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6 protocols using targetamp nano g biotin arna labeling kit

1

Transcriptomic Profile of Mtb-Infected THP-1 Cells

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Total RNA from uninfected and Mtb-infected THP-1 cells, treated or untreated with 100 μM RES for 24 hours, was extracted using the mirVana Isolation Kit (Life Technologies). RNA quality was confirmed using the Agilent Bioanalyzer, and only samples with RNA integrity number >7 were processed. Biotinylated complementary RNA was prepared from 100 ng of total RNA using the Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for the Illumina system, followed by hybridization on Illumina human arrays. Raw expression data were extracted by GenomeStudio Gene Expression v1.9.0 and processed with quantile normalization (51 (link)). Hierarchical clustering analysis with complete linkage algorithms was performed using R (52 ). Heat maps were plotted using Spotfire (TIBCO Software Inc.; Spotfire.tibco.com/">http://Spotfire.tibco.com/). Differential expression analysis was performed using Linear Models for Microarray Data (LIMMA) (52 ). GO analysis was carried out by DAVID. Pathway analysis was carried out using IPA (Ingenuity Systems; www.ingenuity.com).
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2

Transcriptomic Analysis of RNA Samples

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Total RNA was purified using mirVana miRNA Isolation Kit (Invitrogen). RNA integrity was assessed using the Bioanalyzer 2000 (Agilent). Target labeling was carried out using the TargetAmp Nano-g Biotin-aRNA Labeling Kit for the Illumina System (Epicentre). Labeled RNA was hybridized onto HumanHT-12 v4 Expression BeadChips (Illumina). Illumina GenomeStudio version 1.9.0 software was used to subtract background and scale samples to the global average signal intensity. Ingenuity Pathway Analysis (IPA) was applied to reveal transcriptional networks as described (16 (link)).
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3

Biotin-labeled cRNA Gene Expression Analysis

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Biotin labeled cRNA was generated using the TargetAmp Nano-g Biotin-aRNA Labeling Kit for the Illumina System (Epicentre). Biotin labeled cRNA (750 ng) was hybridized to Human HT-12V3 Beadchips (Illumina) and scanned on an Illumina iScan or HiScanSQ system.
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4

Lentivirus-Mediated Gene Silencing in HNSCC

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shRNAs were designed against the open reading frame of FSTL1/DIAPH1 sequences using siRNA wizard software (InvivoGen). shRNAs were cloned in lentiviral shRNA expression vector in which H1 promoter drives the expression of shRNA by RNA polymerase III. Third-generation lentiviruses were produced in Lenti-X 293T cells (Clontech) by cotransfection of shControl/shFSTL1/shDIAPH1 vectors and lentiviral packaging plasmid mix (pMDLg/pRRE, pRSV-Rev, and pMD2.G). HNSCC cell lines were transduced with either control lentivirus encoding a scrambled shRNA or shRNA against FSTL1/DIAPH1. Cells with stable integration of lentiviruses were selected with 2 µg puromycin for 2 wk. Total RNA was isolated from cells using the Exiqon miRcury RNA isolation kit. 250 ng total RNA was converted into biotinylated complementary RNA using a TargetAmp Nano-g Biotin-aRNA labeling kit (Epicenter). 750 ng biotinylated cRNA was hybridized to HT-12 V4 expression bead chip (Illumina) using samples in triplicate. Hybridization, washing, and scanning were performed according to the manufacturer’s protocol. Data extracted was normalized and analyzed using Illumina BeadStudio. Microarray data has been deposited in Gene Expression Omnibus database, accession no. GSE 63329.
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5

Transcriptional Profiling of Cholinergic Pathways

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The expression profiles of the genes related to ACh metabolism and signaling transduction pathways were analyzed using the Illumina iScan system with MouseRef-8 Expression BeadChips (Illumina, San Diego, CA, USA) that contain probes that detect over 24 000 transcripts. Total RNAs were isolated by Sepasol-RNA I super solution (Nacalai Tesque, Kyoto, Japan) from the striatum and globus pallidus in wild-type and DD mice. We used the area that includes the neostriatum, ventral striatum, and globus pallidus but not thalamus or hypothalamus in the present study. Total RNA (50 ng) was then applied to RNA amplification that was performed with the TargetAmp Nano-g Biotin-aRNA Labeling Kit (EPICENTRE Biotechnologies, Madison, WI, USA) according to the instructions of the manufacturer. Briefly, first-strand cDNA was synthesized with T7-oligo (dT) primer from total RNAs, and second-strand cDNA synthesis was then performed with synthesized first-strand cDNA. The in vitro transcription reaction was performed with the product of second-strand cDNA synthesis as the template for producing biotin-cRNAs by incorporating biotin-UTP into the RNA transcripts. Finally, 750 ng of biotin-cRNA was hybridized to the MouseRef-8 Expression BeadChips and then reacted with streptavidin-Cy3. The expression intensity of the transcripts on the BeadChips was detected with an Illumina iScan reader.
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6

PBMC RNA Isolation and Illumina Profiling

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Total RNA was isolated from PBMCs using Sigma Aldrich Tri-reagent (cat #T9424), as recommended, with the following modifications: 1 ug of linear acrylamide was added to the sample before Tri-reagent extraction to ensure more efficient precipitation of RNA and 1 ul of RNAsin (an RNAse inhibitor) was added to the Tri-reagent aqueous phase before continuing to the ethanol precipitation. Following RNA isolation, 100 ng of RNA was amplified using Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit (cat # TAN07924) to generate amplified cRNA. Biotinylated, amplified cRNA at 750 ng was hybridized to the Illumina HumanHT-12 v4 Expression BeadChips. All arrays were processed in the Wistar Institute Genomics Facility. Gene expression data is available in the Gene Expression Omnibus (GEO) under the accession number GSE50834.
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