|
| Status |
Public on Mar 25, 2020 |
| Title |
cobB-1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Yersinia pestis |
| Characteristics |
strain: cobB mutant of Yersinia pestis biovar Microtus str. 91001
growth stage: mid-log phase
|
| Growth protocol |
The cobB and yfiQ mutants and the wild-type strain were individually inoculated in duplicate into fresh TMH medium from the overnight cultures and grown at 26°C to an OD620 of about 0.6. The cultures were pelleted, resuspended in equal amounts of fresh TMH medium and then cultivated at 26°C to mid-log phase (OD620 ≈ 1.2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Ambion PureLinkTM RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software was used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
Bowtie2-2.2.3. (Langmead, B. and S.L. Salzberg, 2012) was used to map clean reads to the reference genome of Yersinia pestis biovar Microtus str. 91001 (NC_005810) to map clean reads to reference gene.
Genome_build: NC_005810
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Mar 25, 2018 |
| Last update date |
Mar 25, 2020 |
| Contact name |
Zongmin Du |
| E-mail(s) |
zmduams@163.com
|
| Organization name |
Beijing Institute of Microbiology and Epidemiology
|
| Street address |
No. 20, Fengtai Dongdajie Street
|
| City |
Beijing |
| ZIP/Postal code |
100071 |
| Country |
China |
| |
|
| Platform ID |
GPL24209 |
| Series (1) |
| GSE112313 |
Protein Acetylation Mediated by YfiQ and CobB Is Involved in the Virulence and Stress II |
|
| Relations |
| BioSample |
SAMN08793980 |
| SRA |
SRX3844060 |
