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Status |
Public on Jun 30, 2021 |
Title |
metZ-3 |
Sample type |
SRA |
|
|
Source name |
metZ deletion mutant after24 h of curdlan fermentation
|
Organism |
Agrobacterium sp. CGMCC 11546 |
Characteristics |
genotype: metZ deletion
|
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
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|
|
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 HTSeq was used to count reads. Genome_build: Agrobacterium fabrum str. c58 Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
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|
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Submission date |
May 14, 2019 |
Last update date |
Jun 30, 2021 |
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 (1) |
GSE131215 |
Methionine biosynthetic pathway genes metH and metZ affect curdlan synthesis in Agrobacterium sp. CGMCC 11546 |
|
Relations |
BioSample |
SAMN11644463 |
SRA |
SRX5830933 |