|
| Status |
Public on Jan 21, 2023 |
| Title |
Escherichia coli K-12 novobiocin treated culture replicate 2 (VCE non-enriched 5’ end of primary transcripts) |
| Sample type |
SRA |
| |
|
| Source name |
Escherichia coli K-12 novobiocin treated culture
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: K-12
condition: novobiocin treated
|
| Treatment protocol |
Logarithmic culture of E. coli on rich medium was treated with tetracycline (20 mg / L, 30 min.), rifampicin (50 mg / L, 30 min.), and novobiocin (100 mg / L, 20 min.).
|
| Growth protocol |
Escherichia coli K-12 was grown on Luria broth at 37°C without antibiotics up to the logarithmic phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent (Thermo Fisher Scientific, Waltham, MA USA). The RNA samples were treated with a TURBO DNA-free™ kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions. The RNA content was determined in a Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity, purity, and concentration were assessed with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
The Cappable-Seq procedure was performed as previously described [Ettwiller et al., 2016]. The Ultra directional libraries was prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA)
library strategy: Cappable-Seq/Ultra directional
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
total RNA
Cappable-Seq library of Escherichia coli K-12 novobiocin treated culture (VCE non-enriched 5’ end of primary transcripts)
|
| Data processing |
Demultiplexed reads were trimmed against adapters and ribosomal RNA with bbduk.
Clean reads were mapped against the Escherichia coli K-12 full genome (GCA_000005845.2) with Bowtie2 in local mode (L-16).
The reads per transcript coverage of Ultra directional libraries were evaluated with Salmon (Patro et al., 2017).
The reads per tss were evaluated with perl script as previously described (https://github.com/Ettwiller/TSS).
Assembly: GCA_000005845.2
Supplementary files format and content: Tabular file include operon coverage values for each sample .
|
| |
|
| Submission date |
Oct 12, 2022 |
| Last update date |
Jan 21, 2023 |
| Contact name |
Alexander S Balkin |
| E-mail(s) |
freelivingresearcher@gmail.com
|
| Phone |
0079096071417
|
| Organization name |
Institute for Cellular and Intracellular Symbiosis
|
| Lab |
Laboratory og Biomedical technologies
|
| Street address |
11 Pionerskaya st.
|
| City |
Orenburg |
| ZIP/Postal code |
460000 |
| Country |
Russia |
| |
|
| Platform ID |
GPL15010 |
| Series (1) |
| GSE215300 |
Transcriptomic data of Escherichia coli K-12 control and antibiotic-treated cultures |
|
| Relations |
| BioSample |
SAMN31251276 |
| SRA |
SRX17858421 |
