|
| Status |
Public on Mar 30, 2019 |
| Title |
2 mM sialic acid |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial liquid culture
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: WT
time induction: 20 minutes
treatment: 2 mM sialic acid
|
| Treatment protocol |
Sialic acid was made as a 100 mM stock and then dissolved 1:100 into cultures for a final concentration of 1 mM at OD~0.6. Sialic acid was incubated for 20 minutes with cultures before RNA extraction.
|
| Growth protocol |
Separate P. aeruginosa colonies were picked from LB agar plates. Overnight cultures (12-16 hrs) were grown at 37°C in LB. Cultures were back diluted 1:100 in the morning and grown up to OD~0.6 before the addition of sialic acid.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the MasterPure Complete DNA and RNA Purification Kit (see publication for more details).
Purified RNA was submitted to the MIT MicroBio core for processing and library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Single-end reads mapped to PA14 genome using bowtie2 with default settings.
Genes with fewer than 200 read counts were eliminated. To normalize data, the total number of reads across all genes was calculated for + and - sialic acid conditions. The normalized read count for each gene was calculated by dividing each raw read count by the total read count for both + and - sialic acid conditions.
To calculate fold change of each gene, the ratio between the normalized read count of each gene in the + sialic acid vs. the - sialic acid condition was calculated. Data in the paper is shown as the log2 transformation of this data.
Genome_build: NC_008463.1
Supplementary_files_format_and_content: All_RNAseqdata_20min.csv is a file containing the counts of all genes from the processed RNA-seq data in both + and - sialic acid conditions.
|
| |
|
| Submission date |
Mar 15, 2018 |
| Last update date |
Mar 30, 2019 |
| Contact name |
Benjamin Wang |
| Organization name |
MIT
|
| Street address |
31 Ames Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02141 |
| Country |
USA |
| |
|
| Platform ID |
GPL18644 |
| Series (1) |
| GSE111903 |
Sialic acid relieves RetS-dependent inhibition of GacS to induce a chronic infection state of Pseudomonas aeruginosa |
|
| Relations |
| BioSample |
SAMN08719531 |
| SRA |
SRX3799630 |
