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Sample GSM613993 Query DataSets for GSM613993
Status Public on Feb 05, 2011
Title [E-MTAB-387] E_coli_K12_MG1655_RNAseq_LB_Early_exponential
Sample type SRA
 
Source name E_coli_K12_MG1655_RNAseq_LB_Early_exponential
Organism Escherichia coli
Characteristics material type: whole_organism
strainorline: K-12 substr. MG1655
genotype: wide_type
growth condition: early-exponential
Growth protocol grow | The E. coli K-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1). Luria-Bertani (0.5% NaCl) broth and agar (15 g/liter) were used for routine growth.
Extracted molecule total RNA
Extraction protocol nucleic_acid_extraction | To prepare cells for RNA extraction, 100 ml of fresh LB was inoculated 1:200 from an overnight culture in a 250 ml flask and incubated with shaking at 180 r.p.m. in a New Brunswick C76 waterbath at 37C. Two biological replicates were performed for each strain and samples were taken at early-exponential, mid-exponential, transition-to-stationary and stationary phase. The cells were pelleted by centrifugation (10000 g, 10 min, 4¡C), washed in 1xPBS and pellets were snap-frozen and stored at -80C until required. RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's protocol until the chloroform extraction step. The aqueous phase was then loaded onto mirVanaTM miRNA Isolation kit (Ambion Inc.) columns and washed according to the manufacturer's protocol. Total RNA was eluted in 50µl of RNAase free water. The concentration was then determined using a Nanodrop ND-1000 machine (NanoDrop Technologies), and RNA quality was tested by visualization on agarose gels and by Agilent 2100 Bioanalyser (Agilent Technologies).
sequencing | Standard Illumina protocol for cDNA sequencing
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description Provider: EMBL_Heidelberg
Data processing Sequences obtained from the Illumina Genome Analyzer were mapped to both strands of the E. coli K12 MG1655 genome using BLAT allowing no gaps and up to two mismatches. Only reads which mapped to a single region of the genome were considered for further analysis. For each base position on the genome, the number of reads that mapped to that position was calculated.
 
Submission date Oct 28, 2010
Last update date May 15, 2019
Organization European Bioinformatics Institute
E-mail(s) miamexpress@ebi.ac.uk
Lab ArrayExpress
Street address Wellcome Trust Genome Campus
City Hinxton
State/province Cambridgeshire
ZIP/Postal code CB10 1SD
Country United Kingdom
 
Platform ID GPL10328
Series (1)
GSE24998 [E-MTAB-387] RNA sequencing in E. coli K12
Relations
SRA ERX007970

Supplementary file Size Download File type/resource
GSM613993_Early_Exponential.basecount.txt.gz 11.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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