|
| Status |
Public on Aug 23, 2019 |
| Title |
NH4+_plus_2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria_Ammonia
|
| Organism |
Bacillus velezensis |
| Characteristics |
strain: LG37
culture condition: minimal medium containing 10 mmol/L NH4+-N
time point: late log phase (0.4 - 0.7 OD)
|
| Growth protocol |
Bacteia were growth in minimal medium with initial OD600=0.02
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were lysed by constantly grinding in the presence of liquid nitrogen with the total RNA extracted using TRIzol reagent (Invitrogen), and finally dissolved in 50 μL RNase-free water.
The total RNA quality was evaluated after ribosomal RNAs were removed. The RNA was then fragmented and used as a template for a randomly primed PCR. Strand-specific cDNA libraries were prepared by standard techniques for subsequent Illumina sequencing (Illumina HiSeq 2000)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The quality of the raw sequence data were first assessed by FastQC and the sequences were then filtered and trimmed by Trimmomatic
The remaining reads were used to map to the reference genome of B. velezensis FZB42 (NC_009725.1) by Bowtie2
Alignments reported from Bowtie2 were further processed by the BEDTools software
Differential expression of all of transcripts was quantified through DEGseq software
Differential expressed genes were simply defined as at least 2-fold change with Q value <0.05.
Genome_build: B. velezensis FZB42 (NC_009725.1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 22, 2019 |
| Last update date |
Aug 26, 2019 |
| Contact name |
guangxin liu |
| E-mail(s) |
guangxinliu777@gmail.com
|
| Phone |
13006130090
|
| Organization name |
zhongkai university of agriculture and engineering
|
| Street address |
501 Zhongkai Road, Haizhu District, Guangzhou
|
| City |
guangzhou |
| ZIP/Postal code |
510225 |
| Country |
China |
| |
|
| Platform ID |
GPL27131 |
| Series (1) |
| GSE136178 |
Bacillus velezensis LG37: Transcriptome profiling and functional verification of GlnK and NmtA in ammonia (NH4+) assimilation |
|
| Relations |
| BioSample |
SAMN12619362 |
| SRA |
SRX6750644 |
