|
| Status |
Public on Oct 17, 2022 |
| Title |
TPA·2Na |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Piscinibacter sakaiensis |
| Characteristics |
strain: 201-F6
cell type: bacterial cell
genotype: wild-type
time: 20 h
|
| Growth protocol |
Cells were cultured in a test tube containing YSV medium with a PET film, TPA·2Na, or EG as the primary carbon source for 20 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-Free DNase Set (Qiagen).
Bacterial 16S and 23S ribosomal RNAs were removed from total RNA with the Ribo-Zero rRNA removal kit for gram-negative bacteria (Illumina, San Diego, CA). The enriched mRNA fraction was converted to an RNA-Seq library with multiplexing adaptors.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
CLC Genomics Workbench v 20.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to ASM129352v1 using CLC genomic workbench (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: ASM129352v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jun 10, 2022 |
| Last update date |
Oct 17, 2022 |
| Contact name |
Shosuke Yoshida |
| E-mail(s) |
ssk-yoshida@bs.naist.jp
|
| Organization name |
Nara Institute of Science and Technology
|
| Street address |
8916-5 Takayama-cho
|
| City |
Ikoma |
| State/province |
Nara |
| ZIP/Postal code |
630-0192 |
| Country |
Japan |
| |
|
| Platform ID |
GPL32339 |
| Series (1) |
| GSE205843 |
RNA-seq of Ideonella sakaiensis 201-F6 when grown on PET, TPA·2Na, and EG |
|
| Relations |
| BioSample |
SAMN28963196 |
| SRA |
SRX15670307 |
