Comment[ArrayExpressAccession]	E-GEOD-58765
MAGE-TAB Version	1.1			
Public Release Date	2014-06-25
Investigation Title	DOCK8 regulates protective immunity by controlling the function and survival of RORγt+ ILCs			
Comment[Submitted Name]	DOCK8 regulates protective immunity by controlling the function and survival of RORγt+ ILCs
Experiment Description	Retinoic-acid receptor-related orphan receptor-γt-positive (RORγt+) innate lymphoid cells (ILCs) produce interleukin (IL)-22 and IL-17, which are critical for protective immunity against enteric pathogens. The molecular mechanism underlying the development and survival of RORγt+ ILCs is not thoroughly understood. Here we show that Dedicator of cytokinesis 8 (DOCK8), a scaffolding protein involved in cytoskeletal rearrangement and cell migration, is essential for the protective immunity against Citrobacter rodentium. A comparative RNA sequencing-based analysis reveals an impaired induction of antimicrobial peptides in the colon of DOCK8-deficient mice, which correlates with high susceptibility to infection and a very low number of IL-22-producing RORγt+ ILCs in their GI tract. Furthermore, DOCK8-deficient RORγt+ ILCs are less responsive to IL-7 mediated signaling, more prone to apoptosis and produce less IL-22 due to a defect in IL-23-mediated STAT3 phosphorylation. Our studies reveal an unsuspected role of DOCK8 for the function, generation and survival of RORγt+ ILCs. Control and DOCK8 KO mice were infected with 2X109 CFU of Citrobacter rodentium and day 8 post infection mice were sacrificed and their colons were harvested (n=5) . Total RNA was purified from the infected colons with RNeasy mini kit (Qiagen). RNA sequencing was performed (pooled RNA sample from five mice in each group) at Genomic Core Facility Southwestern Medical Center, University of Texas.			
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	Singh	Singh	Oukka	
Person First Name	Akhilesh	Akhilesh	Mohamed	
Person Mid Initials	K	K		
Person Email	geo@ncbi.nlm.nih.gov			
Person Affiliation	Seattle Childrens Research Institute			
Person Address	Center for Immunity and Immunotherapies, Seattle Childrens Research Institute, 1900, 9th AVE, Seattle, WA, USA			
Person Roles	submitter			
Protocol Name	P-GSE58765-4	P-GSE58765-1	P-GSE58765-3	P-GSE58765-2
Protocol Description	base-calling - Illumina OLB version 1.9.3 demultipexing- Python custom program alignment-CLCBIO- version 6.5 Genome_build: mm8 Supplementary_files_format_and_content: RPKM- Genes - tab-delimited file	Mice Infected with C. rodentium	C. rodentium infected mice colons were harvested at day and cleaned with ice cold PBS. Colon samples were homogenized and total RNA was purified by using RNeasy mini kit (Qiagen) Libraries were prepared for sequencing using Illumina's instructions accompanying the TrueSeq RNA sample preparation V2.	N/A
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	PHENOTYPE			
Experimental Factor Type	phenotype			
PubMed ID	25091235			
Comment[SecondaryAccession]	GSE58765			
Comment[GEOReleaseDate]	2014-06-25			
Comment[ArrayExpressSubmissionDate]	2014-06-24			
Comment[GEOLastUpdateDate]	2014-08-08			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[AdditionalFile:Data1]	GSE58765_DOCK8_RNA-SEQ_RPKM.txt			
Comment[SecondaryAccession]	SRP043526			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1449899-SRR1449900			
SDRF File	E-GEOD-58765.sdrf.txt