SmartChip Human Long Non-Coding RNA-1 Panel
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Understand the role of long noncoding RNA: the new ‘dark matter’ Long described as transcriptional noise or “dark matter”, lncRNAs are now seen as key regulators of transcription and epigenetic modification, with possible involvement in processes as diverse as cancer progression, embryonic pluripotency, and differentiation (see Figure 1). Next generation sequencing (NGS) is responsible for a rapid expansion in the discovery of lncRNAs and a resulting need for precise, methods with low error rates to validate your findings. Real-time PCR offers precision, specificity, and sensitivity—and the results are easy to interpret. Couple this ideal validation technique with the high throughput capabilities of WaferGen Biosystems SmartChip Human lncRNA-1 Panel, and you can now interrogate samples for expression of 1,700 well- characterized lncRNA species in about an hour. MIQE-compliant assays developed to enhance your experimental success The field of lncRNA research is in the midst of a rapid discovery phase, but that doesn’t mean your reagents have to be “experimental”. In collaboration with Biogazelle, we’ve designed the SmartChip Human lncRNA-1 Panel to maximize your investigation of lncRNA expression. They contain triplicate, predispensed PCR assays that have been extensively validated and annotated. In addition, we’ve ensured that the lncRNA assays in this SmartChip Panel are both compliant with the Minimum Information for Publication of Quantitative Real- Time PCR Experiments (MIQE) guidelines, and curated against the latest versions of genomic databases. To understand lncRNA expression levels across a wide variety of well-characterized biological samples and simultaneously validate the the SmartChip Human lncRNA Panel, we profiled lncRNA expression in the NCI-60 cell lines. These are a set of 59 human, cancer cell-lines derived from diverse tissues, such as brain, blood, bone marrow, breast, colon, kidney, lung, ovary, prostate, and skin. As can be seen in Figure 2, the resulting heatmap shows that 97% of the 1700 lncRNA assayed are expressed reproducibly in at least one of the cell lines. A snapshot of the tissue-specificity, that appears to be a hallmark of lncRNA expression, was confirmed with well-characterized HULC and GOMAFU lncRNAs and is shown in Figure 3. SmartChip Human Long Non-Coding RNA-1 Panel Reproducible Results. Novel Content. NGS Validation. Advancing the science of tomorrow today. Figure 1. Four proposed mechanism of lncRNA function. 1) Signaling transcription factors to promote transcription 2) Competing with transcription factors through a decoy mechanism 3) Recruiting chromatin-modifying enzymes as guide molecules 4) Acting as scaffolds to bring together ribonucleoprotein complexes. Figure 2. Profiling expression of 1700 lncRNAs in NCI-60 cell lines using SmartChip Human lncRNA-1 Panel. The data clearly demonstrate the wide range of expression levels of these 1700 lncRNAs. As indicated by the heat- map, lncRNA expression patterns can be largely grouped by tissue types. I. Signal II. Decoy III. Guide IV. Scaffold MDA-MB-435 M14 MALME-3M SK-MEL-5 UACC-62 UACC-257 SK-MEL-28 SK-MEL-2 SR HL-60 SF-295 SNB-75 LOXIMVI OVCAR-8 NCI/ADR-RES NCI-H226 SN12C UO-31 CAKI-1 786-0 A498 TK-10 ACHN U251 SNB-19 HOP-92 Hs-578T RXF-393 SF-539 BT-549 MDA-MB-231 SF-268 K562 RPMI-8226 MCF-7 MOLT-4 CCRF-CEM KM12 COLO-205 HCT-15 HCT-116 HCC-2998 HT29 OVCAR-5 SW-620 MDA-MB-468 T-47D NCI-H322M NCI-H522 NCI-H23 EKVX NCI-H460 A549ATCC HOP-62 DU145 SK-OV-3 PC-3 IGR-OV1 OVCAR-4 OVCAR-3 -6 -2 2 4 6 Value Color Key Product Note
Transcript of SmartChip Human Long Non-Coding RNA-1 Panel
Understand the role of long noncoding RNA: the new ‘dark matter’
Long described as transcriptional noise or “dark matter”, lncRNAs are now seen as key regulators of transcription and epigenetic modification, with possible involvement in processes as diverse as cancer progression, embryonic pluripotency, and differentiation (see Figure 1). Next generation sequencing (NGS) is responsible for a rapid expansion in the discovery of lncRNAs and a resulting need for precise, methods with low error rates to validate your findings. Real-time PCR offers precision, specificity, and sensitivity—and the results are easy to interpret. Couple this ideal validation technique with the high throughput capabilities of WaferGen Biosystems SmartChip Human lncRNA-1 Panel, and you can now interrogate samples for expression of 1,700 well-characterized lncRNA species in about an hour.
MIQE-compliant assays developed to enhance your experimental success
The field of lncRNA research is in the midst of a rapid discovery phase, but that doesn’t mean your reagents have to be “experimental”. In collaboration with Biogazelle, we’ve designed the SmartChip Human lncRNA-1 Panel to maximize your investigation of lncRNA expression. They contain triplicate, predispensed PCR assays that have been extensively validated and annotated. In addition, we’ve ensured that the lncRNA assays in this SmartChip Panel are both compliant with the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, and curated against the latest versions of genomic databases.
To understand lncRNA expression levels across a wide variety of well-characterized biological samples and simultaneously validate the the SmartChip Human lncRNA Panel, we profiled lncRNA expression in the NCI-60 cell lines. These are a set of 59 human, cancer cell-lines derived from diverse tissues, such as brain, blood, bone marrow, breast, colon, kidney, lung, ovary, prostate, and skin. As can be seen in Figure 2, the resulting heatmap shows that 97% of the 1700 lncRNA assayed are expressed reproducibly in at least one of the cell lines. A snapshot of the tissue-specificity, that appears to be a hallmark of lncRNA expression, was confirmed with well-characterized HULC and GOMAFU lncRNAs and is shown in Figure 3.
SmartChip Human Long Non-Coding RNA-1 PanelReproducible Results. Novel Content. NGS Validation.
Advancing the science of tomorrow today.
Figure 1. Four proposed mechanism of lncRNA function.1) Signaling transcription factors to promote transcription2) Competing with transcription factors through a decoy mechanism3) Recruiting chromatin-modifying enzymes as guide molecules4) Acting as scaffolds to bring together ribonucleoprotein complexes.
Figure 2. Profiling expression of 1700 lncRNAs in NCI-60 cell lines using SmartChip Human lncRNA-1 Panel. The data clearly demonstrate the wide range of expression levels of these 1700 lncRNAs. As indicated by the heat-map, lncRNA expression patterns can be largely grouped by tissue types.
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Product Note
Figure 3. The predicted high expression levels of HULC and GOMAFU in liver and brain, respectively, are clearly demonstrated in these experiments.
SmartChip Human Long Non-Coding RNA-1 PanelProduct Note
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Advancing the science of tomorrow today
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. © Copyright 2012, WaferGen Biosystems. All rights reserved. Information in this document is subject to change without notice. WaferGen Biosystems assumes no responsibility for any errors that may appear in this document. WaferGen and WaferGen Biosystems (Design), WaferGen Biosystems are trademarks of WaferGen Biosystems or its subsidiaries in the U.S. and/or certain other countries. All other trademarks are the sole property of their respective owners. MKT-018
Ordering Information
Part Number Description
430-000103 SmartChip Human lncRNA-1 Panel V1.0
450-000013 SmartChip Human lncRNA-1 Panel V1.0 Application Run, per sample
Integrate mRNA, miRNA and lncRNA expression information to advance biological understanding
As the paradigm of DNA → messenger RNA (mRNA) → protein shifts to include noncoding RNAs such as microRNA (miRNA), and now lncRNA, understanding the interactions between these transcription products is extremely important. Now a single platform—the SmartChip Real-Time PCR System—makes these experiments achievable. Our expression analysis of the NCI-60 cell lines also included both mRNA and miRNA targets to provide a detailed view of the interactions of the different RNA species. Specifically, we used the SmartChip Human Oncology Panel, which targets ~1,200 mRNAs associated with cancer and cancer-related pathways, and the SmartChip Human miRNA Panel, which is collection of assays for ~1,100 biologically relevant miRNAs. Figure 4 shows some of the RNA interactions that we were able to document in the NCI-60 cell lines using the SmartChip Real-Time PCR System. Together, this type of integrated coding and noncoding RNA analysis can reveal complex interactions that may prove to be pivotal in the understanding of gene regulation and its effect on development, cancer, and other diseases, and neurobiology.
Please contact us to learn more about the complete NCI-60 study, and how we can help you achieve your research goals. We offer thousands of validated PCR assays across biological pathways and, for other targets, we can design assays for you.
If you are planning a new study, validating existing research, want us to run some of your samples, or have an idea you want to bounce off us, get in touch and we’ll be happy to help.
For science: [email protected] sales: [email protected] support: [email protected] general information: [email protected]
Figure 4. LncRNA, miRNA, and mRNA are subject to complex interactions. Profile, validate, and quantify them using the SmartChip Real-Time PCR System.
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