|
| Status |
Public on Aug 28, 2020 |
| Title |
PA14 glycans 15 m |
| Sample type |
SRA |
| |
|
| Source name |
Planktonic bacterial cultures
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PA14
growth medium: ABTGC medium
growth time: 15 m
|
| 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 or (0.1%) MUC5AC glycans and grown for 15 minutes or 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 biotinylated rRNA probes (as described in Culviner and Laub, 2019).
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 |
Counts_MUC5AC_MUC5B_Glycans_5h.csv
|
| 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 PA14 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 PA14
Supplementary_files_format_and_content: comma-delimited text files with raw read counts
|
| |
|
| Submission date |
Aug 27, 2020 |
| Last update date |
Aug 28, 2020 |
| 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) |
| GSE156995 |
Transcriptomic profiles of Pseudomonas aeruginosa PA14 grown in the presence or absence of mucins or mucin-glycans |
|
| Relations |
| BioSample |
SAMN15924721 |
| SRA |
SRX9024472 |
