|
| Status |
Public on Mar 05, 2013 |
| Title |
plasmid cured rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Xuzhou21 cured of the pO157_Sal plasmid
|
| Organism |
Escherichia coli O157:H7 |
| Characteristics |
strain: Xuzhou21m
genotype: plasmid cured strain
|
| Treatment protocol |
For total RNA isolation, the bacteria were inoculated in 5 ml LB broth at 37℃with shaking for 16 h. 50 µl of the above culture was inoculated in 5 ml fresh LB broth and the culture was shaken at 37°C for about 2.5 h until the OD600 reached 0.6. 500 µl of the culture were mixed with 1 ml RNA protect bacterial reagent (Qiagen, Hilden, Germany) to stabilize RNA according to the manufacturer’s instructions.
|
| Growth protocol |
The bacteria were routinely grown in Luria-Bertani (LB) broth or on LB agar plates (pH 7.2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were then isolated according to the standard protocol using an RNeasy mini kit (Qiagen). Genomic DNA were extracted from both Xuzhou21 and Xuzhou21m using Wizard Genomic DNA purification kit (Promega, Madison, WI, USA) according to the manufacturer’s protocols.
The total RNA extracted from Xuzhou21 and Xuzhou21m were first treated with Ribo-Zero™ rRNA Removal kit to remove rRNA. The mRNA was fragmented and produced cDNA libraries primed with random hexamers. cDNA was selected by size, amplificated using PCR and and then sent to sequencing using Illumina HiseqTM 2000 commercially.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
total RNA
|
| Data processing |
All RNA data were mapped to the reference genome Xuzhou21 using SOAP2.
The distribution of reads was plotted by its location in the reference genome, and then divided into gene region and intergenic region. Genome and gene coverage was calculated by counting the number of reads mapped to the genome and individual genes respectively.
The gene expression was calculated using the RPKM method
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Mar 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
qing hong zhao |
| E-mail(s) |
zhaohq1209@163.com
|
| Organization name |
china cdc
|
| Street address |
changbai road 155
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL16748 |
| Series (1) |
| GSE44846 |
Global transcriptional and phenotypic analyseis of Escherichia coli O157:H7 strain Xuzhou21 and its pO157_Sal cured mutant |
|
| Relations |
| SRA |
SRX248463 |
| BioSample |
SAMN01974761 |
