Table 1.

Summary of types of experimental techniques used in ENCODE

Feature Class	Experimental Technique(s)	Abbreviations	References	Number of Experimental Data Points
Transcription	Tiling array, Integrated annotation	TxFrag, RxFrag, GENCODE	Harrow et al 117 Emanuelsson et al118 Rozowsky et al 19 Kapranov et al 119	63,348,656
5′ Ends of transcripts *	Tag sequencing	GIS-PET, CAGE	Ng et al 121 Carninci et al 13	864,964
Histone modifications	Tiling array	Histone nomenclature†, RFBR	Koch et al 46	4,401,291
Chromatin structure +	QT-PCR, Tiling array	DHS, FAIRE	Dorschner et al42 Sabo et al43 Crawford et al 44 Giresi et al122	15,318,324
Sequence- specific factors	Tiling array, tag sequencing, Promoter assays	STAGE, ChIP- Chip, ChIP- PET, RFBR	Bieda et al 52 Bhinge et al120 Euskirchen et al11 Rada-Iglesias et al123 Thurman et al81 Cawley et al 34 Kim et al 41 Kim et al 51 Kim et al 124 Heintzman et al49 Cooper et al 33 Wei et al 40	324,846,018
Replication	Tiling array	TR50	Jeon et al 59 Karnani el al75	14,735,740
Computational analysis	Computational methods	CCI, RFBR Cluster	Greenbaum et al80 Halees & Weng 125 Zhang et al 10 Guigo et al 126 Bajic et al 127 Zheng & Gerstein 128	NA
Comparative sequence analysis *	Genomic sequencing, multi- sequence alignments, computational analyses	CS	Cooper et al 87 Margulies et al 86 Washietl et al26	NA
Polymorphisms *	Resequencing, copy number variation	CNV	The International HapMap Consortium 103 Stranger et al 129	NA

^*= Not all data generated by ENCODE Project.

⁺= Also contains histone modification.

^†= Histone code nomenclature follows the Brno nomenclature as described by Turner¹³⁰