Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing

ABSTRACT: High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing

PROVIDER: PRJNA124943 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing

Project description: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 permit to enable researchers to analyze digital tags from many 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 were expected and several examples of its applications were introduced in the present study, including analyses of laser-microdissected cells, biological replicates or tag extraction using different anchoring enzymes.

2010-10-01 | GSE20682 | GEO

High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing

2010-09-30 | E-GEOD-20682 | biostudies-arrayexpress

High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing.

Project description: Not available

| S-EPMC2917361 | biostudies-literature

Isolation and molecular characterisation of Dunaliella tertiolecta with truncated light-harvesting antenna for enhanced photosynthetic efficiency.

Project description:Digital gene expression analysis by Ht-SuperSAGE (Matsumura et al. 2011. High-Throughput SuperSAGE. Methods Mol Biol.) was carried out to compare gene expression between wild type and mutant cell lines of the green algae Dunaliella tertiolecta under different light levels.

2020-06-30 | GSE129614 | GEO

Digital transcriptome analysis of genes on sex chromosomes in papaya (Carica papaya)

2012-07-16 | GSE30366 | GEO

High-throughput SuperSAGE for transcript profiling in berry tissues of Vitis vinifera L. under different light regimes

Project description:SuperSAGE is a method of digital gene expression profiling that allows isolation of 26bp tag fragments from expressed transcripts. Because its tag size is larger than that of conventional SAGE, SuperSAGE allowed a secure tag-to-gene annotation using BLAST search against grape genome databases.Transcript profiles in nine samples of grape berry tissues under different light conditions were obtained by SuperSAGE analysis and used for screening the genes which have co-ordinated transcript profiles with the change in the flavonoid composition in the samples analyzed. Candidate genes related to flavonoid biosynthesis and regulation were identified.

2014-06-03 | GSE55473 | GEO

Analysis of gene expression in rice mature leaf and cultured cell suspension using Rice SuperSAGE Array1

Project description:We developed a novel platform for genome-wide gene expression analysis in any eukaryotic organism, that we coin SuperSAGE Array. The SuperSAGE Array is a microarray onto which oligonucleotides of 26 nucleotides corresponding to SuperSAGE tag sequences are directly synthesized. A SuperSAGE Array combines the advantages of the highly quantitative SuperSAGE expression analysis with the high-throughput microarray technology. Highly reproducible gene expression profiling by the SuperSAGE Array was demonstrated for a thousand of genes (tags) in rice. Keywords: Tissues, SuperSAGE, 26base oligonucleotide

2006-07-28 | GSE4685 | GEO

Analysis of gene expression in Nicotiana benthamiana following NbCD1- or NbCD3-overexpression using SuperSAGE Array1

Project description:We developed a novel platform for genome-wide gene expression analysis in any eukaryotic organism, that we coin SuperSAGE Array. The SuperSAGE Array is a microarray onto which oligonucleotides of 26 nucleotides corresponding to SuperSAGE tag sequences are directly synthesized. A SuperSAGE Array combines the advantages of the highly quantitative SuperSAGE expression analysis with the high-throughput microarray technology. This technology was also applied to the detailed study of expressed genes identified by SuperSAGE in Nicotiana benthamiana, an organism without available DNA database. Keywords: transgene overexpression, transient expression

2006-07-28 | GSE4686 | GEO

High-throughput tissue dissection and cell purification with digital cytometry

Project description:High-throughput tissue dissection and cell purification with digital cytometry

| PRJNA524853 | ENA

Digital transcriptome analysis of genes on sex chromosomes in papaya (Carica papaya)

Project description:For identifying genes for sex determination in papaya, digital gene expression analysis by Ht-SuperSAGE (Matsumura et al., 2010) was carried out in flowers from male, female and hermaphrodite plants of papaya. Total more than 9,273,744 26bp-tags were obtained by sequence analysis using SOLiD3 and mapped on papaya primitive sex chromosome sequences. 6 samples examined: male young flowerbud, male mature flower bud, female young flower bud, female mature flower bud, hermaphrodite young flower bud, hermaphrodite mature flower bud

2012-07-15 | E-GEOD-30366 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data