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All data was produced in a MIAME-compliant format [46], with the normalised output from the microarray presented as File S1.
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Once this is successfully completed, the script starts and manages the whole process that can be roughly divided in two parts: the first in which all data is produced and stored and the second in which a restricted part of this data is selected.
A numerical file of all the data was produced and any transcript that did not generate a detection P-value <0.05 [ 70] for at least one chip was removed from the analysis (the default P-value cut-off for a 'present' expression call is 0.065).
All the imported data was produced in at least two replicated experiments and the imported values represent the average of the replicated values.
All sequencing data was produced by the Genomic Analysis Facility (BioSune, Shanhai, China) and analyzed with Meglign 7.0 and Chromas 2.33 software.
All ChIP-seq and RNA-seq data was produced as part of the ENCODE consortium, and is available at (http://genome.ucsc.edu); all data used in this study is past the nine month moratorium.
The YouGov data was produced for the Wednesday conference, at which the Guardian is a media partner.
The company reports data was produced in 84.81 percent of these cases.
The protein data was produced from tandem affinity purification (TAP) of TAP-tagged S. cerevisiae ORFs.
Genomic data was produced at the Department of Energy Joint Genome Institute (Walnut Creek, CA, USA).
Sequence data was produced by Genotyping-By-Sequencing (GBS) [ 49].
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