Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe

BMC Genomics

Table 1 Genome-wide RNA kinetic data in S. cerevisiae

Name	Reference	Method	Measured	Computed	Poly(A) enrichment	Quantification
Young	[52]	rbp1-1	Half-life	Synthesis rate	oligo(dT) selection	Microarray
Brown (1)	[50]	rbp1-1	Half-life	Synthesis rate^a	None	Microarray
Brown (2)	[50]	rbp1-1	Half-life	Synthesis rate^a	oligo(dT) priming	Microarray
Hughes	[53]	rbp1-1	Half-life	Synthesis rate^a	oligo(dT) selection	Microarray
Peltz	[51]	rbp1-1	Half-life	Synthesis rate^a	oligo(dT) selection	Microarray
Pilpel	[54]	rbp1-1	Half-life	Synthesis rate^a	oligo(dT) priming	Microarray
Perez-Ortin	[77]	GRO	Synthesis rate	Half-life	None	Microarray
Cramer (1)	[44]	4sU labeling	Half-life	Synthesis rate	oligo(dT) priming	Microarray
Weis	[45]	4tU chase	Half-life	Synthesis rate^a	oligo(dT) selection	RNA-seq
Cramer (2)	[48]	4tU labeling	Half-life	Synthesis rate	oligo(dT) priming	Microarray
Struhl	[8]	rbp1-frb	Half-life	Synthesis rate^a	oligo(dT) priming	DRS
Gresham	[46]	4tU labeling	Half-life	Synthesis rate	None	RNA-seq
Coller (1)	[10]	rbp1-1	Half-life	Synthesis rate^a	None	RNA-seq
Coller (2)	[10]	rbp1-1	Half-life	Synthesis rate^a	oligo(dT) selection	RNA-seq

^aThe values were computed from mRNA half-lives in the source data and mRNA abundance obtained by Ito and colleagues [71]

ISSN: 1471-2164