|
| Status |
Public on Mar 06, 2020 |
| Title |
CTRL-1 WASH |
| Sample type |
RNA |
| |
|
| Source name |
Cortex/Striatum, 6 week-old
|
| Organism |
Mus musculus |
| Characteristics |
genotype: CTRL
group: WASH
replicate: 1
tissue: Cortex/Striatum
age: 6 week-old
rna fraction: Enriched in short poly(A)-tail RNA
|
| Growth protocol |
All mice were housed in animal facility. Mice were housed four per cage with food and water available ad libitum and maintained in a temperature-controlled environment on a 12/12 h light-dark cycle with light onset at 08:00. Animal housing and maintenance protocols followed the guidelines. Animal experiments were performed under approved protocols.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The cortex and striatum together were quickly dissected, homogenized and total RNA (Input) was extracted using the Maxwell® 16 LEV simplyRNA Tissue Kit (Promega). The poly(A) RNA fraction was purified by poly(U) chromatography (Poly(U)-agarose, Sigma). Differential elution with 25% or 90% formamide yielded two fractions of mRNAs enriched for short (WASH) or long (ELUTED) poly(A)-tails, respectively. The RNA of the two poly(A) fractions was precipitated with isopropanol and purified by Phenol:Chloroform protocol.
|
| Label |
biotin
|
| Label protocol |
5 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2). Amplification was performed for 21 cycles. 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)
|
| Scan protocol |
Arrays were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)
|
| Data processing |
Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)
|
| |
|
| Submission date |
Apr 30, 2018 |
| Last update date |
Mar 06, 2020 |
| Contact name |
Camille Stephan Otto Attolini |
| Organization name |
IRB Barcelona
|
| Department |
Biostatistics and bioinformatics Unit
|
| Street address |
Baldiri Reixac 10
|
| City |
Barcelona |
| State/province |
Select a State or Province |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11180 |
| Series (2) |
| GSE113840 |
Genome-wide analysis of mRNA polyadenylation in Cortex/Striatum of CPEB4 modified mice [II] |
| GSE113842 |
Autism-like phenotype and risk gene-RNA deadenylation by CPEB4 mis-splicing |
|
