|
| Status |
Public on Feb 27, 2011 |
| Title |
siGAPDH_2 [exon-level] |
| Sample type |
RNA |
| |
|
| Source name |
HeLa cells (ATCC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
trasfection: siRNA anti-GAPDH
|
| Treatment protocol |
siRNAs were synthesized as ON-TARGET-PLUS grade from Dharmacon. Anti-HP1 and anti-GAPDH siRNAs were transfected twice consecutively with Dharmafect #1 (Dharmacon) according to the manufacturer’s instructions.
|
| Growth protocol |
HeLa cells were grown in DMEM (Invitrogen) supplemented with 7% (v/v) fetal calf serum and 100 U.ml-1 penicillin-streptomycin.
|
| Extracted molecule |
cytoplasmic RNA |
| Extraction protocol |
RNA was isolated with the RNeasy Mini Kit (Qiagen) with DNAseI (10U, Roche) treatment, according to the 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 EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
|
| |
|
| Submission date |
Nov 12, 2010 |
| Last update date |
Feb 27, 2011 |
| Contact name |
Violaine Saint-André |
| Organization name |
Institut Curie
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE25282 |
HP1gamma Knock Down in Human cells |
|
| Relations |
| Alternative to |
GSM622060 (gene-level analysis) |
