|
| Status |
Public on Mar 05, 2018 |
| Title |
Mutant |
| Sample type |
SRA |
| |
|
| Source name |
Mutant
|
| Organism |
Agrobacterium fabrum str. C58 |
| Characteristics |
strain: C58
genotype: lsrB mutant
od600: 0.5-0.6
|
| Growth protocol |
Subcultures were started by inoculation of 50 mL of fresh TY medium with 5% of overnight cultures and allowed to grow to log phase (OD600 = 0.5-0.6)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIZOL Reagent (Invitrogen, 15596026)
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 Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Agrobacterium tumefaciens C58 whole genome using bowtie2(version: 2- 2.0.5)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using protocol from Mortazavi A et al., Nat Methods, 2008; Anders S et al, Bioinformatics, 2015; Robinson MD, Ge nome Biol, 2010.
Genome_build: Agrobacterium fabrum C58, ASM9202v1
Supplementary_files_format_and_content: EXCEL files include RPKM values for each Sample
|
| |
|
| Submission date |
Jan 08, 2018 |
| Last update date |
Mar 05, 2018 |
| Contact name |
tang gui rong |
| E-mail(s) |
qingxiong51@126.com
|
| Phone |
18516262462
|
| Organization name |
University of Chinese Academy of Sciences
|
| Department |
Shanghai Institutes for Biological Sciences
|
| Street address |
fenglin road 300
|
| City |
上海 |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL24478 |
| Series (1) |
| GSE108845 |
The LsrB protein is required for Agrobacterium tumefaciens interaction with host plants |
|
| Relations |
| BioSample |
SAMN08324513 |
| SRA |
SRX3583313 |
