br Experimental design materials and methods br Acknowledgme

Experimental design, materials and methods
Acknowledgments The authors would like to acknowledge the generous support of Dr. Elena Hidalgo (Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain) for kindly providing the yeast strain, Dr. Ranjan K. Nandy (Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India) for providing the DNA sequencing facility, Dr. Sandipan Ganguly (Division of Parasitology, National Institute of Cholera and Enteric Diseases, Kolkata, India) for providing the Real Time PCR facility. We thank all the funding agencies for their financial support. The consumables for the entire work were supported by DBT, Govt. of India, Grant no. BT/PR12551/BRB/10/02/2009 dated September 3, 2010, DBT-IPLS, UPE and UGC CAS Phase II Govt. of India for providing infrastructural facility. CSIR, Govt. of India for providing fellowship to PB and DBT, Govt. of India for providing fellowship to UM. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data Table S1, chromosomal location of housekeeping (HK) genes exclusively detected by MA alone, sequencing alone, as well as jointly. Table S2, Nanaomycin A cost count, total exon length, total intron length, and GC content of HK genes exclusively detected by MA alone, sequencing alone, as well as jointly. Table S3, detection breadth and the normalized maximum expression quantity of each HK gene exclusively detected by MA alone, sequencing alone, as well as jointly.
Experimental design, materials and methods The data included here were downloaded from 15 published human housekeeping studies, i.e. Warrington [2], Hsiao [3], Eisenberg_03 [4], Tu [5], Dezso [6], She [7], Chang [8], Shyamsundar [9], Zhu_MA, Zhu_EST [10], Podder [11], Reverter [12], Ramskold [13], Eisenberg_13 [14] and Fagerberg [15], in which nine studies used microarray (MA) analysis, i.e. Warrington [2], Hsiao [3], Eisenberg_03 [4], Tu [5], Dezso [6], She [7], Chang [8], Shyamsundar [9], Zhu_MA, and the rest used sequencing analysis. The gene identifiers used in different studies were first converted to entrez gene ID using Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 (http://david.abcc.ncifcrf.gov/) [16,17] as detailed in [1,18]. The chromosomal location was queried against National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov.eleen.top). Genes with unknown genome locations were removed. The obtained entrez gene list was further converted to Refseq mRNA IDs using DAVID, and the Refgene information on exon count, exon starting and ending position as well as the coding sequences were obtained by querying the Refgene information from University of California, Santa Cruz (UCSC) genome browser (http://genome.ucsc.edu/index.html) against the latest human genome assembly (GRCh38) [19]. The total intron length was calculated by the total gene length minus total exon length. The GC content was deduced by the coding sequence only. Again transcripts could not be mapped to Refgene in UCSC database, and those without exon count or exon starting or ending information as well as sequencing information, were removed from the table. The expression quantity was collected from Chang [8], Eisenberg_03 [4], She [7], Warrington [2], Shyamsundar [9] and Fagerberg [15]. The raw expression quantity was first normalized against the maximum value in each individual list to make them comparable. For entrez genes having multiple quantification values in a single list (for example in cases where a single entrez gene ID was mapped to several IDs, each IDs in that particular study had an expression value), the maximum normalized expression value was used. The detective breadth (DB) [1,18] described the number of studies, in which a HK gene had been identified. For example, if a gene was detected in 8 out of 9 MA studies, its DB value would be 8, and similarly if a gene was detected in 5 out of 6 sequencing studies, its DB value would be 5.