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Nanodrop 2100 spectrophotometer

Manufactured by Agilent Technologies
Sourced in United States

The Nanodrop 2100 spectrophotometer is a compact and versatile instrument designed for the measurement of UV-Vis absorbance. It utilizes a patented sample retention technology to enable direct measurement of sample volumes as low as 0.5 μL without the need for cuvettes or other sample containers.

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3 protocols using nanodrop 2100 spectrophotometer

1

Transcriptome Analysis of Plant Tissues

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The total RNA of each sample was extracted separately using the Magen Plant RNA Kit (HiPure HP Plant RNA Mini Kit, Guangzhou) following the instructions of the manufacturer. The quality of the total RNA was investigated by using agarose gel electrophoresis and a Nanodrop 2100 spectrophotometer (Agilent, USA). The 15 cDNA libraries in this study (Ro_1, Ro_2, Ro_3, St_1, St_2, St_3, LB_1, LB_2, LB_3, ML_1, ML_2, ML_3, Fr_1, Fr_2, and Fr_3) were constructed and sequenced using the Illumina HiSeq™ 4000 (Illumina, USA) platform at Novegene Bioinformatics Technology Co. Ltd. (Beijing, China). Sequence adaptors, reads with more than 10% N bases and low-quality reads (Q phred ≤20 for > 50% read) were removed to obtain clean data according to the method described by Lv et al. [55 (link)]. After quality control procedures, the unigenes were de novo assembled using Trinity software [56 (link)]. All of the transcriptome data were used as a reference dataset to calculate the read count of each unigene among the samples and converted to the expected number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) as described by Trapnell et al. [57 (link)].
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2

Quantitative Analysis of Inflammatory Markers

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Cortical penumbra tissue and cell samples were lysed with TRIzol reagent (Invitrogen), total RNA was extracted according to the manufacturer’s protocol, and the quality of the RNA was assessed with a Nanodrop 2100 spectrophotometer (Agilent). Reverse transcription from RNA to cDNA was performed with the PrimeScript RT regent kit (Vazyme, Nanjing, China, R323-01). Quantitative real-time PCR was performed in a Roche LightCycler® 96 system (Roche, Mannheim, Germany) with a SYBR green kit (Accurate, Wuhan, China, AG11701). The primers are as follows:
CXCL3: forward primer- CCAGACAGAAGTCATAGCCAC, reverse primer-CTTCATCATGGTGAGGGGCTT;
CXCL11: forward primer- GGCTTCCTTATGTTCAAACAGGG; reverse primer- GCCGTTACTCGGGTAAATTACA;
CCL20: forward primer- GCCTCTCGTACATACAGACGC, reverse primer- CCAGTTCTGCTTTGGATCAGC;
CCL22: forward primer- AGGTCCCTATGGTGCCAATGT; reverse primer- CGGCAGGATTTTGAGGTCCA;
IL12a: forward primer- CTGTGCCTTGGTAGCATCTATG; reverse primer- GCAGAGTCTCGCCATTATGATTC;
IL23a: forward primer- ATGCTGGATTGCAGAGCAGTA; reverse primer- ACGGGGCACATTATTTTTAGTCT;
Serpine1: forward primer- TTCAGCCCTTGCTTGCCTC; reverse primer- ACACTTTTACTCCGAAGTCGGT;
GAPDH: forward primer- AGGTCGGTGTGAACGGATTTG, reverse primer-TGTAGACCATGTAGTTGAGGTCA;
β-actin: forward primer- GGCTGTATTCCCCTCCATCG, reverse primer- CCAGTTGGTAACAATGCCATGT.
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3

Transcriptional Analysis of Cortical Arterioles

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Cortical arterioles and cell samples were lysed with TRIzol reagent (Invitrogen). Total RNA was isolated according to the standard protocol provided by Invitrogen and the quality of the RNA was assessed with a Nanodrop 2100 spectrophotometer (Agilent). Then, the RNA was reverse-transcribed into cDNA with a PrimeScript RT reagent Kit (Takara, #RR037A). Quantitative real-time PCR was performed on an ABI 7500 PCR instrument (Applied Biosystems) with a SYBR green Kit (Takara, #DRR820A). The mRNA expression in each sample was calculated by the 2-(ΔΔCt) method after normalization to the expression of the internal control GAPDH. The primer sequences are shown in the Table S1.
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