|
| Status |
Public on Oct 02, 2009 |
| Title |
FLX sequencing of Piwi-associated small RNAs extracted from Drosophila ovarian somatic cells (OSC) |
| Sample type |
SRA |
| |
|
| Source name |
ovarian somatic cell (OSC)
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: ovarian somatic cell (OSC)
method: immunoprecipitation
target: Piwi protein
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Piwi was immunopurified from OSC using a specific antibody. Total RNAs were isolated from the immunoprecipitates with phenol:chloroform and precipitated with ethanol. Cloning of small RNAs associated with Piwi in OSC was carried out.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
454 GS FLX |
| |
|
| Description |
After immunoprecipitation, total RNAs were isolated from the immunoprecipitates with phenol:chloroform and precipitated with ethanol. RNAs were dephosphorylated with 16 CIP (NEB) and labeled with 32P-gamma-ATP with T4 polynucleotide kinase (TaKaRa) for visualization.
|
| Data processing |
The adapter sequences attached to 5' and 3' end of every sequence produced from Roshe/454 FLX system were removed. We used NCBI bl2seq program (-p BLASTN -g F -W 10 -e 10 -D 1) to detect fragments of the adapter sequences in the raw sequence and extracted 21,211 sequences. Sequences containing ambiguous Ns were discarded. Among the extracted sequences, 21,089 sequences were mapped onto Drosophila melanogaster genome (dm3). 21,089 sequences were boiled down to 10,890 unique sequence set.
|
| |
|
| Submission date |
Mar 06, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Toutai MITUYAMA |
| Organization name |
National Institute of Advanced Industrial Science and Technology (AIST)
|
| Department |
Artificial Intelligence Research Team
|
| Lab |
Computational Omics Research Team
|
| Street address |
2-4-7 Aomi
|
| City |
Koto-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
135-0064 |
| Country |
Japan |
| |
|
| Platform ID |
GPL9333 |
| Series (1) |
| GSE15137 |
FLX sequencing of Piwi-associated small RNAs extracted from Drosophila ovarian somatic cells (OSC) |
|
| Relations |
| SRA |
SRX012414 |
| BioSample |
SAMN00004746 |
