10 protocols
AccessionType
bioassay_data_transformation
ID_REF =
VALUE = log2 vsn normalized gene level expression values from Bioconductor
image_aquisition
Affymetrix Gene ChIP Scanner 3000 7G
labeling
Samples were labelled with WT target labelling Kit (Affymetrix, Fremont, USA), washed and stained using the HWS Kit (Affymetrix).
feature_extraction
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)
feature_extraction
Statistical analysis was done with the statistical computing environment R (version 2.8.1). Additional software packages (affy_1.20.2, vsn_3.8.0, geneplotter_1.20.0, multtest_1.23.3) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
hybridization
Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.
nucleic_acid_extraction
RNA from 25,000 GFP-positive cells was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA was amplified with the WT expression Kit (Ambion, Austin, USA)
specified_biomaterial_action
U-HO1 and L-1236 cells were transduced with shRNAs against GATA-3 or non-functional control shRNAs, cultured for three days, and sorted according to their GFP positivity.
grow
Cell lines were purchased from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal calf serum (Biochrom; Berlin, Germany), 2 mM glutamine (Invitrogen; Groningen, The Netherlands) and 1% penicillin G/streptomycin sulfate (Invitrogen).UHO-1 cells were cultured as above but in IMDM.
feature_extraction
probe group file: Unsupported Human Gene 1.0 ST Array CDF Files