Comment[ArrayExpressAccession]	E-MTAB-2996
MAGE-TAB Version	1.1					
Investigation Title	Sequencing of LPS-stimulated immune cells from chicken					
Comment[Submitted Name]	Sequencing of LPS-stimulated immune cells from chicken
Experiment Description	RNAs were analysed from bone marrow derived dendritic cells from 6 week old birds (control and LPS stimulated), bone marrow derived macrophages from 6 week old birds (control and LPS stimulated) and heterophils isolated from blood of day-old chicks (control and LPS stimulated).					
Comment[AEExperimentDisplayName]	RNA-seq of coding RNA from bone marrow derived dendritic cells, bone marrow derived macrophages and heterophils isolated from blood of day-old chicks which were control or LPS stimulated					
Experimental Design	stimulus or stress design					
Experimental Design Term Source REF	EFO					
Experimental Design Term Accession Number	EFO_0001762					
Experimental Factor Name	stimulus	cell type				
Experimental Factor Type	stimulus	cell type				
Experimental Factor Term Source REF		EFO				
Experimental Factor Term Accession Number		EFO_0000324				
Person Last Name	Smith	Kaiser				
Person First Name	Jacqueline	Pete				
Person Mid Initials						
Person Email	Jacqueline.smith@roslin.ed.ac.uk	pete.kaiser@roslin.ed.ac.uk				
Person Phone						
Person Fax						
Person Address	University of Edinburgh  Easter Bush  Midlothian  EH25 9RG  Scotland UK  					
Person Affiliation	The Roslin Institute	The Roslin Institute				
Person Roles	submitter	investigator				
Date of Experiment	2013-06-20					
Public Release Date	2015-04-01					
Protocol Name	P-MTAB-41557	P-MTAB-41558	P-MTAB-41559	P-MTAB-41560	P-MTAB-41561	P-MTAB-41562
Protocol Type	growth protocol	treatment protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	high throughput sequence alignment protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Term Accession Number	EFO_0003789	EFO_0003969	EFO_0002944	EFO_0004184	EFO_0004170	EFO_0004917
Protocol Description	Macrophages and dendritic cells were cultured from bone marrow by standard methods (Garceau et al. 2010 and Wu et al. 2010, respectively), and heterophils isolated from blood by standard methods (Kogut et al. 1995).	Cells were cultured with or without LPS for 24 h before RNA was isolated	Standard Trizol extraction method	Samples were prepared for mRNA sequencing using 2ug of total RNA starting material following the Illumina TruSeq RNA Sample Preparation v2 kit protocol. 	Resulting libraries were quality checked on an Agilent DNA 1000 bioanalyzer (Agilent Technologies, South Queensferry, UK) and then clustered onto a paired end flowcell using the Illumina TruSeq Rapid PE Cluster kit at an 8pM concentration. 100 cycle paired-end sequencing was carried out on the Illumina HiSeq 2500 using an Illumina TruSeq Rapid SBS kits (Illumina, Little Chesterford, UK). The Illumina HiSeq 2500 platform generated 13-18 million RNAseq tags per sample (191 million in total), each 100 nucleotides in length, resulting in 46.5 Gb of data. This was carried out at the Edinburgh Genomics facility within Roslin Institute, Midlothian, UK.	Tophat version 2.0.9 was used with Bowtie2  version 2.1.0 for alignment of reads. Reads were aligned to the Galgal 4 genome assembly from the Ensembl 72 release.   
Protocol Hardware					Illumina HiSeq 2500	
Protocol Software						
Term Source Name	EFO
Term Source File	http://www.ebi.ac.uk/efo/					
Term Source Version						
Comment[AEExperimentType]	RNA-seq of coding RNA					
Comment[SecondaryAccession]	ERP007205
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR652848-ERR652853
SDRF File	E-MTAB-2996.sdrf.txt