LncRNA Array V3.0. Arraystar Human LncRNA Array V3.0 was used to profile expression of lncRNAs, which was performed by KangChen Bio-tech (Shanghai, China) according to a previous study (26) . Briefly, RNA samples from BMNCs were further purified to remove rRNA, and transcribed into fluorescent cRNA as probes to hybridize to the Human LncRNA Array V3.0 (8660 K; Arraystar). The array contains 30,586 lncRNAs and 26,109 coding transcripts, which were collected from the most authoritative databases (such as RefSeq, UCSC, Knowngenes, and Ensembl) and related literature. Array data were then analyzed by MultiExperiment Viewer software for upregulation or downregulation of lncRNA expression in AML samples compared to control samples with a cut-off point of 2-fold for upregulation and a cut-off point of 0.5-fold for downregulation.
Human lncrna array v3
Manufactured by Arraystar
Sourced in United States, China
The Human LncRNA Array v3.0 is a high-throughput microarray platform designed for the comprehensive analysis of human long non-coding RNAs (lncRNAs). The array includes probes targeting well-annotated lncRNAs, allowing for the simultaneous detection and quantification of thousands of lncRNA transcripts in a single experiment.
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Lab products found in correlation
Agilent scanner g2505c, by Agilent Technologies (4 mentions)
Quick amp labeling kit, by Agilent Technologies (2 mentions)
Genespring gx v11, by Agilent Technologies (2 mentions)
Nanodrop nd 1000, by Thermo Fisher Scientific (2 mentions)
Genepix4000b chip scanner, by Molecular Devices (1 mentions)
Genepix pro v6, by Molecular Devices (1 mentions)
Agilent feature extraction software v10.7, by Agilent Technologies (1 mentions)
Agilent gene expression hybridization kit, by Agilent Technologies (1 mentions)
Dnase 1, by New England Biolabs (1 mentions)
Rna bee, by Tel-Test (1 mentions)
Tri reagent, by Merck Group (1 mentions)
G2505b scanner, by Agilent Technologies (1 mentions)
Trizol reagent, by Thermo Fisher Scientific (1 mentions)
Feature extraction software, by Agilent Technologies (1 mentions)
Genechip scanner 3000 7g system, by Thermo Fisher Scientific (1 mentions)
Genechip 3 in vitro transcription express kit, by Thermo Fisher Scientific (1 mentions)
Agilent feature extraction software version 11.0.1.1, by Agilent Technologies (1 mentions)
Genespring gx, by Agilent Technologies (1 mentions)
Scanner g2505c, by Agilent Technologies (1 mentions)
Human circrna array, by Arraystar (1 mentions)
19 protocols using human lncrna array v3
1
Profiling lncRNA Expression in AML
2
Profiling lncRNA Expression in ESCC
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Total RNA of the ESCC tissues and adjacent normal tissues were extracted with RNA enzyme inhibitor RNAiso Plus and delivered to Shanghai Kangcheng Biological Co., LTD for chip service. First, rRNA and DNA were removed from 1 μg of total RNA, then the template was amplified and reversely transcribed into fluorescent cDNA with random primers. The labeled cDNA was hybridized with Human LncRNA Array v3.0 (8 × 60K; Arraystar, Rockville, MD, USA), the chip was washed, and the fluorescence signal intensity of the chip was scanned by a GenePix4000B chip scanner (Molecular Devices, San Jose, CA, USA). Finally, GenePix Pro V6.0 (Molecular Devices) was used for hierarchical clustering analysis of raw data. The screening conditions for differentially expressed genes were as follows: |Fold| ≥ 2, p < 0.05, and false discovery rate (FDR) < 0.05.
3
Microarray Analysis of GC Tissue Samples
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Six match-paired sets of tissues for microarray were obtained from patients who were newly diagnosed with GC and received radical resection at the First Affiliated Hospital of China Medical University. Total RNA was extracted from the above tissues. The Quick Amp Labeling kit (Agilent Technologies, Palo Alto CA, USA) was used to amplify and transcribe the RNA into cRNA, then the labeled cRNA was hybridized onto the Human LncRNA Array v3.0 (8 × 60 K, ArrayStar, Rockville, MD, USA) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Total miRNAs were labeled using the miRCURYTM (Hy3TM/Hy5TM) power labeling kit (Exiqon Life Sciences, Vedbaek, Denmark) and hybridized onto the miRCURY LNA microRNA array (v18.0) (Exiqon Life Sciences). The arrays were scanned with an Axon GenePix 4000B microarray scanner following the washing step. The acquired array images were extracted and analyzed using Agilent Feature Extraction Software v10.7. Raw signal intensities were normalized in a quantile method by GeneSpring GX v11.5.1 (Agilent Technologies), and low intensity lncRNAs, mRNAs, and miRNAs were filtered. LncRNAs, mRNAs, and miRNAs that were significantly differentially expressed were identified using box plot and scatter plot filtering. The threshold used to screen upregulated or downregulated lncRNAs, mRNAs and miRNAs was fold change > 2.0 with a P-value < 0.05.
4
Genome-wide lncRNA Expression Analysis
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Total RNA was isolated with RNA-Bee (Tel-Test Inc.) using the protocol provided by the manufacturer. Total RNA (5–10 μg) was treated with DNase I (NEB) according to the manufacturer’s instructions and ethanol precipitated overnight. Genome-wide lncRNA microarray analysis was performed with ArrayStar using Human LncRNA Array v3.0 (8 x 60K, Arraystar). A fold change cut-off of 2.0 was applied to filter lncRNAs into different categories (upregulated, downregulated and rescued) for further analyses. Three technical replicates for each of the three samples were analyzed.
5
Profiling Long Noncoding RNAs in Monocytes
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RNA was isolated from purified monocytes with Tri Reagent (Sigma-Aldrich, Dublin, Ireland) as per the manufacturer’s instructions. The quality and the concentration of pooled RNA samples were monitored at absorbance ratios of A260/A280 and A260/A230 using a NanoDrop 8000 spectrophotometer. Expression profiling studies were performed on RNA by Arraystar, Inc. (Rockville, MD, USA). Briefly, labeled cRNAs were hybridized onto the Human LncRNA Array v3.0 (8 × 60 K, Arraystar) and after having washed the slides, the arrays were scanned by the Agilent Scanner G2505C. Approximately 30,600 lncRNAs and 26,109 coding transcripts can be detected using this microarray [11 (link)].
6
Differential lncRNA Expression Analysis
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LncRNA microarrays of RIF or non-RIF tissues were conveyed by KangChen Biotech (Shanghai, China). Hybridization was conveyed using Human LncRNA Array v3.0 (Arraystar, Rockville, MD, USA). Array images were analyzed using Agilent Feature Extraction software. We performed quantile normalization and data processing using GeneSpring GX v11.5.1 (Agilent Technologies, Santa Clara, CA, USA). Differential expression of lncRNA was analyzed by volcano plot.
7
LncRNA Profiling in LUAD Metastasis
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For LncRNAs microarray analyses, six LUAD tissue samples (three LUAD tissues with lymph node metastasis and three without) were obtained from the Affiliate Hospital of Weifang Medical University. The levels of LncRNAs were profiled using Human LncRNA Array V3.0 (Arraystar, Rockville, Maryland, USA), and analyzed by KangChen Bio-tech Inc. (Shanghai, China). The differentially expressed genes were employed for cluster analysis of samples and heat map generation.
8
TGF-β1 Regulation of lncRNA Expression
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ARPE-19 cells were treated with 10 ng/ml recombinant TGF-β1 or a solvent control for 48 h, and then the cells were harvested. Total RNA was extracted with TRIzol reagent (Invitrogen), transcribed into fluorescent cRNA with a Quick Amp labeling kit (Agilent Technologies, Palo Alto, CA), and hybridized to a Human LncRNA Array v3.0 (8 × 60 K, ArrayStar, Rockville, MD). Microarrays were scanned with an Agilent Scanner G2505B, and microarray images were analyzed using Agilent Feature Extraction software. The experiment was performed in triplicate. The threshold values we used to define upregulation or downregulation were fold change >2 and P < 0.05.
9
Microarray Analysis of lncRNA Expression
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Microarray analysis was conducted as a previous report [18 (link)]. In brief, total RNA from 5 pairs of CC and paracancerous tissues was extracted. Next, cDNA was synthesized using 0.5 μg total RNA via a GeneChip 3’In-vitro Transcription Express Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA, 902789). Then the cDNA was fragmented and hybridized with human LncRNA Array V3.0 (Arraystar Inc., USA, AS-LNC-H-V4.0). After that, the chips were washed and scanned using a GeneChip™ Scanner 3000 7G system (Thermo Fisher, 000213).
10
Differential Transcriptome Analysis of Bladder Cancer
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Four pairs of carcinoma and para-carcinoma tissues were used for microarray assay to determine differentially expressed lncRNA, circRNA and mRNAs comparing bladder cancer and normal control. The microarray hybridization was performed based on the manufacturer's standard protocols (Agilent Technology) including purifying RNA, transcribing into fluorescent cRNA, and then hybridizing onto the Human lncRNA Array v3.0 (Arraystar) and Human circRNA Arrays (Arraystar). Finally, the hybridized slides were washed, fixed and scanned to images by the Agilent Scanner G2505C. And the data collection was performed using Agilent Feature Extraction software (version 11.0.1.1). The raw data were quantile normalized and further data analysis was performed with R software package, GeneSpring GX (Agilent Technologies) and gene expression dynamics inspector (GEDI). The statistical significance of differentially regulated lncRNAs, circRNAs and mRNAs between bladder carcinoma group and normal control group was identified through p-value and FDR filtering. Significant differential expressed transcripts were retained by screening fold change ≥2.0, P < 0.05 and FDR <0.05. Hierarchical clustering was performed to generate an overview of the characteristics of expression profiles based on values of all expressed transcripts and significant differential expressed transcripts.
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