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Sample GSM253841 Query DataSets for GSM253841
Status Public on Jan 01, 2008
Title Atrium Animal 284 zeitgeber time 6 Wildtype
Sample type RNA
 
Source name Atria
Organism Mus musculus
Characteristics Wildtype
zeitgeber time 6
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 45.82378 0.03836634
scl0018000.2_112-S -4.062364 0.5569307
scl018000.14_10-S -15.41348 0.8335396
ri|5430412N19|PX00102B18|AK030668|1883-S 1.590382 0.4282178
scl0024050.1_59-S 38.04612 0.05569307
scl024050.9_20-S -1.761445 0.496906
scl41084.12.1_14-S 45.2168 0.03836634
scl018951.1_6-S 33.43927 0.06497525
ri|C920001C06|PX00178G14|AK083302|3392-S 6.602921 0.3236386
scl0002894.1_595-S 2.671149 0.4028465
scl0002914.1_42-S -3.378128 0.5365099
scl0056526.1_262-S 32.98709 0.06621287
ri|A530023M17|PX00140B11|AK040766|2258-S 38.78434 0.05569307
ri|D430043E23|PX00195I14|AK052529|2864-S 42.84547 0.04517327
scl0235072.13_139-S 71.61157 0.01175743
scl41564.10_42-S 7.70925 0.3038366
scl40689.20_176-S -37.57719 0.9975247
scl0002080.1_55-S -11.75085 0.7549505
scl093684.5_156-S 138.4737 0
scl22501.2_29-S -1.454486 0.4931931

Total number of rows: 46120

Table truncated, full table size 1762 Kbytes.




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

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