|
| Status |
Public on Aug 08, 2018 |
| Title |
S1_L001: Control rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Control
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
antibioic treatment: 1 ug/mL of ciprofloxacin
fatty acid treatment: None
treatment time: 1 hour
|
| Treatment protocol |
Cells were divided to two cultures with 25 mL each. The one culture was treated with 1 µg/ml of ciprofloxacin as a control, and the other culture was treated with both 1 µg/ml of ciprofloxacin and 500 µM of ET2DA. After one-hour incubation, cells were pelleted by centrifuging at 12,000 ´g for 5 min and washed twice with 25 mL of cold 0.85% NaCl. The cell pellet was resuspended in 2 mL of RNAlater (Invitrogen, Carlsbad, CA) and incubated for one hour at 4°C. Then, RNAlater was removed by centrifugation, and the cell pellet obtained was stored in -80°C until use.
|
| Growth protocol |
Overnight culture of E. coli BW25113 was diluted 100 times with LB medium and incubated at 37°C with shaking (220 rpm) until OD = 0.5. Cells were washed twice using 0.85% NaCl and resuspended with fresh LB to adjust the OD = 1.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Zymo RNA isolation kit (Zymo Research, Irvine, CA) by following the manufacturer’s suggested protocol. Total RNA was quantified by Qubit and the RNA integrity (RIN) was assessed by Agilent 2200 TapeStation. Ribo-Zero rRNA removal Kit (Illumina, San Diego, CA) was used to remove ribosomal RNA from 1 µg of total RNA sample by following the protocol supplied in the kit.
cDNA was synthesized by reverse transcription and amplified to generate library using ScriptSeq Complete Kit (Epicenter, Madison, WI) and thermal cycler by following the library preparation protocol provided by the manufacturer. Libraries were sequenced on an Illumina NextSeq500 with 2x75bp reads on a Mid Output Sequencing Flow Cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
gene expression during persister cell formation
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to E.Coli MG1655 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: E. coli MG1655
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Mar 30, 2018 |
| Last update date |
Aug 08, 2018 |
| Contact name |
Seok Hoon Hong |
| E-mail(s) |
shong26@iit.edu
|
| Phone |
3125678950
|
| Organization name |
Illinois Institute of Technology
|
| Department |
Chemical and Biological Engineering
|
| Street address |
10 West 33rd Street, Perlstein Hall 127
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60616-3730 |
| Country |
USA |
| |
|
| Platform ID |
GPL21117 |
| Series (1) |
| GSE112545 |
Medium chain unsaturated fatty acid ethyl esters inhibit persister formation of Escherichia coli via antitoxin HipB |
|
| Relations |
| BioSample |
SAMN08822982 |
| SRA |
SRX3867272 |
