|
| Status |
Public on Mar 01, 2024 |
| Title |
S.rapa, without PQQ, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Streptomyces rapamycinicus |
| Characteristics |
cell type: bacteria
genotype: without PQQ operon
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA of each sample was extracted using Total RNA Extractor kit (B511311, Sangon, China) according to the manufacturer’s protocol. The extracted RNA was then sent to the Sangon Biotech (Shanghai) Co., Ltd. for library construction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
srpqq.csv
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the streptomyces rapamycinicus NRRL5491(CP085193.1) and streptomyces griesus DSM 40236 (GCA_900105705.1) genome assembly using bowtie2（version: 2-2.0.5）.
Gene expression level was calculated by DESeq2 R package (v.1.20.0), displaying as average values of three clones from each group.
Assembly: streptomyces rapamycinicus NRRL5491(CP085193.1) and streptomyces griseus DSM 40236 (GCA_900105705.1)
Supplementary files format and content: csv files include values as follows: BaseMean (the average of the normalized counts for samples with and without PQQ operon); log2FoldChange (The log2-transformed fold change of averaged gene expression with and without PQQ operon); lfcSE (The standard error associated with the log2FoldChange): stat (The Wald test statistic for testing the null hypothesis that the log2FoldChange is equal to zero (i.e., no differential expression)); pvalue (The p-value associated with the Wald test).
|
| |
|
| Submission date |
Feb 20, 2024 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Xinran Wang |
| E-mail(s) |
xr.wang@siat.ac.cn
|
| Phone |
17841120985
|
| Organization name |
Shenzhen Institute of Advanced Technology, Chinese Acadamy of Science
|
| Department |
Center for Synthetic Biochemistry
|
| Lab |
Keasling and Luo Lab
|
| Street address |
No.1068 Xueyuan Avenue
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518100 |
| Country |
China |
| |
|
| Platform ID |
GPL34215 |
| Series (1) |
| GSE256209 |
Elucidation of genes enhancing natural product biosynthesis through co-evolution analysis |
|
| Relations |
| BioSample |
SAMN40002184 |
| SRA |
SRX23671883 |
