|
| Status |
Public on Dec 10, 2024 |
| Title |
Vcor OCN008 wild-type RNA, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Vibrio coralliilyticus |
| Characteristics |
cell line/strain: OCN008
genotype: wild-type
condition: ~OD600=1.5
cell type: Bacterial
|
| Treatment protocol |
Samples originate from two sets Vibrio coralliilyticus strains, OCN008 and BAA-450, and two genotypes, wild-type (reference sample) and VcpR-null. Each sample set (i.e. OCN008 wild-type, OCN008::ΔvcpR, BAA-450 wild-type, BAA-450::ΔvcpR) received the same treatment.
|
| Growth protocol |
All Vcor samples grew in sterile LB marine (LM) medium (Lysogeny broth supplemented with 10 g NaCl L-1 and dissolved in purified water) in a shaking incubator (275 RPM) at 30°C. Samples were backdiluted 1:1,000 and grown to an OD600=1.5, which corresponds to high cell density in Vibrio. Once grown, cells pellets were collected, freezed in liquid nitrogen, and stored in a -80°C freezer until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Thawed pellets resuspended in TRIZOL (Invitrogen; 5 min. incubation) and chloroform (5 min. incubation) then pelleted at 4°C.Trasfered upper aqueous phase to new tube and mixed with isopropanol (incubated 10 min.). Centrifuged (max speed; supernatant discarded) and resuspended pellet in EtOH (75%). Centrifuged (supernatant discarded) and pellet resuspended in RNA-free water then incubated 15 min. at 56°C. Samples DNase treated (Ambion DNase-free kit protocol, included DNaseI inactivation step) and cleaned via QIAGEN RNeasy kit. Extracted RNA stored in -80°C freezer.
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The raw RNA-seq reads were cleaned using Trimmomatic version 0.38 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the corresponding genome reference (Vibrio coralliilyticus ATCC BAA-450 reference from the assembly GCF_000176135.1_ASM17613v1 for BAA-450 reads and Vibrio coralliilyticus OCN008 reference from the assembly GCF_011212705.1_ASM1121270v1 for OCN008 reads) using bowtie2 version 2.4.2 (Langmead et al. 2012).
Individual gene expression was quantified by counting the number reads mapping to each of the annotated genes using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s 2 -p -B -C)
Assembly: Vibrio coralliilyticus ATCC BAA-450 reference from the assembly GCF_000176135.1_ASM17613v1 for BAA-450 reads and Vibrio coralliilyticus OCN008 reference from the assembly GCF_011212705.1_ASM1121270v1 for OCN008 reads
Supplementary files format and content: Tab deliminted text files containing counts of reads overlapping with coding regions of the genes.
|
| |
|
| Submission date |
May 18, 2023 |
| Last update date |
Dec 10, 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 |
GPL33420 |
| Series (1) |
| GSE232809 |
Quorum sensing regulates virulence factors in the coral pathogen Vibrio coralliilyticus. |
|
| Relations |
| BioSample |
SAMN35158839 |
| SRA |
SRX20421431 |
