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5 protocols using superscript 3 first strandsynthesis system supermix

1

Isolation and Characterization of Murine Nucleic Acids

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Genomic DNAs were extracted from peripheral blood specimens of PL mice using the DNeasy Blood & Tissue kit (Qiagen, Valencia, CA), according to the manufacturer’s protocol.
For RNA extraction, brain, heart, liver, lung, spleen, kidney, intestine, skin, testis, thymus, and bone marrow were obtained from euthanized PL mice, submerged in the RNALater RNA stabilization reagent (Qiagen), and subjected to total RNA extraction using the RNeasy Mini kit (Qiagen) with DNase, following the manufacturer's instruction. Extracted total RNA was applied for first-strand cDNA synthesis using the SuperScript III First-Strand Synthesis System SuperMix (Invitrogen, Carlsbad, CA), according to the manufacturer’s protocol.
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2

Quantification of Adenosine Receptor Subtypes

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Adenosine receptor subtype (A1,
A
2A, A2B, and
A
3), was assayed by quantitative PCR (qPCR) in IEC-6,
HCT-8, or in mouse cecum epithelial cells. Purified TcdA and TcdB were provided
by David Lyerly from TECHLAB, Inc. (USA). Each sample was suspended in 350 μL of
RLT lysis buffer and the RNA was extracted using Qiagen RNeasy mini kit (USA),
according to manufacturer's instructions. RNA was quantified by standard
spectrophotometry (Biophotometer, Eppendorf, Germany). In order to remove the
genomic DNA carried over from RNA extraction, DNase I (Ambion, USA) treatment
was performed following the manufacturer's instructions. Synthesis of cDNA by
reverse transcriptase PCR was performed using SuperScript III First-Strand
Synthesis System SuperMix (Invitrogen, USA) with the use of oligo (dT) as
primers. cDNA was used in quantitative PCR for measuring A1,
A
2A, A2B, and A3
expression compared to GAPDH expression. The Invitrogen Fast SYBR green
cells-to-CT one-step kit was used according to the manufacturer's instructions,
as previously described (26 (link)). The
relative gene expression was determined using the 2−ΔΔCt (25 (link)) method using GAPDH as the housekeeping gene.
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3

Quantification of IGF-1 and BCL-2 Expression

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Samples were taken immediately from necropsied animals and frozen in liquid nitrogen.
After freezing, the samples were stored at -80°C until analysis. Samples were thawed
and total RNA was extracted using Qiagen RNeasy mini kit (QIAGEN Biotecnologia Brasil
Ltda, Brazil) according to the manufacturer's instructions. RNA concentration was
quantified and checked spectrophotometrically (Biophotometer; Eppendorf, Germany) for
purity by UV absorbance at 260 nm and 280 nm (A260:280 ratio). Synthesis of cDNA by
reverse transcriptase PCR was performed using the SuperScript III First-Strand
Synthesis System SuperMix (Invitrogen, Life Technologies, Brazil) with the use of
oligo (dT) as primers. cDNA was used in qPCR for measuring IGF-1 and BCL-2 expression
compared with actin expression (used as the housekeeping gene). The
primers for murine IGF-1 and BCL-2 were purchased from Invitrogen and their
nucleotide sequences are shown in Table 2.
Amplification consisted of 10 min at 95°C, followed by 40 cycles of 25 s at 95°C, 25
s at the respective annealing temperature for each pair of primers (60°C), and 20 s
at 72°C, followed by 40 cycles of 10 s starting at 75°C, with 0.5°C increments for
the melt curve. Fluorescence was measured during the annealing step of each cycle.
The relative gene expression was determined using the 2−ΔΔCt method.
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4

Quantifying Gene Expression via RT-PCR

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RT-PCR was used to determine the influence of the DMRs identified on gene expression. cDNA was generated using random primers with Invitrogen’s Superscript III First-Strand Synthesis System SuperMix. PCR reactions were prepared using TaqMan Fast Advanced Master Mix and TaqMan Gene Expression Assays (Applied Biosystems) as specified by the manufacturer. RT-PCR was performed and analyzed on the ViiA 7 Real-Time PCR System with ViiA 7 1.22 software (Applied Biosystems). The quantification of target gene transcription relative to that of GAPDH was assessed using the 2ΔΔCT method. Unpaired Student’s t tests were used to identify differential expression between HTNPREG and controls using a significance threshold of P < 0.05. Data are expressed as means ± SD.
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5

miRNA and mRNA Expression Analysis

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Total RNA was extracted with TRIzol reagent (Invitrogen) and treated with RNase-free DNase I (Qiagen, Hilden, Germany). For miRNA expression analysis, 1 μg of DNase I-treated RNA was converted into cDNA using the TaqMan microRNA reverse transcription kit (Applied Biosystems, Foster City, CA). Expression levels of mature miR-301a were measured using a TaqMan microRNA assay (Applied Biosystems) by normalizing to U6 snRNA. For analysis of SOCS6 transcript levels, 1 μg of DNase I-treated RNA was reverse transcribed using the SuperScript III first-strand synthesis system supermix (Invitrogen). A SYBR Green PCR kit (TaKaRa, Dalian, China) was used to quantify the SOCS6 mRNA levels. β-actin mRNA was amplified as an internal control. Expression levels of miR-301a or SOCS6 were calculated using the 2-ΔΔCT method.
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