The rats were decapitated, and brains were extracted based on our previous study. The rats were killed by rapid decapitation without anesthesia 1.5 h after the end of fear conditioning. The hippocampal CA1 region was removed from the brain, snap-frozen in liquid nitrogen, and stored at −80 °C until analysis. Total RNA of CA1 tissues was isolated using the RNApre Pure Tissue kit (TIANGEN BIOTECH CO., LTD Beijing China) according to manufacturer’s instructions, including a DNase digestion step. After having passed RNA measurement on the NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA) by measuring absorbance (A280, A260, A230), RNA concentrations and quantity, and then denaturing gel electrophoresis. For microarray analysis, Agilent Array platform (Shanghai KANGCHEN, Shanghai China) was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Rat LncRNA Array (4 × 44 K, Arraystar, KangChen Bio-tech Inc. Shanghai China). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.
Agilent array platform
Manufactured by Agilent Technologies
Sourced in United States, China
The Agilent Array platform is a high-performance microarray system designed for comprehensive genomic and transcriptomic analysis. It provides a flexible and scalable solution for array-based experimentation, enabling researchers to explore genome-wide patterns and relationships.
Automatically generated - may contain errors
Lab products found in correlation
Genespring gx v11, by Agilent Technologies (11 mentions)
Agilent scanner g2505c, by Agilent Technologies (9 mentions)
Agilent feature extraction software, by Agilent Technologies (9 mentions)
Trizol reagent, by Thermo Fisher Scientific (7 mentions)
Genespring gx v12, by Agilent Technologies (7 mentions)
Agilent scanner g2505b, by Agilent Technologies (6 mentions)
Rneasy mini kit, by Qiagen (5 mentions)
Nanodrop nd 1000, by Thermo Fisher Scientific (5 mentions)
Agilent s quick amp labeling protocol, by Agilent Technologies (3 mentions)
Feature extraction software, by Agilent Technologies (3 mentions)
Mrna only eukaryotic mrna isolation kit, by Illumina (3 mentions)
Agilent dna microarray scanner g2505c, by Agilent Technologies (3 mentions)
Rat lncrna microarray v2, by Arraystar (3 mentions)
Agilent feature extraction v11, by Agilent Technologies (3 mentions)
Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (3 mentions)
Human lncrna microarray v3, by Arraystar (3 mentions)
Quick amp labeling protocol, by Agilent Technologies (2 mentions)
Flash rna labeling kit, by Arraystar (2 mentions)
Scanner g2505c, by Agilent Technologies (2 mentions)
Human lncrna array v2, by Arraystar (2 mentions)
47 protocols using agilent array platform
1
Hippocampal RNA Profiling in Rats
2
Transcriptome Profiling of NK and T Cells
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For transcriptome profiling analysis, lncRNA and mRNA microarray hybridization in human decidual NK cells, peripheral blood NK cells, umbilical cord blood NK cells and peripheral blood T cells was performed using an Agilent Array platform (Agilent Technologies). During array hybridization, three donors were mixed into a single pool for each of dNK cells, cNK cells, pNK cells and T cells to balance individual differences. Heat map and red-blue color scales for differentially expressed lncRNAs and for lncRNA expression correlation analysis were exported using MEV 4.8.1 software. lncRNA-mRNA interactions were predicted using the database of Shanghai Biotechnology Corporation (SBC; http://www.shbio.com/sas.html ), and mRNA-mRNA interactions were predicted using STRING [42 (link)] (http://string-db.org ). lncRNA-mRNA interaction networks were exported using Cytoscape v3.1.0 software.
3
Microarray Analysis of JAK2V617F-positive cMPNs
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The Agilent Array platform was employed for microarray analysis [14 (link)]. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. The arrays were scanned by the Agilent Scanner G2565BA . Differentially expressed mRNA or lncRNA with an absolute value of fold change (FC) ≥ 1.5 and the false discovery rate (FDR) < 0.05 were considered statistically significant. In-depth mining of microarray data including pathway enrichment, co-expression analysis, cis-regulatory gene analyses, and trans-regulatory gene analysis were performed to better annotate the roles of lncRNAs and related-mRNAs in JAK2V617F-positive cMPNs.
4
Agilent Mouse Gene Expression Analysis
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Gene chip expression analysis was performed by Kangcheng Biotechnology Co., Ltd. using the Agilent array platform. First, the RNA quantity and quality were assessed using a NanoDrop ND‐1000 UV Spectrophotometer (Implen). RNA integrity of each sample was identified by standard denaturing agarose gel electrophoresis. Second, sample labeling and chip hybridization were performed according to the Agilent One‐Color Microarray‐Based Gene Expression Analysis protocol (Agilent). The samples were labeled by using the Agilent Quick Amp Labeling kit and hybridization experiments were performed by using the Agilent SureHyb. Specifically, the total RNA of each sample was linearly amplified and labeled with Cy3‐UTP; the labeled complementary RNAs (cRNAs) were purified by using the RNeasy Mini Kit (Qiagen), and the concentration and activity were detected with a NanoDrop ND‐1000 UV spectrophotometer. The purified Cy3‐UTP‐labeled cRNAs were hybridized with Agilent mouse 4 × 44 K gene expression profiling chip v2 (Agilent). The hybridization chip was washed, fixed, and scanned by using Agilent DNA Microarray Scanner (part number G2505C); Chip probe signal values were acquired by using Agilent Feature Extraction software (v11.0.1.1) to obtain raw data. Finally, the quantile normalization of raw data and subsequent data processing were performed by using GeneSpring GX v12.1 software (Agilent).
5
Human Gene Expression Microarray Protocol
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Infected cell samples were pelleted and frozen. Samples were sent to Arraystar (Rockville, MD) for RNA extraction and microarray analysis with the Agilent Human 4 x 44K gene expression array. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, the Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies). After washing the slides, the arrays were scanned by the Agilent Scanner G2505C.
6
Differential Expression of T-UCRs in Samples
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This study was previously detected by our team at Kangcheng Bio (Shanghai, China). The total RNA of each sample was quantified with NanoDrop ND-1000 (Thermo Fisher Scientific), and RNA integrity was evaluated by standard denaturing agarose gel electrophoresis. For microarray analysis, the Agilent array platform (Agilent Technologies, Santa Clara, California) was employed. Sample preparation and microarray hybridization were performed according to the manufacturer’s standard protocol. In short, the purified mRNA and LncRNA were amplified by random primer method (Arraystar Flash RNA Labeling Kit, Arraystar) and transcribed into fluorescent cRNA along the full length of the transcript. The labeled cRNA was hybridized to human T-UCR array (8×60K, Arraystar). After cleaning the slides, the array was scanned by the Agilent scanner G2505C (Agilent Technologies). The extracted data was normalized using Agilent GeneSpring GX v12.1 software. Use GeneSpring GX v12.1 and a signal processing algorithm called Otsu method for further data analysis. Finally, the differentially expressed T-UCRs between the samples were identified by fold change filtering.
7
Microarray Analysis of Eukaryotic LncRNA
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RNA quality and integrity of each sample were assessed by NanoDrop ND-1000 and agarose gel electrophoresis, respectively. The Agilent Array platform was employed to perform microarray analysis. Sample preparation and hybridization were performed according to the manufacturer’s protocol. Briefly, rRNA was removed from total mRNA (mRNA-only™ Eukaryotic mRNA Isolation Kit, Epicenter, Madison, WI, USA). Then, samples was amplified and transcribed into fluorescent cRNA without 3’ bias by using a random prime, and labeled cRNAs were hybridized to microarray (8 × 60 K, Arraystar, Rockville, MD, USA,). After washing, the slides was scanned into images by an Agilent G2505C scanner and were analyzed by Agilent Feature Extraction software (version 11.0.1.1). The GeneSpring GX v11.5.1 software package (Agilent Technologies, Santa Clara, CA, USA) was used to perform quantile normalization and subsequent data processing. LncRNA, which has flags in present or marginal at least 3 out of 6 samples (“All Targets Value”), were chosen for further research. Differentially expressed LncRNAs between two groups were screened through fold change filtering.
8
Differential Expression Analysis of LncRNAs and mRNAs
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LncRNA and mRNA microarrays were carried out by Arraystar Inc. (Rockville, MD) using the Mouse LncRNA Microarray V3.0, a Agilent Array Platform (Agilent Technologies, Inc., Santa Clara, CA, USA)16 (link). LncRNAs and the differentially expressed protein-coding genes were identified, and fold changes as well as P values from the statistics t-test were calculated. The up- or down-regulated lncRNAs were set as fold change ≥ 2.0 and P value ≤ 0.05 and shown in volcano plots and heat maps. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were applied to explore the potential roles that the differentially expressed mRNAs played in biological pathways or GO terms, including the following three categories: biological process, cellular component, and molecular function16 (link).
9
Microarray Analysis of LncRNA and mRNA
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Total RNA from the samples was quantified using the NanoDrop ND-1000. Microarray analysis was performed using the Agilent Array platform (Agilent Technologies, Santa Clara, CA, USA). Sample preparation and microarray hybridization were performed according to the manufacturer's standard protocols with minor modifications. Briefly, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3′ bias using a random priming method. The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 × 60 K, Arraystar). Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent). Differentially expressed lncRNAs and mRNAs with statistical significance were identified through volcano plot filtering and fold-change filtering. Finally, hierarchical clustering was performed based on differentially expressed mRNAs and lncRNAs using Cluster Tree view software (Stanford University, Palo Alto, CA, USA).
10
Transcriptome Analysis of hMSC Chondrogenesis
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Two groups of cells (hMSCs from the same patient undergoing expansion and chondrogenic induction to chondrogenesis), which each contained the mixture of cell sources from three parallel experiment, were prepared, and total RNA was isolated using TRIzol reagent. RNA quality and quantity were measured by Nanodrop 2000 (Thermo Fisher Scientific). RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. All labeled lncRNAs were hybridized onto an Arraystar Human LncRNA Microarray version -3.0 (Arraystar, Kangcheng, Shanghai, China). The microarray screening data have been submitted to the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128533 ). A heatmap was exported using Agilent Feature Extraction software (version 11.0.11, Agilent Technologies). Differentially expressed lncRNAs with statistical significance between the two samples were identified through fold change filtering.
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