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6 protocols using gdna digester plus

1

Hypothalamus Total RNA Extraction and qRT-PCR

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Total RNA was extracted from the hypothalamus tissues using Molpure® TissueTotal RNA Kit (YEASEN Biotechnology (Shanghai) Co., Ltd.). In addition, the cDNA was synthesized using a gDNA digester plus (YEASEN Biotech Co., Ltd.). Then, the Hieff UNICON® Universal Blue SYBR Green Master Mix (YEASEN Biotech Co., Ltd.) was used to execute an amplification reaction in Gene-9660 System (Bioer Technology, Hangzhou, China). The amplification conditions were 95°C for 5 min, 40 cycles at 95°C for 10 s, and 60°C for 30 s. Relative fold change was calculated using the −2ΔΔCT method using Gapdh as the control marker. Primer sequences are demonstrated in Supplementary Table 1.
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2

Quantification of AKT3 Transcripts in Aged Mice

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RT PCR for AKT3 transcripts was performed as previously reported [15 (link)]. Total RNA (2 μg) extracted from the hippocampi of aged mice was reverse transcribed to cDNA using the Hifair® III 1st strand cDNA synthesis kit containing gDNA digester plus (Yeasen, China). The hippocampi of mice were injected with the recombinant adeno-associated virus to overexpress circAKT3 (rAAV-hSyn-mmu-circAKT3-nEF1α-EGFP) or the empty vector (rAAV-hSyn-EGFP) to exclude the interference of rAAV injections. Next, cDNA was amplified using 2 × Phanta® Max Master Mix with Dye Plus (Vazyme, China) and common sense primer (5′-GGACTATCTACATTCCGGAAAG-3′) with AKT3 transcript 1 primer (5′-GGTGAAGACCCTTGGCTGGTC-3′) or AKT3 transcript 2 primer (5′-GGGTCTAGATTACTTTTTATTATCATTTTTTTTCCAGTTAC-3′). The primer sequences were synthesized as reported previously [15 (link)]. And the PCR protocol consisted of preliminary denaturation (95 ℃, 3 min), repeated 35 cycles containing denaturation (95 ℃, 15 s), annealing (54 ℃, 15 s) and extension (72 ℃, 30 s), and a further extension at 72 ℃ for 5 min. Afterwards, the Semiquantitative RT-PCR was scored by agarose gel electrophoresis (1%) mixed with GelRed nucleic acid dye (Yeasen, China) and photographed by the ultraviolet imaging system.
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3

Transcriptome Analysis via RT-qPCR

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The TRIzol reagent (Invitrogen, USA) was used for the extraction of total RNA from cells and tissues. A gDNA kit (TransGen Biotech, Beijing, China) was used to isolate gDNA from cells. The reverse transcription reaction utilized 1st Strand cDNA Synthesis SuperMix (gDNA Digester Plus) (Yeasen). For the RT-qPCR, 2 μL of cDNA template was employed with qTOWER3 (link) system (Analytik Jena, Germany) using qPCR SYBR Green Master Mix (Yeasen). GAPDH and U6 were used as internal controls to standardize the transcript levels based on the 2-△△Ct method. Primers employed in this study were synthesized by Sangon Biotech from Shanghai, China (Shanghai, China) (Table S1).
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4

RNA Extraction and Quantitative PCR Analysis

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Total RNA from MC‐3T3 cells was extracted using TRIeasy Total RNA Extraction Reagent, provided by Yeasen Biotechnology in Shanghai, China. This RNA was then converted to cDNA using the Hifair III First‐Strand cDNA Synthesis SuperMix, suitable for quantitative polymerase chain reaction (qPCR) with gDNA digester plus (also from Yeasen). The RT‐qPCR was performed using a CFX96 RT‐PCR Detection System from Bio‐Rad, CA, USA, and the Hieff qPCR SYBR Green Master Mix (Low ROX Plus) by Yeasen. Primer sequences are listed in Table 1. The qPCR cycling protocol was in accordance with the method described by Li et al. (2021). Relative mRNA expression levels were quantified using the comparative 2−ΔΔCt method and normalized against the internal control gene, Glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH).
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5

Total RNA Extraction and RT-qPCR Analysis

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For PCR, 1 ml of Total RNA Extraction Reagent (Shanghai Yeasen Biotechnology Co., Ltd.) was used to extract the total RNA from 100 mg of tissue. The 1st Strand cDNA Synthesis kit, gDNA Digester Plus (Shanghai Yeasen Biotechnology Co., Ltd.) was applied for reverse transcription of total RNA. The reaction program involved heating to 95°C for denaturation and holding at 4°C for 40 cycles (95°C, 15 sec; 55-60°C, 10 sec; 72°C, 20 sec). RT-qPCR was performed using SYBR Green Master Mix (Shanghai Yeasen Biotechnology Co., Ltd.). All procedures were performed according to the manufacturer's protocols. GAPDH was applied to normalize the expression of mRNAs. The experiment was repeated 3 times for each sample. The Ct (threshold cycle) was defined as the number of cycles required for the fluorescence signal to exceed the detection threshold. The 2−ΔΔCq method was used to calculate the differential expression of genes (20 (link)). The related primers are listed in Table SI.
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6

Workflow for Circular RNA Quantification

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Total RNA was extracted using TRIzol reagent (Yeasen Biotech, Shanghai, China). NanoDrop 2000c was used to measure RNA quality. RNase R treatment was performed for 20 min at 37°C using 3 U/mg RNase R (Epicenter Biotechnologies, Madison, Wisconsin, USA). For hsa_circ_0017620, SFMBT2 expression, and KRT5, 500 ng of RNA was reversed transcribed into cDNA using cDNA Synthesis reagents with gDNA digester plus (Yeasen Biotech). For miR‐520a‐5p expression, cDNA synthesis kit (Thermo Fisher, Waltham, MA, USA) was used to detect. Quantitative RT‐PCR was performed with the use of SYBR Green Master Mix (Yeasen Biotech). Primer sequences are shown in Table 1.
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