|
| Status |
Public on Feb 05, 2021 |
| Title |
Geobacillus thermoglucosidasius DSM2542 at 4 h with 1% xylose |
| Sample type |
SRA |
| |
|
| Source name |
Cells of Geobacillus thermoglucosidasius DSM2542 harvested at 4 h after fermentation
|
| Organism |
Parageobacillus thermoglucosidasius |
| Characteristics |
synonymn: Geobacillus thermoglucosidasius
strain: DSM2542
genotype: wild type
treatment: treated with 1% xylose
timepoint: 4h
|
| Treatment protocol |
Cell pellets were quickly harvested by fast filtration and flash frozen in liquid nitrogen, and then ground into powder
|
| Growth protocol |
Geobacillus thermoglucosidasius DSM2542 were cultivated in 250 mL shake flask with 50 mL USYE medium containing 40 mM each (final concentrations) of Bis-Tris, PIPES, and HEPES at pH 7.0 at 60 °C, 250 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. 3 ug of total RNA was used for RNA-seq
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 |
| |
|
| Description |
Global gene expression profile of Geobacillus thermoglucosidasius DSM2542 at 4 h with 1% xylose
|
| Data processing |
For RNA-seq raw reads of fastq format were firstly processed to remove low quality reads and those containing adapter.
The clean reads were mapped against predicted transcripts of the Geobacillus thermoglucosidasius DSM2542 genome (https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP012712.1) by using SOAPaligner/SOAP2.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene, and then the FPKM was calculated based on the gene length and mapped read counts.
Genome_build: https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP012712.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample of RNA_seq.
|
| |
|
| Submission date |
Feb 04, 2021 |
| Last update date |
Feb 05, 2021 |
| Contact name |
Junyang Wang |
| E-mail(s) |
junyang199036@126.com
|
| Phone |
13718683829
|
| Organization name |
Institute of Microbiology, Chinese Academy of Sciences
|
| Street address |
1 Beichen West Road, Chaoyang District, Beijing,
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL29694 |
| Series (1) |
| GSE166135 |
Time-series RNA-seq data of Geobacillus thermoglucosidasius DSM2542 |
|
| Relations |
| BioSample |
SAMN17776088 |
| SRA |
SRX10020151 |
