8 protocols
AccessionType
bioassay_data_transformation
ID_REF =
VALUE = dChip signal intensity
image_aquisition
Affymetrix standard protocol.
nucleic_acid_extraction
Total RNA from duplicate experiments of HPBALL infected cells with pLKO-.1 Luc and pLKO.1 shTLX3 was extracted with the RNeasy kit (Qiagen) according to the manufacturer's instructions
specified_biomaterial_action
Lentiviral plasmids plKO.1 Luc and pLKO.1 shTLX3 and the correspondent packaging plasmids were transfected in HEK293T by using JetPEI transfection agent . The viral surnatant was collected 48 hrs after transfection, filtered and used to infect target cells. All the infections were performed by spinoculation of viral supernatants produced in HEK293T cells. After infection, HPB-ALL cells were selected for 5 days in puromycin and ficolled the day before the experiments.
hybridization
Affymetrix standard protocol.
labeling
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
grow
HPBALL cell line were mantained in RPMI supplemented with 20% FBS and 1% P/S
feature_extraction
Array normalization was performed by DNAChip-Analyzer (dChip) on Genepattern website.