|
| Status |
Public on Jan 01, 2020 |
| Title |
GBE HCC Replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
GBE HCC 1
|
| Organism |
Mus musculus |
| Characteristics |
cohort: GBE HCC
replicate: 1
barcode: BC15561-179
|
| Treatment protocol |
B6C3F1 mouse were either treated with vehicle control or various doses of Ginkgo biloba extract by oral gavage for 2 years as part of National Toxicology Porgram (NTP) Toxicology and Carcinogenesis studies.
|
| Growth protocol |
B6C3F1 mouse were used for this study for a period of 2 years.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were isolated from these selected samples using the Invitrogen PureLink Mini Kit® (Life Technologies Corporation, Carlsbad, CA). RNA quality was assessed using an Agilent Bioanalyzer®. (Agilent Technologies, Inc; Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
Array slides were double stained with streptavidin/phycoerythrin and washed using the EukGE-WS2v5 protocol from the Affymetrix Fluidics Station FS450 for antibody amplification.
|
| |
|
| Hybridization protocol |
15 µg of amplified biotinylated cDNAs were fragmented and hybridized for 16 hours at 45oC as per Affymetrix protocol
|
| Scan protocol |
Arrays were scanned in an Affymetrix Scanner 3000, and GeneChip1 Command Console Software (AGCC; Version 1.1) was used to obtain the data. Fluorescent pixel intensity measurements were processed using the MAS5 algorithm (Hubbell, Liu, and Mei 2002), and signals were background subtracted and averaged across probes within a probeset using a mean Tukey biweight function.
|
| Description |
Gene Expression data for GBE HCC Replicate 1
|
| Data processing |
The CEL files were processed using R, proprocessCore package to compute RMA normalized Signal for each probe set
|
| |
|
| Submission date |
Jun 11, 2019 |
| Last update date |
Jan 02, 2020 |
| Contact name |
Deepak Mav |
| Organization name |
Sciome LLC
|
| Street address |
2 Davis Drive
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE132575 |
Expression Profiling of Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Exposure to Ginkgo biloba Extract (GBE) in B6C3F1/N Mice [Expression] |
| GSE132578 |
Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Exposure to Ginkgo biloba Extract (GBE) in B6C3F1/N Mice |
|
