Comment[ArrayExpressAccession]	E-GEOD-49449
MAGE-TAB Version	1.1				
Public Release Date	2014-05-12
Investigation Title	RNA-seq analysis of IL-10 treatment of wildtype and Ptpn1-/- knockout peritoneal macrophages				
Comment[Submitted Name]	RNA-seq analysis of IL-10 treatment of wildtype and Ptpn1-/- knockout peritoneal macrophages
Experiment Description	We report here the deep sequencing of the mRNA from peritoneal exudate cells (macrophages) purified from wildtype or Ptpn1 (PTP1B) knockout mice, either treated or untreated with IL-10. In periotenal macrophages IL-10 activates the transcription factor STAT3 to execute and anti-inflammatory gene expression programme. The tyrosine phosphatase PTPN1 targets STAT3 for dephosphorylation and leads to the deactivation of STAT3. In this study we examined the role of PTP1B in controlling the normal homeostatic level phosphorylation of STAT3 by comparing the IL-10/STAT3-mediated anti-inflammatory gene expression programme. We find that loss of PTP1B leads to an up-regulation of the activity of STAT3, both at the level of phosphorylation and also in enhanced expression of anti-inflammatory gene products. RNA-seq of wildtype and Ptpn1 (PTP1B) knockout mouse peritoneal macrophages, treated or untreated with IL-10				
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	Hutchins	Hutchins	Miranda-Saavedra	Pike	Tremblay
Person First Name	Andrew	Andrew	Diego	Kelly	Michel
Person Mid Initials	Paul	P		A	L
Person Email	andrew@gibh.ac.cn				
Person Affiliation	Guangzhou Institutes of Biomedicine and Health				
Person Address	Bioinformatics, Guangzhou Institutes of Biomedicine and Health, 190 KaiYuan Rd., Guangzhou, China				
Person Roles	submitter				
Protocol Name	P-GSE49449-3	P-GSE49449-1	P-GSE49449-2		
Protocol Description	rsem-calculate-expression --phred64-quals -seed-length 28 --bowtie-m 50 Only keep genes >1.0 in >=2 samples EDASeq: withinLaneNormalization(data, gc, which=full) EDASeq:betweenLaneNormalization(data, which=full) mean expression values between replicates Genome_build: mm9 Supplementary_files_format_and_content: TSV file containing gene annotations (Ensembl) and expression values in normalised abundance estimates	Peritoneal cells were allowed to adhere to plastic for 24 hours	TRIzol Illumina Standard protocol		
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol		
Experimental Factor Name	TREATMENT	GENOTYPE			
Experimental Factor Type	treatment	genotype			
Publication Title	Protein tyrosine phosphatase 1B is a regulator of the interleukin-10-induced transcriptional program in macrophages.				
Publication Author List	Pike KA, Hutchins AP, Vinette V, Th�berge JF, Sabbagh L, Tremblay ML, Miranda-Saavedra D				
PubMed ID	24803538				
Publication DOI	10.1126/scisignal.2005020				
Comment[SecondaryAccession]	GSE49449				
Comment[GEOReleaseDate]	2014-05-12				
Comment[ArrayExpressSubmissionDate]	2013-08-01				
Comment[GEOLastUpdateDate]	2014-06-18				
Comment[AEExperimentType]	RNA-seq of coding RNA				
Comment[AdditionalFile:Data1]	GSE49449_genes_cpm_expression.tsv				
Comment[SecondaryAccession]	SRP028380				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR946753-SRR946760				
SDRF File	E-GEOD-49449.sdrf.txt