|
| Status |
Public on Jan 18, 2007 |
| Title |
HDAC2 KO E17.5 Ventricle 1B |
| Sample type |
RNA |
| |
|
| Source name |
Mouse wt heart ventricular tissue at E17.5, pool of 3
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6 X SV129, Age: Embryonic Day 17.5, Tissue: Heart Venticlee
|
| 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) |
epsteinj@mail.med.upenn.edu
|
| 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 |
