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Sample GSM45830 Query DataSets for GSM45830
Status Public on Apr 15, 2005
Title Night_6hr_pool_v_light_6hr_rat_102
Sample type RNA
 
Channel 1
Source name Individual Rat 102
Organism Rattus norvegicus
Extracted molecule total RNA
 
Channel 2
Source name Pool
Organism Rattus norvegicus
Extracted molecule total RNA
 
 
Description One µg of total RNA from either an
individual rat or from a pooled sample was amplified and labeled with a
fluorescent dye (either Cy3 or Cy5) using the Low RNA Input Linear Amplification
Labeling kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s
protocol. The amount and quality of the resulting fluorescently labeled cRNA
was assessed using a Nanodrop ND-100 spectrophometer and an Agilent
Bioanalyzer. Equal amounts of Cy3- or Cy5-labeled cRNA were hybridized to the
Agilent Rat Oligo Microarray (Agilent Technologies, Inc., Palo Alto, CA) for 17
hrs, prior to washing and scanning. Data was extracted from the resulting
images using Agilent’s Feature Extraction Software (Agilent Technologies, Inc.,
Palo Alto, CA). For day/night comparisons, two types of complementing
hybridizations were performed: hepatic RNA from individual day rats was
hybridized against a pool made up of RNA from 12 hour offset night rats, and
RNA from individual night rats was hybridized against a pool made up of RNA
from 12-hour offset day rats. Specifically, hepatic RNA samples from three
individual day rats collected ten hours after light on (CT10) were hybridized
against a pooled RNA sample composed of equal aliquots of RNA from the livers
of six night rats collected ten hrs after lights off (CT22); and RNA samples from
Page 8
three individual night rats collected at CT22 were hybridized against a pooled
RNA sample composed of equal aliquots of RNA from the livers of six day rats
collected at CT10. This was replicated in a second study for a total of 24
hybridizations of 12 hour offset samples.
For time of day comparisons, equal aliquots of RNA from the livers of six
rats collected at each of four different times of the circadian day (CT4, CT10, C16
and CT22) were pooled. The two replicate studies thus resulted in 8 pools (two
replicate pools/time point times four time points); each pool was hybridized
against a Universal Rat Reference RNA Standard (Stratagene, La Jolla, CA).
 
Submission date Mar 23, 2005
Last update date Oct 28, 2005
Contact name Gary A Boorman
E-mail(s) boorman@niehs.nih.gov
Phone (919) 541-3440
Organization name NIEHS
Department Division of Intramural Research Environmental Toxicology Program
Street address MD B3-08, P.O. BOX 12233
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL890
Series (1)
GSE2441 Hepatic Gene Expression Changes Throughout the Day in the Fischer Rat

Data table header descriptions
ID_REF
VALUE night_6hr_pool_v_light_6hr_rat_102

Data table
ID_REF VALUE
3 -0.18420677
4 0.29933608
5 0.16118096
6 0.13815515
8 0.016003024
9 0.23025852
10 -0.25328434
11 0.115129255
12 0.3453878
13 0.04605171
15 -0.046051696
16 0.023025876
17 0.06907751
18 0.06907751
19 1.60E-04
20 0.115129255
22 0.115129255
23 0.2532843
24 0.13815515
25 -0.460517

Total number of rows: 20222

Table truncated, full table size 338 Kbytes.




Supplementary data files not provided

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