|
| Status |
Public on Apr 01, 2017 |
| Title |
3w TH-MYCN_Passage sphere_rep.3-2 |
| Sample type |
RNA |
| |
|
| Source name |
3-week-old TH-MYCN_Passage sphere
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 129+Ter/SvJcl
genotype/variation: TH-MYCN hemizygote (TH-MYCN+/-)
age: 3 weeks
tissue/cell type: passage sphere
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from spheres were isolated using ISOGEN II (317-07363, Nippon Gene) according to the manufacture’s instruction. Total RNA quantity and quality was examined by Agilent RNA6000 Nano Kit (5067-1511, Agilent Technologies) and Agilent 2100 Bioanalyzer (Agilent Technologies) according to the manufacture’s instruction. Total RNA samples with over RNA Integrity Number 8 were subjected to microarray analysis.
|
| Label |
Cy3
|
| Label protocol |
40 or 200 ng of total RNAs were labeled with Cyanine3 using Low Input Quick-Amp Labeling Kit (one color, 5190-2305, Agilent technologies) according to the manufacture’s instruction, followed by probe purification with RNeasy Mini Kit (74104, QIAGEN).
|
| |
|
| Hybridization protocol |
Purified labelled total RNAs were hybridized to SurePrint G3 Mouse Gene Expression 8x60K Microarray (G4852A, Agilent Technologies).
|
| Scan protocol |
Hybridization, scanning of microarrays, and data extraction from scanned images were conducted using the SureScan Microarray Scanner (G4900DA, Agilent Technologies) according to the Agilent protocol version 6.9 and Feature Extraction (version 13.1) software.
|
| Description |
Gene expression of 3-week-old TH-MYCN passage sphere rep.3-2 passaged 5 times
SAMPLE 30
|
| Data processing |
Scanned signals were analyzed using Subio Platform (Subio inc., Japan). Low signal cutoff was set to 1.0. Log transformation was applied with base 2. Global normalization was cunducted at percentage 75. Centering was applied by Mean. The normalized data (included in the sample table) was further filtered out (1) if Entrez gene ID is not annotated, (2) if Refseq number starts from either XM or XR (which is predicted gene), and (3) if the gene name contains "Predicted gene". It was further filtered out if 50% of gIsWellAboveBGs flag is zero at all sample groups (which signals are lower than background signal). The resulting data (with 23330 data rows) was considered as reliable probes. In the analysis, the normalized data was further filtered out if mean of normalized signals are between -1 to 1 at all sample groups (which signals are not varying), and filtered out if standard deviation of normalized signals are over 2 at one of each sample group (which signals are fluctuating within a sample group). The resulting data (with 7232 data rows) was considered as differentially expressed probes among four groups.
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| |
|
| Submission date |
Oct 10, 2016 |
| Last update date |
Apr 01, 2017 |
| Contact name |
Shoma Tsubota |
| E-mail(s) |
tsubota@med.nagoya-u.ac.jp
|
| Organization name |
Nagoya University Graduate School of Medicine
|
| Department |
Department of Molecular Biology
|
| Street address |
65 Tsurumai-cho, Showa-ku
|
| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
466-8550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10787 |
| Series (2) |
| GSE87782 |
MYCN-transformed neuroblasts from TH-MYCN mice are selectively isolated and maintained as spheres in vitro |
| GSE87784 |
Emerging role of polycomb repressive complex 2 in the early neuroblastoma tumorigenesis in TH-MYCN transgenic mice and its association with human neuroblastoma |
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