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Sample GSM156165 Query DataSets for GSM156165
Status Public on Jan 18, 2007
Title HDAC2 WT E17.5 Ventricle 1A
Sample type RNA
 
Source name Mouse wt heart ventricular tissue at E17.5, pool of 2
Organism Mus musculus
Characteristics Strain: C57BL/6 X SV129, Age: Embryonic Day 17.5, Tissue: Heart Venticle
Extracted molecule total RNA
Extraction protocol Triazol extraction of total RNA was performed according to the manufecturer's protocol.
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.
Description Gene expression data during developmental stage of heart at E17.5
Data processing Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
 
Submission date Jan 17, 2007
Last update date Aug 28, 2018
Contact name Jonathan A Epstein
E-mail(s) [email protected]
Phone 215-898-8731
Fax 215-573-2094
URL http://www.med.upenn.edu/mcrc/epstein_lab/
Organization name University of Pennsylvania, School of Medicine
Department Cell and Developmental Biology
Lab 954, BRB II
Street address 421, Curie Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL1261
Series (1)
GSE6770 Gene Expression Data in HDAC2 KO Myocardium
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF ID_REF
VALUE VALUE
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 109.3 P 0.004484
AFFX-BioB-M_at 137.2 P 0.000225
AFFX-BioB-3_at 70.1 P 0.006871
AFFX-BioC-5_at 294 P 0.00011
AFFX-BioC-3_at 377.7 P 0.000052
AFFX-BioDn-5_at 521.8 P 0.000052
AFFX-BioDn-3_at 1644.4 P 0.00039
AFFX-CreX-5_at 4328.7 P 0.000052
AFFX-CreX-3_at 5554.7 P 0.000044
AFFX-DapX-5_at 504.1 P 0.000044
AFFX-DapX-M_at 736.3 P 0.000225
AFFX-DapX-3_at 766 P 0.000052
AFFX-LysX-5_at 46.5 P 0.000753
AFFX-LysX-M_at 99.8 M 0.054213
AFFX-LysX-3_at 199 P 0.000052
AFFX-PheX-5_at 76.3 P 0.00011
AFFX-PheX-M_at 93.8 P 0.001796
AFFX-PheX-3_at 103.2 P 0.000258
AFFX-ThrX-5_at 96.7 P 0.002867
AFFX-ThrX-M_at 123.5 P 0.000094

Total number of rows: 45101

Table truncated, full table size 1196 Kbytes.




Supplementary file Size Download File type/resource
GSM156165.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM156165.TXT.gz 840.7 Kb (ftp)(http) TXT

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