|
| Status |
Public on Aug 01, 2022 |
| Title |
R+T+V_P8_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organisms |
Vibrio hepatarius; Ruegeria pomeroyi DSS-3; Thalassospira sp. HF15 |
| Characteristics |
v. hepatarius strain: Vibrio hepatarius HF70
time point: P8
|
| Growth protocol |
All bacteria were grown on marine basel medium supplemented with 1.25 mM ectoine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from filters using the ZymoBIOMICS RNA Miniprep Kit (Zymo Research), treated with Turbo DNase (Invitrogen, Waltham, MA, USA), and cleaned using RNA Clean & Concentrator (Zymo Research). Ribosomal rRNA was removed using the NEBNext® rRNA Depletion Kit (NEB, Ipswich, MA, USA).
Stranded RNA-seq libraries were prepared and sequenced using an Illumina NextSeq 500 SE75 High Output flow cell at the Georgia Genomics and Bioinformatics Core (University of Georgia). Mono-culture samples of three bacterial species were pooled together for RNA-seq library prep and sequencing run.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
P8_R_RVT_3
P8_V_RVT_3
P8_T_RVT_3
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx
|
| Data processing |
FASTX toolkit was used to retain reads with a minimum quality score of 28 over 70% of read length
rRNA reads were filtered using SortMeRNA (30) and a custom-curated rRNA database
The remaining mRNA reads were mapped to the respective genomes using STAR (2.6.1c-foss-2016b) and counted using HTSeq
Genes with zero reads mapping in all samples were removed from further analysis. Counts were converted to transcripts per million (TPM)
Supplementary files format and content: Matrix table with raw gene counts for every gene of each bacterium in different conditions
|
| |
|
| Submission date |
Mar 30, 2022 |
| Last update date |
Oct 28, 2022 |
| Contact name |
He Fu |
| E-mail(s) |
biofuhe@gmail.com
|
| Organization name |
University of Georgia
|
| Department |
Microbiology
|
| Street address |
120 Cedar St
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL32094 |
| Series (1) |
| GSE199797 |
Transcriptome of a Synthetic Microbial Community |
|
| Relations |
| BioSample |
SAMN27107708 |
| SRA |
SRX14670137 |
