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23 protocols using quantitative real time pcr kit

1

RNA Isolation and Real-Time qPCR Analysis

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Total RNA isolation was carried out using the RNA Purification Kit (Yi Shan Biotechnology Company, Shanghai, China). The complementary DNA (cDNA) was synthesized and amplified with the reverse transcription kit (Takara, Osaka, Japan). A quantitative real-time PCR kit (Takara, Osaka, Japan) was used to prepare cDNA from various cell samples, along with GAPDH as an internal control, and specific primers were used for amplification (NRF2: forward 5′-TCTGCCAACTACTCCCAGGT-3′ and reverse 5′- AATGTCTGCGCCAAAAGCTG -3′; P62: forward 5′-CCCTCTCCCAGATGCTGTCCAT-3′ and reverse 5′-G CCGCTCCGAT GTCATAGTTCT-3′; Keap1: forward 5′-CGTGGCTGTCCTCAATCGTCTC-3′ and reverse 5′-CGCTTCGGATGGTGTTCATTGC-3′; GAPDH: forward 5′-CAAATTCCATGGCACCGTCA-3′ and reverse 5′-AGCATCGCCCCACTTGATTT-3′).
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2

Resveratrol Modulates PI3K/Akt Signaling

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Resveratrol (purity > 99%) was obtained from Nanjing Spring & Autumn Biological Engineering Co., Ltd. (Nanjing, China). PI3Kp85, phospho-PI3Kp85 (Tyr458), Akt, phospho-Akt (Ser473), phospho-PKD1 (Ser916), c-Myc, and Cav-1 antibodies were purchased from Cell Signaling Technology Inc. (Beverly, MA, USA). PKD1 was from Novus (Novus Biologicals, Littleton, Colorado). Klf5 antibody was obtained from Abcam (Cambridge, MA, USA). The phosphoserine antibody was purchased by Santa Cruz Biotechnology Inc. (Santa Cruz, USA). GAPDH antibodies were purchased from proteintech (Wuhan, China). Trizol was from Invitrogen Inc. (Carlsbad, CA, USA). Reverse transcription reaction Kit was from Toyobo Co.Ltd. (Osaka, Japan) and quantitative Real-time PCR kit was purchased from TAKARA Bio Inc. (Otsu, Shiga, Japan). All other chemicals were of the highest grade commercially available.
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3

Quantifying mRNA Expression in SW982 Cells

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Upon reaching an 80 percent density within 6-well plates post lentivirus infection over 6 days, SW982 cells were harvested and thrice rinsed with PBS. Subsequent extraction of total RNAs was performed employing TRIzol reagent (Invitrogen, US), following the manufacturer’s instructions. The reverse transcription process was aided by the Prime ScriptTM RT reagent kit (Takara, China) to procure a single cDNA strand. mRNA quantification was then achieved via a Quantitative Real-Time PCR kit utilizing SYBR master mixture (DRR041B, Takara, China). The PCR reaction mixture (20 μl) included: 10 l SYBR PremixEx Taq (2), 0.8 μl Forward primers (10 μM), 0.8 μl Reverse primers (10 μM), 2 μl cDNA, 0.4 μl ROX Reference Dye (50×), as well as 6.0 μl ddH2O. The following procedure parameters were established: 95 °C for five seconds, then 60 °C for thirty seconds (for a total of 40 cycles), followed by a holding period at 4 °C. The 2−ΔΔCT approach determined the fold changes in mRNA expression, with experimental outcomes being assessed in relation to GAPDH normalization. The sequences of the primers are shown in Appendix 1.
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4

Regulation of STAT3 Signaling and Apoptosis

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The restriction enzymes were obtained from New England Biolabs (Beijing, China). p-nitrophenyl α-D-galactopyranoside, guggulsterone, CDCA, yeast nitrogen base without amino acids, dimethyl sulfoxide (DMSO) and glucose were all purchased from Sigma (Shanghai, China). The dropout supplement free from leucine and tryptophan (-Leu/-Trp DO supplement) and quantitative real-time PCR kit were bought from Takara (Dalian, China). Dulbecco's modified Eagle's Medium (DMEM) and fetal bovine serum (FBS) was from Gbico (Shanghai, China). 293Fect was purchased from Pregene (Beijing, China). Dual-Luciferase Reporter Assay System was obtained from Promega (Beijing, China). RNA extraction reagent and reverse transcription kit were purchased from Toyobo (Shanghai, China). Rabbit anti-phosphorylated-STAT3, rabbit anti-total-STAT3 and caspase9 were from Bioworld Technology, Inc (Nanjing, China). GAPDH antibody was obtained from Kangcheng Bio-tech (Shanghai, China). All NSAIDs were purchased from Sigma.
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5

Gene Expression Analysis by qRT-PCR

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Hierachization clustering analysis (conducted by MEV version 4.9.0) was used to visualize the variance of different individual samples for all DEGs. To validate the gene expression profiling result, quantitative real-time PCR was performed to analyze several selected genes expression. Total RNA was used synthesize cDNA using a Kit (CWbio, Beijing, China). With the synthesized cDNA of each sample, ABI 7500 Real-Time PCR system (Applied Biosystems, Foster City, CA, USA) and a quantitative real-time PCR kit (Takara, Japan) were used. The primers used in this experiment were listed in (Supplementary Table S8). GAPDH was used as an endogenous control. Relative gene expression level was calculated by 2−ΔΔCt method51 (link). Student t-test was used to test hypotheses.
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6

Quantifying Ferroptosis-Related Gene Expression

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Total RNA was isolated from intestinal tissues with TRIzol (Invitrogen, USA) and then reverse transcribed into cDNA using a reverse transcription kit (TaKaRa, Japan). With GAPDH as internal control, the relative mRNA expression of the ferroptosis-related genes ACSL4 and IREB2 was detected using a quantitative real-time PCR kit (TaKaRa, Japan). The primer sequences of the target genes were as follows: ACSL4, forward 5′-TTGTATTGCTGCCTGTCCACTTGTT-3′ and reverse 5′-ATTCTCTTTGCCATAGCGTTTTTCT-3′; IREB2, forward 5′-ATTCTGCCTTACTCAATACGGGTCC-3′ and reverse 5′-ATTGCTTTGTTTGGTTTTCCAGTCC-3′; GAPDH, forward 5′-CGTGTTCCTACCCCCAATGT-3′ and reverse 5′-TGTCATCATACTTGGCAGGTTTCT-3′.
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7

Quantifying mRNA levels in mouse tissues

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Total RNA in tissues(cells number: 2x106) was extracted using TRIzol® reagent (Thermo Fisher Scientific, Inc.). The first-stand cDNA was synthesized using First Strand cDNA Synthesis kit with gDNA Eraser according to the manufacturer's protocol. PCR was performed using cycling conditions: Denaturation 95˚C for 30 sec, annealing 60˚C for 40 sec and extension at 72˚C for 60 sec; 35 cycles) (Takara, Osaka, Japan). RT-qPCR was performed with SYBR Green Master Mix to examine the relative mRNA levels of indicated genes with an AJ qTOWER 2.2 Real-Time PCR system (Analytik Jena AG) by using a quantitative real-time PCR kit (Takara Bio, Inc.). Sequences for RT-qPCR primers were: Mouse Cpt1a, 5'-CTCCGCCTGAGCCATGAAG-3', mouse GAPDH: 5'-AGGTCGGTGTGAACGGATTTG3'. GAPDH was used as an internal control. Relative gene expression level was calculated by 2-ΔΔCq method (10 (link)).
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8

Quantification of RyR1 and RyR3 mRNA

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Cells used for total RNA extraction obtained from 3 separate experiments (different batches of cells and on different days). Total RNA was extracted from cells using HiPure Total RNA Mini Kit (Magen, Beijing, China), and then reverse-transcribed into cDNA using a PrimeScript™ RT reagent Kit with gDNA Eraser (Takara, Osaka, Japan). Synthesized cDNA was used for RT-qPCR analysis by employing a quantitative real-time PCR kit (Takara, Osaka, Japan) with an AJ qTOWER 2.2 Real-Time PCR system (Analytik Jena AG, Jena, Germany) according to standard procedures. All samples were measured in triplicate. The primers used in the experiment were listed in Table S1. To compare the mRNA expression of RyR1 and RyR3 in cells, the amplification efficiency of their primers was used to rectify the qRT-PCR cycle number. GAPDH (glyceraldehyde-3-phosphate dehydrogenase) was used as an internal control. Relative gene expression level was calculated by 2−ΔΔCt method [31 (link)].
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9

Huh-7 Cell Line Hepatocellular Carcinoma Protocol

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Hepatocellular carcinoma cell line (Huh-7) (Cell repository, National Centre for Cell Science, Pune, India), DMEM complete growth media (D5796, Sigma Aldrich, USA), fetal bovine serum (F2442, Sigma Aldrich, USA), trypsin-EDTA (T4049, Sigma Aldrich, USA), antibiotic-antimycotic (P4333, Sigma Aldrich, USA), gentamycin sulphate (G13970, Sigma Aldrich, USA), phosphate buffered saline (P3813, Sigma Aldrich, USA), acridine orange (A6014, Sigma Aldrich, USA), TRIzol reagent (162710, Invitrogen, USA), chloroform (AS039, Himedia, India), analytical grade ethanol (Hayman, UK), isopropanol (00270, Lobachemie, India), and quantitative real-time PCR kit (RR086A, TaKaRa, Japan) were the materials and reagents used in this study.
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10

Huh-7 Cell Line Hepatocellular Carcinoma Protocol

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Hepatocellular carcinoma cell line (Huh-7) (Cell repository, National Centre for Cell Science, Pune, India), DMEM complete growth media (D5796, Sigma Aldrich, USA), fetal bovine serum (F2442, Sigma Aldrich, USA), trypsin-EDTA (T4049, Sigma Aldrich, USA), antibiotic-antimycotic (P4333, Sigma Aldrich, USA), gentamycin sulphate (G13970, Sigma Aldrich, USA), phosphate buffered saline (P3813, Sigma Aldrich, USA), acridine orange (A6014, Sigma Aldrich, USA), TRIzol reagent (162710, Invitrogen, USA), chloroform (AS039, Himedia, India), analytical grade ethanol (Hayman, UK), isopropanol (00270, Lobachemie, India), and quantitative real-time PCR kit (RR086A, TaKaRa, Japan) were the materials and reagents used in this study.
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