|
| Status |
Public on Jul 26, 2014 |
| Title |
female |
| Sample type |
SRA |
| |
|
| Source name |
female gonad (adult of one years old from the F1 progeny of family "G3")
|
| Organism |
Magallana gigas |
| Characteristics |
developmental stage: adult (one year old)
colony: F1 progeny of "G3" family
tissue: female gonad
exptl group: tissue
|
| Treatment protocol |
small RNA is extracted by TRIzol Reagent
|
| Growth protocol |
The embryo were cultured in sea water with a volume of 20 cubic meters. The temperature of the sea water is 26 ºC and the salinity is 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. Juvenile and adult individuals were cultured in natural sea.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For smRNA-seq, we gel-purified 18-30 nts RNAs from the samples utilized for RNA-seq. Illumina 5â and 3â RNA adapter were sequentially ligated to the RNA fragments and the ligated products were size-selected on denaturing polyacrylamide gels. The adapter-linked RNA was reverse transcribed with small RNA RT primers and amplified with 15 cycles of PCR using small RNA PCR primer 1 and 2 (Illumina). The libraries were sequenced with the Illumina Genome Analyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sequenced reads were generated from the female gonad of an individual of "G3" family in Crassostrea gigas.
|
| Data processing |
use oyster_v9 genome as reference, sequenced reads were aligned onto the corresponding reference using SOAP2.20 with default parameters except -M 0 -l 17 -v 0 -p 7 -r 2
|
| |
|
| Submission date |
Jul 28, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Fei Xu |
| E-mail(s) |
xufei@qdio.ac.cn
|
| Phone |
+86-13791940813
|
| Organization name |
Institute of Oceanology, Chinese Academy of Sciences
|
| Street address |
7 Nanhai Road
|
| City |
Qingdao |
| ZIP/Postal code |
266071 |
| Country |
China |
| |
|
| Platform ID |
GPL13986 |
| Series (1) |
| GSE31009 |
miRNA of Pacific oyster Crassostrea gigas for different organs and developmental stages |
|
| Relations |
| SRA |
SRX085377 |
| BioSample |
SAMN00690285 |
