|
| Status |
Public on May 15, 2020 |
| Title |
RNAseq_C. beijerinckii: B. subtilis cocultured cathodic MEC-connected, nitrate-enriched wastewater, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cathodic MEC-connected using nitrate-enriched wastewater
|
| Organism |
Clostridium beijerinckii |
| Characteristics |
protocol: B. subtilis cocultured cathodic MEC-connected using nitrate-enriched wastewater
|
| Treatment protocol |
Two two-chamber H-Cell MECs (Adams & Chittenden Scientific Glass) were used for conducting bioelectrochemcial experiments. 50 ml of 10 g/L NaCl and graphite felt anode (3.75 cm2 and 2 mm thickness) were used in the anodic chamber. The anode chamber and the cathode chamber (volume 50 mL) were separated using a membrane (Nafion 117, perfluorinated membrane, 0.007in. thick). Wastewater supplemented with 1% glucose, a graphite rod cathode (2.4 cm length and 0.6 cm diameter), an Ag/AgCl (3M NaCl) reference electrode (Bioanalytical Systems, Inc. BASi) were used as the cathodic compartment. 5 ×106 cells/ml from B. subtilis and OE-NasDEF were inoculated to 50 ml of wastewater for B. subtilis + MC and OE-NasDEF+ MC systems, respectively and MC system was used as the control setup without additional bacteria inoculation. Anode and cathode were contacted via wire (0.025 cm diameter) to the outside of the MEC. The MEC was connected to a two-channel potentiostat/galvanostat (MLab) to record the current and potential during 48 h of run. The MEC was operated at 37 °C. Nitrogen gas sparged into the cathodic compartment to enhance anaerobic condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed through RNeasy Mini Kit (Qiagen), and the quality examination was performed by Bioanalyzer (Agilent) through Agilent RNA 6000 Nano Kit.
After removing rRNA from total RNA samples through Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina), library was prepared through TruSeq mRNA stranded Bacteria HT (Illumina).
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A2C_S4_L001_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis cocultured cathodic MEC-connected using nitrate-enriched wastewater-rep1
|
| Data processing |
Pre-processing of paired-end Illumina RNA reads was performed using GEO2RNAseq pipeline. Briefly, quality of reads was analyzed before and after trimmung using FastQC (v. 0.11.8). Quality control of reads was performed with Trimmomatic (v. 0.36). Mapping reads to reference genomes was performed using HiSat2. The ammonium and nitrate-enriched sequences were mapped on the reference genome of the Clostridium_beijerinckii (NCBI Assembly accession: ASM83310v2; GCF_000833105.2) and Clostridium butyricum (NCBI Assembly accession: ASM145606v2; GCF_001456065.2), respectively. In total 284,907,998 2x75 bp sequences were mapped on the reference genomes. Each sample was sequenced four times to ensure sufficient sequencing depth. Samples contained between 2,904,757 to 4,678,797 reads. The SAMtools package was used to convert, sort and index sequence alignment files for downstream data analysis. Gene abundances were estimated per sample using featureCounts tool.
Supplementary_files_format_and_content: csv including raw gene counts
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| |
|
| Submission date |
May 14, 2020 |
| Last update date |
May 15, 2020 |
| Contact name |
Shadi Rahimi |
| E-mail(s) |
shadi.mahshad@gmail.com, shadir@chalmers.se
|
| Organization name |
Chalmers University of Technology
|
| Department |
Department of Biology and Biological Engineering
|
| Street address |
Kemivägen 10
|
| City |
Goteborg |
| ZIP/Postal code |
41296 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL23579 |
| Series (1) |
| GSE150480 |
Co-culturing Bacillus subtilis and wastewater microbial community in a bio-electrochemical system enhances denitrification and butyrate formation |
|
| Relations |
| BioSample |
SAMN14923762 |
| SRA |
SRX8340854 |
