17 protocols
AccessionType
normalization data transformation protocol
Transcript-level gene expression estimates were generated via the robust multichip average (RMA) algorithm within each batch using the Entrez Gene CDF v11 (http://brainarray.mbni.med.umich.edu) in R v2.9.2. ID_REF = VALUE = Quantile normalized transcript level expression using the RMA algorithm with the Entrez Gene CDF v11 (http://brainarray.mbni.med.umich.edu)
array scanning protocol
Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.
hybridization protocol
cDNA was fragmented end-labeled with a biotinylated dideoxynucleotide using terminal transferase and added to a hybridization cocktail, loaded on a Human Gene1.0 ST GeneChip and hybridized for 16 hours at 45 ºC under rotation (60 rpm). Following hybridization, the array was washed and stained according to the standard Affymetrix protocol.
labelling protocol
The total RNA was converted to cDNA and subsequently amplified and biotin-labeled.
growth protocol
H1299 cells were cultured in RPMI 1640 growth medium (ATCC) and plated at a 50% confluence in 60mm plates 24h before transfection.
sample treatment protocol
Plasmids containing empty vector as a control were transfected using Lipofectamine 2000 (Invitrogen) as per manufacturer’s protocol.
nucleic acid extraction protocol
Total RNA was isolated using the miRNeasy mini kit (Qiagen) as per manufacturer’s instructions.
growth protocol
H2170 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.
sample treatment protocol
H2170 cells were  transduced with a lentivirus overexpressing an empty vector as a control using polybrene at a concentration of 1ug/ml.
sample treatment protocol
H2170 cells were  transduced with a lentivirus overexpressing miR-4423 using polybrene at a concentration of 1ug/ml.
sample treatment protocol
SW900 cells were  transduced with a lentivirus overexpressing an empty vector as a control using polybrene at a concentration of 1ug/ml.
growth protocol
SW900 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.
sample treatment protocol
SW900 cells were  transduced with a lentivirus overexpressing miR-4423 using polybrene at a concentration of 1ug/ml.
sample treatment protocol
Calu6 cells were  transduced with a lentivirus overexpressing an empty vector as a control using polybrene at a concentration of 1ug/ml.
growth protocol
Calu6 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.
sample treatment protocol
Calu6 cells were  transduced with a lentivirus overexpressing miR-4423 using polybrene at a concentration of 1ug/ml.
sample treatment protocol
Plasmids containing miR-4423 were transfected using Lipofectamine 2000 (Invitrogen) as per manufacturer’s protocol.