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8 protocols using qpcr master mix

1

Quantifying nWASP Transcripts in Tissue Samples

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Total RNA was isolated from the homogenized tissues (150 pairs of specimens) or from cultured cells using Total RNA Isolation Reagent (ABgene™). Reverse transcription was performed using the Reverse Transcription kit (Primer design). QPCR was performed on the Icycler IQ5 system (Bio-Rad, Hammel Hemstead, UK) to quantify the level of nWASP transcripts in the samples (shown as copies/μl from internal standard normalised to actin). The QPCR technique utilised the Amplifluor system™ (Intergen Inc., England) and QPCR master mix (BioRad). nWASP QPCR primers: Forward: 5’AGTCCCTCTTCACTTTCCTC’3 and Reverse: 5’ACTGAACCTGACCGTACAACATCTCTGTGGATTGTCCT’3. Real-time QPCR conditions were 95 °C for 15 min, followed by 60 cycles of 95 °C for 20 s, 55 °C for 30 s and 72 °C for 20 s. nWASP transcript expression was then analysed and correlated with patient’s pathological and clinical information.
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2

Quantitative RT-PCR Protocol for Gene Expression

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For all qPCR experiments 2 µg of purified RNA was converted to cDNA using a cDNA synthesis kit (ABI). cDNA was then subjected to Taqman Real-Time qPCR using the cognate probes, qPCR master mix (Biorad) and PCR conditions as per the manufacturer's instructions (Invitrogen).
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3

qPCR Quantification of POLQ Knockdown

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Cellular RNA was extracted using the Direct-zol RNA Microprep kit. mRNA was reverse transcribed using the GoScript Reverse Transcription kit and qPCR was performed using GoTaq qPCR Master Mix and previously-published anti-POLQ qPCR primers41 (link) by a Bio-Rad CFX 96 C1000 real-time PCR instrument. The cycling parameters used were: (1) 95°C for 3 min, (2) 95°C for 10 s, (3) 64°C for 30 s, (4) 72°C for 40 s, with steps 2 to 4 repeated for 40 cycles. The fold change knock-down of POLQ mRNA was calculated relative to the non-targeting control using the ΔΔCq method as described.77 (link) The non-coding 18S rRNA was used as an internal control.
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4

qPCR Analysis of XBP1 Expression

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For qPCR, β-cells were lysed, and mRNA was harvested as previously described [105 (link)]. qPCR was performed using the Life Technologies Quant Studio 6 Detection System and Software (Thermo Fisher), using SYBR green primers and qPCR master mix (Bio-Rad, Hercules, CA, USA), as previously described [105 (link)] for Total XBP1, sXBP1, and PPIA. Relative mRNA levels for Total XBP1 and sXBP1 were calculated using the Delta CT method, with PPIA being used as a housekeeping gene. Sequences are available upon request.
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5

Quantifying NOD1 and TLR4 Expression

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Total RNA of lung tissues from the above treated mice was extracted via Invitrogen Trizol (Carlsbad, USA) following the protocol of manufacturer. 1 μg RNA was reversely transcribed into cDNA by using the M-MLV reverse transcriptase (Promega, Madison, USA). The Bio-Rad qPCR Master Mix (Hercules, USA) was used to conduct qRT-PCR on the 7500 Real-Time PCR system. GAPDH were used to normalize the expression level of NOD1 and TLR4. The relative expression levels of NOD1 and TLR4 were calculated by using the 2−ΔΔCT method. Primers were listed below: NOD1: Forward: 5’-AGGAGGCCAACAGACGCC-3’, Reverse: 5’-CTGACCTAGAGGGTATCG-3’; TLR4: Forward: 5’-AGCTCCTGACCTTGGTCTTG-3’, Reverse: 5’- CGCAGGGGAACTCAATGAGG-3’. GAPDH: Forward: 5’-CATCACTGCCACCCAG AAG ACTG-3’, Reverse: 5’-ATGCCAGTGAGCTTCCCGTTCAG-3’.
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6

Transcriptional Analysis of Co- and Mono-Cultured Samples

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The transcriptional expression level of the genes in co- and mono-cultured systems at different sampling times was evaluated by qPCR. All the data were normalized to 16S rDNA of each species. The entire RNA was extracted from the samples with the ApexPrep RNA Miniprep Kit (APExBio). HiTaq EvaGreen qPCR MasterMix (APExBio) was used and the quantitative PCR reactions were performed on a CFX96 real time PCR system (Bio-Rad) with a total volume of 20 μL containing diluted cDNA (2 μL), qPCR MasterMix (10 μL),and forward primer and reverse primer (0.8 μL).
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7

Quantitative RT-PCR Analysis of Psoriasin

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TRIzol Reagent (Sigma-Aldrich; Merck KGaA) was used for total RNA extraction and cDNA was synthesised using iScript cDNA Synthesis kit (Bio-Rad Laboratories, Inc.). REDTaq ReadyMix PCR reaction mix (primer sequences presented in Table I) was utilised for PCR under the following cycling conditions: 95°C for 5 min, followed by 36 cycles at 95°C for 30 sec, 55°C for 30 sec, 72°C for 40 sec and a final extension at 72°C for 10 min.
qPCR of BC cell cDNA samples was performed using the Icycler IQ5 system (Bio-Rad Laboratories, Inc.), the Amplifluor system (Intergen, Inc.) and qPCR Mastermix (Bio-Rad Laboratories, Inc.) to identify Psoriasin transcript expression, along with standards and negative controls. Psoriasin primers were designed using Beacon design software (Premier Biosoft International), with additional Z sequence (5′-ACTGAACCTGACCGTACA) on the reverse primer complementary to the universal Z probe (Intergen, Inc.). Reaction conditions were as follows: 95°C for 12 min, followed by 90 cycles at 95°C for 15 sec, 55°C for 40 sec and 72°C for 20 sec.
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8

Quantification of Lung Inflammatory Markers

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Total RNA was isolated from the lung tissue of 27 pups (9 in each group) using TRIzol reagent (Invitrogen, Carlsbad, California). Using 1 µg of RNA, reverse transcription was completed using qScript cDNA SuperMix (Quanta Biosciences, Gaithersburg, Maryland) and S1000 Thermal Cycler (Bio-Rad Laboratories, Hercules, California). qRT-PCR was performed using advanced qPCR Master Mix and CFX384 Real-Time System (Bio-Rad Laboratories, Hercules, California). The primers used were as follows: NLRP3 (forward: CCCTTGGACCAGGTTCAGTG, reverse: AGACTTGAGAAGAGACCACGGC), Il-1β (forward: AGTGTGGATCCCAAGCAATACCCA, reverse: TGTCCTGACCACTGTTGTTTCCCA), TLR4 (forward: GCTCCTGGCTAGGACTCTGA, reverse: TGTCATCAGGGACTTTGCTG), and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (forward: GGGGTCCCAGCTTAGGTTCAT, reverse: CGAAGGTGGAAGAGTGGGAG). CFX Manager 3.1 (Bio-Rad Laboratories, Hercules, California) was used to analyze data. Expression levels were normalized to the reference housekeeping gene GAPDH.
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