10 protocols
AccessionNameType
P-GSE46162-1
normalization data transformation protocol
The raw data pair files were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6.0.0 (Roche NimbleGen, Inc.). ID_REF = VALUE = normalized gene-level signal intensity
P-GSE46162-10
array scanning protocol
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.NimbleGen.com.
P-GSE46162-9
hybridization protocol
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.NimbleGen.com.
P-GSE46162-8
labelling protocol
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.NimbleGen.com.
P-GSE46162-6
growth protocol
Transgenic PF T. brucei cells harbouring tetracycline-inducible constructs were grown in SDM-79 medium in 27 °C. Cells were seeded at 1.3E+6 cells/ml and harvested after 24h or 48h.
P-GSE46162-7
nucleic acid library construction protocol
Total RNA was extracted using TRIzol Reagent (Invitrogen) and was further purified using RNeasy Mini Kit (Qiagen) as per manufacturers’ intsructions. RNA quality was examined using Agilent 2100 Bioanalyzer.
P-GSE46162-5
sample treatment protocol
The cells were treated with 1ug/ml tetracycline to induce RNAi and 100ng/ml tetracycline to induce over-expression, for a duration of 48h (except for Tb927.8.6650 RNAi which was treated for a duration of 24h)
P-GSE46162-2
sample treatment protocol
The cells were treated with 100ng/ml tetracycline, for a duration of 48h.
P-GSE46162-4
nucleic acid library construction protocol
Tandem affinity purification was performed as described before (Panigrahi et al., http://www.ncbi.nlm.nih.gov/pubmed/12649499). Total RNA or RNA associated with Tb927.8.6650 was extracted using TRIzol Reagent (Invitrogen) as per manufacturers’ intsructions. RNA quality was examined using Agilent 2100 Bioanalyzer.
P-GSE46162-3
growth protocol
Transgenic PF T. brucei cells harbouring tetracycline-inducible constructs were grown in SDM-79 medium in 27 °C. Cells were seeded at 1.3E+6 cells/ml and harvested 48h after tet-induction at a density of 3.0E+7 cells/ml.