|
| Status |
Public on May 03, 2020 |
| Title |
sod_12h rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole cells
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
treatment: sodium hypochlorite
time: 12h
|
| Treatment protocol |
One of 10 biocides (disinfectants and antiseptics).
|
| Growth protocol |
Escherichia coli MG1655 was grown in minimal media (M9 with 0.4% w/v glucose) for 12h (mid to late exponential growth) at 37°C (pre-inoculum).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cold 5% (v/v) phenol:ethanol was added (1.5 mL per 3 mL sample) to each tube. The cells were pelleted by centrifugation at 4000 RPM at 4°C for 10 min and stored at -80°C for up to two weeks.
Total RNA was recovered from pelleted cells with the RNeasy mini kit (Qiagen) and on-column DNase digestion (Qiagen). Ribosomal RNA was removed with capture oligonucleotide mix (MICROBExpress, Ambition). RNA clean-up was performed with NucleoSpin RNA Clean-up (Macherey-Nagel).
For the library preparation, the KAPA Stranded RNA-Seq Library Preparation kit for Illumina platforms (Kapa Biosystems) was used according to the manufacturer’s instructions. An extra step of size selection was performed using Agencourt AMPure XP magnetic beads (Beckman Coulter).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Bacteria grown in M9 for 12h, followed by 1:100 dilution in M9 + sodium hypochlorite (3.64 uM) and growth to mid-exponential.
processed data file: processed_data_file_ecoli_biocides.xlsx
|
| Data processing |
Adapters and low-quality reads were removed from the raw reads by Trimmomatic.
Alignment to the reference files for E. coli MG 1655 by Bowtie2.
Bam files generated by Bowtie2 were fed into FeatureCounts.
Differentially expressed genes (DEGs) were identified using edgeR and Deseq-2 with a false discovery rate of 0.05 as the threshold for calling differential expression.
Gene ontology terms (GO: biological process) were captured from Ecocyc for all DEGs.
Genome_build: E. coli MG1655 (GenBank U00096.3)
Supplementary_files_format_and_content: *_raw.csv: Comma-separated text files include raw counts.
Supplementary_files_format_and_content: *_norm.csv: Comma-separated text files include normalized counts.
Supplementary_files_format_and_content: processed_data_file_ecoli_biocides.xlsx: Excel file containing DEGs and GO biological process terms.
|
| |
|
| Submission date |
Jan 04, 2019 |
| Last update date |
May 05, 2020 |
| Contact name |
Ilias Tagkopoulos |
| E-mail(s) |
itagkopoulos@ucdavis.edu
|
| Phone |
5307524821
|
| Organization name |
UC Davis
|
| Lab |
5212 GBSF
|
| Street address |
451 Health Science Dr.
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL17024 |
| Series (1) |
| GSE124673 |
Escherichia coli exposed to biocides (antiseptics and disinfectants) |
|
| Relations |
| BioSample |
SAMN10693089 |
| SRA |
SRX5204079 |
