|
| Status |
Public on Dec 13, 2016 |
| Title |
wt, EtOH, 30 min, 30C |
| Sample type |
SRA |
| |
|
| Source name |
Caulobacter crescentus_wt, EtOH, 30 min, 30C
|
| Organism |
Caulobacter vibrioides |
| Characteristics |
strain: NA1000
genotype: wildtype
|
| Treatment protocol |
Mid-log cells were treated with 4% EtOH for 30 min before sampling.
|
| Growth protocol |
Cultures were grown in mid-log phase in rich medium (PYE) while shaking.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNAeasy kit (Qiagen) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols (done by Genewiz)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
sample4
Processed data file: Sample4 vs. Sample1.xlsx
Gene expression changes (fold changes) in EtOH-treated cells (30min) compared to untreated cells
|
| Data processing |
Data processing was performed by Genewiz.
Sequence reads were trimmed to remove low quality bases at ends, mapped to the reference genome (C. crescentus NA1000), hit counts were calculated and RPKM values for genes determined
Samples were compared to determine relative changes in gene expression (fold changes)
Genome_build: C. crescentus NA1000
Supplementary_files_format_and_content: Excel files containing differentially expressed genes (fold-change of original RPKM values and the normalized RPKM values)
|
| |
|
| Submission date |
Nov 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kristina Jonas |
| E-mail(s) |
kristina.jonas@su.se
|
| Organization name |
Stockholm University
|
| Department |
Department of Molecular Biosciences, The Wenner-Gren Institute
|
| Lab |
Jonas lab
|
| Street address |
Svante Arrheniusväg 20 C
|
| City |
Stockholm |
| ZIP/Postal code |
10691 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL18006 |
| Series (1) |
| GSE90030 |
A kinase-phosphatase switch transduces environmental information into a bacterial cell cycle circuit |
|
| Relations |
| BioSample |
SAMN06036135 |
| SRA |
SRX2359288 |
