|
| Status |
Public on Dec 22, 2020 |
| Title |
Tumor2-1 |
| Sample type |
RNA |
| |
|
| Source name |
mouse2 tumor
|
| Organism |
Homo sapiens |
| Characteristics |
marker: CD44+ cells
cell tyep: PDX cells
sample type: primamary tumor
|
| Treatment protocol |
Cancer stem cell marker CD44-positive PDX cells were collected from the PDX tumor at the primary site and the liver of PDX mice using a cell sorter.
|
| Growth protocol |
Human breast cancer patient-derived xenograft (PDX) mouse model was established by xenotransplantation of the breast cancer tissue into mammary fat pad regions of female immunodeficient NSG mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
From the 2,000 sorted PDX cells, total RNA was extracted using RNesy mini kit (Qiagen) according to the manufacturer's instructions. Tehn, cDNA was synthesized and amplified from total RNA exploiting Ovation Pico WTA System V2 (NuGEN).
|
| Label |
Cy3
|
| Label protocol |
cDNA samples were labeled with cyanine 3-dUTP exploiting SureTag DNA Labeling Kit (Agilent Tech.) according to the manufacturer's instructions/
|
| |
|
| Hybridization protocol |
cDNA were subjected to fragmentation and hybridized on SurePrint G3 Human GE ver3.0 8x60K Microarray (Agilent Tech.) following manufacture’s instruction. Then, slides were washed in Agilent Gene Expression Wash Buffers 1 and 2 (Agilent Tech.).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of primamary tumor
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih two filters with GeneSpring software (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values separately for mouse1 and mouse2 (two tumor and two liver data (in total four data) for each mouse). In the first filter, when the value of a probe was lower than 20 percentile value in all samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. After flitering, the common probes in mouse1 and mouse 2 were extacted ,and control probes were excluded. Then log scale values were transformed into normal scale, and theprobes of which coefficient of variation was over 0.5 in any four samples (mouse1 tumor, mouse1 liver, mouse2 tumor, mouse2 liver) were omitted. Finally, the probes for whcih the gene symbol were not assigned were also omitted.
|
| |
|
| Submission date |
May 26, 2020 |
| Last update date |
Dec 22, 2020 |
| Contact name |
Nishimura Tatsunori |
| E-mail(s) |
tatsunori323@med.nagoya-u.ac.jp
|
| Organization name |
Nagoya University
|
| Department |
Graduate School of Medicine
|
| Lab |
Division of Cancer Biology
|
| Street address |
65 Tsurumai-cho, Showa-ku
|
| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
466-8550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21185 |
| Series (1) |
| GSE151191 |
Gene expression of breast cancer stem cells. |
|
