NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM253863 Query DataSets for GSM253863
Status Public on Jan 01, 2008
Title Ventricle Animal 206 zeitgeber time 0 Transgenic
Sample type RNA
 
Source name Ventricles
Organism Mus musculus
Characteristics Transgenic
zeitgeber time 0
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 25.11629 0.09344059
scl0018000.2_112-S -5.842298 0.582302
scl018000.14_10-S 2.114908 0.3824258
ri|5430412N19|PX00102B18|AK030668|1883-S -0.6927468 0.4504951
scl0024050.1_59-S 2.665659 0.3669555
scl024050.9_20-S -20.47006 0.8892327
scl41084.12.1_14-S 41.64972 0.03527228
scl018951.1_6-S 19.65505 0.1311881
ri|C920001C06|PX00178G14|AK083302|3392-S 12.22934 0.2233911
scl0002894.1_595-S 3.12192 0.3576733
scl0002914.1_42-S -7.918851 0.6423267
scl0056526.1_262-S 13.53029 0.2042079
ri|A530023M17|PX00140B11|AK040766|2258-S 39.28487 0.04207921
ri|D430043E23|PX00195I14|AK052529|2864-S 43.12107 0.03155941
scl0235072.13_139-S 53.07189 0.0105198
scl41564.10_42-S -15.6009 0.8211634
scl40689.20_176-S -44.11743 1
scl0002080.1_55-S -10.64245 0.7122525
scl093684.5_156-S 35.65354 0.05136139
scl22501.2_29-S -1.139852 0.4647277

Total number of rows: 46120

Table truncated, full table size 1765 Kbytes.




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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap