|
| Status |
Public on Jul 01, 2010 |
| Title |
TSS_FWAF_logphase |
| Sample type |
SRA |
| |
|
| Source name |
G. sulfurreducens PCA, grown in FWAF medium, mid-log phase
|
| Organism |
Geobacter sulfurreducens PCA |
| Characteristics |
strain: PCA
genotype: wild type
condition: fresh water acetate-fumarate (FWAF) medium
|
| Growth protocol |
G. sulfurreducens PCA strain was cultured in FWAF medium, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen) and DNA was removed by DNase digestion. RNA quality and concentration was determined by analysis with a Thermo NanoDrop 1000.
RNA with 5’-monophosphate end was removed with 5’-phosphate-dependent exonuclease. The 5’-triphosphate end of primary RNA was then converted to 5’-monophosphate end with RNA 5’ polyphosphatase. 5’ sRNA adapter was ligated to the 5’ end of mRNA. cDNAs were then synthesized from the adapter-ligated mRNA using 3’-adapter. Fraction of the cDNA between 100 bp and 300 bp was then gel purified and PCR amplified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Alignment: The data were aligned onto the G. sulfurreducens PCA genome (NC_002939.4) using the Mosaik Aligner (http://bioinformatics.bc.edu/marthlab/Mosaik), hash size = 15, mismatch=0. These data are in the *bed files.
5' end: the 5' end of unique aligned reads were counted and considered as potential transcription start sites. These data are in the *wig files.
|
| |
|
| Submission date |
Jun 30, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Bernhard Palsson |
| E-mail(s) |
palsson@ucsd.edu
|
| Phone |
858-534-5668
|
| Fax |
858-822-3120
|
| URL |
http://systemsbiology.ucsd.edu
|
| Organization name |
UCSD
|
| Department |
Bioengineering
|
| Lab |
Systems Biology Research Group
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92122 |
| Country |
USA |
| |
|
| Platform ID |
GPL10638 |
| Series (2) |
| GSE22511 |
Genome-wide transcription start site determination of Geobacter sulfurreducens under multiple growth conditions |
| GSE22512 |
Analysis of Geobacter sulfurreducens under multiple growth conditions |
|
| Relations |
| SRA |
SRX023132 |
| BioSample |
SAMN00016912 |
