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Sample GSM3767759 Query DataSets for GSM3767759
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
 
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.
 
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

Supplementary file Size Download File type/resource
GSM3767759_metZ_3_RPKM.txt.gz 43.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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