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Comparing the human behaviour with the behaviour realization of the technical system on the higher levels, a human reference model can be identified.
After elimination of the duplicate reads, the remaining reads of at least 18 nt were mapped to a human reference genome (hg19) using SOAP V2.0.
After elimination of duplicate reads, the remaining reads of at least 18 nt were mapped to a human reference genome (hg19) using SOAP V2.0 [30].
In this way we compiled a mouse reference TSS set containing 98,682 sequences (MTSS) and a human reference TSS set containing 113,814 sequences (HTSS).
To identify overrepresented categories of genes, we inputted the overexpressed RefSeq genes into the PANTHER (Protein Analysis Through Evolutionary Relations) database (http://panther.appliedbiosystems.com) and compared them to a human reference list of transcribed genes [52].
All of the 17-bp sequences next to the possible Nla III restriction sites in a human reference genome (hg19) and the 4-bp CATG restriction enzyme-digested site were extracted and concatenated as a new reference [65].
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The authors of the above study used two RNA sample types and two mixtures of the original samples: Sample A, a universal human reference RNA; Sample B, a human brain reference RNA; Sample C, which consisted of 75 and 25% of sample A and B respectively; and Sample D, which consisted of 25 and 75% of sample A and B respectively.
The evaluation based on POG was done with 12 datasets produced by the MAQC project [ 21] in which two RNA sample types and two mixtures of the original samples were used: Sample A, a universal human reference RNA; Sample B, a human brain reference RNA; Sample C, which consisted of 75 and 25% of Sample A and B respectively; and Sample D, which consisted of 25 and 75% of Sample A and B respectively.
MAQC-I sample A is a universal human reference RNA (UHRR) prepared by pooling RNA from multiple cell lines [ 10] and MAQC-I sample B consists of human brain reference RNA (HBRR) prepared from multiple individuals [ 1].
A common human reference RNA served as an internal standard (Universal Human Reference RNA, Stratagene Corp., La Jolla, CA).
The two RNA sample types used were a universal human reference RNA (UHRR) from Stratagene and a human brain reference RNA (HBRR) from Ambion.
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