Comment[ArrayExpressAccession] E-MEXP-3807 Investigation Title BMT_aGvHD_Intestine Comment[Submitted Name] BMT_aGvHD_Intestine Comment[AEExperimentDisplayName] Transcription profiling by array of intestinal tissues from mice receiving bone marrow transplantation with or without T-cell stimulation Comment[MIAMExpressLogin] Dietmar_Pfeifer Comment[MIAMExpressSubmissionID] 8579 Experiment Description Mice received TBI and allogeneic bone marrow transplantation. One group without and one group with T cells. On day 14 after transplantation mice were sacrificed and the intestinal tract was isolated. RNA was isolated from the intestinal tract of the two experimental groups. Experimental Design in_vivo_design co-expression_design stimulus_or_stress_design Comment[AEExperimentType] transcription profiling by array Experimental Factor Name disease Experimental Factor Type disease Person Last Name Pfeifer Person First Name Dietmar Person Email dietmar.pfeifer@uniklinik-freiburg.de Person Phone 49 761 270 3210 Person Affiliation University Clinics medical Center Person Address hematology, Hugstetterstr.55, Freiburg, BW, 79106, Germany Person Roles submitter Person Roles Term Source REF MGED Ontology Quality Control Type spike_quality_control biological_replicate Comment[QualityControlDescription] cRNA concentration, cRNA Bioanalyser profile, cDNA concentration, biotin incorporation, fragmentation Public Release Date 2013-01-16 Comment[ArrayExpressSubmissionDate] 2013-01-16 16:26:41 Publication Status Protocol Name P-MTAB-30625 P-MTAB-30626 P-MTAB-30627 P-MTAB-30628 P-MTAB-30629 P-MTAB-30630 Protocol Description Scanning was done as described in the Affymetrix GeneChip Expression Wash, Stain and Scan User manual (P/N 702731) (Parameters: Scanning hardware = GeneChip Scanner 3000 [Affymetrix], Scanning software = Scanning software) CEL files are preprocessed using GC background subtraction (antigenomic background probes)and RMA for quantile normalization and subsequent median Polish condensation. C57BL/6 (H-2b, Thy-1.2) and BALB/c (H-2d, Thy-1.2) mice were purchased either from Charles River Laboratory (Sulzburg, Germany) or from the local stock of the animal facility at Freiburg University. Recipients between 6 and 12 weeks of age and only gender matched combinations were used for transplant experiments. The mice were housed under specific pathogen-free conditions (SPF)in a normal night-day rhythm under standard conditions of temperature and humidity. The animal protocols (G-10/62, X-10/13H) were approved by the University Committee on the Use and Care of Laboratory Animals at Albert-Ludwigs-University Freiburg, Germany. (Parameters: time unit = seconds, temperature unit = C) RNA was isolated according to a standard protocol (Qiagen RNA isolation kit).Quantity and integrity of the RNA were verified using RNA 6000 nano chips (Agilent 2100 Bioanalyser, Palo Alto, CA, USA). RNA samples with an RNA integrity number of greater than 7 were further processed. (Parameters: Extracted product = total_RNA, Amplification = RNA polymerases) Hybridization, Washing and Staining is performed using the Affymetrix Hybridization, Wash and Stain kit exactly as described by the manufacturer. (Parameters: Chamber type = OTHER: Affymetrix GeneChip Oven 645, Quantity of label target used = 2.75, Mass unit = Micro gram, time = 17, Tiny time unit = hours, Volume = 80, Volume unit = Micro litre, temperature = 45) For Bone marrow transplantation (BMT) experiments, recipients were injected intravenously with 5x10e6 bone marrow (BM) cells after lethal irradiation with 900cGy. To induce aGvHD, 3x10e5 CD4+/CD8+ Tc were given (C57BL/6 ---> BALB/c) intravenously on d0. Intestinal tissue dissection and RNA isolation from the whole intestines was performed from mice that received either bone marrow alone or bone marrow and T cells on day 14 after transplatation. After removal, the small intestine was cut into 2 pieces of equal size which were then opened longitudinally in order to wash out feces by cold PBS. The tissue was next directly submitted to RNA isolation Protocol Type image_acquisition bioassay_data_transformation grow nucleic_acid_extraction hybridization specified_biomaterial_action Protocol Term Source REF MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology Term Source Name MGED Ontology ArrayExpress Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress SDRF File E-MEXP-3807.sdrf.txt Publication Title Inflammatory neovascularization during graft-versus-host disease is regulated by αv integrin and miR-100. Publication Author List Leonhardt F, Grundmann S, Behe M, Bluhm F, Dumont RA, Braun F, Fani M, Riesner K, Prinz G, Hechinger AK, Gerlach UV, Dierbach H, Penack O, Schmitt-Gräff A, Finke J, Weber WA, Zeiser R PubMed ID 23327924 Publication DOI 10.1182/blood-2012-07-442665