|
| Status |
Public on Sep 20, 2023 |
| Title |
B. subtilis 9407 derived strain, active PNPase, PNPase group |
| Sample type |
SRA |
| |
|
| Source name |
B. subtilis 9407
|
| Organism |
Bacillus subtilis |
| Characteristics |
tissue: Bacteria
strain: 9407
cell type: Overexpressed
rip antibody: Anti-6X His tag monoclonal rabbit antibodies (Abcam, #ab200537)
treatment: Control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Target mRNAs were extracted using TRIzol reagent (Invitrogen), followed by determination of RNA concentration and quality analysis conducted by Seqhealth Technology Co., Ltd (Wuhan, China).
The stranded RNA sequencing library was constructed using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Seqhealth) following the manufacturer's instruction. The library products corresponding to 200-500 bps were enriched, quantified, and finally sequenced using the PE150 model on a Novaseq 6000 sequencer (Illumina).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PNPase_1
|
| Data processing |
Raw sequencing data were filtered using Trimmomatic (version 0.36) to discard low-quality reads and trim reads contaminated with adaptor sequences.
The de-duplicated consensus sequences were mapped to the reference genome of B. subtilis 9407, which was obtained from NCBI's GenBank database (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/835/225/GCF_002835225.1_ASM283522v1/) and aligned using STAR software (version 2.5.3a) with default parameters.
The RSeQC (version 2.6) was used for analyzing read distribution.
The exomePeak (Version 3.8) software was used for peak calling with a more stringent significance threshold (FDR < 0.05 and log2 FC ≥ 2).
Peaks were annotated using Bedtools (Version 2.25.0). DeepTools (Version 2.4.1) was used for analyzing peak distribution.
Assembly: GCA_002835225.1
Supplementary files format and content: D493A_peaks.tsv: Peaks of D493A group in tsv format
Supplementary files format and content: D493A_peaks_anno.tsv: Gene Annotation information of D493A group in tsv format
Supplementary files format and content: PNPase_peaks.tsv: Peaks of PNPase group in tsv format
Supplementary files format and content: PNPase_peaks_anno.tsv: Gene Annotation information of PNPase group in tsv format
|
| |
|
| Submission date |
Sep 15, 2023 |
| Last update date |
Sep 20, 2023 |
| Contact name |
Xiaofei Gu |
| E-mail(s) |
guxiaofei19911012@hotmail.com
|
| Organization name |
China Agricultural University
|
| Street address |
NO 2 Yuanmingyuan West Road , Haidian District, Beijing
|
| City |
Beijing |
| State/province |
China |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL30886 |
| Series (1) |
| GSE243342 |
RIP-seq of RNA associated in vivo with the PNPase and PNPaseD493A proteins, performed in Bacillus subtilis 9407 |
|
| Relations |
| BioSample |
SAMN37411409 |
| SRA |
SRX21787271 |
