ArticleNucleic acids research2004
aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 34 citations in OpenAlex.
- The successes and future prospects of the linear antisense RNA amplification methodology.Nature protocols · 2018Article
- KLF4-mediated negative regulation of IFITM3 expression plays a critical role in colon cancer pathogenesis.Clinical cancer research : an official journal of the American Association for Cancer Research · 2011Article
- Analysis of microRNAs in pancreatic fine-needle aspirates can classify benign and malignant tissues.Clinical chemistry · 2008Article
- MicroRNA expression alterations are linked to tumorigenesis and non-neoplastic processes in pancreatic ductal adenocarcinoma.Oncogene · 2007Article
- Single molecule transcription profiling with AFM.Nanotechnology · 2007Article
- Collagen type I-induced Smad-interacting protein 1 expression downregulates E-cadherin in pancreatic cancer.Oncogene · 2007Article
- Discarding duplicate ditags in LongSAGE analysis may introduce significant error.BMC bioinformatics · 2007Article
- Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.Genome research · 2007Article
- Global analysis of gene expression in mammalian kidney.Pflugers Archiv : European journal of physiology · 2005Review
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale gene expression analyses of microdissected primary tissue are still difficult because generally only a limited amount of mRNA can be obtained from microdissected cells. The introduction of the T7-based RNA amplification technique was an important step to reduce the amount of RNA needed for such analyses. This amplification technique produces amplified antisense RNA (aRNA), which so far has precluded its direct use for serial analysis of gene expression (SAGE) library production. We describe a method, termed 'aRNA-longSAGE', which is the first to allow the direct use of aRNA for standard longSAGE library production. The aRNA-longSAGE protocol was validated by comparing two aRNA-longSAGE libraries with two Micro-longSAGE libraries that were generated from the same RNA preparations of two different cell lines. Using a conservative validation approach, we were able to verify 68% of the differentially expressed genes identified by aRNA-longSAGE. Furthermore, the identification rate of differentially expressed genes was roughly twice as high in our aRNA-longSAGE libraries as in the standard Micro-longSAGE libraries. Using our validated aRNA-longSAGE protocol, we were able to successfully generate longSAGE libraries from as little as 40 ng of total RNA isolated from 2000-3000 microdissected pancreatic ductal epithelial cells or cells from pancreatic intraepithelial neoplasias.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.