|
| Status |
Public on Feb 04, 2014 |
| Title |
0h nitrogen starved cell rep1 |
| Sample type |
SRA |
| |
|
| Source name |
0h nitrogen starved cell rep1
|
| Organism |
Rhodopseudomonas palustris CGA009 |
| Characteristics |
time point: 0h
strain: CGA009
|
| Treatment protocol |
When cells reached the mid-logarithmic phase of growth, the headspace was flushed with argon gas for 10 min (t0), cells were starved for nitrogen for 12, 30, 50, 90 140, and 180h, and harvested for RNA purification
|
| Growth protocol |
R. palustris CGA009 was grown anaerobically in the light in mineral medium with nitrogen gas as the sole nitrogen source and 20mM acetate as the sole carbon source
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified by using the QIAGEN miRNeasy Mini kit followed by Ambion's Turbo DNase treatment
RNA-seq library was constructed by using R. palustris-specific selective primers and NuGENs Ovation Ultralow DR Multiplex System
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Xpression was used for filtering reads
Xpression called BWA to align reads against the R. palustris strain CGA009 genome (BX571963.1)
Xpresssion was used for quantifying, normalizing, and visualizing read counts
DESeq was used for identifying differentially expressed genes
Genome_build: ASM19577v1, GI:39748133
Supplementary_files_format_and_content: Processed data contains raw read count and reads per kilobase per million uniquely mapped (RPKM) number
|
| |
|
| Submission date |
Oct 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yasuhiro Oda |
| E-mail(s) |
yasuhiro@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Department of Microbiology
|
| Lab |
Harwood
|
| Street address |
Box 357242, 1705 N.E. Pacific Street, HSB K-354
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-7242 |
| Country |
USA |
| |
|
| Platform ID |
GPL17852 |
| Series (1) |
| GSE51825 |
Non-growing Rhodopseudomonas palustris increases the hydrogen gas yield from acetate by shifting from the glyoxylate shunt to the tricarboxylic acid cycle |
|
| Relations |
| BioSample |
SAMN02387045 |
| SRA |
SRX369387 |
