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| Status |
Public on Sep 15, 2024 |
| Title |
RNC S1K247Q-3 |
| Sample type |
SRA |
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| Source name |
bacteria
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| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
cell type: bacteria
genotype: S1K247Qoverexpression
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| Treatment protocol |
When strains cultrued to OD600 0.6，1mM IPTG was added to the strains. After induction for 3h, strains were collected respectively.
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| Growth protocol |
LB（Luria-Bertani） medium
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial samples were treated with pre-chilled cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer): 20 mM HEPES-KOH (pH 7.4), 15 mM MgCl2, 200 mM KCl, 100 𝜇g/ml cycloheximide, and 2 mM dithiothreitol]. After a 30 min ice bath, cell lysates were collected and transferred to pre-chilled 1.5 mL tubes. After that, cell debris was removed by centrifuging at 4 °C for 10 min. Supernatants were transferred to the surface of sucrose buffer (30% sucrose in ribosome buffer), then ultracentrifuged at 4°C by T-865 fixed angle rotor (ThermoFisher, Germany) to pellet RNCs. Pellets were then resuspended with RB buffer.
Isolation of total RNA was carried out by the Trizol Reagent (Invitrogen, USA) according to the manufacturer's instructions. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The obtained RNA-Seq library was sequenced on Illumina NovaSeq 6000.
Low-quality reads were trimmed by using Cutadapt (v4.3).
Assembly: Escherichia coli K-12 MG1655 (NCBI,ASM584v2)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jan 24, 2024 |
| Last update date |
Sep 15, 2024 |
| Contact name |
利 赵 |
| E-mail(s) |
y10190077@mail.ecust.edu.cn
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| Phone |
18963566353
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| Organization name |
华东理工大学
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| Street address |
梅陇路130号
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| City |
上海 |
| State/province |
State/Province |
| ZIP/Postal code |
200237 |
| Country |
China |
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| Platform ID |
GPL26592 |
| Series (1) |
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| Relations |
| BioSample |
SAMN39600367 |
| SRA |
SRX23384791 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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