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Typhoon 9500 scanner

Manufactured by GE Healthcare
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The Typhoon 9500 scanner is a versatile imaging system designed for high-performance detection and analysis of a wide range of biomolecules, including proteins, nucleic acids, and small molecules. It utilizes fluorescence and phosphor imaging technologies to capture and quantify signals from these biomolecules in various experimental applications.

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Lab products found in correlation

Northernmax reagents, by Thermo Fisher Scientific (5 mentions) Imagequant software, by GE Healthcare (4 mentions) Imagequant, by GE Healthcare (3 mentions) Bis tris gel, by Thermo Fisher Scientific (3 mentions) Rnase r, by Illumina (2 mentions) Trizol, by Thermo Fisher Scientific (2 mentions) Silica gel 60 tlc plate, by Merck Group (1 mentions) Cy5 labeled secondary antibody, by Thermo Fisher Scientific (1 mentions) Lambda phage dna, by New England Biolabs (1 mentions) Ultrahyb oligo hybridization buffer, by Thermo Fisher Scientific (1 mentions) Hybond n membrane, by GE Healthcare (1 mentions) Quantity one software, by Bio-Rad (1 mentions) Prism 8, by GraphPad (1 mentions) Branson sonifier 450, by Emerson (1 mentions)

Close spelling variants of this product

Typhoon FLA 9500 laser-based scanner Typhoon FLA 9500 fluorescence scanner Typhoon FLA 9500 gel scanner Typhoon 9500 laser scanner Typhoon™ FLA 9500 variable mode laser scanner Typhoon FLA 9500 scanner Typhoon FLA 9500 laser scanner Typhoon 9500 Typhoon scanner Scanners

15 protocols using typhoon 9500 scanner

1

Northern Blot Analysis of RNA

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Northern blots using NorthernMax reagents (Life Technologies) and oligonucleotide probes were performed as previously described (Wilusz et al. 2008 (link)). All oligonucleotide probe sequences are provided in Supplemental Table 1. Blots were viewed and quantified with the Typhoon 9500 scanner (GE Healthcare). Representative blots are shown. For RNase R treatments, 20 μg of total RNA was treated with 10 U of RNase R (Epicentre) for 10 min at room temperature. mFold was used to calculate hairpin stabilities, assuming a 7-nt linker (AGAAUUA) between the two repeat sequences.
Kramer M.C., Liang D., Tatomer D.C., Gold B., March Z.M., Cherry S, & Wilusz J.E. (2015). Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes & Development, 29(20), 2168-2182.
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2

Northern Blotting with Oligonucleotide Probes

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Northern blots using oligonucleotide probes and NorthernMax reagents (Thermo Fisher Scientific) were performed as previously described in detail [41 (link)]. Probes used for Drosophila cell experiments: Laccase2 Exon 2 XmaI (5′-GCTGAGCTCCCCGGG-3′), Drosophila β-actin (5′-AGCACAGTGTTGGCGTACAG-3′), and HygroR (5′-GACATATCCACGCCCTCCTA-3′). Probes used for human cell experiments: Laccase2 Exon 2 (5′-GCTAGGATTGAGGATGGAGCTCC-3′), cGFP (5′-TCCATGCCGTGGGTGATGCC-3′), and human β-actin (5′-AGCACTGTGTTGGCGTACAG-3′). All blots were viewed with a Typhoon 9500 scanner (GE Healthcare) and quantified using ImageQuant.
Liang D., Tatomer D.C, & Wilusz J.E. (2021). Use of circular RNAs as markers of readthrough transcription to identify factors regulating cleavage/polyadenylation events. Methods (San Diego, Calif.), 196, 121-128.
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3

Thin-Layer Chromatography of NBD-Sphingolipids

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After liquid-phase lipid extraction, samples were separated by thin layer chromatography using Silica Gel 60 TLC plates (Merck KGaA, Darmstadt, Germany) with a mobile phase of CHCl3/CH3OH/H2O (60/35/8). After development and drying, the separated, NBD–sphingolipids were visualized using a Typhoon 9500 scanner (GE Healthcare Life Sciences, Piscataway, NJ) at excitation wavelength 457 nm and emission wavelength 532 nm. A NBD-S1P standard was a generous gift from Dr. Brian W. Wattenberg (University of Louisville).
Jonnalagadda D., Sunkara M., Morris A.J, & Whiteheart S.W. (2014). Granule-Mediated Release of Sphingosine-1-Phosphate by Activated Platelets*. Biochimica et biophysica acta, 1841(11), 1581-1589.
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4

CheA Disulfide Formation Assay

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Strain UU2806 co-transformed with cysteine-reporter derivatives of pPA114 and pGP32 (or pGP34) was grown at 30°C with aeration in tryptone broth supplemented with 12.5 µg/ml chloramphenicol, 50 µg/ml ampicillin, 0.6 µM sodium salicylate and 75 µM IPTG. At OD600nm ~0.5, a 1.5-ml aliquot of the culture was withdrawn, washed twice with 1 ml of PBS, finally resuspended in 1 ml of PBS and treated with 300 µM Cu2+-phenanthroline for 10 min at 35°C to induce disulfide formation, as previously described [21 (link)]. Whole cell lysates were separated by SDS/PAGE and CheA-containing species were detected by immunoblotting with a polyclonal anti-HA antibody (Pierce) and a Cy5-labeled secondary antibody (Invitrogen). Western blots were imaged under fluorescence mode in a Typhoon 9500 scanner (GE Healthcare), and bands were quantified with ImageQuant software (GE Healthcare).
Piñas G.E., DeSantis M.D, & Parkinson J.S. (2018). Noncritical signaling role of a kinase-receptor interaction surface in the Escherichia coli chemosensory core complex. Journal of molecular biology, 430(7), 1051-1064.
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5

Northern Blot Analysis of RNA

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Northern blots using NorthernMax reagents (ThermoFisher Scientific) and oligonucleotide probes were performed as previously described (Tatomer et al., 2017 (link)). All oligonucleotide probe sequences are provided in Table S1. Blots were viewed and quantified with the Typhoon 9500 scanner (GE Healthcare) and quantified using ImageQuant (GE Healthcare). Representative blots are shown. For RNase R treatments, 20 μg of total RNA was treated with 10 U RNase R (Epicentre RNR07250) at 37°C for 10 min.
Liang D., Tatomer D.C., Luo Z., Wu H., Yang L., Chen L.L., Cherry S, & Wilusz J.E. (2017). The output of protein-coding genes shifts to circular RNAs when the pre-mRNA processing machinery is limiting. Molecular cell, 68(5), 940-954.e3.
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6

Quantitative Northern Blot Analysis

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Northern blots using NorthernMax reagents (ThermoFisher Scientific) and oligonucleotide probes were performed as described previously (Tatomer et al. 2017 (link)). All probe sequences are in Supplemental Table S5. Blots were viewed with a Typhoon 9500 scanner (GE Healthcare) and quantified using ImageJ. Representative blots are shown.
Huang C., Liang D., Tatomer D.C, & Wilusz J.E. (2018). A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs. Genes & Development, 32(9-10), 639-644.
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7

Histone Exchange Assay for SWR Chromatin Remodeling

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The histone exchange assay was conducted using a protocol modified from (32 (link)). Each reaction is 25 μl and is composed of three parts. Part A, which constitutes 60% of the reaction volume, contains 4 nM purified SWR in 25 mM HEPES–KOH (pH 7.6), 0.5 mM EGTA, 0.1 mM EDTA, 5 mM MgCl2, 0.17 μg/μl BSA, 50 mM NaCl, 10% glycerol, 0.02% NP-40. Part B, which constitutes 20% of the reaction volume, contains 75 nM Cy3-labeled AA nucleosome and 550 nM H2A.Z–H2BFL dimers in 10 mM Tris–HCl (pH 7.5), 1 mM EDTA, 50 mM NaCl. Part C is 1 mM ATP and represents 20% of the reaction volume. Part A and Part B were mixed together before Part C was added to initiate the reaction. The reaction was left at room temperature (∼22°C) for the indicated times before they were quenched by the addition of 62.5 ng of lambda phage DNA (New England Biolabs). Five microliter of Nap1 at 3.5 μM in buffer S [70% (w/v) sucrose, 10 mM Tris–HCl (pH 7.8), 1 mM EDTA] was added to the reaction immediately before resolving the nucleosomes on 6% polyacrylamide/0.5× TBE gels. In-gel Cy3 fluorescence was detected by a Typhoon 9500 scanner (GE Healthcare) and densitometry was performed using the ImageQuant software. For the Swc5 rescue experiments, Swc5 and/or H2A–H2B dimer were added to the Part A and B mixture at the indicated final concentrations before adding in Part C.
Sun L, & Luk E. (2017). Dual function of Swc5 in SWR remodeling ATPase activation and histone H2A eviction. Nucleic Acids Research, 45(17), 9931-9946.
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8

Small RNA Isolation and Detection

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Total RNA was isolated using Trizol (Thermo Fisher Scientific 15596018) as per the manufacturer’s instructions. Small RNAs were separated by 8% denaturing polyacrylamide gel electrophoresis (National Diagnostics EC-833) and electroblotted/UV crosslinked to Hybond N+ membrane (GE Healthcare RPN303B). ULTRAhyb-oligo hybridization Buffer (Thermo Fisher Scientific AM8663) was used as per the manufacturer’s instructions. All oligonucleotide probe sequences are provided in Table S3. Blots were viewed and quantified with the Typhoon 9500 scanner (GE Healthcare) and quantified using ImageQuant (GE Healthcare). Representative blots from ≥3 experiments are shown.
Elrod N.D., Henriques T., Huang K.L., Tatomer D.C., Wilusz J.E., Wagner E.J, & Adelman K. (2019). The Integrator complex attenuates promoter-proximal transcription at protein-coding genes. Molecular cell, 76(5), 738-752.e7.
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9

Northern Blot Analysis of Guide RNAs

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Northern blots using 1.2% denaturing formaldehyde agarose gels, NorthernMax reagents (Thermo Fisher Scientific), and oligonucleotide probes were performed as previously described (44 (link)). Oligonucleotide probe sequences are provided in Supplementary Table S3. Blots were hybridized with individual oligonucleotide probes, washed, and viewed with the Typhoon 9500 scanner (GE Healthcare) followed by quantification using ImageQuant (GE Healthcare). They were then subsequently re-probed with additional oligonucleotide probes so that all blots shown in a figure panel are derived from the same experiment. To confirm expression of the guide RNAs, 8% polyacrylamide gels rather than denaturing formaldehyde agarose gels were used.
Ai Y., Liang D, & Wilusz J.E. (2022). CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells. Nucleic Acids Research, 50(11), e65.
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10

Southern and Western Blot Quantification

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All experiments were repeated at least three times. DNA signals from Southern blot analysis were detected by phosphorimaging using a Typhoon 9500 scanner (GE Healthcare Life Sciences) and quantified using Quantity One software (Bio-Rad). Protein signals from Western blot analysis were detected and quantified using the Bio-Rad Chemi-Doc (ImageLab) system. Statistical analysis was performed using the two-tailed, unpaired Student t test with Excel.
Luo J., Luckenbaugh L., Hu H., Yan Z., Gao L, & Hu J. (2020). Involvement of Host ATR-CHK1 Pathway in Hepatitis B Virus Covalently Closed Circular DNA Formation. mBio, 11(1), e03423-19.
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