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20 protocols using β actin

1

Stable WI-38 Cell Line Creation

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WI-38 cells were plated in 96 well plates at 25,000 cells/well. After 24 hours, cells were transfected using NanoJuice Transfection Reagent (Novagen) according to product literature. Cells were transfected with one of three plasmids: pAcGFP1-Actin (β-Actin, #632453, Clontech), pcDNA3-EGFP-RhoA-T19N (dnRhoA, a gift from Gary Bokoch, #12967, Addgene), and pEmGFP-N1 (GFP, a gift from L. E. O. Darling, Wellesley College). Once cells reached 80–90% confluence post-transfection, cells were trypsinized and re-plated at low densities in 6-well plates in WI-38 culture media supplemented with 400 μg/mL Geneticin. After 4–7 days, when positively transfected colonies were visible (based on GFP fluorescence), 3–5 colonies were picked and expanded under antibiotic conditions. Colonies were grown and developed into stable cell lines in the presence of antibiotics.
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2

Measuring ATP Synthesis in 661W Cells

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ATP formation from ADP and inorganic phosphate (Pi) in 661W cells was measured by the luciferin/luciferase chemiluminescent method (Roche Applied Science), as described previously [38] . Cells (5 µg protein) were permeabilized with 0.03 mg/mL digitonin for 1 min, centrifuged for 9 min at 1000 rpm and resuspended in 50 mM Tris HCl (pH 7.4), 5 mM KCl, 1 mM EGTA, 5 mM MgCl 2 , 0.6 mM ouabain, 5 mM KH 2 PO 4 , 5 mM pyruvate and 2.5 mM malate and ampicillin (25 µg/mL). ATP synthesis was induced by adding 0.3 mM ADP.
2.9 β-actin and Mitochondrial Calcium Transfections 0.2 µg of each pAcGFP1-Actin (Clontech Laboratories, USA) and mito-GcaMP2 (Dr. Wang, Peking University) plasmids were used to transfect the cells for β-actin and mitochondrial calcium ([Ca 2+ ] mito ). Cells were transfected using Lipofectamine 2000 (Invitrogen, Germany) according to manufacturer's protocol. 4 h after transfection, complete growth medium was added and left undisturbed until the next morning.
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3

Quantification of Apoptosis-Related Genes

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Total RNA of above 50 μL supernatants was extracted from by using a RNA extraction kit (TaKaRa Biotechnology (Dalian) Co., Ltd., Dalian, China). Specific primers for Bcl-2, bax, and caspase-3 genes were designed and synthesized by TaKaRa (β-actin, forward primer: CACGATGGAGGGGCCGGACTCATC, reverse primer: TAAAGACCTCTATGCCAACACAGT; Bcl-2, forward primer: GGTGAACTGGGGGAGGATTG, reverse primer: GCATGCTGGGGCCATATAGT; bax, F: GGCGATGAACTGGACAACAA, R: CAAAGTAGAAAAGGGCAACC; and Caspase-3, forward primer: GGACCTGTGGACCTGAAAAA, reverse primer: GCATGCCATATCATCGTCAG). Reverse transcription was performed as follows: 42°C, 1 h; 95°C, 5 min. cDNA was used for a multiplex qRT-PCR by using real-time PCR system instrument (Thermo Fisher Scientific, Waltham, MA, USA) and SYBR Green Master Mix (Applied Biosystems, Foster City, CA, USA). RT-PCR reactions were performed under the following conditions: one cycle of 95°C for 5 min, followed by 45 cycles of 95°C for 10 s, 60°C for 15 s, and 72°C for 20 s. β-Actin was used as a control. Fold change was calculated as 2-ΔΔCt.
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4

Quantitative Real-Time PCR for Gene Expression Analysis

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Quantitative real-time PCR (qRT-PCR) was performed with the One-Step PrimeScript RT-PCR Kit (Takara, Japan) according to manufacturer's instructions. Samples were normalized to β-actin (Takara, Japan), as indicated. Primers used for qRT-PCR were:

miR-205 Fw 5′-TGGGCTGAGTCCCTCT-3′

miR-205 Rev 5′-GAGGGACGGGTGATGGGCAGATTGG-3′

CXCL11 Fw 5′- TGCCCAAAGGAGTCCAACAA −3′

CXCL11 Rev 5′- TTTCCGACCAATGGTAGCCT −3′

IL-1α Fw 5′-ACCAC TG TTC TCT TCTCTACCC-3′

IL-1α Rev 5′-TAGGAGGAAGGGAGAAA TCG TG-3′

IL-1β Fw 5′-CAGGATGAGGACCCAAGCAC-3′

IL-1β Rev 5′-GTCGTCATCATCCCACGAGT-3′

IL-8 Fw 5′-TTGGCAGCCTTCCTGATTTC-3′

IL-8 Rev 5′-AACTTCTCCACAACCCTCCTG-3′

IL-6 Fw 5′- TTCGGTCCAGTTGCCTTCT-3′

IL-6 Rev 5′-GTACTCATCTGGACAGCTC-3′

MMP3 Fw 5′- AACAATGGACAAAGGATACAACAGG-3′

MMP3 Rev 5′-CATCTTGAGACAGGCGGAACC-3′

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5

EGFR Gene Expression Quantification

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To detect EGFR gene expression level, cells were harvested after being treated with aX-Td@bsiRNA, free siRNA, and lipo3000@siRNA for 48 h. Total RNA was extracted from cells using RNeasy Mini Kit (QIAGEN, Germany), then reverse-transcribed with HiScript® Q Select RT SuperMix for qPCR (+gDNA wiper) (Vazyme Biotech Co., Ltd., Nanjing, China) to obtain cDNAs. Real-time PCR was performed using SYBR® Premix Ex Taq™ II (Tli RNaseH Plus), ROX Plus (TAKARA, Dalian, China) and amplified with Applied Biosystems Stepone™ (Thermo Fisher Scientific, USA). All samples’ EGFR mRNA expression levels were normalized by β-actin amplification. Primer sequences used for EGFR (forward 5ʹ-AGACGCAGATAGTCGCCCAAAG-3ʹ, reverse 5ʹ-TCCATCAGGGCACGGTAGAAG-3ʹ) were designed and synthesized by TAKARA (Dalian, China). β-Actin (forward 5ʹ-AAATCGTGCGTGACATTAA-3ʹ, reverse 5ʹ-CTCGTCATACTCCTGCTTG-3ʹ)38 (link) was synthesized by TAKARA (Dalian, China).
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6

Quantifying Gli1 Expression in NSCLC Cells

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Total RNA from NSCLC cells was isolated using RNAiso Plus extraction reagent and cDNA was produced using PrimeScript Reverse Transcriptase (Takara Bio, Inc., Otsu, Japan) according to the manufacturer’s instructions. RT-qPCR reactions were then conducted with SYBR Premix Ex Taq II (Takara Bio, Inc.) in 25 μl reactions with 2 μl cDNA and 0.4 μM each of the forward and reverse primers using the following thermocycling conditions: 95°C for 30 sec, 95°C for 5 sec and 60°C for 30 sec. Data was collected over 40 cycles and all expression levels were normalized to β-actin. The following primers were used: Gli1, F 5′-CTG GAC CTG CAG ACG GTT ATC-3′ and R 5′-AGC CTC CTG GAG ATG TGC AT-3′; β-actin, F 5′-TGA CGT GGA CAT CCG CAA AG-3′ and R 5′-CTG GAA GGT GGA CAG CGA GG-3′ (Sangon Biotech Co., Ltd., Shanghai, China).
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7

Quantitative Gene and miRNA Expression Analysis

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Total RNA was extracted using the RNeasy Plus Mini Kit (50) (Qiagen, Hilden, Germany), and miRNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Then, cDNA was synthesized using a PrimeScript RT reagent kit (TaKaRa, Dalian, China). The SYBR Premix Ex Taq II (TaKaRa) was used to amplify the double-stranded cDNA of interest. qPCR primers for miR-520b and U6 were purchased from RuiBo Bio (Guangzhou, China). qPCR primers for GATA6, CREB1 and ACTB (β-actin) were synthesized by TaKaRa (Dalian, China). The levels of U6 and ACTB were used as internal controls for miRNA and mRNA, respectively. The 2–ΔΔCt method was used to determine the relative expression level of RNA between groups. The primer sequences are listed in Supplementary Table S1.
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8

Calreticulin Expression Analysis Protocol

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DATS (98% pure) was purchased from LKT Laboratories, Inc. (Minneapolis, MN, USA). Dulbecco's modified Eagle's medium (DMEM) and fetal bovine serum (FBS) were obtained from Gibco (Thermo Fisher Scientific, Inc., Waltham, MA, USA). Rabbit anti-human polyclonal CRT antibody (cat. no. ab227444) and mouse anti-human polyclonal β-actin antibody (cat. no. ab8227) were purchased from Abcam (Cambridge, UK). Fluorescein isothiocyanate (FITC)-labeled goat anti-rabbit immunoglobulin G antibody (FITC-IgG; heavy and light chain; cat. no. E031220-01) was obtained from EarthOx Life Sciences (Millbrae, CA, USA). Horseradish peroxidase (HRP)-conjugated goat anti-rabbit IgG antibodies (cat. no. sc-2004) were obtained from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA). The primer sequences were as follows: CRT upstream, 5′-TTGGAAGAGATTGGGACT-3′ and downstream, 5′-GCCAAAGTTATCATAGGCATAGA-3′; β-actin upstream, 5′-CTCCCTGGAGAAGAGCTACGA-3′ and downstream, 5′-CGATCCACACGGAGTACTTGC-3′ (Takara Biotechnology Co., Ltd., Dalian, China).
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9

Optimized Primer Design for Gene Expression

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The primers of CpG ODN 2006, β-actin, Nfatc, c-fos, RANK, matrix metalloproteinase 9 (MMP9), and 6-carboxyfluorescein (FAM)-labeled ODN (ODN and phosphorothioate ODN) were synthesized by TaKaRa Bio (Dalian, China), and the sequences are listed in Table 1. These FAM-labeled ODNs shows green signal when excited by blue light. N-Ac-L-Leu-PEI and branched PEI25K (Sigma–Aldrich, St. Louis, USA) were provided by the School of Life Sciences, Jilin University (Jilin, China). The PrimerScript® RT reagent kit and SYBR Green Premix Ex Taq kit were purchased from TaKaRa Bio (Dalian, China). Antibodies to Nfatc, c-fos, RANK, MMP9, β-actin, and horseradish peroxidase (HRP)-conjugated goat anti-rabbit secondary antibodies were all purchased from ABclonal (Boston, MA, USA). The RAW264.7 cells (SCSP-5036) were purchased from the cell bank at the Chinese Academy of Sciences (Shanghai, China).

The Primer Sequences of CpG ODN 2006, β-Action, Nfatc, c-fos, RANK and MMP9

NameSequence
20065ʹ-TCGTCGTTTTGTCGTTTTGTCGTT-3’
β-actin5ʹ-CATCCGTAAAGACCTCTATGCCAAC-3ʹ5ʹ-ATGGAGCCACCGATCCACA-3’
Nfatc5ʹ-CAAGTCTCACCACAGGGCTCACTA-3ʹ5ʹ-TCAGCCGTCCCAATGAACAG-3’
c-fos5ʹ-ACGTGGAGCTGAAGGCAGAAC-3ʹ5ʹ-AGCCACTGGGCCTAGATGATG-3’
RANK5ʹ-GGCTTACCTGCCCAGTCTCATC-3ʹ5ʹ-AAGCATCATTGACCCAATTCCAC-3’
MMP95ʹ-GCCCTGGAACTCACACGACA-3ʹ5ʹ-TTGGAAACTCACACGCCAGAAG-3’
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10

Western Blot Analysis of Apoptosis Markers

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The cells were digested with trypsin, washed three times with PBS solution, added with an appropriate amount of protein extract (Beijing Soleibo Technology Co., Ltd., China), and shaken in an ice bath for 15 min. After centrifugation (10,000 × g, 4°C) for 20 min, the supernatant was collected and aliquoted into EP tubes, followed by protein purity determination via the BCA kit (Abcam, USA) method. Afterward, 30 μg of protein was subjected to SDS–PAGE (Thermo Fisher, USA) and transferred onto a PVDF membrane (Sigma–Aldrich, USA), followed by 2 h of immersion in 5% skim milk and subsequent overnight incubation with antibodies against Bax (1 : 1000), Caspase-3 (1 : 1000), and β-actin (1 : 1000) (TaKaRa, Japan) at room temperature. The next day, the membranes were washed three times with TBST, followed by a 1 h incubation with the secondary antibody (1 : 2000). Subsequently, the membranes were also washed three times with TBST, followed by exposure and development. A gel imaging system (iBright, Thermo Fisher, USA) and the ImageJ software (National Institutes of Health) were used to analyze the gray value and calculate the relative protein expression.
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