|
| Status |
Public on Oct 01, 2010 |
| Title |
zebrafish embryo 16.5h after fertilization |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish developing embryo
|
| Organism |
Danio rerio |
| Characteristics |
anchor: NlaIII
tag length: 22
tag count: 466332
strain: Tg(fli1:EGFP)y1albino b4/b4)
tissue: whole embryo after fertilization
developmental stage: 16.5h after fertilization
|
| 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 |
Embryo was collected at 16.5h after fertilization.
|
| 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 |
GPL9319 |
| Series (1) |
| GSE20682 |
High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing |
|
| Relations |
| BioSample |
SAMN02196167 |
