ArticlePloS one2010
High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 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
50 citing papers in PubMed, 109 citations in OpenAlex.
- Applications of artificial intelligence multiomics in precision oncology.Journal of cancer research and clinical oncology · 2023Review
- Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella.Plant cell reports · 2022Article
- The Importance of ATM and ATR inGenes · 2020Article
- HT-SuperSAGE of the gut tissue of a Vip3Aa-resistant Heliothis virescens (Lepidoptera: Noctuidae) strain provides insights into the basis of resistance.Insect science · 2019Article
- Developmental toxicity and apoptosis in zebrafish embryos induced by low-dose γ-ray irradiation.Environmental science and pollution research international · 2019Article
- Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling.PloS one · 2019Article
- Cowpea and abiotic stresses: identification of reference genes for transcriptional profiling by qPCR.Plant methods · 2018Article
- Improvement of Drought Tolerance in Rice (BioMed research international · 2018Review
- High-throughput SuperSAGE for gene expression analysis of Nicotiana tabacum-Rhizoctonia solani interaction.BMC research notes · 2017Article
- A gene expression atlas of adult Schistosoma mansoni and their gonads.Scientific data · 2017Article
- Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis.Applied and environmental microbiology · 2017Article
- End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data.Genome research · 2016Article
- DNA Methylation Analysis: Choosing the Right Method.Biology · 2016Review
- 'Candidatus Liberibacter asiaticus', Causal Agent of Citrus Huanglongbing, Is Reduced by Treatment with Brassinosteroids.PloS one · 2016Article
- Current status of tropical fruit breeding and genetics for three tropical fruit species cultivated in Japan: pineapple, mango, and papaya.Breeding science · 2016Review
- Performance evaluation of indel calling tools using real short-read data.Human genomics · 2015Article
- Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells.BMC genomics · 2015Article
- Genome sequence comparison reveals a candidate gene involved in male-hermaphrodite differentiation in papaya (Carica papaya) trees.Molecular genetics and genomics : MGG · 2015Article
- Selection and validation of potato candidate genes for maturity corrected resistance to Phytophthora infestans based on differential expression combined with SNP association and linkage mapping.Frontiers in genetics · 2015Article
- Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways.Frontiers in plant science · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined "High-Throughput (HT-) SuperSAGE". SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes allow researchers to analyze digital tags from transcriptomes of many samples in a single sequencing run by simply pooling the libraries. Here, we demonstrated that HT-SuperSAGE provided highly sensitive, reproducible and accurate digital gene expression data. By increasing throughput for analysis in HT-SuperSAGE, various applications are foreseen and several examples are provided in the present study, including analyses of laser-microdissected cells, biological replicates and tag extraction using different anchoring enzymes.
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.