|
| Status |
Public on Dec 21, 2020 |
| Title |
WT3_S3_L004_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
WT_control_exponential growth phase
|
| Organism |
Geobacter sulfurreducens PCA |
| Characteristics |
strain: PCA
treatment: without cobalt
growth phase: Exponential
|
| Treatment protocol |
Addition of cobalt chloride 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 QIAseq FastSelect – 5S/16S/23S rRNA depletion (QIAGEN). 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).
Genome_build: ASM798v2
Supplementary_files_format_and_content: xls file with filtering steps (false discovery rate FDR<0.05, log CPM>5, and a log2 FC<-1 (downregulated genes) or >1 (upregulated genes) )
Supplementary_files_format_and_content: csv output file give by SPARTA software
|
| |
|
| Submission date |
Aug 30, 2020 |
| Last update date |
Apr 25, 2022 |
| 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 |
GPL29085 |
| Series (1) |
| GSE157146 |
Cobalt resistance via detoxification and mineralization in the iron-reducing bacterium Geobacter sulfurreducens |
|
| Relations |
| BioSample |
SAMN15942367 |
| SRA |
SRX9036259 |
