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