|
| Status |
Public on Dec 31, 2024 |
| Title |
N2_S5_L006_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
Exponential growth phase
|
| Organism |
Trichlorobacter lovleyi |
| Characteristics |
strain: SZ
treatment: with nitrate
|
| Treatment protocol |
Addition of sodium nitrite into the culture media
|
| Growth protocol |
Anaerobic growth in liquid media without agitation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction following manufacturer's recommendation for QIAGEN RNeasy kit (QIAGEN)
rRNA depletion used an Illumina TruSeq Total RNA Library Preparation kit with RiboZero Bacteria rRNA depletion beads. Libraries were quantified using Qubit and Advanced Analytical Fragment Analyzer High Sensitivity DNA NGS assays. The libraries were then pooled in equimolar amounts for multiplexed sequencing and the pool was quantified using the Kapa Biosystems Illumina Library Quantification qPCR kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
SPARTA pipeline https://sparta.readthedocs.io/en/latest/
raw data output file from SPARTA
raw data counts obtained in csv file were filtered base on the cuttoff parameters as follow: false discovery rate FDR< 0.05, log CPM>5, and a log2 FC<-1 (downregulated genes) or > 1 (upregulated genes) (Johnson et al., 2016).
|
| |
|
| Submission date |
Jan 13, 2021 |
| Last update date |
Dec 31, 2024 |
| Contact name |
MARCELA TABARES |
| Organization name |
MICHIGAN STATE UNIVERSITY
|
| Department |
MMG
|
| Lab |
REGUERA LAB
|
| Street address |
567 WILSON RD
|
| City |
EAST LANSING |
| State/province |
MI |
| ZIP/Postal code |
48823 |
| Country |
USA |
| |
|
| Platform ID |
GPL29599 |
| Series (1) |
| GSE164776 |
Low levels of nitrate rather than high carbon-nitrogen ratios induce Dissimilatory Nitrate Reduction to Ammonia (DNRA) in Geobacter lovleyi SZ. |
|
| Relations |
| BioSample |
SAMN17308655 |
| SRA |
SRX9844013 |
