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| Status |
Public on Sep 08, 2016 |
| Title |
Lzd_treated |
| Sample type |
SRA |
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| Source name |
Exponential E. coli cells
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| Organism |
Escherichia coli |
| Characteristics |
strain: BWDK (-tolC)
treatment: 400 µg/mL LZD
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosome profiling was carried out using the antibiotic hypersusceptible E. coli strain BWDK, a derivative of the strain BW25113 with inactivated tolC gene. The overnight culture grown in LB medium was diluted 100 fold into three conical baffled 1 L flasks with 100 ml of LB supplemented with 0.2% glucose and grown with vigorous shaking at 37°C. When the culture density reached OD600 ~ 0.5, CHL or LZD were added to a final concentration of 100 µg/ml or 800 µg/ml (100 x fold MIC) and incubation continued for 2.5 min. The control culture did not receive a drug treatment. Cells were harvested by rapid filtration, frozen in liquid nitrogen and processed for ribosome profiling as described. The library for Illumina sequencing was prepared using RNA fragments ranging in size between 28 and 42 nt. Analysis of ribosome profiling was carried out using the GALAXY pipeline. The first position of the P site codon was assigned at 15 nt away from the 3’ end of the read.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Ribosomal Footprint
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| Data processing |
Wig files were generated using the Galaxy pipeline described in Kannan et al., Proceedings of the National Academy of Sciences, 2014
Ribosome P-site were assigned as 15 nt from the 3' end of the sequencing read
Genome_build: U00093.3
Supplementary_files_format_and_content: WIG file
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| Submission date |
Sep 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
James Marks |
| E-mail(s) |
marksjp@nih.gov
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| Phone |
502-931-1657
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| Organization name |
NIAMS/NIH
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| Street address |
50 South Drive
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL18133 |
| Series (1) |
| GSE86536 |
Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center |
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| Relations |
| BioSample |
SAMN05736497 |
| SRA |
SRX2145674 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2305306_LZD_fwd.wig.gz |
756.4 Kb |
(ftp)(http) |
WIG |
| GSM2305306_LZD_rev.wig.gz |
823.5 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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