|
| Status |
Public on Sep 26, 2018 |
| Title |
Condition A rep3 |
| Sample type |
SRA |
| |
|
| Source name |
ATCC 27594
|
| Organism |
Serratia liquefaciens |
| Characteristics |
strain: ATCC 27592
atmosphere: CO2
temperature: 0C
pressure: 7 mbar
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected using a bench top centrifuge, and RNA was extracted using the RiboPureTM RNA Purification Kit (Thermo Fisher Scientific, Waltham, MA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina HiSeq Control Software v2.2.37 was used for basecalling.
Sequenced reads were trimmed to remove low-quality base-calls. Trimmed sequences were mapped to the ATCC 27592 genome using bowtie2 v2.3.2. Aligned sequences were quantified at the gene level using HTSeq v0.6.1.
Gene counts for each sample were imported into R v3.4.2 using limma v3.33.7. Differential expression analysis was done using the default parameters in limma and a significance cut-off of 2 fold with a p value < 0.01.
Genome_build: RefSeq NC_021741.1
Supplementary_files_format_and_content: .csv files include the raw count values for each sample, and the limma normalized abundant output for each condition comparison.
|
| |
|
| Submission date |
Sep 24, 2018 |
| Last update date |
Sep 27, 2018 |
| Contact name |
Wayne Nicholson |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Florida
|
| Department |
Microbiology and Cell Science
|
| Street address |
Space Life Sciences Laboratory 505 Odyssey Way Room 201B
|
| City |
Merritt Island |
| State/province |
FL |
| ZIP/Postal code |
32953 |
| Country |
USA |
| |
|
| Platform ID |
GPL25602 |
| Series (1) |
| GSE120390 |
Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere. |
|
| Relations |
| BioSample |
SAMN10127601 |
| SRA |
SRX4737354 |
