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| Status |
Public on Jun 03, 2020 |
| Title |
ΔhbtRC+pVSV105_3 |
| Sample type |
SRA |
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| Source name |
Bacterial culture
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| Organism |
Aliivibrio fischeri |
| Characteristics |
strain: ES114
genotype: deltahbtRC
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| Growth protocol |
Bacteria were grown in liquid seawater-tryptone medium with 1.75 mM IPTG to mid-log phase
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with RNAprotect Bacterial Reagent (Qiagen). RNA was extracted with RNeasy Mini Kit (Qiagen). DNA was degraded with TURBO Dnase (Invitrogen).
Ribosomal reduction (RiboZero) and strand-specific library preparation (TruSeq) were performed at the University of Minnesota Genomics Center per standard Illumina protocols. Paired-end 50-bp sequence analysis was performed on an Illumina HiSeq 2500 on high-output mode.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Ribosome-depleted RNA
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| Data processing |
Reads were trimmed and filtered with Trimmomatic to remove adaptor sequences and discard reads not matching the V. fischeri genome (maximum mismatch:1, LEADING:3, TRAILING:3, SLIDINGWINDOW:4,20, MINLEN:35).
Reads were mapped to the V. fischeri genome with Bowtie2 (-un-con, --sensitive).
Reads were counted with featureCounts (-p disabled, -t=gene, -g=locus_tag, -Q=10, -s).
Differential expression was analyzed with DESeq2 (outliers filtering and independent filtering turned on).
Genome_build: NC_006840.2, NC_006841.2, NC_006842.2
Supplementary_files_format_and_content: Tab-delimited text files containing normalized read counts for each gene.
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| Submission date |
Jun 02, 2020 |
| Last update date |
Jun 03, 2020 |
| Contact name |
Brittany Dawn Bennett |
| E-mail(s) |
[email protected], [email protected]
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| Organization name |
University of Hawaii
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| Department |
Pacific Biosciences Research Center
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| Lab |
Ruby
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| Street address |
41 Ahui St.
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| City |
Honolulu |
| State/province |
HI |
| ZIP/Postal code |
96813 |
| Country |
USA |
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| Platform ID |
GPL28616 |
| Series (1) |
| GSE151621 |
HbtR, a heterofunctional homolog of the virulence regulator TcpP, facilitates the transition between symbiotic and planktonic lifestyles in Vibrio fischeri. |
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| Relations |
| BioSample |
SAMN15081249 |
| SRA |
SRX8453165 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4586747_tcp-del_3_filtered.txt.gz |
17.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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