Comment[ArrayExpressAccession]	E-GEOD-45180
MAGE-TAB Version	1.1				
Public Release Date	2013-12-31
Investigation Title	Gene expression data from CD11b-positive myeloid cells infiltrating tumors after local irradiation				
Comment[Submitted Name]	Gene expression data from CD11b-positive myeloid cells infiltrating tumors after local irradiation
Experiment Description	Analysis of global gene expression in myeloid cells infiltrating tumors after irradiation. Cell death induces recruitment of myeloid cells into irradiated tumors thereby stimulating tumor recurrence. Results provide insights into molecular mechanisms regulating tumorigenic functions of myeloid cells in tumors re-growing after radiation therapy. Samples were collected at day 4 from irradiated tumors in WT, TLR9KO and Stat3KO (MxCre/Stat3flox). There were total 11 samples with  3-4 replicates of each sample type.				
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl			
Person Last Name	Li	Kortylewski	Gao	Kozlowska	Li
Person First Name	Haiqing	Marcin	Chan	Anna	Haiqing
Person Email	hali@coh.org				
Person Affiliation	Beckman Research Institute of City of Hope				
Person Phone	626-256-4673				
Person Address	Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, USA				
Person Roles	submitter				
Protocol Name	P-GSE45180-4	P-GSE45180-1	P-GSE45180-3	P-GSE45180-2	
Protocol Description	Basecalls and barcode analysis were performed using CASAVA version 1.7 Sequenced reads were mapped to mm9 whole genome using rnaseq alignment tool tophat 1.3.1 (bowtie ver 0.12.7) with parameters --max-insertion-length 10 --max-deletion-length 10 --segment-length 20. Other configuarions were kept default. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genome Suite ver 6.12.0713. An expectation/maximization algorithm was used to determine relative isoform abundance levels, and the isoform abundance counts were summarized to the gene level for normalized gene expression abundance counts. Genome_build: mm9 Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (normalized gene expression abundance counts)	Subcutaneously implanted tumors were locally irradiated at 15 Gy and harvested four days later.	CD11b-positive tumor-infiltrating myeloid cells were enriched using specific antibodies and magnetic bead isolation (StemCell Technologies). The total RNA was isolated by using miRVana™ kit (Ambion). RNA libraries were prepared for sequencing using standard Illumina protocols	Freshly isolated primary myeloid cells without in vitro culture.	
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol	
Experimental Factor Name	GENOTYPE				
Experimental Factor Type	genotype				
Comment[SecondaryAccession]	GSE45180				
Comment[GEOReleaseDate]	2013-12-31				
Comment[ArrayExpressSubmissionDate]	2013-03-14				
Comment[GEOLastUpdateDate]	2014-01-01				
Comment[AEExperimentType]	RNA-seq of coding RNA				
Comment[SecondaryAccession]	SRP019455				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR774574-SRR774584				
SDRF File	E-GEOD-45180.sdrf.txt