA1 pyramidal neurons in young-middle aged Ts65Dn mice

doi: 10.1002/cne.23663

Figure Lengend Snippet: Bar graphs and color coded heatmaps illustrating relative transcript levels in Ts65Dn (n = 9) and 2N (n = 7) mice at 4-9 months of age in CA1 neurons. (A) Several neurotrophins and cognate neurotrophin receptors displayed downregulation, including CNTF, NTF4/5, p75NTR, TrkA, TrkB, and TrkC (B) No significant changes in GluR subunits were observed. (C) Alterations in AD-related transcripts included SAA4, KCNIP3, MAPT4, and NPC2 (*p < 0.01), (**p < 0.005), and (*** p < 0.001) (t= trend 0.02< p < 0.05). Error bars indicate standard error of the mean (SEM).

Article Snippet: Taqman qPCR primers (Life Technologies) were utilized for qPCR, TrkB (Mm01341760_m1; targeting the exon 16-17 boundary), TrkC (Mm01317842_m1; targeting the exon 12-13 boundary), NTF3 (Mm00435413_s1; targeting exon 3), BDNF (Mm04230607_s1; targeting exon 8) and the housekeeping gene succinate dehydrogenase complex, subunit A, flavoprotein (SDHA; Mm01352360_m1; targeting the exon 14-15 boundary).

Techniques:

Journal: The Journal of comparative neurology

Article Title: Expression profile analysis of vulnerable CA1 pyramidal neurons in young-middle aged Ts65Dn mice

doi: 10.1002/cne.23663

Figure Lengend Snippet: (A) BDNF showed no difference in mRNA expression levels, however, the BDNF receptor TrkB (NTRK2) showed significant downregulation, in accordance with the microarray results. NTF3 showed a trend for downregulation and the NTF3 receptor TrkC (NTRK3) was significantly downregulated. ddCT was expressed as percent of 2N control for all qPCR results. Key, (* p < 0.05) and (t p < 0.1). Error bars indicate SEM.

Article Snippet: Taqman qPCR primers (Life Technologies) were utilized for qPCR, TrkB (Mm01341760_m1; targeting the exon 16-17 boundary), TrkC (Mm01317842_m1; targeting the exon 12-13 boundary), NTF3 (Mm00435413_s1; targeting exon 3), BDNF (Mm04230607_s1; targeting exon 8) and the housekeeping gene succinate dehydrogenase complex, subunit A, flavoprotein (SDHA; Mm01352360_m1; targeting the exon 14-15 boundary).

Techniques: Expressing, Microarray

Journal: The Journal of comparative neurology

Article Title: Expression profile analysis of vulnerable CA1 pyramidal neurons in young-middle aged Ts65Dn mice

doi: 10.1002/cne.23663

Figure Lengend Snippet: Immunoblot analysis using regional hippocampal dissections was performed to assess whether selected transcriptional alterations resulted in commensurate protein level changes in Ts65Dn mice compared to 2N littermates at 4-6 months of age. (A) Representative immunoblots for pro-BDNF, mature BDNF, NTF3, TrkB-FL, TrkB-T1, TrkC-FL, and TrkC-T1. β-tubulin (TUBB) expression was used as a loading control. (B) Normalized expression levels compared to TUBB expression show upregulation of pro-BDNF (p<0.02), a trend towards downregulation of TrkB-FL (p =0.09) and TrkC-T1 (p= 0.069), but no significant changes in NTF3, mature BDNF, TrkB-T1 and TrkC-FL expression. Key: 2N black, Ts65Dn grey.

Article Snippet: Taqman qPCR primers (Life Technologies) were utilized for qPCR, TrkB (Mm01341760_m1; targeting the exon 16-17 boundary), TrkC (Mm01317842_m1; targeting the exon 12-13 boundary), NTF3 (Mm00435413_s1; targeting exon 3), BDNF (Mm04230607_s1; targeting exon 8) and the housekeeping gene succinate dehydrogenase complex, subunit A, flavoprotein (SDHA; Mm01352360_m1; targeting the exon 14-15 boundary).

Techniques: Western Blot, Expressing

Journal: Cancer Medicine

Article Title: Serum CXCL13 as a Novel Biomarker in Oral Squamous Cell Carcinoma

doi: 10.1002/cam4.70263

Figure Lengend Snippet: Novel biomarker candidates for OSCC identified using microarray analysis.

Article Snippet: TaqMan probes and primers for CXCL13 (Hs00757930_m1) and HMBS (Hs00609297_m1) were obtained from Thermo Fisher Scientific.

Techniques: Biomarker Discovery, Microarray, Binding Assay

Journal: Cancer Medicine

Article Title: Serum CXCL13 as a Novel Biomarker in Oral Squamous Cell Carcinoma

doi: 10.1002/cam4.70263

Figure Lengend Snippet: Expression of CXCL13 mRNA in primary OSCC tissues by RT‐qPCR. (A) CXCL13 expression was higher in tumor tissues compared to adjacent normal tissues in all cases. (B) Significant upregulation of CXCL13 mRNA was observed in tumor tissues. ** p < 0.01 compared to adjacent normal tissues.

Article Snippet: TaqMan probes and primers for CXCL13 (Hs00757930_m1) and HMBS (Hs00609297_m1) were obtained from Thermo Fisher Scientific.

Techniques: Expressing, Quantitative RT-PCR

Journal: Cancer Medicine

Article Title: Serum CXCL13 as a Novel Biomarker in Oral Squamous Cell Carcinoma

doi: 10.1002/cam4.70263

Figure Lengend Snippet: Serum levels of CXCL13 protein in patients with OSCC. (A) The average serum CXCL13 protein in 125 patients with OSCC was 72.8 ρg/mL. (B) The average serum CXCL13 protein in healthy individuals was 33.5 ρg/mL. (C) The reference value determined by the ROC curve for maximizing the TPF/FPF ratio was 53.0 ρg/mL. FPF, false‐positive fraction; TPF, true‐positive fraction.

Article Snippet: TaqMan probes and primers for CXCL13 (Hs00757930_m1) and HMBS (Hs00609297_m1) were obtained from Thermo Fisher Scientific.

Techniques:

Journal: Cancer Medicine

Article Title: Serum CXCL13 as a Novel Biomarker in Oral Squamous Cell Carcinoma

doi: 10.1002/cam4.70263

Figure Lengend Snippet: Serum CXCL13 levels in patients with OSCC.

Article Snippet: TaqMan probes and primers for CXCL13 (Hs00757930_m1) and HMBS (Hs00609297_m1) were obtained from Thermo Fisher Scientific.

Techniques:

Journal: Cancer Medicine

Article Title: Serum CXCL13 as a Novel Biomarker in Oral Squamous Cell Carcinoma

doi: 10.1002/cam4.70263

Figure Lengend Snippet: Diagnostic sensitivity of serum CXCL13 and SCC in patients with OSCC.

Article Snippet: TaqMan probes and primers for CXCL13 (Hs00757930_m1) and HMBS (Hs00609297_m1) were obtained from Thermo Fisher Scientific.

Techniques: Diagnostic Assay

Journal: Cancer Medicine

Article Title: Serum CXCL13 as a Novel Biomarker in Oral Squamous Cell Carcinoma

doi: 10.1002/cam4.70263

Figure Lengend Snippet: Serum CXCL13 and clinicopathological factors in patients with OSCC. (A) Serum CXCL13 protein levels in T classification. The serum CXCL13 proteins increased in accordance with primary tumor size. The serum CXCL13 levels in T1 were significantly higher than in T3 and T4. (B) The serum CXCL13 proteins in recurrence. The serum levels of CXCL13 proteins in patients with recurrence were significantly elevated. (C) Patients with recurrence were classified into primary recurrence, neck LNM, and distant metastasis (including multiple responses). The serum levels of CXCL13 proteins in neck LNM were significantly elevated. * p < 0.05, ** p < 0.01.

Article Snippet: TaqMan probes and primers for CXCL13 (Hs00757930_m1) and HMBS (Hs00609297_m1) were obtained from Thermo Fisher Scientific.

Techniques:

Journal: Cancer Medicine

Article Title: Serum CXCL13 as a Novel Biomarker in Oral Squamous Cell Carcinoma

doi: 10.1002/cam4.70263

Figure Lengend Snippet: Serum CXCL13 and prognosis in patients with OSCC. A comparison of overall survival (OS) and disease‐free survival (DFS) in patients with OSCC was made among the two groups, which were classified based on the median serum CXCL13 level using the Kaplan–Meier method with a log‐rank test. High expression of serum CXCL13 indicated poor prognosis in both OS (A, p = 0.044) and DFS (B, p = 0.018) across all stages. In Stage I/II, the groups had no significant difference in OS (C, p = 0.696) and DFS (D, p = 0.435). In Stage III/IV, both OS (E, p = 0.020) and DFS (F, p = 0.009) were significantly poorer in patients with high CXCL13 levels.

Article Snippet: TaqMan probes and primers for CXCL13 (Hs00757930_m1) and HMBS (Hs00609297_m1) were obtained from Thermo Fisher Scientific.

Techniques: Comparison, Expressing

Journal: Cancer Medicine

Article Title: Serum CXCL13 as a Novel Biomarker in Oral Squamous Cell Carcinoma

doi: 10.1002/cam4.70263

Figure Lengend Snippet: Visium spatial transcriptome analysis using two cases of primary OSCC tissues. (A) Case 1: Primary tongue SCC tissues were classified into eight clusters based on the gene expression profile. Among these, the tumor area comprised four clusters (Cluster 1, 3, 5, and 6). CXCL13 expression was upregulated in three of four clusters within the tumor area. CD8 expression was detected in all tumor clusters. (B) Case 2: In Case 2, primary tongue SCC tissues were classified into seven clusters. The tumor area consisted of four clusters (Clusters 1, 2, 3, and 6). The expression of CXCL13 and CD8 was upregulated in three of four clusters within the tumor area. CD4 expression was detected only in Cluster 2 in the tumor area but not in Case 1.

Article Snippet: TaqMan probes and primers for CXCL13 (Hs00757930_m1) and HMBS (Hs00609297_m1) were obtained from Thermo Fisher Scientific.

Techniques: Gene Expression, Expressing