|
| Status |
Public on Apr 03, 2015 |
| Title |
LNCaP-ABL KD1 Biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
LNCaP-ABL cells with GNPNAT1 shRNA 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: LNCaP-ABL
lentivirus: GNPNAT1 shRNA 1
sample type: CRPC, contains AR-FL
|
| Treatment protocol |
To generate stable GNPNAT1 KD in 22RV1, LNCaP-ABL and C42 cells, lentiviral transduction of GNPNAT1 shRNA (Sigma Aldrich (Product# CSTVRS), two independent shRNA clones) was carried out using a virus titer of 5 MOI and cells were selected using 0.5ug/ml puromycin
|
| Growth protocol |
22RV1 and LNCaP-ABL were grown in RPMI 1640 medium with 10 % full or charcoal stripped FBS and with or without phenol red respectively. 100 ug/ml of Normocin was added to all the cell culture media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We used RNeasy Mini Kit from QIAGEN for total RNA extraction according to the manusfacturer's protocol
|
| Label |
biotin
|
| Label protocol |
Standard Affimatrix protocol were used at Affymetrix and Microarray Core Facility at UMICH using IVT express kit.
|
| |
|
| Hybridization protocol |
Standard Affimatrix protocol were used at Affymetrix and Microarray Core Facility at UMICH using IVT express kit.
|
| Scan protocol |
Standard Affimatrix protocol were used at Affymetrix and Microarray Core Facility at UMICH.
|
| Data processing |
calculated expression values for each gene using a robust multi-array average (RMA) Irizarry et al. (2003). This is a modeling strategy that converts the PM probe values into an expression value for each gene. Note that the expression values are log2 transformed data.
|
| |
|
| Submission date |
Apr 02, 2015 |
| Last update date |
Apr 03, 2015 |
| Contact name |
Akash Kumar Kaushik |
| E-mail(s) |
akkaushi@bcm.edu
|
| Phone |
9362050781
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Cellular Biology
|
| Lab |
Sreekumar Lab 120D
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE67537 |
Pathway-based integrative analysis reveals a key role for the hexosamine biosynthetic pathway in castrate resistant prostate cancer with therapeutic implications |
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