Approximately 200 ng of total RNA from each sample was used for the lncRNA microarray analysis. LncRNA expression was analyzed using Agilent human lncRNA + mRNA Array V4.0 (4 × 180 K format), with each array containing probes interrogating about 41,000 human lncRNAs and about 34,000 human mRNAs (Agilent, USA). Those lncRNA and mRNA target sequences were merged from multiple databases, 23898 from GENCODE/ENSEMBL, 21488 from LNCipedia, 14353 from Human LincRNA Catalog [35 (link)], 13701 from NRED (ncRNA Expression Database), 7760 from RefSeq, 5627 from USCS, 3019 from LncRNAs-a (Enhancer-like), 1053 from Antisense ncRNA pipeline, 1038 from H-InvDB, 962 UCRs, 848 from Chen Ruisheng lab (Institute of Biophysics, Chinese Academy of Science) and 407 Hox ncRNAs. Each RNA was detected by probes that were replicated 2 times. The array also contained 4974 control probes (Agilent, USA).
Human lncrna mrna array v4
Manufactured by Agilent Technologies
Sourced in United States
The Human lncRNA + mRNA Array V4.0 is a high-density microarray platform designed for the comprehensive analysis of long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression in human samples. The array contains probes targeting over 58,000 lncRNA and 34,000 mRNA transcripts, providing a comprehensive coverage of the human transcriptome.
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5 protocols using human lncrna mrna array v4
1
Comprehensive lncRNA Expression Analysis
2
Profiling Differential lncRNA and mRNA Expression
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LncRNA and mRNA expressions were determined using a CapitaBio Technology Human LncRNA Array v4 (CapitalBio, Beijing, China). Double‐stranded complementary DNAs (cDNAs) were synthesized from 1 μg total RNA. cDNA was labeled with Cy3‐dCTP or Cy5‐dCTP (GE Healthcare, Piscataway, NJ) and hybridized onto a human lncRNA + mRNA Array V4.0 (4 × 180 K; Agilent, Santa Clara, CA), comprising 40,916 human lncRNAs and approximately 34,000 human mRNAs. The lncRNA and mRNA target sequences were merged from ENSEMBL, human long intervening/intergenic ncRNA, and the LNCipedia catalog.
Threshold values of ≥2 and ≤2‐fold change and a Benjamini‐Hochberg corrected p = .05 were used to identify differentially expressed genes. The data were analyzed using hierarchical clustering with average linkage. Java Treeview software (Stanford University School of Medicine, Stanford, CA) was employed to visualize the microarray results. The primers are listed in Table S1.
Threshold values of ≥2 and ≤2‐fold change and a Benjamini‐Hochberg corrected p = .05 were used to identify differentially expressed genes. The data were analyzed using hierarchical clustering with average linkage. Java Treeview software (Stanford University School of Medicine, Stanford, CA) was employed to visualize the microarray results. The primers are listed in Table S1.
3
Comprehensive lncRNA Profiling by Microarray
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Approximately 200 ng of RNA from each sample was applied for the lncRNA microarray analysis. The lncRNA expression profiles were analysed using an Agilent Human lncRNA + mRNA Array V4.0 (4 × 180K format) that contained 41000 human lncRNA probes and approximately 34000 human mRNA probes. The lncRNAs and their mRNA target sequences were obtained from multiple databases, including GENCODE/ENSEMBL, LNCipedia, the Human LincRNA Catalog, the ncRNA Expression Database (NRED), RefSeq, the University of California, Santa Cruz (UCSC), and the Chen Ruisheng laboratory (Institute of Biophysics, Chinese Academy of Science). Each RNA was detected two times by probes.
4
Agilent Human lncRNA + mRNA Array V4.0
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The microarray employed in the current study was Agilent human lncRNA + mRNA Array V4.0, which was designed with four identical arrays per slide (4 × 180 K format) with each array containing probes interrogating about 41,000 human lncRNAs and about 34,000 human mRNAs. The lncRNA target sequences were selected from multiple databases including GENCODE/ENSEMBL, Human LincRNA Catalog, RefSeq, UCS, NRED (ncRNA Expression Database), LNCipedia, H-InvDB, LncRNAs-a (Enhancer-like), Antisense ncRNA pipeline, Hox ncRNAs, UCRs, and 848 unpublished lncRNAs from the Chen Runsheng laboratory (Institute of Biophysics, Chinese Academy of Science, Beijing, China). The mRNAs were collected from RefSeq Build 50, Ensemble Release 52, Unigene Build 216, GenBank (April 2009), and Broad Institute TUCP transcripts catalog (Nov 2011) by Agilent, which have also been used in Agilent-039494 SurePrint G3 Human GE v2 8 × 60 K Microarray. The array also contains 4974 Agilent control probes for hybridization quality control.
5
Comprehensive Profiling of lncRNA, mRNA, and circRNA in Breast Cancer Cell Lines
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The Agilent human lncRNA + mRNA Array V4.0 was used for the profiling of lncRNA and mRNA in MCF-7, LCC2, and LCC9 cell lines. Each array contains probes that could interrogate around 41,000 lncRNAs and 34,000 mRNAs in human genome. The target sequences for these lncRNA and mRNA were derived from a wide range of databases: 23,898 from GENCODE/ENSEMBL, 21,488 from LNCipedia, 14,353 from Human LincRNA Catalog (13 (link)), 13,701 from NRED (ncRNA Expression Database), 7,760 from RefSeq, 5,627 from USCS, 3,019 from LncRNAs-a (Enhancer-like), 1,053 from Antisense ncRNA pipeline, 1,038 from H-InvDB, 962 UCRs, 848 from Chen Ruisheng lab (Institute of Biophysics, Chinese Academy of Science), and 407 Hox ncRNAs.
The CapitalBiotech human circRNA Array V2.0 was used for the profiling of circRNA in MCF-7, LCC2, and LCC9 cell lines. Each array contains probes capable of interrogating approximately 170,340 human circRNAs, the target sequences of which are from Circbase, Deepbase and publication of Rybak-Wolf (14 (link)). Each circRNA was simultaneously detected by a long probe and a short probe.
The CapitalBiotech human circRNA Array V2.0 was used for the profiling of circRNA in MCF-7, LCC2, and LCC9 cell lines. Each array contains probes capable of interrogating approximately 170,340 human circRNAs, the target sequences of which are from Circbase, Deepbase and publication of Rybak-Wolf (14 (link)). Each circRNA was simultaneously detected by a long probe and a short probe.
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