Comment[ArrayExpressAccession]	E-MTAB-1446
MAGE-TAB Version	1.1
Investigation Title	Mapping of genotype-phenotype diversity amongst clinical isolates of Mycobacterium tuberculosis by RNA-seq
Comment[Submitted Name]	Mapping of genotype-phenotype diversity amongst clinical isolates of Mycobacterium tuberculosis by RNA-seq
Experiment Description	Mapping of genotype-phenotype diversity amongst clinical isolates of Mycobacterium tuberculosis by RNA-seq
Experimental Design	strain_or_line_design	in_vitro_design	co-expression_design
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[AEExperimentDisplayName]	RNA-seq of M. tuberculosis to investigate genotype-phenotype diversity amongst clinical isolates
Experimental Factor Name	strain or line
Experimental Factor Type	strain or line
Quality Control Type
Public Release Date	2013-09-19
Person Last Name	Rose
Person First Name	Graham
Person Mid Initials
Person Email	grahamdrose@gmail.com
Person Phone	02088162475
Person Address	MRC NIMR The Ridgeway, Mill Hill, London  NW7 1AA
Person Affiliation	MRC NIMR
Person Roles	submitter
PubMed ID
Publication Author List	Rose G	 Cortes M	 Comas I	 Coscolla M	 Gagneux S	 Young D
Publication Title	Mapping of genotype-phenotype diversity amongst clinical isolates of Mycobacterium tuberculosis by RNA-seq
Publication Status	Submitted
Protocol Name	P-MTAB-30502	P-MTAB-30503	P-MTAB-30504	P-MTAB-30505	P-MTAB-30506	P-MTAB-30507
Protocol Type	grow	specified_biomaterial_action	nucleic_acid_extraction	sequencing	scanning	nucleic acid library construction protocol
Protocol Description	Single colony bacterial stocks were grown in Middlebrook 7H9 supplemented with 0.5% glycerol, 10% Middlebrook ADC, and 0.05% Tween-80 in roller bottle culture.	Exponential phase cultures were harvested at an optical density of 0.4-0.8 (OD600); growth curves were performed to ensure calibration of exponential growth phase of the clinical strains. Stationary phase cultures were harvested one week after the cultures reached 1.0 OD600	Isolation of RNA was performed using the FastRNA Pro blue kit from QBiogene/MP Bio according to manufacturer's instructions. All RNA samples were treated with Turbo DNase free (Ambion). 	A single flow cell lane was used per library. Single end sequencing of cDNA.	Reference based assembly was performed using the reference genome H37Rv	Construction of strand-specific cDNA libraries was carried out with 2-3_g total RNA using the Illumina directional mRNA-Seq protocol (Part # 15018460 Rev. A), but with exclusion of polyA-tail and size selection to capture all RNA species. Terminator-5'-phosphate-dependent exonuclease (Epicentre Biotechnologies) was used to deplete processed RNAs in cDNA samples used for TSS mapping analysis (vertis Biotechnologie AG).
Protocol Hardware				Illumina HiSeq 2000
Comment[SecondaryAccession]	ERP002122
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR219193-ERR219205
SDRF File	E-MTAB-1446.sdrf.txt