|
| Status |
Public on Oct 08, 2024 |
| Title |
escherichia coli, BL21(DE3), 5mM AcK-3 |
| Sample type |
SRA |
| |
|
| Source name |
BL21 (DE3)
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BL21 (DE3)
transformed with: 5mM AcK
|
| Treatment protocol |
The resulting colonies were inoculated into seed cultures, which were then diluted 1:100 into LB media containing 50 μg/mL kanamycin and incubated at 37 ˚C.
|
| Growth protocol |
BL21 (DE3) cells grown on LB-agar plates containing 50 μg/mL kanamycin overnight at 37 ˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
When the OD600 reached 0.1-0.2, the cells were induced with 0.2 mM IPTG, and the AcK group was supplied with 5 mM AcK. Subsequently, the cells were moved to 30 ˚C and harvested when the OD600 reached 0.5-0.6.
RNA was harvested using FreeZol Reagent (vazyme, catalog no. R711) and Bacteria RNA Enhancement Reagent (vazyme, catalog no. R412-C5) .
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
fpkm all samples(Kac_3)
|
| Data processing |
Illumina NovaSeq6000 reads were trimmed and clipped for quality control in Fastp v0.22.0
High quality reads in each sample were mapped to the reference genome Escherichia coli BL21(DE3) GCF_000022665.1 using analysis tool: Hisat2
rRNA contamination assessment using Blast
Expression analysis Quantify gene and transcript abundances from paired-end RNA-Seq data using RSEM
Differential expression analysis was performed using the DESeq2 v1.4.5
Assembly: BL21(DE3)(https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000022665.1/)
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Oct 02, 2024 |
| Last update date |
Oct 08, 2024 |
| Contact name |
Jinyuan Xu |
| E-mail(s) |
meng0108004@outlook.com
|
| Phone |
15896273656
|
| Organization name |
Nanjing University of Traditional Chinese Medicine
|
| Street address |
No. 138, Xianlin Street, Qixia District, Nanjing City, Jiangsu Province
|
| City |
Nanjing |
| ZIP/Postal code |
210038 |
| Country |
China |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
| GSE278616 |
RNA-seq analysis of BL21 (DE3) cells for AcK biosynthesis |
|
| Relations |
| BioSample |
SAMN44025088 |
| SRA |
SRX26261209 |
