|
| Status |
Public on Oct 20, 2019 |
| Title |
ABTGC rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Planktonic bacterial cultures
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
growth medium: ABTGC defined medium
growth time: 5 h
|
| Growth protocol |
Batch cultivation of Pseudomonas aeruginosa was carried out shaking at 37 °C in LB. Overnight cultures were diluted to an OD600 of 0.01 medium with or without (0.5%) MUC5AC, (0.5%) MUC5B, or (0.01%) MUC5AC-glycans and grown for 5 h at 37 °C in a static 96-well microtiter plate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the MasterPure RNA Purification kit (Lucigen) and residual DNA was removed using the Turbo DNA-free kit (Ambion). The integrity of the total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). 16S, 23S, and 5S rRNA were removed using the Ribo-Zero Magnetic Kit (Bacteria) (Epicentre).
Gene expression analysis was conducted via Illumina RNA sequencing (RNA-seq). Libraries were produced using the KAPA RNA HyperPrep kit (Kapa Biosystems). Libraries were sequenced using the Illumina HiSeq platform with a single-end protocol and read lengths of 40 nt or 52 nt.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Planktonic bacterial cultures
|
| Data processing |
Illumina genome analyzer modules Firecrest and Bustard were used for image analysis and base-calling, respectively.
Sequence reads were mapped onto the P. aeruginosa PAO1 reference genome, which is available for download from the Pseudomonas Genome Database (http://www.pseudomonas.com) using the Burrows Wheeler algorithm on the Galaxy server.
Read counts were quantified in R thes files are provided as processed data)
Gene expression values were normalized based on library size and differentially expressed genes were identified using a negative binomial test with a false discovery rate (FDR) less than 0.05.
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: comma-delimited text files with raw read counts
|
| |
|
| Submission date |
Aug 21, 2019 |
| Last update date |
Oct 20, 2019 |
| Contact name |
Katharina Ribbeck |
| E-mail(s) |
ribbeck@mit.edu
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Biological Engineering
|
| Lab |
Ribbeck
|
| Street address |
21 Ames St
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL18644 |
| Series (1) |
| GSE136097 |
Transcriptomic profiles of Pseudomonas aeruginosa PAO1 grown in the presence or absence of mucins or mucin-glycans |
|
| Relations |
| BioSample |
SAMN12613381 |
| SRA |
SRX6747257 |
