|
| Status |
Public on Apr 20, 2024 |
| Title |
RNA sequencing of Vibrio natriegens CL-2 without salt stress ( 1) |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Vibrio natriegens |
| Characteristics |
cell type: bacterial cell
stress: without salt stress
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The bacterial cells were lysed using Qiagen bacterial lysis buffer, the lysate containing RNA was passed to silica membrane of Qiagen RNeasy spin column, and the total RNA was eluted using nuclease free water. The quality of the RNA was analysed through Agilent Bioanalyzer.
QIAseqFastSelect – 5S/16S/23S Kit for Bacterial Ribodepletion and QIAseq Stranded RNA Library Kit for Library preparation following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
CL-2(C0)
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using trimgalore (Phred score threshold of 20)
Trimmed sequence reads were mapped to reference genome using Bowtie2 aligner.
Read count extraction was done using featureCounts and normalization and DEG identification was done using DESeq2.
Assembly: GCF_001456255.1, GCF_002220285.1
Supplementary files format and content: tab delimited text file include normalized counts for each sample
|
| |
|
| Submission date |
Apr 13, 2024 |
| Last update date |
Apr 20, 2024 |
| Contact name |
Rajnish Prakash Singh |
| E-mail(s) |
[email protected]
|
| Organization name |
Jaypee Institute of Information Technology
|
| Street address |
A 10, A Block, Block A, Industrial Area, Sector 62, Noida
|
| City |
Noida |
| ZIP/Postal code |
201309 |
| Country |
India |
| |
|
| Platform ID |
GPL34383 |
| Series (1) |
| GSE263917 |
RNA sequencing of bacterial samples under salt stress [CL2] |
|
| Relations |
| BioSample |
SAMN40951415 |
| SRA |
SRX24242350 |
