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Superscript 3 first strand synthesis kit

Manufactured by Thermo Fisher Scientific
Sourced in United States, United Kingdom, Germany, China, Japan

The SuperScript III First-Strand Synthesis kit is a laboratory product used for the reverse transcription of RNA into complementary DNA (cDNA). It is designed to generate high-quality cDNA from a variety of RNA templates.

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875 protocols using superscript 3 first strand synthesis kit

1

Quantifying SMAD3 and SMAD7 Gene Expression by RT-PCR

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Relative quantification of gene expression was determined by real-time RT-PCR. The expression of SMAD3 and SMAD7 genes was quantified using TaqMan Gene Expression assays as described previously [1 (link)]. Briefly, total RNA was isolated from freshly cut sections of cryopreserved jejunum previously embedded in OCT compound using the Purelink FFPE RNA isolation Kit protocol (Life Technologies). The total RNA was purified using RNA Clean and concentrator-25 Kit (Zymo Research, Irvine, CA, USA) with on-column DNase I treatment (Life Technologies) followed by RNA quantification using the Synergy H4 reader (Biotek, Winooski, VT, USA). Superscript III first-strand synthesis kit (Life Technologies) was used to synthesize cDNA from total RNA. TaqMan gene expression assays Rh02621726_m1, Hs00706299_s1, and Hs00178696_m1 (Life Technologies) were employed for the quantification of TGF-β, SMAD3, and SMAD7 transcripts, respectively, using an ABI 7900HT Fast PCR System (ThermoFisher Scientific). The expression of each gene was normalized against 18S rRNA expression using TaqMan 18S rRNA Endogenous Control Assay (Life Technologies). Relative gene expression was determined among different groups using the comparative threshold cycle (CT) method, and fold changes in the expression were evaluated using 2−ΔΔCT [33 (link)].
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2

Quantifying Itih3 Gene Expression in Liver and Brain

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Itih3 gene expression was studied in tissue samples dissected out on an ice-cold platform. The lobe of the right liver (inferior part) as well as the hypothalamus, which is among the brain regions with the highest Itih3 gene expression [16 ], were used for analyses. Tissue samples were homogenized in lysis buffer and total RNA was isolated (mirVana RNA Isolation Kit with TURBO DNAse; Ambion, Austin, TX, USA). The quality/concentration of RNA was checked using NanoDrop (Wilmington, DE, USA). Total RNA (0.4–1 μg) was reverse-transcribed into cDNA with random hexamer primers using the Superscript III First Strand Synthesis Kit (Life Technologies, Grand Island, NY, USA) in a thermal cycler. Quantitative real-time PCR (qRT-PCR) was performed using SYBR Green Master Mix in a 7500 Fast Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) with primers from Integrated DNA Technologies (Coralville, IA, USA) for Itih3 (Forward 5′−CCCGGCGCATTTATGAAGAT-3′; Reverse 5′-ATGGCGTTCTCGGGGTATTC-3′) and the house keeping gene succinate dehydrogenase complex, subunit A, flavoprotein (SDHA; Forward 5′−CCTGTCCTATGTGGACGTTG-3′, Reverse 5′-GTTTTGTCGATCACGGGTCT-3′). Relative Itih3 gene expression was calculated using crossing point (Cp) values and experimentally determined PCR efficiency for Itih3 and SDHA.
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3

Quantitative PCR for Gene Expression

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RNA extracted (described above) from PD, PD-D, and control tissues was processed with the SuperScript III First-Strand Synthesis kit (Life Technologies, Carlsbad, CA) for cDNA synthesis, per the manufacturer's protocol. Quantitative real-time (qRT) PCR was completed using the Roche LightCycler 480 with SYBR Green detection.
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4

Rat Blood RNA Extraction and qPCR

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Rat blood RNA was extracted using the Ribopure RNA Purification kit (Life Technologies). One μg of total RNA was reverse transcribed using the SuperScript III first-strand synthesis kit (Life Technologies). Quantitative PCR (qPCR) was performed in four replicates in the 7900HT Fast Real-time PCR system (Applied Biosystems) using the Power SYBR Green PCR Master Mix (Applied Biosystems). Primers used in qPCR assay are summarized in Table I. Fold changes were calculated using the 2−ΔΔCt method as previously described (Zhao et al. 2013 (link)).
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5

Ube3a Gene Expression Analysis

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Total RNA was extracted from tissue samples using the PureLink RNA Mini Kit (Life Technologies, Carlsbad, CA). First-strand cDNA synthesis was performed using: (1) the Superscript III First-Strand Synthesis kit and oligo-dT primers (messenger RNA [mRNA]; Life Technologies) and (2) the High Capacity RNA to cDNA kit and random hexamer primers (total RNA [toRNA]; Life Technologies). Real-time PCR was performed using the TaqMan Gene Expression Master Mix and TaqMan Gene Expression Assays per manufacturer’s protocol (Life Technologies). Beta-2 microglobulin (TaqMan Assay #Mm00437762_m1) was used as an internal control. TaqMan Assay #Mm00839910_m1 was used to assess Ube3a toRNA and mRNA levels. The primer and probe set targets an amplicon of 121 base pairs that spans exons 6 and 7 of Ube3a isoforms 1 and 3 and exons 8 and 9 of Ube3a isoform 2. The reactions were performed using an ABI 7900HT real-time PCR machine.
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6

Quantitative Analysis of Cytokine and TLR4 Pathways

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Quantitative real-time polymerase chain reaction (Q-PCR) was undertaken to relatively quantify the expression levels of cytokine genes including IFN-γ, IL-1β, IL-8, and TNF-α, and the gene expressions of the MyD88-dependent pathway of TLR4, MyD88, and NF-κB in the livers, spleens, and cecal tissues. At 2 and 6 days of post-infection, Trizol reagent (Invitrogen) was used to extract total RNA from livers, spleens, and cecal tissues according to the manufacturer’s instruction. Nano Drop 2000 spectrophotometer (Thermo Fisher Scientific, MA, United States) was used to determine the concentration and quality of total RNA. SuperScript III First Strand synthesis kit (Life Technologies, Carlsbad, CA, United States) was used to synthesize cDNA with 2 μg of total RNA. The cDNA was stored at -20°C. The Q-PCR was performed with SYBR Green master mix using 7500 Fast Real-Time PCR system (Applied Biosystems, Carlsbad, CA, United States). PCR conditions contained one cycle of 95°C for 30 s, followed by 40 cycles of 95°C for 5 s and 60°C for 34 s. Dissociation analysis of amplification products was performed at the end of each PCR to confirm the specificity of amplicon. The primers for real-time PCR are listed in Table 2. mRNA relative expression was calculated using the 2-ΔΔCt method.
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7

Gene Expression Profiling of Cellular Responses

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RNA was isolated from cells with TRIzol (Life Technologies) following manufacturer’s instructions. Reverse transcription was performed with the SuperScript III first-strand synthesis kit (Life Technologies) and RT-qPCR was performed using the POWER SYBR green PCR mastermix kit (Applied Biosystems) and Applied Biosystems 7000 sequence detection system. The relative expression levels of gene in fold changes were calculated against GAPDH. Primers sequences are GAPDH forward: 5’-AACTTTGGCATTGTGGAAGG-3’, GAPDH reverse: 5’-ACACATTGGGGGTAGGAACA-3’, TGFβ forward: 5’-ATCCTGTCCAAACTAAGGCTCG-3’, TGFβ reverse: 5’-ACCTCTTTAGCATAGTAGTCCGC-3’, arginase forward: 5’-CAGAAGAATGGAAGAGTCAG-3’, arginase reverse: 5’-CAGATATGCAGGGAGTCAC-3’, iNOS forward: 5’-CCCTTCAATGGTTGGTACATGG-3’ and iNOS reverse: 5’-ACATTGATCTCCGTGACAGCC-3’.
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8

Quantification of Spliced XBP1 mRNA

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Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructions and the procedure was repeated to ensure thorough removal of genomic DNA. cDNA synthesis of the extracted RNA was performed using Superscript III First Strand Synthesis kit (Life Technologies). Quantitative PCR was performed using GoTaq qPCR Master Mix (Promega) and forward and reverse primers (Supplementary Table S1) with LightCycler 480 system (Roche). Spliced XBP1 was detected using the Taqman gene expression assay (Life Technologies, Hs03929085_g1) and Light Cycler Probes Master (Roche). To obtain relative target mRNA folds, cycle thresholds (Ct) were normalized to the Ct of Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) or Ribosomal protein L27 (RPL27) reference genes and expressed as fold-change by the 2−▵▵Ct method50 (link).
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9

Reducing ROS and Exhaustion in CAR-T Cells

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Example 6

Human normal donor anti-mesothelin CAR-T cells were stimulated on mesothelin-Fc coated plates for 4 days. CellROX Green Reagent (Life Technologies) was added to the cells at a final concentration of 5 μM and incubated for 30 minutes at 37° C. Cells were washed three times in PBS and analyzed for CellROX Green fluorescence by flow cytometry. Measurement is shown as normalization to CellROX Green fluorescence of non-stimulated anti-mesothelin CAR-T cells.

As shown in FIG. 5A, the presence of the wild type CD28 costimulatory domain in anti-mesothelin CAR increased ROS levels. Replacing the CD28 motif YMNM for the ICOSζ YMFM (SEQ ID NO: 1937) motif significantly reduced the ROS levels.

RNA was collected from non-stimulated human normal donor anti-mesothelin CAR-T cells or cells stimulated on mesothelin-Fc coated plates for 4 or 8 days. cDNA was synthesized according to the SuperScript III First-Strand Synthesis Kit (Life Technologies) protocol. Expression of Tox2 was measured on a Viia 7 Real-Time PCR System (Applied Biosystems) using a Tox2-specific Taqman probe set (Thermo Fisher; Hs00262775_m1).

As shown in FIG. 5B, the CD28-mutant YMFM (SEQ ID NO: 1937) also reduced the RNA level of the exhaustion marker Tox2 on T cells.

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10

RNA Isolation and qRT-PCR Analysis

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Total RNA was isolated from transplanted tumors or endothelial cells from the mouse brain using the Maxwell RSC simplyRNA Tissue Kit (Promega Corp.). cDNA was synthesized using the SuperScript III First-Strand Synthesis Kit (Life Technologies). Quantitative real-time RT-PCR was performed using the StepOnePlus system (Applied Biosystems). The primers used for real-time RT-PCR are listed in Supplementary Table 1. The comparative Ct method was used to analyze the relative gene expression. Two independent experiments were performed in duplicate in each experiment. Beta-actin was used as a housekeeping gene for normalization.
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