ArticleGenome research2007
Gene discovery and annotation using LCM-454 transcriptome sequencing.
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 176 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
176 citing papers in PubMed.
- Single-cell RNA sequencing in stroke and traumatic brain injury: Current achievements, challenges and future perspectives on transcriptomic profiling.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2026Review
- The transcriptomics and differential gene expression of freezing and thawing in a freeze-tolerant vertebrate.BMC genomics · 2026Article
- Review
- Disclosing the development and focus of sequencing and omics studies in kidney neoplasm research.Discover oncology · 2025Article
- Application of Single-Cell Genomics to Animal Models of Periodontitis and Peri-Implantitis.Journal of clinical periodontology · 2025Review
- NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs.Genome biology · 2024Article
- siqRNA-seq is a spike-in-independent technique for quantitative mapping of mRNA landscape.BMC genomics · 2024Article
- Developing a simple and rapid method for cell-specific transcriptome analysis through laser microdissection: insights from citrus rind with broader implications.Plant methods · 2024Article
- Transcriptomic era of cancers in females: new epigenetic perspectives and therapeutic prospects.Frontiers in oncology · 2024Review
- Transcriptome profiling analysis of uterus during chicken laying periods.BMC genomics · 2023Article
- The Lost and Found: Unraveling the Functions of Orphan Genes.Journal of developmental biology · 2023Review
- An Angiogenic Gene Signature for Prediction of the Prognosis and Therapeutic Responses of Hepatocellular Carcinoma.International journal of molecular sciences · 2023Article
- GeneFriends: gene co-expression databases and tools for humans and model organisms.Nucleic acids research · 2023Article
- Application of single-cell sequencing to the research of tumor microenvironment.Frontiers in immunology · 2023Review
- SPECK: an unsupervised learning approach for cell surface receptor abundance estimation for single-cell RNA-sequencing data.Bioinformatics advances · 2023Article
- Novel Insights into the Sinoatrial Node in Single-Cell RNA Sequencing: From Developmental Biology to Physiological Function.Journal of cardiovascular development and disease · 2022Review
- Sequential Isolation of Microglia and Astrocytes from Young and Aged Adult Mouse Brains for Downstream Transcriptomic Analysis.Methods and protocols · 2022Article
- Promoting validation and cross-phylogenetic integration in model organism research.Disease models & mechanisms · 2022Article
- Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut.Genes · 2022Article
- Transcriptome analysis provides new insights into cold adaptation of corsac fox (Ecology and evolution · 2022Article
116 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
454 DNA sequencing technology achieves significant throughput relative to traditional approaches. More than 261,000 ESTs were generated by 454 Life Sciences from cDNA isolated using laser capture microdissection (LCM) from the developmentally important shoot apical meristem (SAM) of maize (Zea mays L.). This single sequencing run annotated >25,000 maize genomic sequences and also captured approximately 400 expressed transcripts for which homologous sequences have not yet been identified in other species. Approximately 70% of the ESTs generated in this study had not been captured during a previous EST project conducted using a cDNA library constructed from hand-dissected apex tissue that is highly enriched for SAMs. In addition, at least 30% of the 454-ESTs do not align to any of the approximately 648,000 extant maize ESTs using conservative alignment criteria. These results indicate that the combination of LCM and the deep sequencing possible with 454 technology enriches for SAM transcripts not present in current EST collections. RT-PCR was used to validate the expression of 27 genes whose expression had been detected in the SAM via LCM-454 technology, but that lacked orthologs in GenBank. Significantly, transcripts from approximately 74% (20/27) of these validated SAM-expressed "orphans" were not detected in meristem-rich immature ears. We conclude that the coupling of LCM and 454 sequencing technologies facilitates the discovery of rare, possibly cell-type-specific transcripts.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.