Comment[ArrayExpressAccession] E-MEXP-3755
Investigation Title Serine protease-mediated wounding identifies localized epidermal wound response genes in Drosophila melanogaster
Comment[Submitted Name] Serine protease-mediated wounding identifies localized epidermal wound response genes in Drosophila melanogaster
Comment[AEExperimentDisplayName] Transcription profiling by array of D. melanogaster whole embryos to investigate localized wound response genes by srine protease-mediated wounding
Comment[MIAMExpressLogin] ghardiman
Comment[MIAMExpressSubmissionID] 8469
Experiment Description We have used trypsin-mediated wounding to amplify the transcriptional response to clean puncture wounding. We studied the transcriptional response of clean puncture wounding and trypsin puncture wounding in relation to unwounded wild-type late-stage embryos. Trypsin puncture wounding generally increases the puncture wounding fold induction relative to unwounded controls.
Experimental Design co-expression_design time_series_design injury_design replicate_design
Comment[AEExperimentType] transcription profiling by array
Experimental Factor Name time individual
Experimental Factor Type time individual
Person Last Name Hardiman
Person First Name Gary
Person Mid Initials T
Person Email gthardiman@ucsd.edu
Person Phone 8588223792
Person Fax 8588223021
Person Affiliation UCSD DEPT OF MEDICINE
Person Address BIOGEM, 9500 Gilman Drive, La Jolla, California, 92093-0724, USA
Person Roles submitter
Person Roles Term Source REF MGED Ontology
Quality Control Type
Public Release Date 2013-08-12
Comment[ArrayExpressSubmissionDate] 2012-10-18 23:13:32
Publication Title Serine proteolytic pathway activation reveals an expanded ensemble of wound response genes in Drosophila.
Publication Status submitted
Protocol Name P-MTAB-28873 P-MTAB-28869 P-MTAB-28870 P-MTAB-28871 P-MTAB-28872 P-AGIL-28 P-AGIL-2
Protocol Description Whole embryos (either wounded or unwounded) were collected and stored frozen in Trizol (Invitrogen). For each replicate, approximately 500 whole embryos were ground in Trizol in microfuge tube with a pestle according to the manufacturer's recommendations. For each sample, 50 micrograms of RNA was further cleaned using the Qiagen RNeasy miniprep kit, according to the manufacturer's recommendations. Sample integrity was assayed using RT-PCR and BioAnalyzer (Agilent) analysis.
(Parameters: Extracted product = total_RNA, Amplification = none) Three different sample types were used: unwounded wild-type, puncture wild-type, and trypsin puncture wild-type stage 15-17 embryos. Unwounded wild-type stage 15-17 embryos were used as controls. Puncture wild-type embryos were wounded with 1mM HCl and dye and allowed to recover for either 30, 60, or 120 minutes at RT before RNA isolation. Trypsin puncture wild-type embryos were wounded with 2mg/mL trypsin soluble in 1mM HCl and dye and were allowed to recover for either 30, 60, or 120 minutes before RNA isolation. Scanning of the agilent microarrays was performed through the standard agilent microarray scanner system protocol.
(Parameters: Scanning hardware = DNA Microarray Scanner BA [Agilent Technologies], Scanning software = Feature Extraction Software [Agilent]) We normalized all samples simultaneously using a multiple-loess technique described in:
Sasik R, Woelk CH, Corbeil J., J Mol Endocrinol. 33:1-9 (2004). Parental wild-type (w1118) flies were raised under standard lab conditions, and the laid embryos were allowed to develop at 25C for approximately 14-16 hours. Gut morphology was used as a guide to ensure proper staging.
(Parameters: time unit = seconds, temperature unit = C)
Protocol Type nucleic_acid_extraction specified_biomaterial_action image_acquisition bioassay_data_transformation grow labeling hybridization
Protocol Term Source REF MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology ArrayExpress ArrayExpress
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-3755.sdrf.txt
PubMed ID 23637905
Publication Author List Patterson RA, Juarez MT, Hermann A, Sasik R, Hardiman G, McGinnis W.
Publication DOI 10.1371/journal.pone.0061773