{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001338","ANALYSIS_ID":"AN002232","VERSION":"1","CREATED_ON":"April 3, 2020, 9:39 am"},

"PROJECT":{"PROJECT_TITLE":"aryl hydrocarbon receptor-related compounds studies","PROJECT_SUMMARY":"The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that responds to a variety of structurally diverse exogenous and endogenous small molecules. Gut microbiota utilizing tryptophan and indole metabolism as a reservoir, has been demonstrated to provide an abundant source of AHR ligands. So differential analysis was performed to find the potential candidates of AHR activator in cecal contents between conventional and germ-free mice with the help of untargeted global profiling.","INSTITUTE":"Pennsylvania State University","LAST_NAME":"DONG","FIRST_NAME":"FANGCONG","ADDRESS":"314 Life Sciences Building, University Park, PA 16802","EMAIL":"fxd93@psu.edu","PHONE":"8148637610"},

"STUDY":{"STUDY_TITLE":"Global profiling for cecal contents","STUDY_SUMMARY":"The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that responds to a variety of structurally diverse exogenous and endogenous small molecules. Gut microbiota utilizing tryptophan and indole metabolism as a reservoir, has been demonstrated to provide an abundant source of AHR ligands. So differential analysis was performed to find the potential candidates of AHR activator in cecal contents between conventional and germ-free mice with the help of untargeted global profiling.","INSTITUTE":"Pennsylvania State University","LAST_NAME":"DONG","FIRST_NAME":"FANGCONG","ADDRESS":"314 Life Sciences Building, University Park, PA 16802","EMAIL":"fxd93@psu.edu","PHONE":"8148637610"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Cecal content_C1",
"Factors":{"Genotype":"wild-type"},
"Additional sample data":{"Treatment":"chow diet","RAW_FILE_NAME":"Cecal content_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Cecal content_C2",
"Factors":{"Genotype":"wild-type"},
"Additional sample data":{"Treatment":"chow diet","RAW_FILE_NAME":"Cecal content_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Cecal content_C3",
"Factors":{"Genotype":"wild-type"},
"Additional sample data":{"Treatment":"chow diet","RAW_FILE_NAME":"Cecal content_C3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Cecal content_C4",
"Factors":{"Genotype":"wild-type"},
"Additional sample data":{"Treatment":"chow diet","RAW_FILE_NAME":"Cecal content_C4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Cecal content_GF1",
"Factors":{"Genotype":"germ-free"},
"Additional sample data":{"Treatment":"chow diet","RAW_FILE_NAME":"Cecal content_GF1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Cecal content_GF2",
"Factors":{"Genotype":"germ-free"},
"Additional sample data":{"Treatment":"chow diet","RAW_FILE_NAME":"Cecal content_GF2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Cecal content_GF3",
"Factors":{"Genotype":"germ-free"},
"Additional sample data":{"Treatment":"chow diet","RAW_FILE_NAME":"Cecal content_GF3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Cecal content_GF4",
"Factors":{"Genotype":"germ-free"},
"Additional sample data":{"Treatment":"chow diet","RAW_FILE_NAME":"Cecal content_GF4.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"C57BL/6J wild type mice were originally purchased from Jackson Laboratories (Bar Harbor, MN, USA). Germ-free (GF) C57BL/6J mice were from the Pennsylvania State University Gnotobiotic Animal Research Facility. Mice were bred in-house and fed on a standard animal chow diet. Animal experiments were performed after approval by the Institutional Animal Care and Use Committee. Fresh cecal contents from conventional and GF mice were collected and stored at -80 °C.","SAMPLE_TYPE":"Cecum"},

"TREATMENT":{"TREATMENT_SUMMARY":"C57BL/6J wild type mice were originally purchased from Jackson Laboratories (Bar Harbor, MN, USA). Germ-free (GF) C57BL/6J mice were from the Pennsylvania State University Gnotobiotic Animal Research Facility. Mice were bred in-house and fed on a standard animal chow diet. Animal experiments were performed after approval by the Institutional Animal Care and Use Committee. Fresh cecal contents from conventional and GF mice were collected and stored at -80 °C."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Each mixture was homogenized with 1 mm zirconium beads using a BeadBlasterTM 24 (Benchmark Scientific, Edison, NJ, USA) homogenizer. All samples were homogenized according to the program parameters: 6500 - 1×30 - 005 (×3). After vortexing, samples were sonicated for 20 min in an ice water bath, prior to centrifugation at 20,000 × g for 20 min at 4 ℃. The supernatants were collected, dried in a Savant SpeedVac (Thermo Scientific, Waltham, MA, USA), and reconstituted in 100 μL of 3% methanol (v/v) containing 1 µM chlorpropamide (internal standard).","SAMPLEPREP_PROTOCOL_FILENAME":"MS_protocol_for_global_profiling.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters Acquity BEH C18 (100 x 2mm, 1.7um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Fusion Tribrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Solvent A was HPLC-grade water with 0.1% formic acid, and solvent B was HPLC-grade acetonitrile with 0.1% formic acid. The initial condition was 97% A and 3% B, increasing to 45% B at 10 min and 75% B at 12 min, where it was held at 75% B until 17.5 min before returning to the initial conditions. Differential analyses were performed by the use of Compound Discoverer (Thermo Fisher Scientific, Waltham, MA, USA)","MS_RESULTS_FILE":"ST001338_AN002232_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}