|
| Status |
Public on Nov 14, 2010 |
| Title |
Mouse M50 hepatocellular carcinoma tumor liver tissue |
| Sample type |
RNA |
| |
|
| Source name |
18 months post- AAV-vector injection mouse M50 tumor tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: frozen liver
gender: male
strain: C57BL/6J
|
| Treatment protocol |
At 18 months post-injection, mice were necropsied and liver (normal and tumor) samples snap frozen in liquid nitrogen
|
| Growth protocol |
Mice were injected with AAV-vector at 2-3 months of age and followed for 18 months under normal conditions with normal diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction with Rneasy kit (Qiagen) was performed according to manufacturers instructions
|
| Label |
biotin
|
| Label protocol |
0.2ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
|
| |
|
| Hybridization protocol |
The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0ST microarrays. 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.
|
| Scan protocol |
A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature
|
| Description |
gene expression data from liver cancer
|
| 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. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. 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.
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| |
|
| Submission date |
Aug 18, 2010 |
| Last update date |
Nov 14, 2010 |
| Contact name |
Hojun Li |
| E-mail(s) |
[email protected]
|
| Phone |
215-590-0674
|
| Fax |
215-590-3660
|
| Organization name |
Children's Hospital of Philadelphia
|
| Department |
Hematology
|
| Lab |
Dr. Katherine A. High
|
| Street address |
3501 Civic Center Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE23680 |
Expression data from hepatocellular carcinoma and adjacent normal liver tissue |
|
