|
| Status |
Public on Jul 15, 2024 |
| Title |
Vh-WT-Rep2T |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial lysate
|
| Organism |
Vibrio campbellii |
| Characteristics |
strain: BB120
genotype: WT (BB120)
agent: Terminator Exonucleae
|
| Treatment protocol |
When indicated samples were treated with Terminator Exonucleae (TEX; epicentre)
|
| Growth protocol |
Cells were grown at 30°C in LM media to an OD600 of 1.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Reagent followed by Dnase I treatment
For Illumina sequencing of cDNA molecules, the libraries were constructed by vertis Biotechnology AG, Germany. The cDNA libraries were sequenced using a NextSeq 500 machine (Illumina) in single-read mode
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping (READemption 0.3.0)
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.0)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.3.0)
Genome_build: CP000789.1, CP000790.1, CP000791.1
Supplementary_files_format_and_content: wiggle
|
| |
|
| Submission date |
Aug 27, 2021 |
| Last update date |
Jul 15, 2024 |
| Contact name |
Julia van Kessel |
| E-mail(s) |
[email protected]
|
| Phone |
812-856-2235
|
| Organization name |
Indiana University
|
| Department |
Biology
|
| Lab |
van Kessel
|
| Street address |
1001 E 3rd Street, Biology Building
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL27117 |
| Series (1) |
| GSE182898 |
dRNA-Seq data for Vibrio campbellii BB120 (ATCC BAA-1116, previously designated as Vibrio harveyi) |
|
| Relations |
| BioSample |
SAMN21019577 |
| SRA |
SRX11947271 |
