|
| Status |
Public on Aug 11, 2015 |
| Title |
TDP-WT_TET_siTDP43_2 (exon-level) |
| Sample type |
RNA |
| |
|
| Source name |
TDP-WT siTDP43
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK-293
genotype/variation: siTDP43-treated HEK-293 cells overexpressing a flagged-wildtype TDP-43
|
| Treatment protocol |
Flp-In HEK293 (Invitrogen) carrying inducible siRNA resistant FLAG-tagged wild type TDP-43, F4L mutant, and TDP43-12XQ/N constructs were induced (to obtain tagged TDP-43 expression) with 1μg/ml tetracycline (Sigma). Depletion of endogenous TDP-43 was performed by RNA interference using HiPerFect Transfection Reagent (Qiagen) and siRNA specific for TDP-43 (Dharmacon; target sequence 5’-aagcaaagccaagaugagccu-3’).
|
| Growth protocol |
Cells were cultured under DMEM(10%FBS, 1% penicillin-streptomycine). Atmosphere: air, 95%; carbon dioxide (CO2), 5%. Temperature, 37.0°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNeasy Mini Kit (Qiagen) following manufacturer´s instructions
|
| 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
|
| Data processing |
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
HJAY_r2.pgf
HJAY_r2.full.mps
|
| |
|
| Submission date |
Mar 24, 2015 |
| Last update date |
Aug 11, 2015 |
| Contact name |
Pierre de la Grange |
| E-mail(s) |
pierre.delagrange@genosplice.com
|
| Organization name |
GenoSplice technology
|
| Department |
Paris Biotech Santé
|
| Street address |
29, rue du Faubourg Saint-Jacques
|
| City |
Paris |
| ZIP/Postal code |
75014 |
| Country |
France |
| |
|
| Platform ID |
GPL15106 |
| Series (1) |
| GSE67195 |
TDP-43 can directly affect splicing profiles and isoform production of genes involved in the apoptotic and mitotic cellular pathways |
|
| Relations |
| Reanalyzed by |
GSM1642489 |
