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6 protocols using dnase 1

1

TIMP2 and TIMP3 Binding Analysis

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Prostate cancer cells were lysed with RIPA buffer containing RNase inhibitor (CWBio, Beijing China) and cell lysates was incubated with biotin-labeling oligonucleotides for the specific-region sets of TIMP2 and TIMP3 overnight at 4°C. Then the biotin-oligonucleotides-protein-RNA complexes were pulled down with ImmunoPure streptavidin-agarose beads (20 μl/sample, Pierce, Rockford, IL, USA) and the complexes were freed from streptavidin-agarose beads by using 0.1 M biotin. The solution containing the complexed was treated with DNase I (CWBio) and Proteinase K (CWBio) before the RNA extracted with Trizol reagent, and then the RNA was reverse-transcribed to cDNA and PCR was performed to detect DANCR, and the primer sequences are as followings: F:5′-GCCACTATGTAGAGGGTTTC-3′, R:5′-AC-CTGCGCTAAGAACTGAGG-3′.
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2

Nucleic Acid and Protein Analysis in sCABs

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The nucleic acids and proteins in sCABs were obtained with TRIzol according to the manufacturer's instructions. After the enzymatic hydrolysis reaction with DNaseI (CW2090s, CWBIO, China) and RNaseA (EN0531, Thermo Scientific, USA) separately, the concentrations of RNA and DNA were analyzed based on the absorbance at OD260 by the NanoDrop One instrument (Thermo Fisher Scientific, USA). The samples of RNA and DNA were then separated by urea‐denatured polyacrylamide gel electrophoresis (5%) and a 1% agarose gel. The gels were imaged with a UV transilluminator (Gel Doc 2000, Hercules, USA) after ethidium bromide (0.1%) staining.
The proteins were washed with guanidine hydrochloride (0.3 м) at least 2 times and resuspended in sodium dodecyl sulfate (SDS) (200 μL, 1%). The samples were then subjected to LC‐MS analysis on a Shimadzu UFLC 20ADXR HPLC system connected in line with an AB Sciex 5600 Triple TOF mass spectrometer (AB SCIEX, USA). The proteins were analyzed by searching the mouse taxon of the UniProtKB/SwissProt database (release 2011_11). Gene ontology (GO) (http://geneontology.org/) was used to classify the proteins based on cellular components and molecular functions. The proteins were clustered according to pathway terms identified from KEGG database.
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3

Quantitative RT-PCR for Insect Tissues

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Total RNA from antennae, proboscis and maxillary palps was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA). The extracted RNA was quantified and qualified using a NanoDrop ND-1000 spectrophotometer and 2% agarose gel electrophoresis, respectively. The RNA was treated with DNase I (Cwbio, Beijing, China) to remove genomic DNA contamination. Approximately 1 μg of RNA was reverse transcribed into the first-strand cDNA using the SuperScript III RT Kit (Invitrogen, Carlsbad, CA, USA). The RT-qPCR was performed using PrimeScript™ RT Master Mix (Takara, Dalian, China) in a 25-μl system that contained 200 nM forward and reverse primers, 200 μM dNTPs, 2.5U TB Green Premix Ex Taq II and 1 μl cDNA template (approximately 40 ng). The thermal cycling conditions were as follows: 95 °C for 30 s, 40 cycles of 95 °C for 5 s and 60 °C for 30 s. Three biological and three technical replicates were performed for each sample. The data were analyzed by the 2−ΔΔCT method [53 (link)], and results were expressed as log2-transformed fold change values. A housekeeping gene, RpS7, was used as an internal control. Gene-specific primers that spanned exon-intron boundaries were designed using Primer 5.0 and are listed in Additional file 1: Table S1.
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4

Sucrose Consumption and Fluoxetine in BDNF

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In this study, sucrose (Amresco; 20140319) was employed in the sucrose consumption test, and fluoxetine (Eli Lilly and Company, Suzhou 215021, China; 4126A) was used as the standard control for acupuncture. ELISA Kit of BDNF (BlueGene Biotech CO., LTD., China; E02B0029) was used to detect the expression of BDNF in serum. The antibodies and some reagents used for WB analysis included rabbit polyclonal anti-BDNF (LifeSpan BioSciences; LS-C343943), rabbit polyclonal anti-acH3K9 (Cell Signaling Technology; 9649S), mouse anti-HDAC2 (Cell Signaling Technology; 5113S), β-actin (Zhongshanjinqiao Biotechnology Co., Ltd., Beijing, China; TA-09), goat anti-rabbit IgG (Jackson; 111-035-003), rabbit anti-H3 (Cell Signaling Technology, 4499S), ECL (Millipore; WBKLS0500), and bicinchoninic acid (BCA) protein assay kit (Cwbiotech; 02912E). Furthermore, the reagents used for RT-PCR and methylation-specific quantitative real-time PCR analysis included ultrapure RNA kit (Cwbiotech), HiFi-MMLV Reverse Transcriptase (Cwbiotech), SYBR Green PCR Mixture (Cwbiotech), and Dnase I (Cwbiotech), etc.
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5

Rice Seedling Response to Cyanide Exposure

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After 2 days of exposure, the CNtreated rice seedlings were collected, rinsed with deionized water, and divided into the root and shoots. Treated and untreated plant tissues (0.2 g) were precisely weighted, immediately frozen in liquid nitrogen, and ground into fine powder. The total RNA was extracted from both the root and shoot of all rice samples by using an Ultrapure RNA Kit (CWBio, Taizhou, China). DNase I (CWBio, Taizhou, China) was used to remove genomic DNA contamination if any from the RNA extract. Then, the total RNA was purified with an RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany).
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6

RNA Extraction from Rice Tissues

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Total RNA was extracted from rice tissues of the Cr-treated and non-treated seedlings by using an Ultrapure RNA Kit (CWBio, Taizhou, China). DNase I (CWBio, Taizhou, China) was used to clear away genomic DNA contamination in RNA extract. After that, an RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany) was selected to purify the total RNA. Four biological replicates were prepared for each sample.
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