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Status |
Public on Feb 05, 2011 |
Title |
[E-MTAB-387] E_coli_K12_MG1655_RNAseq_LB_Early_exponential |
Sample type |
SRA |
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Source name |
E_coli_K12_MG1655_RNAseq_LB_Early_exponential
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Organism |
Escherichia coli |
Characteristics |
material type: whole_organism strainorline: K-12 substr. MG1655 genotype: wide_type growth condition: early-exponential
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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.
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer II |
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Description |
Provider: EMBL_Heidelberg
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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.
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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 |