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5 protocols using ribospin 2 kit

1

Maturation and Injury Assessment of hCO

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To characterize hCO maturation total RNA was extracted from NPC and from hCO
after 14 or 60 days in vitro (DIV). To assess OGD effects on hCO, samples were
collected three days after injury, immediately frozen on dry ice and stored at
−80°C until analysis. Total RNA was extracted with a Quiagen kit or Ribospin II
kit (GeneAll). Samples were treated with DNase (Life Technologies) and
reverse-transcribed with random hexamer primers using Multi-Scribe Reverse
Transcriptase (Life Technologies). Real-time reverse transcription PCR was done
with b-actin as housekeeping gene. Relative gene expression was determined by
the ΔΔCt method using mean Ct from three replicates per sample. Data are
expressed as the log 2-fold difference over the NPC or CTRL groups. Genes and
primer sequences are listed in Table 1.
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2

Comprehensive RT-qPCR Analysis of Injury Response

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Total RNA was extracted from the cortex with a Ribospin II kit (GeneAll, #314-103). Samples were reverse transcribed with random hexamer primers using Multi-Scribe Reverse Transcriptase (Life Technologies). Real-time reverse transcription PCR was done with RPL27 as the housekeeping gene. Relative gene expression was determined by the ΔΔCt method [19 (link)]. Data are expressed as the log2-fold difference compared to the control group. Genes and primer sequences are listed in Additional file 1: Table S2. The exploratory analysis included the following genes: microtubule-associated protein 2 (MAP2); glial fibrillary acid protein (GFAP); cluster of differentiation molecule 11ß (CD11ß); platelet and endothelial cell adhesion molecule 1 (PECAM-1); caspase 3 and 8 (CASP-3 and CASP-8), and heme oxygenase 1 (HO-1). These genes were chosen to provide a representative picture of the tissue reaction to the injury from multiple viewpoints, including structural cellular integrity, inflammation, apoptosis, endothelial function, and oxidative stress.
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3

Quantification of XylB Gene Expression

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XylB transcripts were measured by quantitative PCR (qPCR) using rpoA as a reference. The total RNA of the VXA38D and VXA38C strains in the mid-log phase were extracted using a Ribospin II kit (GeneAll, Seoul, Korea). Complementary DNA of rpoA and xylB mRNA for each sample was synthesized using M-MLV Reverse Transcriptase (Elpis-Biotech, Daejeon, Korea) and rpoA_RT_R and xylB_RT_R primers. qPCR was performed in technical triplicates using TOPreal™ qPCR 2 × PreMIX (SYBR Green with high ROX) (Enzynomics, Daejeon, Korea) and rpoA_RT_F/R and xylB_RT_F/R primer sets, designed to amplify 200 bp regions of each gene (Additional file 1: Table S10). A StepOnePlus Real-time PCR system (Applied Biosystems, Foster City, CA, USA) was used for amplification and signal detection. To determine the relative transcript amount, the comparative CT method (2−ΔΔCT) was utilized [71 (link)].
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4

Quantitative RT-PCR Analysis of RNA Extraction

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Total RNA was extracted from cells that were pretreated with SA (100, 200, and 400 μM) followed by treatment with 50 μM of 6-OHDA using the Ribospin™ II kit (GeneAll Biotechnology Co., LTD, Seoul, Korea). After measuring the total RNA concentration using a UV/Vis Nano Spectrophotometer (MicroDigital Co., Ltd., Sungnam, Korea), 1 μg of total RNA from each group was reverse transcribed to synthesize cDNA using the GoScript Reverse Transcription System Kit (Promega Co., Madison, WI, USA). qRT-PCR was performed using a TaKara Thermal Cycler Dice Real-Time System (Takara Bio. Inc., Shiga, Japan) using the TOPreal™ qPCR 2× PreMIX Kit (Enzynomics Co., Daejeon, Korea). The primer sequences are as shown in Table 1.
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5

Copper Modulation of Mitochondrial Biogenesis

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Total RNA was isolated from the cells treated with 500 μM H2O2 alone or pretreated with 0.1, 0.5, and 1 μM Cu I followed by treatment of 500 μM H2O2 for 24 h by using a Ribospin™ II kit (GeneAll Biotechnology Co., LTD, Seoul, Korea). To examine the expression levels of mitochondrial biogenesis genes, 1 μg total RNA from the cells in each group was reverse transcribed into cDNA using ImProm II reverse transcriptase (Promega Co., Madison, WI, USA) with oligo-dT priming. qRT-PCR was performed using a Takara Thermal Cycler Dice Real-Time System (Takara Bio. Inc., Shiga, Japan) with SYBR Green (Takara) as a fluorescent dye. The primer sequences were as follows: peroxisome proliferator-activated receptor α (PPARα), forward 5′-GGC AAT GCA CTG AAC ATC GAG-3′ and reverse 5′-GCC GAA TAG TTC GCC GAA AG-3′; peroxisome proliferator-activated receptor γ coactivator- (PGC-) 1β, forward 5′-GTG AGA TAG TCG AGT GCC AGG TG-3′ and reverse 5′-TTC TCA GGG TAG CGC CGT TC-3′; estrogen-related receptor α (ERRα), forward 5′-GCT GAA AGC TCT GGC CCT TG-3′ and reverse 5′-TGC TCC ACA GCC TCA GCA T-3′; nuclear respiratory factor- (NRF-) 1, forward 5′-CAC TCT GGC TGA AGC CAC CTT AC-3′ and reverse 5′-TCA CGG CTT TGC TGA TGG TC-3′; and 18S, forward 5′-TTC TGG CCA ACG GTC TAG ACA AC-3′ and reverse 5′-CCA GTG GTC TTG GTG TGC TGA-3′.
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