|
| Status |
Public on Oct 01, 2005 |
| Title |
ST01-298 |
| Sample type |
RNA |
| |
|
| Source name |
cellular uterine leiomyoma
|
| Organism |
Homo sapiens |
| Characteristics |
Histological type: Cellular
Karyotype: 44,XX,del(1)(p11-12),-19,-21/44,idem,del(13)(q14q22)
|
| Biomaterial provider |
Bradley J. Quade, M.D., Ph.D., Division of Women’s and Perinatal Pathology, Brigham and Women’s Hospital
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
|
| Label |
biotin
|
| Label protocol |
by standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
by standard Affymetrix protocol
|
| Scan protocol |
by standard Affymetrix protocol
|
| Description |
Cellular uterine leiomyoma with karyotype = 44,XX,del(1)(p11-12),-19,-21/44,idem,del(13)(q14q22). Total RNA was isolated with Trizol and converted to labeled cRNA by standard Affymetrix protocols. Before analysis, Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis.
|
| Data processing |
Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis.
|
| |
|
| Submission date |
Aug 08, 2005 |
| Last update date |
Aug 09, 2005 |
| Contact name |
Bradley J Quade |
| E-mail(s) |
bquade@partners.org
|
| Phone |
617-732-5475
|
| Fax |
617-738-6996
|
| URL |
http://www.bwhpathology.org/gynpath/
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Pathology
|
| Lab |
Division of Women's and Perinatal Pathology
|
| Street address |
75 Francis Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL80 |
| Series (2) |
| GSE764 |
Comparison of Gene Expression in Uterine Smooth Muscle Tumors |
| GSE9511 |
Characterization of Plexiform Leiomyomata Provide Further Evidence for Genetic Heterogeneity Underlying Uterine Fibroids |
|
| Data table header descriptions |
| ID_REF |
Affymetrix Identifier |
| VALUE |
Normalized (Avg Diff) Average Difference hybridization intensity value (see sample description for normalization) |
| POSITIVE |
number of pairs with positive signal |
| NEGATIVE |
number of pairs with negative signal |
| PAIRS_USED |
number of pairs used for analysis |
| PAIRS_IN_AVG |
trimmed probe pair set |
| POS_FRACTION |
#positive probe pairs/#of probe pairs used |
| LOG_AVG |
log average ratio (see Affymetrix literature for formula) |
| AVG_DIFF |
raw Avg Diff value prior to normalization |
| ABS_CALL |
absolute call of Presence or Absence of gene transcript in sample |
| SELECTED_SMOOTH_MUSCLE_TUMOR_GENE |
boolean (true/false) variable to identify genes selected by ANOVA and combined Ratio/Threshold filter |
