ArticleGenome research2007
Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
- Article
- Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development.BMC genomics · 2015Article
- The transcription start site landscape of C. elegans.Genome research · 2013Article
- A gene expression atlas of the domestic pig.BMC biology · 2012Article
- Article
- Deep SAGE analysis of the Caenorhabditis elegans transcriptome.Nucleic acids research · 2010Article
- Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries.BMC genomics · 2009Article
- Next-generation tag sequencing for cancer gene expression profiling.Genome research · 2009Article
- Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity.Nucleic acids research · 2009Article
- A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas.Bioinformatics (Oxford, England) · 2009Article
- ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult.Developmental biology · 2009Article
- Protection of specific maternal messenger RNAs by the P body protein CGH-1 (Dhh1/RCK) during Caenorhabditis elegans oogenesis.The Journal of cell biology · 2008Article
- Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing.Nucleic acids research · 2008Article
- Identification of a set of genes showing regionally enriched expression in the mouse brain.BMC neuroscience · 2008Article
- Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.BMC biology · 2008Article
- Modeling transcriptome based on transcript-sampling data.PloS one · 2008Article
- Specific expression of long noncoding RNAs in the mouse brain.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Identification of transcripts with enriched expression in the developing and adult pancreas.Genome biology · 2008Article
- Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data.BMC genomics · 2007Article
- Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data.BMC plant biology · 2007Article
Corrections and comments
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Authors and funding
25 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe the details of a serial analysis of gene expression (SAGE) library construction and analysis platform that has enabled the generation of >298 high-quality SAGE libraries and >30 million SAGE tags primarily from sub-microgram amounts of total RNA purified from samples acquired by microdissection. Several RNA isolation methods were used to handle the diversity of samples processed, and various measures were applied to minimize ditag PCR carryover contamination. Modifications in the SAGE protocol resulted in improved cloning and DNA sequencing efficiencies. Bioinformatic measures to automatically assess DNA sequencing results were implemented to analyze the integrity of ditag structure, linker or cross-species ditag contamination, and yield of high-quality tags per sequence read. Our analysis of singleton tag errors resulted in a method for correcting such errors to statistically determine tag accuracy. From the libraries generated, we produced an essentially complete mapping of reliable 21-base-pair tags to the mouse reference genome sequence for a meta-library of approximately 5 million tags. Our analyses led us to reject the commonly held notion that duplicate ditags are artifacts. Rather than the usual practice of discarding such tags, we conclude that they should be retained to avoid introducing bias into the results and thereby maintain the quantitative nature of the data, which is a major theoretical advantage of SAGE as a tool for global transcriptional profiling.
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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.