|
| Status |
Public on Sep 09, 2014 |
| Title |
Undifferentiated NPC culture from SVZ of Naive rat, rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
SVZ Naive
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Dark Agouti
cell type: NPC culture
npc culture propagated from: SVZ
differentiation stage: Undifferentiated
disease state: Healthy
|
| Growth protocol |
NPC cultures propagated from different segments of the central nervous system: subventricular zone (SVZ) and the cervical, thoracic and caudal parts of the spinal cord. The segments were isolated from either healthy (naive) rats or rats with EAE.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction and on-column DNase treatment was performed using the RNeasy mini kit from Qiagen.
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
NPC culture harvested after second passage
Healthy rats
|
| Data processing |
Data processing involved background signal correction using the GC composition-based background correction algorithm (PM-GCBG), array normalization with global median and signal summarization using the probe logarithmic intensity error estimation (plier), all steps performed in the GeneChip Expression console from Affymetrix.
To calculate the statistical significance between naïve and EAE groups two-sided unpaired student’s t-test was used. The false discovery rate (FDR) was calculated using the q-value plugin for R and an FDR level of 5% was set. The functional analysis and canonical pathway analysis of the entire data set was generated with Ingenuity Pathway Analysis
probe group file: RaGene-1_0-st-v1.r4.pgf
meta-probeset file: RaGene-1_0-st-v1.r4.mps
|
| |
|
| Submission date |
Apr 25, 2013 |
| Last update date |
Sep 09, 2014 |
| Contact name |
Ruxandra Covacu |
| E-mail(s) |
ruxandra.covacu@ki.se
|
| Phone |
+46736915255
|
| Organization name |
Karolinska Institutet
|
| Street address |
CMM, L8:04
|
| City |
Stockholm |
| ZIP/Postal code |
SE-17176 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE46373 |
Change of fate comitment in adult neural progenitor cells subjected to chronic inflammation |
|
