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Sample GSM1592993 Query DataSets for GSM1592993
Status Public on Jun 01, 2015
Title Clockwise shifts_fourteen days recovery_8h_nr347
Sample type RNA
 
Source name liver RNA
Organism Mus musculus
Characteristics strain: FVB
light rotation: Clockwise shifts
group: fourteen days recovery
zeitgeber time: 8h
mouse id: 347
Treatment protocol Prior to the first shift, animals (n=24) were sacrificed around the clock at four hour intervals (n=4 at each time point). Subsequently, the remaining group of animals underwent six shifts in either a clockwise (CW) or counterclockwise (CCW) rotating light schedule. Specifically, mice were exposed to a phase delay or phase advance of eight hours every five days, respectively. After one shift, six shifts, five days recovery and fourteen days recovery n=30 animals per group were sacrificed around the clock with four hour intervals (n=5 per time point).
Growth protocol Female FVB mice, 8 to 12 weeks of age, were kept under a normal 12:12 hour light-dark (LD) cycle for approximately three weeks, with Zeitgeber Time 0 (ZT0) corresponding to lights on. Animals were group-housed and food and water were provided ad libitum.
Extracted molecule total RNA
Extraction protocol RNA was extracted from livers (n=4 per time point at baseline and n= 2 per time point for the CCW and CW groups) using the miRNeasy Mini Kit (Qiagen Benelux, Venlo, The Netherlands). RNA concentrations were measured using a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA), and RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands).
Label Cy3
Label protocol RNA was processed for gene expression analysis using the methods described in [Pennings et al, PLoS One, 2011. 6(4): p. e18866.]. Experimental samples (each corresponding to RNA from one individual mouse) were labelled with Cy3 and the common reference sample (made by pooling equimolar amounts of RNA from experimental samples) was labelled with Cy5.
 
Hybridization protocol Samples were hybridized to Nimblegen Mus musculus 12 x 135 k microarrays (Roche NimbleGen, Germany). This type of microarray contains 44,170 gene probes with three spots per probe.
Scan protocol Slides were scanned with an Agilent G2565CA DNA microarray scanner. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen), resulting in a table containing individual probe signal intensities for both dyes.
Description channel #2 in FTR file corresponds to Cy5-labeled common reference
Data processing The raw data were subjected to a set of quality control checks to ensure comparable signal average and distribution. Raw microarray data for gene-coding probes were normalized in R (www.r-project.org) using a four step approach [Pennings et al, PLoS One, 2011. 6(4): p. e18866.]: (1) natural log-transformation, (2) quantile normalization of all scans, (3) correcting the sample spot signal for the corresponding reference spot signal and (4) averaging data from replicate probe spots. The normalized data of 44,170 probes were further analysed in R and Excel (Microsoft Corporation, USA).
 
Submission date Jan 27, 2015
Last update date Jun 01, 2015
Contact name Jeroen Pennings
E-mail(s) Jeroen.Pennings@rivm.nl
Phone +31 88 689 2214
Organization name Natl. Inst. Public Health & Environment
Street address A. van Leeuwenhoeklaan 9
City Bilthoven
ZIP/Postal code 3721MA
Country Netherlands
 
Platform ID GPL10192
Series (1)
GSE65346 Liver gene expression response to circadian rhythm disruption

Data table header descriptions
ID_REF
VALUE Natural log-transformed signal intensity

Data table
ID_REF VALUE
AB000096 6.8769
AB000490 6.8898547
AB001425 7.0399226
AB001435 6.7564125
AB001539 7.105492
AB001750 8.2076032
AB001926 6.9500597
AB003502 9.0210769
AB004048 6.5985896
AB005662 6.7399483
AB005665 5.7080667
AB005909 6.1917901
AB006034 6.7149608
AB006103 6.696285
AB007407 6.4941393
AB008928 6.7301749
AB009369 6.3530036
AB010088 7.4877735
AB010122 7.4372376
AB011499 6.1536845

Total number of rows: 44170

Table truncated, full table size 833 Kbytes.




Supplementary file Size Download File type/resource
GSM1592993_537083A06.ftr.gz 4.0 Mb (ftp)(http) FTR
Processed data included within Sample table

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