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Sample GSM1592926 Query DataSets for GSM1592926
Status Public on Jun 01, 2015
Title Counterclockwise shifts_two shifts_16h_nr208
Sample type RNA
 
Source name liver RNA
Organism Mus musculus
Characteristics strain: FVB
light rotation: Counterclockwise shifts
group: two shifts
zeitgeber time: 16h
mouse id: 208
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 7.0519685
AB000490 6.9583375
AB001425 7.0547259
AB001435 6.9431446
AB001539 7.2374066
AB001750 8.099931
AB001926 7.0025765
AB003502 9.0449083
AB004048 6.7126615
AB005662 6.6973808
AB005665 5.7228293
AB005909 6.4268312
AB006034 6.7668993
AB006103 6.7079549
AB007407 6.6140274
AB008928 6.7254538
AB009369 6.3989501
AB010088 7.5487494
AB010122 7.2740786
AB011499 6.1539338

Total number of rows: 44170

Table truncated, full table size 833 Kbytes.




Supplementary file Size Download File type/resource
GSM1592926_537136A05.ftr.gz 3.9 Mb (ftp)(http) FTR
Processed data included within Sample table

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