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3 protocols using rneasy fibrosis mini kit

1

RNA Extraction and Quality Assessment

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RNA extraction was performed as described previously. Tissue was dissociated using Precellys® 24 tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) and total RNA purified using the automated QIAcube with RNeasy Fibrosis Mini kit (Qiagen, CA, United States) according to the manufacturer’s instructions. The RNA integrity was assessed with the Bioanalyzer 2,100 system (Agilent, CA, United States), and RIN values > 8 accepted as suitable for PCR profiling. RNA concentrations were then measured using the Nanodrop 2000 (Labtech International, East Sussex, United Kingdom).
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2

Quantitative PCR Analysis of Soleus Muscle RNA

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Total RNA was extracted from soleus muscle homogenate using an RNeasy Fibrosis Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. The purity and quantity of total RNA were assessed using a NanoDrop system (NanoDrop Technologies, Wilmington, DE). Total RNA was reverse transcribed into cDNA using a high-capacity cDNA Reverse Transcription Kit (Applied Biosystems, Waltham, MA) according to the manufacturer’s instructions. PCR was performed with a 7300 real-time PCR system (Applied Biosystems) using PowerUp SYBR Green PCR Master Mix (Applied Biosystems). The thermal profiles consisted of denaturation at 95°C for 10 min followed by 40 cycles of 95°C for 15 s and annealing at 60°C for 60 s. The expression of β-actin mRNA was used as a housekeeping control, and all data were normalized to the β-actin mRNA level. Data are expressed as fold change relative to the values of ND/Sed group. Specific PCR primer pairs for each gene are shown in Table 2.
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3

Highly Sensitive RNA Sequencing of Mouse Ears

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Mouse ears (9 mice/group) were stabilized by addition of RNAlater (Ambion) and homogenized using TissueLyzer II (Qiagen). Total RNA was extracted using the RNeasy Fibrosis mini kit (Qiagen) and quantified using a Qubit Fluorometer. RNA integrity was assessed using the RNA ScreenTape on Agilent TapeStation (Agilent), with RIN (RNA integrity number) ≥ 8 set as an inclusion cutoff. Indexed libraries were constructed from 2000 ng of total RNA using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instruction. The quantity and quality of the libraries were also assessed by Qubit and D1000 ScreenTape on Agilent TapeStation (Agilent), respectively. To maximize CDR3 reads, the average library size was 400 bp. The libraries’ molar concentration was validated by qPCR for library pooling. Sequencing was performed on the Illumina HiSeq 4000 platform using PE150 chemistry (Illumina).
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