|
| Status |
Public on Jul 26, 2014 |
| Title |
man_l_13d |
| Sample type |
SRA |
| |
|
| Source name |
left mantle
|
| Organism |
Magallana gigas |
| Characteristics |
developmental stage: adult
tissue: left mantle
exptl group: tissue
|
| Treatment protocol |
total RNA is extracted by TRIzol Reagent
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3â dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using a 1G Illumina Genome Analyzer and the paired-end sequencing module.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sequenced reads were generated from the left mantles of the treated oyster individuals sampled at 13th day after shell breakage.
|
| Data processing |
use oyster_v9 genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except -r 20 --mate-std-dev 5 -g 20 -I 10000 --solexa1.3-quals
|
| |
|
| 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) |
| GSE31011 |
Transcriptome sequencing of Pacific oyster Crassostrea gigas |
|
| Relations |
| SRA |
SRX093532 |
| BioSample |
SAMN00714406 |
