|
| Status |
Public on Oct 10, 2012 |
| Title |
WU-BC4, mouse passage3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Stratagene Human Reference total RNA from 10 human cell lines: 1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte. Also, mRNA spiked in from MCF7 and ME16C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extractions followed by Dnase treatment and column purification.
|
| Label |
Cy3
|
| Label protocol |
Agilent Low Input Linear Amplification Kit and protocol
|
| |
|
| Channel 2 |
| Source name |
primary breast tumor, WU-BC4, xenograft passage3
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue type: primary breast tumor
sample type: oct block from human:mouse xenograft which contained at least 50% tumor cellularity
clinical er: Negative
clinical pgr: Negative
clinical her2: Negative
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extractions followed by Dnase treatment and column purification.
|
| Label |
cy5
|
| Label protocol |
Agilent Low Input Linear Amplification Kit and protocol
|
| |
|
| |
| Hybridization protocol |
Agilent 60-mer oligo microarray processing protocol
|
| Scan protocol |
Microarrays were scanned with an Agilent B Scanner using 5um, single pass scanning mode and eXtended dynamic range.
|
| Description |
PAM50 Basal Subtype
|
| Data processing |
txt files and tif images generated by Agilent's Feature Extraction, v9.5.3.1, were uploaded into the UNC Microarray database. Final loess, normalized log2 ratios (Cy5-sample/Cy3-control) for each probe were retrieved.
|
| |
|
| Submission date |
Apr 26, 2011 |
| Last update date |
Dec 26, 2023 |
| Contact name |
Cynthia Ma |
| E-mail(s) |
cynthiaxma@wustl.edu
|
| Phone |
3143628903
|
| Organization name |
Washington University
|
| Department |
Medical Oncology
|
| Lab |
Dr. Cynthia Ma Lab
|
| Street address |
4515 Mckinley, 4515 Mckinley
|
| City |
st louis |
| State/province |
Missouri |
| ZIP/Postal code |
63627 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE28860 |
WU-BC 3, 4, and 5 PAM50 Subtypes with Passage and Gene Expression Comparison Between Xenografts and Primary Tumors |
| GSE41685 |
WHIM Gene Expression Data_Update Through WHIM 26 |
|
| Relations |
| Reanalyzed by |
GSM4486586 |
