|
| Status |
Public on Jul 17, 2023 |
| Title |
Strain_2251_LBS_25˚C_Biol_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
2251
|
| Organism |
Aliivibrio fischeri |
| Characteristics |
strain: 2251
genotype: ES114 {delta}binK
treatment: LBS _Media_25C
|
| Growth protocol |
V. fischeri strains were grown as 500uL colony spots on either LBS or LBS-10 mM Calcium agar plates for 48 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Colony material was scrapped from plates and processed using a QIAgen RNeasy PowerBiofilm kit, followed by an additional purification and on-column DNA digestion with the QIAgen Rneasy MinElute kit. For each sample, 500ng of total RNA was used for library construction.
Libraries were constructed using the Illumina Ribo-Zero Plus rRNA Depletion with Stranded Total RNA kit, with an addition of V. fischeri specific rRNA depeletion probes. Library preparation was conducted at the University of Wisconsin - Madison Biotechnology Center Gene Expression Center & DNA Sequencing Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
X225125R3_S415
|
| Data processing |
Raw FASTQ files were first processed using FASTP v0.20.1 for read quality control.
FASTP processed files were mapped using BWA-MEM v0.7.17.
Mapped reads were enumerated by loci using HTSeq v0.13.5
Differential expression analysis was conducted using EdgeR v3.32.1.
Assembly: Vibrio fischeri ES114 Chromosome 1: CP000020.2, Chromosome 2: CP000021.2, pES100 Plasmid: CP000022.1
Supplementary files format and content: Tab delimited file containing the mapped raw sequencing read pairs for each sample produced by HTSeq.
Supplementary files format and content: Tab delimited file containing the TPM values for each gene within the tested samples.
|
| |
|
| Submission date |
Jul 12, 2023 |
| Last update date |
Jul 17, 2023 |
| Contact name |
Jacob Alan Vander Griend |
| E-mail(s) |
[email protected]
|
| Phone |
858-248-7199
|
| Organization name |
University of Wisconsin - Madison
|
| Department |
Medical Microbiology and Immunology
|
| Lab |
Mandel
|
| Street address |
1550 Linden Drive
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53711 |
| Country |
USA |
| |
|
| Platform ID |
GPL33575 |
| Series (1) |
| GSE237189 |
Biofilm transcriptional pathways in the model symbiont Vibrio fischeri |
|
| Relations |
| BioSample |
SAMN36417203 |
| SRA |
SRX20995560 |
