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| Status |
Public on Dec 05, 2022 |
| Title |
LEVO, TREATMENT, REP1 |
| Sample type |
SRA |
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| Source name |
K12 MG1655
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| Organism |
Escherichia coli |
| Characteristics |
strain: K12 MG1655
genotype: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan
media: M9 glucose
treatment: LEVO
time: 30 mins treatment
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| Treatment protocol |
Cells were treated with 5 µg/ml LEVO or 5 µg/ml MOXI or 5 µg/ml MMC for 1) 30 mins at 37˚C with shaking before RNA extraction, or 2) 5 h at 37˚C with shaking, followed by removal of drug, and 30 mins recovery in LB media.
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| Growth protocol |
Cells were culutred in 25ml M9 glucose media for 20 h O/N shaking at 37 ˚C to reach stationary phase.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was stablized using RNAprotect bacteria reagent (Qiagen, Germantown, MD). Total RNA was extracted using RNeasy Mini Kit with on-column DNA digestion with DNase I (Qiagen, Germantown, MD) following manufacturer’s instruction. rRNA depletion was performed using RiboCop rRNA Depletion Kit (Lexogen, Greenland, NH).
RNA libraryies was prepared using PrepX RNA-seq library preparation kit (Takara Bio, San Jose, CA).
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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 |
Reads qualities were assessed and mapped to Mu_origin 1 as reference genome using STAR.
Gene expression was quantified using featureCounts (Galaxy version 1.6.4+galaxy1).
DESeq2 v1.34.0 (code available at: https://github.com/CathyTJC/GCS-seq/blob/main/DEseq.R ) was performed to identify differential gene expression in both the drug treatment period and the recovery period.
Assembly: E.coli MG1655 U00096.3 modified to incorporate the Mu sequence. FASTA file and annotation file inlucded in the records
Supplementary files format and content: fasta file and *.gtf annoation file
Supplementary files format and content: text files containing the raw read counts mapped to each feature (gene)
Supplementary files format and content: tab-delimited text files containing the log2FoldChange and p-values from differntial gene analysis
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| Submission date |
Jun 21, 2022 |
| Last update date |
Dec 07, 2022 |
| Contact name |
Juechun Tang |
| E-mail(s) |
juechunt@princeton.edu
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| Organization name |
Princeton University
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| Department |
Chemical and Biological Engineering
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| Lab |
Brynildsen Group
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| Street address |
25 william streeet
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| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08540 |
| Country |
USA |
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| Platform ID |
GPL25368 |
| Series (2) |
| GSE206609 |
Effect of fluoroquinolone-induced gyrase cleavage sites on gene expression during drug treatment period and recovery period on E. coli |
| GSE206610 |
Fluoroquinolone-induced gyrase cleavage sites |
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| Relations |
| BioSample |
SAMN29229274 |
| SRA |
SRX15818693 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6257892_30min_LEVO_1_counts.txt.gz |
18.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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