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Sybr fast qpcr master mix

Manufactured by Roche
Sourced in United States, China

SYBR FAST qPCR Master Mix is a ready-to-use solution for quantitative real-time PCR (qPCR) experiments. It contains all the necessary components, including a fast-acting DNA polymerase, buffer, and SYBR Green I dye, to facilitate efficient and sensitive qPCR reactions.

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91 protocols using sybr fast qpcr master mix

1

RNA Isolation and qPCR Analysis

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RNA isolation and cDNA preparation were performed as previously reported [27 (link)] except either five (for saa, mpx, and il1b primers) or 18 (for mmp9 and tnfα primers) dissected intestines were pooled. RNA was harvested by homogenizing and extracting with Trizol reagent (Invitrogen). Contaminating genomic DNA was eliminated using the Turbo DNA-free kit (Ambion) per manufacturer’s instructions. The RNA (100 ng for saa, mpx, and il1b primers; 320 ng for mmp9 and tnfα primers) was used as templates for generating cDNA with Superscript III Reverse Transcriptase and random primers (Invitrogen) following manufacturer’s instructions. The cDNA was measured in a qPCR reaction with SYBR Fast qPCR master mix (Kapa Biosystems). Assays were performed in triplicate using ABI StepOne Plue RealTime. Data were normalized to elfa and analyzed using ΔΔCt analysis. Sequences and annealing temperatures are presented in S1 Table.
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2

RNA Extraction and qPCR Analysis

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RNA extraction was conducted using the NucleoSpin RNA Plus RNA purification kit (Macherey-Nagel, Düren, Germany). RNA samples were stored at −80 °C, and RNA integrity was tested with bleach agarose gel [111 (link)]. cDNA was synthesized using the PrimeScript™ 1st strand cDNA Synthesis Kit (Takara Bio USA, San Jose, CA, USA). Real-time quantitative PCRs (qPCRs) were performed in duplicates using 5 ng of cDNA per reaction amplified by SYBR FAST qPCR Master Mix (KK4602, Kapa Biosystems, Wilmington, MA, USA) in a StepOne™ Real-Time PCR System (Applied Biosystems™, Warrington, UK) and a 7500 Fast Dx Real-Time PCR Instrument (Applied Biosystems™, Warrington, UK). CYLD qPCR primers recognize a region from exon 2 to exon 3 (spanning from 645 to 753, transcript NM_173369.3). The complete list of primer sequences can be found in Table S1.
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3

Adipose and Liver RNA Extraction and qPCR

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Total RNA of epididymal adipose tissue and liver were isolated using the RNeasy Lipid Mini kit (QIAGEN), and cDNA was synthesized using Superscript®II Reverse Transcriptase kit (Thermo Fischer Scientific, Waltham, MA). The mRNA expression levels of genes were analyzed using a Real-Time PCR system (Bio-Rad, Hercules, CA) and the SYBR FAST qPCR Master Mix (Kapa Biosystems, Wilmington, MA). Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was used as a reference gene. Relative gene expression levels were calculated using the 2−ΔΔCt method. The sequence of the primers used in this study is shown in Table 1.
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4

Quantification of Bacteroidetes Species

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Cells were harvested by centrifugation for quantification. DNA was isolated using a DNeasy blood and tissue kit according to the manufacturer’s instructions (Qiagen). DNA (10 ng) was assayed in duplicate in a Mastercycler EP Realplex system (Eppendorf) using SYBR Fast qPCR master mix (Kapa Biosystems, Inc., Wilmington, MA) and species-specific primers for 40 cycles of 95°C for 3 s, 55°C for 20 s, and 72°C for 8 s. Species-specific primers used for B. ovatus and B. thetaiotaomicron were BACOVA03426 and BT3854, respectively (Table S2). Purified genomic DNA standards (range, 80, 20, 2, 0.4, 0.08, and 0.01 ng) of each species were included in duplicate in each qPCR run. A standard curve generated from these standards was used to calculate the relative abundances of species in each sample.
See Text S1 for descriptions of other experimental procedures used in our study.
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5

Immunoprecipitation of PARP1-associated Proteins

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The immunoprecipitation of selected proteins likely associated with PARP1 promoter was carried out according to Saccani Nat. Immunol. 3, 69–75 (2002). In brief, cells were cross-linked with 1% formaldehyde solution, isolated chromatin was sheared with the ultrasonic homogenizer Bandelin Sonopuls (HD 2070). After overnight incubation with antibody-conjugated magnetic beads (Dynabeads Protein G) the immunoprecipitated chromatin was washed and decrosslinked overnight at 65 °C. The DNA was isolated with phenol:chlorophorm:isoamyl alcohol and analyzed with real-time PCR. The immunoprecipitated fragment of DNA, which spans PU.1 binding site was quantified with Kapa Sybr Fast qPCR Master Mix, while GC rich fragment spanning SP1/E2F binding sites was quantified with KAPA HiFi™ HotStart ReadyMix supplemented with EvaGreen® Dye and 7% DMSO. The list of primers used for PARP1 promoter are listed in Suppl. Table 1.
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6

Quantifying Chicken TUFM Knockdown

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Because anti-TUFM antibody was incapable of recognizing chTUFM expressed in DF-1 cells, the knockdown efficiency of si-chTUFM-1 and si-chTUFM-2 was evaluated by quantitative reverse transcription (qRT)-PCR instead of Western blotting. The first-strand cDNA synthesis was reverse transcribed with oligo(dT) and then subjected to qPCR with specific forward (TGGGCATGCTGACTACGTTAAG; nt 327 to 348) and reverse (TTCACATACACCACCACGTGC; nt 465 to 485) primers of chTUFM. Reactions were prepared with SYBR fast qPCR master mix (KAPA). PCR was performed on the LightCycler 480 (Roche) in the default run mode with SYBR green I. Chicken GAPDH (primers CATCATCCCAGCGTCCA and AGCACCCGCATCAAAGG; 283 bp) was used as a reference.
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7

Quantitative PUL Expression Analysis

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PUL expression analyses were performed as previously described (24 (link)). Briefly, cells were harvested by centrifugation of the aliquots at 13,000 rpm for 10 min; cells were then treated with RNAprotect (Qiagen) and stored at −80°C until further processing. Total RNA was extracted from cells using an RNeasy minikit (Qiagen) and treated with Turbo DNase I (Ambion). Reverse transcription was performed using SuperScript III reverse transcriptase (Invitrogen) according to the manufacturer’s instructions. cDNA quantification was performed with a Mastercycler EP Realplex system (Eppendorf) using SYBR Fast qPCR master mix (Kapa Biosystems, Inc., Wilmington, MA) for 40 cycles of 95°C for 3 s, 55°C for 20 s, and 72°C for 8 s. All transcript levels were normalized based on 16S rRNA abundance, and transcript levels at time zero were used as references. Primers used are given in Table S2; they targeted previously validated sentinel susC-like genes, as previously reported (21 (link)).
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8

Quantitative RT-PCR Gene Expression Analysis

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cDNA was synthesized with the cDNA synthesis kit (Bio-Rad, Cat# 1708890). qRT-PCR was performed using a Roche LC480 Real-time PCR machine and SYBR Fast qPCR master mix (Kapa Biosystems) as described (Iskusnykh et al., 2021 (link)). Gene expression was normalized to that of the reference gene Gapdh. All samples were tested in triplicate using the primers listed in Table 1.
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9

Quantitative Real-Time PCR Analysis

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Cells of the wild type strain XL280 and the indicated strains were cultured in YPD liquid medium at 30°C for 16 hr. Three biologically replicates were used. Total RNA samples were extracted using the PureLink® RNA Mini Kit (Life Technology) and their integrity was confirmed with RNA gel electrophoresis. Each RNA sample (8 μg) was treated with DNase (TURBO DNA-free™) according to the manufacture’s instruction. DNase-treated RNA samples were used as templates in the synthesis of the first strand cDNA using GoScript™ Reverse Transcription System (Promega) per the instruction from the manufacture. The resulting cDNA products were diluted to 8 ng/μl and 2 μl was used as template for quantitative real-time PCR (qRT-PCR). qRT-PCR was performed using the SYBR FAST qPCR master mix (KAPA Biosystems, Wilmington, MA) on a realplex2 instrument (Eppendorf). The house-keeping gene TEF1 was used as the internal control for each sample to normalize the gene transcript level as we described previously (Chacko et al., 2015 (link)). The relative levels of transcripts were quantified using the ΔΔCt method as we described previously (Wang et al., 2014 (link); Wang et al., 2012 (link)). We used One-Way ANOVA for multiple comparison and P values ≤ .05 were considered statistically significant. Primers for qRT-PCR are included in the Supplemental Table 2.
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10

Quantitative analysis of gene expression

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Total RNA was isolated using Trizol reagent (Invitrogen) and cDNA prepared using Reverse Transcriptase and Oligo-dT primers (Promega). Quantitative PCR done using SYBR FAST qPCR master mix (Kapa Biosystems) in BioRad CFX96 Real Time System. Primers used are listed in supplementary text.
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