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| Status |
Public on Jun 30, 2016 |
| Title |
TB |
| Sample type |
SRA |
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| Source name |
Gluconobacter oxydans cells
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| Organism |
Gluconobacter oxydans |
| Characteristics |
genotype: pqqB-overexpression mutant
strain: Gluconobacter oxydans WSH003
culture phase: exponential growth phase
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| Extracted molecule |
total RNA |
| Extraction protocol |
The bacterial total RNA extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer’s instructions and adding lysozyme (Sinopharm, Shanghai, China).
RNA libraries 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 MiSeq |
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| Data processing |
FastQC v0.11.3 software used for basecalling.
Cutadapt software used forremoving the adapter sequences using Cutadapt software,and then removed low overall quality reads which base qulity values Q≤20 is over 50% using FASTX-ToolKit software, and then filter reads containing ambiguous bases or trimming flanking ambiguous bases using NGS QC Toolkit.
The aligment of clean reads were mapped against the G. oxydans genome WSH003 using Bowtie 2.
To obtain and visualize the differences data in gene expression between two samples, Cufflinks and cummeRbund were used according to the described.
Genome_build: ASM31176v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Oct 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hui Wan |
| E-mail(s) |
zhoujw1982@jiangnan.edu.cn
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| Phone |
8651085918312
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| Organization name |
Jiangnan University
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| Street address |
No 1800 Lihu Avenue
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| City |
Wuxi |
| State/province |
Jiangsu |
| ZIP/Postal code |
214122 |
| Country |
China |
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| Platform ID |
GPL21079 |
| Series (1) |
| GSE74431 |
Transcriptome sequencing of Gluconobacter oxydans with different PQQ production |
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| Relations |
| BioSample |
SAMN04208318 |
| SRA |
SRX1370287 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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