 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 01, 2010 |
| Title |
High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing |
| Organisms |
Arabidopsis thaliana; Oryza sativa; Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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.
|
| |
|
| Overall design |
27 different tissue samples from three different life organisms were analyzed. About 2 samples, three different anchoring enzymes were employed.
|
| |
|
| Contributor(s) |
Matsumura H, Yoshida K, Luo S, Kimura E, Fujibe T, Albertyn Z, Barrero RA, Krüger DH, Kahl G, Schroth GP, Terauchi R |
| Citation(s) |
20700453 |
| |
| Submission date |
Mar 08, 2010 |
| Last update date |
Nov 27, 2017 |
| Contact name |
Hideo Matsumura |
| E-mail(s) |
hideoma@shinshu-u.ac.jp
|
| Phone |
81-268-21-5800
|
| Organization name |
Shinshu University
|
| Department |
Gene Research Center
|
| Street address |
Tokita 3-15-1
|
| City |
Ueda |
| State/province |
Nagano |
| ZIP/Postal code |
3868567 |
| Country |
Japan |
| |
|
| Platforms (3) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
| GPL9316 |
Illumina Genome Analyzer II (Oryza sativa) |
| GPL9319 |
Illumina Genome Analyzer II (Danio rerio) |
|
| Samples (31)
|
| GSM518275 |
rice seedling-1 (5-cycles of PCR) |
| GSM518276 |
rice seedling-2 (5-cycles of PCR) |
| GSM518277 |
rice seedling-3 (5-cycles of PCR) |
| GSM518278 |
M.grisea-infected rice cells (30h) |
| GSM518279 |
M.grisea-infected rice cells (48h) |
| GSM518280 |
rice pollen cells |
| GSM518281 |
rice anther wall tissue |
| GSM518282 |
lm1 rice mutant seedling |
| GSM518283 |
M.grisea-infected rice leaf tissue |
| GSM518284 |
CM552 seedling (allele of lm1) |
| GSM518285 |
SG0807 seedling (allele of lm1) |
| GSM518286 |
rice germinating seed (c.v.Dunghan shali at low temp) |
| GSM518287 |
rice germinating seed (c.v. Kakehashi at low temp) |
| GSM518288 |
rice germinating seed (c.v.Dunghan shali,submerged) |
| GSM518289 |
rice germinating seed (c.v. Kakehashi,submerged) |
| GSM518290 |
wild type rice (cv. Sasanishiki) leaf |
| GSM518291 |
Pex33-overxpressing rice leaf |
| GSM518292 |
zebrafish embryo 10.5h after fertilization |
| GSM518293 |
zebrafish embryo 12h after fertilization |
| GSM518294 |
zebrafish embryo 13.5h after fertilization |
| GSM518295 |
zebrafish embryo 15h after fertilization |
| GSM518296 |
zebrafish embryo 16.5h after fertilization |
| GSM518297 |
Arabidopsis leaves (NlaIII) |
| GSM518298 |
Arabidopsis leaves (DpnII) |
| GSM518299 |
Arabidopsis leaves (BfaI) |
| GSM518300 |
Arabidopsis stems (NlaIII) |
| GSM518301 |
Arabidopsis stems (DpnII) |
| GSM518302 |
Arabidopsis stems (BfaI) |
|
| Relations |
| BioProject |
PRJNA124943 |
| Supplementary data files not provided |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...