|
| Status |
Public on Apr 07, 2017 |
| Title |
WT_12h_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria cells
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BW25113
product: Butanol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries 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 |
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively
Genome_build: CP009273.1
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample
|
| |
|
| Submission date |
Mar 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chunhua Zhao |
| E-mail(s) |
jeil0901@163.com
|
| Organization name |
Institute of Microbiology, Chinese Academy of Sciences
|
| Street address |
No.1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL14548 |
| Series (1) |
| GSE96551 |
Genome-wide analysis of the differentially expressed genes between a butanol-producing wild type strain and a pykA mutant during fermentation |
|
| Relations |
| BioSample |
SAMN06564546 |
| SRA |
SRX2636840 |
