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The array covers angles from 5° to 18° in the 4π Array at the National Superconducting Cyclotron Laboratory at Michigan State University.
The array covers 251 megabases of the genome at 92 base-pair resolution.
Of the 5542 identified genes, the array covers 5396 genes (97.4%) including protein coding, rRNA, tRNA, snRNA and pseudogenes.
Of these genes, 1,701 are represented on the Affymetrix HG-U95A2 microarray platform, common to all data sets considered in the present study (Table S1) Although the array covers only about 40% of the whole Membranome (Fig. 1A), the internal representation of all major functional classes – as defined by Panther [22] - is strictly maintained (Fisher exact test p-value<0.001 p-value<0.001
Of the 5542 identified P. falciparum genes, the array covers 4741 genes (85%).
The array covers the promoter, 5′-untranslated region, first exon, gene body, and 3′-untranslated region of each gene.
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Labeled cDNAs were combined in a hybridization mixture (27 µl formamide, 15 µl 20xSSC and 0.6 µl 10% SDS), applied to the array, covered with a lifter slip (Erie Scientific, NH) in a hybridization chamber (Arrayit, CA) and incubated at 42°C overnight (16 20 hrs).
After blocking the array in blocking buffer (PBS, 1% BSA, 0.1% Tween 20) for 1 h at 4°C, 10 µg aliquots of biotinylated NEMO or GST control diluted in 120 µl of probing buffer (PBS containing 0.5 mM DTT, 5 mM MgCl2, 5% glycerol, 0.05% Triton X-100 and Calbiochem protease inhibitor cocktail) were added to the array and the array covered and incubated at 4°C for a further 1.5 h.
The probes on the array cover a total of >30,000 coding transcripts, including alternative splice variants, and >11,000 lincRNA.
The array covered the NTD lower lobe, the NTD-LBD linker, the LBD and the transmembrane sector (schematic in Figure 4B).
The sequences on the array cover a total of 227 GO terms, with 73% of all the sequences having at least one GO entry assigned to it.
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