|
| Status |
Public on Oct 01, 2010 |
| Title |
Arabidopsis leaves (NlaIII) |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis mature leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
anchor: NlaIII
tag length: 22
tag count: 399106
ecotype: Wassilevskija
tissue: rosetta leaves
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ds-cDNA was synthesized using biotinylated dT primer. After digestion of cDNA with anchoring enzymes (NlaIII, DpnII or BfaI), digested fragments were associated with streptavidin magnetic beads. Adapters were ligated to cDNA ends on the beads and adapter-cDNA was digested with EcoP15I. Released fragments after enzyme digestion were ligated to adapter encoding barcode. Obtained fragments were once amplified PCR and applied to sequence analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
RNA was extracted from leaves. Synthesized cDNA was separated in three tubes and digested with each different enzyme (NlaIII, DpnII, BfaI).
|
| Data processing |
Sequece reads were sorted by barcode into separate files. From each read in each file, 26-bp sequence upstream anchoring enzyme site (CATG, GTAC or CTAG) was extracted. Extracted 26-bp sequences (tags) were count. These process was done by script written in Perl.
Tags were extracted from sequence data of multiplexed samples, which were analyzed by Illumina Genome Analyzer IIx.
|
| |
|
| Submission date |
Mar 05, 2010 |
| Last update date |
Jun 11, 2013 |
| 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 |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE20682 |
High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing |
|
| Relations |
| BioSample |
SAMN02196168 |
