|
| Status |
Public on May 14, 2018 |
| Title |
Sfpq heterologous knock-out 1 |
| Sample type |
RNA |
| |
|
| Source name |
Sfpq+/- (Sfpq heterologous knock-out)
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: embryo
age: E13.5
tissue: brain (cerebral cortical region)
genotype/variation: Sfpq+/-
|
| Growth protocol |
Embryonic cerebral cortices were disected, isoalted in eppendorf tube, and quickly frozen in Liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cerebral cortical regions of control, Sfpq+/-,and Sfpq+/- brains were extracted using Rneasy Plus Micro (Qiagen) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT Expression Kit (Ambion) and then fragmented and labeled with the WT Terminal Labelingand and Controls Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned.
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Description |
RNA expression value derived from Expression Console software; full-exon analysis
|
| Data processing |
RNA expression value derived from Expression Console software; full-exon analysis
Raw data were processed with the Expression Console 1.2.0.20 (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed according to our previous plublication (Yamashita et al. J. Hum. Genet. 57, 368-374). )R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.
|
| |
|
| Submission date |
Apr 17, 2013 |
| Last update date |
May 14, 2018 |
| Contact name |
Mikako Ito |
| E-mail(s) |
ito@med.nagoya-u.ac.jp
|
| Organization name |
Nagoya University Graduate School of Medicine
|
| Lab |
Neurogenetics
|
| Street address |
65 Tsurumai, Showa-ku
|
| City |
Nagoya |
| ZIP/Postal code |
4668550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6193 |
| Series (1) |
| GSE46138 |
Exon Level Expression Profiling: a Novel Unbiased Transcriptome |
|
