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Sample GSM1642270 Query DataSets for GSM1642270
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

Data table header descriptions
ID_REF
VALUE Quantile gene and normalized gene level expression values (log2) from EASANA (GenoSplice technology)

Data table
ID_REF VALUE
1 9.31879
2 11.84184
3 12.82093
4 13.04906
5 11.5495
6 10.44283
7 8.951209
8 10.8029
9 11.26775
10 10.31809
11 10.53812
12 9.533371
13 10.44589
14 10.90865
15 10.79575
16 10.6615
17 10.39983
18 8.986618
19 11.21519
20 10.73694

Total number of rows: 573410

Table truncated, full table size 8789 Kbytes.




Supplementary file Size Download File type/resource
GSM1642270_TDP-WT_TET_siTDP43_2.CEL.gz 24.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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