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Sample GSM1406483 Query DataSets for GSM1406483
Status Public on May 30, 2017
Title 1M9 rep1
Sample type SRA
 
Source name Whole cell
Organism Escherichia coli str. K-12 substr. MG1655
Characteristics strain: MG1655
treatment: Bacteria grown for 12 h in M9
time: 12 h
Extracted molecule total RNA
Extraction protocol Bacterial was harvested with 0.5 Vol of 5% Phenol in Ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using Rneasy.
Library constructed using KAPA Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Bacteria grown for 12 h in M9
Data processing For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. Trimmed reads were aligned on most recent reference genome of Escherichia coli (U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). Finally, Cufflink is used to generate FPKM-normalized expression value for each gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: vcf, mutations called; fpkm_tracking, fpkm-normalized expression values
 
Submission date Jun 09, 2014
Last update date May 15, 2019
Contact name Ilias Tagkopoulos
E-mail(s) iliast@ucdavis.edu
Organization name university of california at davis
Street address 2063 kemper hall, 1 shields avenue
City davis
State/province CALIFORNIA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL15010
Series (1)
GSE58325 The Genetic and Transcriptional Basis of Short and Long Term Adaptation across Multiple Stresses in Escherichia coli
Relations
BioSample SAMN02847835
SRA SRX581894

Supplementary file Size Download File type/resource
GSM1406483_iADB96_84.genes.fpkm_tracking.gz 108.2 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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