#METABOLOMICS WORKBENCH ehiggins_20210122_122728 DATATRACK_ID:2415 STUDY_ID:ST001659 ANALYSIS_ID:AN002710 PROJECT_ID:PR001064
VERSION             	1
CREATED_ON             	January 22, 2021, 1:24 pm
#PROJECT
PR:PROJECT_TITLE                 	Volatile Biomarkers for a Valley Fever Breath Test
PR:PROJECT_TYPE                  	GCxGC-TOFMS metabolomics
PR:PROJECT_SUMMARY               	Coccidioidomycosis, or valley fever, is prevalent in AZ, with more than 12,000
PR:PROJECT_SUMMARY               	new human infections diagnosed every year. In highly endemic areas, e.g.,
PR:PROJECT_SUMMARY               	Phoenix and Tucson, up to 30% of community-acquired pneumonia may be caused by
PR:PROJECT_SUMMARY               	Valley fever, and cases are on the rise. The current diagnostics for Valley
PR:PROJECT_SUMMARY               	fever are severely lacking due to invasiveness (biopsy) and poor sensitivity
PR:PROJECT_SUMMARY               	(serology), strongly contributing to an unacceptable 23-day median
PR:PROJECT_SUMMARY               	time-to-diagnosis. There is a critical need for sensitive and non-invasive
PR:PROJECT_SUMMARY               	diagnostics for identifying Valley fever lung infections. Our long-term goal is
PR:PROJECT_SUMMARY               	to substantially shorten the time-to-diagnosis for Valley fever through the
PR:PROJECT_SUMMARY               	development of sensitive and specific breath-based diagnostics for
PR:PROJECT_SUMMARY               	coccidioidomycosis lung infections. The overall objective of this application is
PR:PROJECT_SUMMARY               	to identify and validate putative volatile biomarkers of Coccidioides infections
PR:PROJECT_SUMMARY               	via metabolomics analyses of in vitro cultures, mouse model lung infections, and
PR:PROJECT_SUMMARY               	lung specimens from humans with Valley fever. At the completion of the proposed
PR:PROJECT_SUMMARY               	study, we expect to have identified and validated a panel of 10-15 volatile
PR:PROJECT_SUMMARY               	biomarkers for the sensitive and specific detection of valley fever in lung
PR:PROJECT_SUMMARY               	specimens.
PR:INSTITUTE                     	Arizona State University
PR:DEPARTMENT                    	School of Life Sciences
PR:LABORATORY                    	Bean Laboratory
PR:LAST_NAME                     	Bean
PR:FIRST_NAME                    	Heather
PR:ADDRESS                       	PO Box 874501, Tempe, AZ, 85287, USA
PR:EMAIL                         	Heather.D.Bean@asu.edu
PR:PHONE                         	480-727-3395
PR:FUNDING_SOURCE                	Arizona Biomedical Research Centre New Investigator Award to HDB
#STUDY
ST:STUDY_TITLE                   	Identify putative volatile biomarkers of Coccidioides spp. grown in vitro
ST:STUDY_TYPE                    	Untargeted metabolomics
ST:STUDY_SUMMARY                 	Valley fever (coccidioidomycosis) is an endemic fungal pneumonia of the North
ST:STUDY_SUMMARY                 	and South American deserts. The causative agents of Valley fever are the
ST:STUDY_SUMMARY                 	dimorphic fungi Coccidioides immitis and C. posadasii, which grow as mycelia in
ST:STUDY_SUMMARY                 	the environment and spherules within the lungs of vulnerable hosts. The current
ST:STUDY_SUMMARY                 	diagnostics for Valley fever are severely lacking due to poor sensitivity and
ST:STUDY_SUMMARY                 	invasiveness, contributing to a 23-day median time-to-diagnosis, and therefore
ST:STUDY_SUMMARY                 	new diagnostic tools are needed. We are working toward the development of a
ST:STUDY_SUMMARY                 	breath-based diagnostic for coccidioidomycosis, and in this initial study we
ST:STUDY_SUMMARY                 	characterized the volatile metabolomes (or volatilomes) of in vitro cultures of
ST:STUDY_SUMMARY                 	Coccidioides. Using solid-phase microextraction and comprehensive
ST:STUDY_SUMMARY                 	two-dimensional gas chromatography coupled to time-of-flight mass spectrometry
ST:STUDY_SUMMARY                 	(GC×GC–TOFMS), we characterized the VOCs produced by six strains of each
ST:STUDY_SUMMARY                 	species during mycelial or spherule growth. We detected a total of 353 VOCs that
ST:STUDY_SUMMARY                 	were at least two-fold more abundant in a Coccidioides culture versus medium
ST:STUDY_SUMMARY                 	controls and found the volatile metabolome of Coccidioides is more dependent on
ST:STUDY_SUMMARY                 	growth phase (spherule versus mycelia) than on the species. The volatile
ST:STUDY_SUMMARY                 	profiles of C. immitis and C. posadasii have strong similarities, indicating
ST:STUDY_SUMMARY                 	that a single suite of Valley fever breath biomarkers can be developed to detect
ST:STUDY_SUMMARY                 	both species.
ST:INSTITUTE                     	Arizona State University
ST:DEPARTMENT                    	School of Life Sciences
ST:LABORATORY                    	Bean Laboratory
ST:LAST_NAME                     	Bean
ST:FIRST_NAME                    	Heather
ST:ADDRESS                       	PO Box 874501 Tempe, AZ 85287
ST:EMAIL                         	Heather.D.Bean@asu.edu
ST:PHONE                         	4807273395
ST:PUBLICATIONS                  	Lifecycle dominates the volatilome character of the dimorphic fungus
ST:PUBLICATIONS                  	Coccidioides spp Emily A. Higgins Keppler, Heather L. Mead, Bridget M. Barker,
ST:PUBLICATIONS                  	Heather D. Bean bioRxiv 2021.01.15.426916; doi:
ST:PUBLICATIONS                  	https://doi.org/10.1101/2021.01.15.426916
#SUBJECT
SU:SUBJECT_TYPE                  	Fungi
SU:SUBJECT_SPECIES               	Coccidioides posadasii;Coccidioides immitis
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3221 Mycelia_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=B3221 Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3221 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=B3221 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3221 Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=B3221 Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3221 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=B3221 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3221 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=B3221 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3221 Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=B3221 Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3222 Mycelia_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=B3222 Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3222 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=B3222 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3222 Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=B3222 Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3222 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=B3222 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3222 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=B3222 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	B3222 Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=B3222 Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	Media	Control Mycelia_2	treatment:Blank | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=Control Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	Media	Control Mycelia_3	treatment:Blank | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=Control Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	Media	Control Mycelia_4	treatment:Blank | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=Control Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	Media	Control Spherule_1	treatment:Blank | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=Control Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	Media	Control Spherule_2	treatment:Blank | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=Control Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	Media	Control Spherule_3	treatment:Blank | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=Control Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	GT-166 Mycelia_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=GT-166 Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	GT-166 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=GT-166 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	GT-166 Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=GT-166 Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	GT-166 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=GT-166 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	GT-166 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=GT-166 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	GT-166 Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=GT-166 Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2006 Mycelia_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2006 Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2006 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2006 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2006 Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2006 Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2006 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2006 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2006 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2006 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2006 Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2006 Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2009 Mycelia_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2009 Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2009 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2009 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2009 Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2009 Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2009 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2009 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2009 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2009 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2009 Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2009 Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2010 Mycelia_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2010 Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2010 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2010 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2010 Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2010 Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2010 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2010 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2010 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2010 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2010 Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2010 Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC2343 Mycelia_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2343 Mycelia_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC2343 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2343 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC2343 Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2343 Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC2343 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2343 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC2343 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2343 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC2343 Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2343 Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2395 Mycelia_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2395 Mycelia_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2395 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2395 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2395 Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC2395 Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2395 Spherule _1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2395 Spherule _1.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2395 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2395 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC2395 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC2395 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC3505 Mycelia_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC3505 Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC3505 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC3505 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC3505 Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC3505 Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC3505 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC3505 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC3505 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC3505 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RMSCC3505 Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC3505 Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC3506 Mycelia_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC3506 Mycelia_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC3506 Mycelia_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC3506 Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC3506 Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RMSCC3506 Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC3506 Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC3506 Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC3506 Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC3506 Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	RMSCC3506 Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RMSCC3506 Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RS Mycelia_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RS Mycelia_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RS Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RS Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RS Mycelia_4	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=RS Mycelia_4.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RS Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RS Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RS Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RS Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. immitis	RS Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=RS Spherule_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	Silveira Mycelia_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=Silveira Mycelia_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	Silveira Mycelia_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=Silveira Mycelia_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	Silveira Mycelia_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:30°C | culture_conditions:normoxia	RAW_FILE_NAME=Silveira Mycelia_3.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	Silveira Spherule_1	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=Silveira Spherule_1.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	Silveira Spherule_2	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=Silveira Spherule_2.SMP
SUBJECT_SAMPLE_FACTORS           	C. posadasii	Silveira Spherule_3	treatment:Fungi | culture_time (h):96 | culture_medium:RPMI | culture_tempurature:39°C | culture_conditions:10% CO2	RAW_FILE_NAME=Silveira Spherule_3.SMP
#COLLECTION
CO:COLLECTION_SUMMARY            	All Coccidioides isolates were grown under BSL-3 containment, using conditions
CO:COLLECTION_SUMMARY            	that induce mycelial or spherule growth. For mycelial growth, a 50 ml vented
CO:COLLECTION_SUMMARY            	falcon tube containing 10 ml of RPMI media (filter sterilized RPMI 1640, 10%
CO:COLLECTION_SUMMARY            	fetal bovine serum) was inoculated with a 1 cm x 1 cm 2xGYE agar plug for each
CO:COLLECTION_SUMMARY            	strain. These plates were inoculated using 100 µl of glycerol stock, spread
CO:COLLECTION_SUMMARY            	across the plate, and cultured for 30°C for two weeks. Control RPMI media was
CO:COLLECTION_SUMMARY            	inoculated with a plug from sterile 2xGYE agar media. Each sample, including
CO:COLLECTION_SUMMARY            	media control, was prepared in triplicate. Cultures were grown on a shaking
CO:COLLECTION_SUMMARY            	incubator at 150 rpm, 30°C for 96 h. For spherule cultures, a 50 ml vented
CO:COLLECTION_SUMMARY            	falcon tube containing 10 ml of RPMI media was inoculated to a final
CO:COLLECTION_SUMMARY            	concentration of 1.0 x 10^5 arthroconidia/ml in 1xPBS. Arthroconidia were grown
CO:COLLECTION_SUMMARY            	and harvested. Strains RMSCC2343 and RMSCC3505 did not produce enough conidia to
CO:COLLECTION_SUMMARY            	achieve 1.0 x 10^5 arthroconidia/ml, and were inoculated at 7.0 x 10^4 and 4.0 x
CO:COLLECTION_SUMMARY            	10^4 arthroconidia/ml, respectively. Control media was inoculated with 1 ml of
CO:COLLECTION_SUMMARY            	sterile 1xPBS. Cultures were grown on a shaking incubator at 150 rpm, at 39°C
CO:COLLECTION_SUMMARY            	in 10% CO2 for 96 h. Mycelial and spherule cultures were spun at 12,000 x g at
CO:COLLECTION_SUMMARY            	4°C for 10 min to pellet the cells. The supernatant was removed and place in a
CO:COLLECTION_SUMMARY            	Nanosep MF Centrifugal Devices with Bio-Inert® Membrane 0.2 µm spin filter and
CO:COLLECTION_SUMMARY            	centrifuged at 3,200 x g for 4 min. The filtrate was stored at −80°C until
CO:COLLECTION_SUMMARY            	volatile metabolomics analysis. The Coccidioides spp. culture filtrates and
CO:COLLECTION_SUMMARY            	media blanks were allowed to thaw at 4°C overnight, and then 2 ml were
CO:COLLECTION_SUMMARY            	transferred and sealed into sterilized 10 ml GC headspace vials with
CO:COLLECTION_SUMMARY            	PTFE/silicone septum screw caps. All samples were stored for up to 12 d at 4°C
CO:COLLECTION_SUMMARY            	until analyzed.
CO:SAMPLE_TYPE                   	Fungi cells
#TREATMENT
TR:TREATMENT_SUMMARY             	All Coccidioides isolates were grown under BSL-3 containment, using conditions
TR:TREATMENT_SUMMARY             	that induce mycelial or spherule growth. See Collection Protocol for details
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Filtrate samples were heated to 50 degrees Celsius with agitation, and volatiles
SP:SAMPLEPREP_SUMMARY            	were sampled for 10 minutes using solid-phase microextraction (SPME) and
SP:SAMPLEPREP_SUMMARY            	analyzed using comprehensive gas chromatography coupled to time-of-flight mass
SP:SAMPLEPREP_SUMMARY            	spectrometry.
SP:EXTRACTION_METHOD             	Solid-phase microextraction (SPME)
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Samples analyzed using comprehensive two-dimensional gas chromatography (GCxGC).
CH:CHROMATOGRAPHY_SUMMARY        	See attached method file.
CH:CHROMATOGRAPHY_TYPE           	GCxGC
CH:INSTRUMENT_NAME               	Agilent 7890B
CH:COLUMN_NAME                   	Multidimensional column configuration
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Leco Pegasus 4D GCxGC TOF
MS:INSTRUMENT_TYPE               	GC x GC-TOF
MS:MS_TYPE                       	EI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	see attached MS methods
MS:MS_RESULTS_FILE               	ST001659_AN002710_Results.txt	UNITS:Peak areas	Has m/z:No	Has RT:Yes	RT units:Seconds
#END