17 protocols
AccessionNameType
P-GSE48796-1
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)
P-GSE48796-7
array scanning protocol
Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.
P-GSE48796-6
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.
P-GSE48796-5
labelling protocol
The total RNA was converted to cDNA and subsequently amplified and biotin-labeled.
P-GSE48796-3
growth protocol
H1299 cells were cultured in RPMI 1640 growth medium (ATCC) and plated at a 50% confluence in 60mm plates 24h before transfection.
P-GSE48796-8
sample treatment protocol
Plasmids containing empty vector as a control were transfected using Lipofectamine 2000 (Invitrogen) as per manufacturer’s protocol.
P-GSE48796-4
nucleic acid extraction protocol
Total RNA was isolated using the miRNeasy mini kit (Qiagen) as per manufacturer’s instructions.
P-GSE48796-16
growth protocol
H2170 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.
P-GSE48796-17
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.
P-GSE48796-15
sample treatment protocol
H2170 cells were  transduced with a lentivirus overexpressing miR-4423 using polybrene at a concentration of 1ug/ml.
P-GSE48796-14
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.
P-GSE48796-13
growth protocol
SW900 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.
P-GSE48796-12
sample treatment protocol
SW900 cells were  transduced with a lentivirus overexpressing miR-4423 using polybrene at a concentration of 1ug/ml.
P-GSE48796-11
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.
P-GSE48796-10
growth protocol
Calu6 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.
P-GSE48796-9
sample treatment protocol
Calu6 cells were  transduced with a lentivirus overexpressing miR-4423 using polybrene at a concentration of 1ug/ml.
P-GSE48796-2
sample treatment protocol
Plasmids containing miR-4423 were transfected using Lipofectamine 2000 (Invitrogen) as per manufacturer’s protocol.