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Sample GSM253927 Query DataSets for GSM253927
Status Public on Jan 01, 2008
Title Ventricle Animal 303 zeitgeber time 21 Wildtype
Sample type RNA
 
Source name Ventricles
Organism Mus musculus
Characteristics Wildtype
zeitgeber time 21
Treatment protocol Atrial and ventricular tissue samples were collected from wildtype and transgenic animals lacking a functional circadian clock within the cardiomyocytes every three hours for a period of 24 hours (n=4 samples per time point).
Extracted molecule total RNA
Extraction protocol RNA was extracted from all tissues using a standard protocol and Tri-reagent.
Label Cy-3
Label protocol Total RNA was converted to cDNA by reverse transcription using Superscript II reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA.
 
Hybridization protocol A total of 1.5 micrograms of biotin-labeled cRNA was applied to a BeadChip and allowed to hybridize overnight at 55°C for approximately 18 hours, followed by washing and staining with strepavidini-Cy3 prior to visualization.
Scan protocol BeadChips were visualized using the BeadStation scanner, which uses a dual-laser confocal scanner with 0.8 µm resolution to determine fluorescence values for each bead on the chip.
Description Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
Data processing After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA), which calculates the mean fluorescence signal across all replicates of each gene/transcript, along with a probability that the mean signal for each gene/transcript on the chip is greater than background (i.e., detection p-value). Both non-normalized and normalized (qspline) data were generated for each tissue type.
 
Submission date Dec 31, 2007
Last update date Dec 31, 2007
Contact name Molly Bray
E-mail(s) mbray@bcm.edu
Phone 713-798-9311
Fax 713-798-7187
Organization name Baylor College of Medicine
Department Pediatrics/USDA/ARS Children's Nutrition Research Ctr
Street address 1100 Bates, Suite 8070
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6333
Series (1)
GSE10045 Disruption of the Circadian Clock within the Cardiomyocyte

Data table header descriptions
ID_REF
VALUE normalized signal intensity (BeadStudio ver. 3)
Detection Pval

Data table
ID_REF VALUE Detection Pval
scl054204.2_14-S 14.41232 0.1503713
scl0018000.2_112-S -16.23561 0.8087871
scl018000.14_10-S 6.333104 0.2722772
ri|5430412N19|PX00102B18|AK030668|1883-S -8.020551 0.6144802
scl0024050.1_59-S 37.17338 0.0259901
scl024050.9_20-S -10.25208 0.6664604
scl41084.12.1_14-S 39.83421 0.02165841
scl018951.1_6-S -9.6261 0.6503713
ri|C920001C06|PX00178G14|AK083302|3392-S 16.77231 0.1293317
scl0002894.1_595-S 10.27615 0.210396
scl0002914.1_42-S -5.389463 0.5457921
scl0056526.1_262-S 19.80067 0.1008663
ri|A530023M17|PX00140B11|AK040766|2258-S 36.91414 0.0259901
ri|D430043E23|PX00195I14|AK052529|2864-S 28.82878 0.04888614
scl0235072.13_139-S 38.86018 0.02289604
scl41564.10_42-S 21.11908 0.09405941
scl40689.20_176-S 2.566796 0.3490099
scl0002080.1_55-S 45.99015 0.0105198
scl093684.5_156-S 33.16589 0.03774752
scl22501.2_29-S 43.40683 0.01485149

Total number of rows: 46120

Table truncated, full table size 1769 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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