Comment[ArrayExpressAccession] E-MEXP-3933 Investigation Title SCN lightpulse timecourse Comment[Submitted Name] SCN lightpulse timecourse Comment[AEExperimentDisplayName] Transcription profiling by array of mouse suprachiasmatic nucleus after exposure to a light pulse Comment[MIAMExpressLogin] RButler Comment[MIAMExpressSubmissionID] 8814 Experiment Description The aim of the experiment was to identify genes in the mouse suprachiasmatic nucleus whose expression was altered by exposure to a light pulse of 400 lux at CT16 (subjective night). C57BL/6 male mice were entrained to a 12:12 LD cycle and given a 30 min 400 lux light pulse at CT16. Punches of SCN tissue were collected at 30 (LP30), 60 (LP60)and 120 (LP120) mins after the start of the light pulse and flash frozen on dry ice. Sham SCN punches (Sham) were collected from mice not exposed to light at CT16. Total RNA from individual tissue samples was extracted using RNeasy micro kit from Qiagen using the lipid tissue protocol according to manufacturer's recommendations. Individual samples were analyzed for quality using an Agilent Bioanalzyer and only samples with a RIN of 8 and above were used. Samples were quantified by Nanodrop and 300ug of total RNA was used to prepare probes for hybridisation to Affymetrix Mouse Exon arrays. Probe preparation and array hybridisation was carried out according to Affymetrix protocols. Each array represents an individual SCN tissue punch.

Experimental Design in_vivo_design stimulus or stress design time series design co-expression_design Comment[AEExperimentType] transcription profiling by array Experimental Factor Name genotype time irradiate dose Experimental Factor Type genotype time irradiate dose Person Last Name Butler Person First Name Rachel Person Email rachel.butler@ndcn.ox.ac.uk Person Phone 01865234771 Person Affiliation University of Oxford Person Address Clinical Neurosciences, Level 6, West Wing, JR Hospital,, Oxford, Oxfordshire, OX11 6AT, United Kingdom Person Roles submitter Person Roles Term Source REF EFO Quality Control Type Public Release Date 2013-12-16 Comment[ArrayExpressSubmissionDate] 2013-07-10 09:35:18 Publication Title The CRTC1-SIK1 pathway regulates entrainment of the circadian clock Publication Status in press Protocol Name P-MTAB-33708 P-MTAB-33709 Protocol Description C57BL/6 male mice were kept on a 12:12 LD cycle and given a 30 min light pulse (400 lux) at CT16. SCN punches were taken at the end of the light pulse (LP30), 60 mins after the start of the light pulse (LP60) and 120 mins after (LP120). Sham tissue was taken at CT16 from animals that had not received a light pulse. Tissue was flash frozen on dry ice. Total RNA was extracted using Qiagen's micro RNeasy kit after the tissue punch was homogenised in trizol. The protocol was carried out to manufacturers specifications.
(Parameters: Extracted product = total_RNA, Amplification = none) Protocol Type treatment protocol nucleic acid extraction protocol Protocol Term Source REF EFO EFO Term Source Name EFO ArrayExpress Term Source File http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/arrayexpress SDRF File E-MEXP-3933.sdrf.txt PubMed ID 23993098 Publication Author List Jagannath A, Butler R, Godinho SI, Couch Y, Brown LA, Vasudevan SR, Flanagan KC, Anthony D, Churchill GC, Wood MJ, Steiner G, Ebeling M, Hossbach M, Wettstein JG, Duffield GE, Gatti S, Hankins MW, Foster RG, Peirson SN Publication DOI 10.1016/j.cell.2013.08.004