|
| Status |
Public on Apr 04, 2017 |
| Title |
Planktonic cells |
| Sample type |
SRA |
| |
|
| Source name |
Planktonic cells of Pseudoalteromonas sp. SCSIO 11900
|
| Organism |
Pseudoalteromonas sp. SCSIO_11900 |
| Characteristics |
genotype/variation: wild type strain
cell type: Planktonic cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Tiangen RNAprep Pure Cell (Tiangen Biotech, China) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina Hiseq 2000 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file:
11900_Initial_pellicle_vs_planktonic.txt
11900_Mature_pellicle_vs_planktonic.txt
11900_raw_counts.xls
|
| Data processing |
Sequencing was performed on Illumina HiSeq2000 platform
Dirty raw reads were filtered. Clean reads were mapped to reference genome and genes sequences respectively using SOAP2 (Li, 2009).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated as mentioned (Mortazavi, Williams et al. 2008).
Then, the calculated gene expression can be directly used for comparing the difference of gene expression among samples.
Genome_build: genome sequence of Pseudoalteromonas sp. SCSIO 11900: https://www.ncbi.nlm.nih.gov/nuccore/JEMJ00000000
Supplementary_files_format_and_content: xls files including RPKM values for each sample, and difference of gene expression between initial pellicle and planktonic, and between mature pellicle and planktonic.
|
| |
|
| Submission date |
Apr 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Pengxia Wang |
| E-mail(s) |
wangpengxia@scsio.ac.cn
|
| Phone |
+(86) 20 89235490
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
South China Sea Institute of Oceanology
|
| Street address |
164 Xingang West Rd
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510301 |
| Country |
China |
| |
|
| Platform ID |
GPL23248 |
| Series (1) |
| GSE97322 |
Transcriptome analysis of planktonic, initial pellicle, and mature pellicle of Pseudoalteromonas sp. SCSIO 11900 |
|
| Relations |
| BioSample |
SAMN06675918 |
| SRA |
SRX2700627 |
