|
| Status |
Public on Oct 22, 2011 |
| Title |
RNPs TDP-43-IP rep1 |
| Sample type |
RNA |
| |
|
| Source name |
RNPs TDP-43-IP
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NSC-34
cell type: motoneuronal-like cells
cellular fraction: cytoplasm
rip antibody: anti-TDP-43
rip antibody vendor: ProteinTech Group
rip antibody catalog number: 12892-1-AP
rip antibody lot/batch number: 00006802
|
| Growth protocol |
The motoneuronal cell line NSC34 was cultured in DMEM supplemented with 5% fetal bovine serum, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 mg/ml streptomycin.
|
| Extracted molecule |
cytoplasmic RNA |
| Extraction protocol |
Endogenous ribonucleoprotein (RNP) complexes from the cytoplasmic fraction of NSC34 were immunoprecipitated with anti-TDP-43, anti-FUS, or anti-IgG antibodies. mRNA (~100ng) was phenol-cloroform extracted from each triplicate immunoprecipitation sample. RNA integrity was evaluated with Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
mRNA was amplified and biotinylated using the Ambion TotalPrep RNA Amplification Kit according to the manufacturer's protocol and the integrity of the labeled cRNA obtained was evaluated with Agilent 2100 Bioanalyzer.
|
| |
|
| Hybridization protocol |
750ng of biotinylated cRNA per sample was hybridized to the Illumina MouseRef-8 v2.0 BeadChips according to standard Illumina hybridization protocol.
|
| Scan protocol |
Standard Illumina scanning protocol with the BeadArray Reader
|
| Description |
SAMPLE 1
|
| Data processing |
The data were normalised using quantile normalization method and a multiple testing correction using Benjamini and Hochberg False Discovery Rate was also applied.
|
| |
|
| Submission date |
Oct 21, 2011 |
| Last update date |
Nov 14, 2011 |
| Contact name |
Claudia Colombrita |
| Organization name |
IRCCS Istituto Auxologico Italiano
|
| Street address |
Via Zucchi, 18
|
| City |
Cusano milanino |
| ZIP/Postal code |
20095 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE33159 |
Identification of TDP-43 and FUS mRNA targets and pathways in the cytoplasmic compartment of motoneuronal NSC-34 cells |
|
