|
| Status |
Public on Aug 22, 2023 |
| Title |
T0-0689-3 |
| Sample type |
SRA |
| |
|
| Source name |
HD73 cells, cdsR knockdown, T0
|
| Organism |
Bacillus thuringiensis serovar kurstaki str. HD73 |
| Characteristics |
cell type: Bacterial cells
genotype: cdsR knockdown
treatment: T0
|
| Treatment protocol |
Samples of T-1 indicate samples of logarithmic phase, samples of T0 indicate samples of the end of logarithmic growth, and samples of T1 indicate samples of adaptation phase.
|
| Growth protocol |
HD73 and cdsR deletion mutant were cultured in SSM medium until T-1, T0, and T1, respectively. T0 indicates the end of the exponential growth phase and Tn indicates the number of hours before (-) or after T0. The samples were crushed to extract total RNA for sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted using the RN43-EASYspin Plus kit (Aidlab Biotechnologies,Beijing) following the manufacturer's. The total RNA qualityand purity were analysis of Bioanalyzer 2100 system and RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA).
Ribosomal RNA was removed using Epicentre Ribo Zero™ rRNA Removal Kits (bacteria) (Epicentre, USA) . sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
HD73 cells, cdsR knockdown, T0, repeat 3
|
| Data processing |
The raw sequence data were quality filtered using the fastp software.
Filtered fastq files were used for mapping to the reference genome using Rockhopper version 2.0 software with default parameters.
rRNA reads were eliminated by using SortMeRNA v2.1 program together with silva database.
reads were mapped to ribosomal RNA genes by Hisat2.
The DESeq2 suite of programs was used to analysis differential transcripts from in a pairwise fashion.
Assembly: Bacillus thuringiensis serovar kurstaki str. HD73 (NCBI Reference Sequence: NC_020238.1)
Supplementary files format and content: Reads were mapped to ribosomal RNA genes by Hisat2. After that, FeatureCount was employed to do expression calibration.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Oct 21, 2022 |
| Last update date |
Aug 22, 2023 |
| Contact name |
zhang xin |
| E-mail(s) |
zhangxin_live@outlook.com
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Department |
Institute of Plant Protection
|
| Lab |
State Key Laboratory for Biology of Plant Diseases and Insect Pests
|
| Street address |
No.2 West Yuanmingyuan Road
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL32767 |
| Series (1) |
| GSE216307 |
Functional study of a small transcriptional factor CdsR |
|
| Relations |
| BioSample |
SAMN31405017 |
| SRA |
SRX17985128 |
