|
| Status |
Public on Aug 22, 2012 |
| Title |
array3 for Dicer knock-out in MEF cells, biological (exon) rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Dicer knock-out in MEF cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Dicer -/-
cell type: embryonic fibroblast
|
| Treatment protocol |
Cells were grown 3 days until subconfluency (70-80%)
|
| Growth protocol |
MEF cells were grown in DMEM (Invitrogen) supplemented with 7% (v/v) fetal calf serum and 100 U.ml-1 penicillin-streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using phenol-chloroform method. Ethanol-precipitated RNA was resuspended, treated with DNase (RNase free) 1h at 37°C, and cleaned-up using commercially available kits RNA-XS (Macherey-Nagel).
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the Applause WT-Amp Plus ST system Kit (NuGEN)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42°C for 5 minutes centrifuge at max speed for 1 minute. • Transfer 200μl of hyb solution to each array. • Hybridize 16 hours at 45°C at 60 rpm. • Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Data processing |
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), exon level expression were summarized from the corrected intensities and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps
|
| |
|
| Submission date |
Jul 30, 2012 |
| Last update date |
Aug 22, 2012 |
| Contact name |
Eric Batsche |
| Phone |
(33)1 44 27 34 77
|
| Organization name |
IBPS - Institut Biologie Paris Seine
|
| Department |
B2A Biological Adaptation and Ageing - UMR8256 CNRS
|
| Lab |
Epigenetics and RNA metabolism in human diseases
|
| Street address |
7-9, Quai Saint Bernard
|
| City |
Paris |
| ZIP/Postal code |
75006 |
| Country |
France |
| |
|
| Platform ID |
GPL6193 |
| Series (2) |
| GSE39746 |
Argonaute proteins couple chromatin silencing to alternative splicing (exon array) |
| GSE39749 |
Argonaute proteins couple chromatin silencing to alternative splicing |
|
| Relations |
| Alternative to |
GSM978472 (gene level analysis) |
