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Sample GSM4628310 Query DataSets for GSM4628310
Status Public on Jun 25, 2021
Title ML3286 (MG1655 pKVS45-GapR-3xFLAG), in exponential phase, induced with aTc
Sample type SRA
 
Source name Escherichia coli MG1655
Organism Escherichia coli str. K-12 substr. MG1655
Characteristics growth stage: exponential phase
strain: ML3286
media: LB + 25 ng/µL aTc
Treatment protocol As needed, cells were induced with 25 ng/mL anhydrous tetracycline for 2 hr.
Growth protocol Strains were grown in LB, diluted to OD 0.3 and diluted back to OD ~0.01, and 25 ng/mL aTc was added. Cells were grown for 2 hr (OD ~0.3) and RNA was extracted and processed into sequencing libraries as previously reported (Culviner and Laub, 2018).
Extracted molecule total RNA
Extraction protocol RNA was extracted as previously reported (Culviner and Laub, 2018).
Sequencing libraries were processed as previously reported (Culviner and Laub, 2018).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Reads were aligned to Escherichia coli MG1655 (NC_000913.2) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
To calculate mRNA abundance, a pseudocount was added to all positions and the number of reads mapped to a gene was divided by the length of the gene and normalized to yield the mean number of reads per kilobase per million sequencing reads (RPKM).
The change in gene expression was calculated by taking log2-RPKM ratio of each gene from the experimental condition to the control condition (GapR-3xFLAG induced / GapR-3xFLAG uninduced).
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Wiggle files first column containing chromosome positions and second column containing the fraction of reads mapped to the position. For RNA-seq, two files are provided, one for forward and reverse strand.
 
Submission date Jun 19, 2020
Last update date Jun 25, 2021
Contact name Monica S Guo
E-mail(s) msguo@uw.edu
Organization name University of Washington
Department Microbiology
Lab Guo
Street address 750 Republican St
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL21117
Series (2)
GSE152879 High-resolution, genome-wide mapping of positive supercoiling in chromosomes [RNA-seq]
GSE152882 High-resolution, genome-wide mapping of positive supercoiling in chromosomes
Relations
BioSample SAMN15329697
SRA SRX8586152

Supplementary file Size Download File type/resource
GSM4628310_D19-11576-4278G_MG1655_norm_fw.wig.gz 18.1 Mb (ftp)(http) WIG
GSM4628310_D19-11576-4278G_MG1655_norm_rv.wig.gz 18.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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