|
| Status |
Public on Dec 31, 2020 |
| Title |
WHIM6E: whim6_passage E |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: 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.
|
| Growth protocol |
Tumors from xenograft models were cryopreserved. Tumors from patient samples were frozen and stored in OCT compound.
|
| 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 |
xenograft tumor_whim6_passage E
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: xenograft tumor
tissue type: cryopreserved tissue
|
| Growth protocol |
Tumors from xenograft models were cryopreserved. Tumors from patient samples were frozen and stored in OCT compound.
|
| 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 Scanner.
|
| Data processing |
Raw Agilent 4x44K gene expression data were normalized using the BioConductor “limma” package sequentially through background subtraction, loess within-array normalization and quantile between-array normalization. The probe level gene expression data were collapsed to gene level by median expression. ComBat was applied using the R package “sva” to the normalized gene expression data to correct for potential human/mouse batch effect.
|
| |
|
| Submission date |
Apr 20, 2020 |
| 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 |
GPL28436 |
| Series (1) |
| GSE148949 |
BKM120 Treated WHIMs_17 Model Cohort |
|
| Relations |
| Reanalysis of |
GSM611060 |
| Reanalyzed by |
GSM7797112 |
