|
| Status |
Public on Jun 30, 2022 |
| Title |
WT-3. |
| Sample type |
SRA |
| |
|
| Source name |
Agrobacterium sp. CGMCC 11546 after 24 h of curdlan fermentation
|
| Organism |
Agrobacterium sp. CGMCC 11546 |
| Characteristics |
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
bacterial cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA labrarys 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 used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Agrobacterium fabrum str. c58 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
HTSeq software used for calculating RPKM
Genome_build: Agrobacterium fabrum str. c58
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …
|
| |
|
| Submission date |
Jun 29, 2020 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Deming Jiang |
| E-mail(s) |
foodmicrobiolab@163.com
|
| Organization name |
East China Normal University
|
| Street address |
No. 500, Dongchuan Road, Minhang District, Shanghai
|
| City |
Shanghai |
| ZIP/Postal code |
200241 |
| Country |
China |
| |
|
| Platform ID |
GPL26670 |
| Series (2) |
| GSE153505 |
Glutamine synthetase gene glnA plays an important role in curdlan biosynthesis of Agrobacterium sp. CGMCC 11546 |
| GSE153506 |
phbC and glnA play important roles in curdlan biosynthesis of Agrobacterium sp. CGMCC 11546 |
|
| Relations |
| BioSample |
SAMN15399759 |
| SRA |
SRX8633397 |
