p. 2 Table

. Sequences of selected aptamers. . Profile of literature analyzed. 

p. 3 Table


p. 4 Table

 S3. Note: Supplementary files with the reads from alkaline and lambda SELEX are available online. 
Supplementary Table S4 contains curated data from the Aptamer Base and from the literature as described in Table S2. Available online as a downloadable .xlsx spreadsheet. S2. Values for each experiment are available in Table S4. Most publications did not provide the estimates, so we calculated the number of sequences based on the experimental conditions. No significant difference was observed. 

Grouping Sequences of random region

Read Count* Lambda Malaria.1 CCAAACGCGCTGGTTTGGAATGCTTAGAGTTTGATCGATGCCTAA Malaria.2 GTGCAGACAGCTAGTAGTGGTGACTTTCTGTCCAAATCAAGATAA Malaria.3 CACTAGGATCTAGGGAAAAATCTCGTAAATACTATACTCCTGAGC -- ACGTTTTAGCTACACGTGCGGGCAGTACCCTCACTGGGAAACAAC -- ATAGCCCGACTATATCGGCAATACACTGTGCTGGATCTTCAGGGT -- TAGCTGAGTTGTACTCGGATGTGTAGGTTTTTAGGCTAGTAATCA -- ATAAAAAGCAGGTGGCCTTGTGATTGGATTTATATTGAAAGTACA -- GTGCAGACAGCTAGTAGTGGTGACTTTCTGTCCAAATCAAGATGA -- GTGCGGACAGCTAGTAGTGGTGACTTTCTGTCCAAATCAAGATAA -- CCGCTGCAGACGCGCAAGTGAGATCTGTTCTTTATTGTATG Alkaline Malaria.3 CACTAGGATCTAGGGAAAAATCTCGTAAATACTATACTCCTGAGC -- TAATGGTGTATTGTTGACTGTTCGCATCGCCTTTAGCTCCGAGCC -- CAAGTAGAACGATCAAAATAAGATAAAAAGCCTTTTTAAAGCTTA -- AAGATGAGGCATTTGTATCGATAAAACCGCGTATGACGGTTCCTA -- TTAGCCTGGCCAAGTTTGTTGTAAATGTGATAATTTCGTTCGAGC -- CGCGGAAATATCGAATAATGAGGATGAGTGAGTTAAGATGGTGAA -- GCAGGGTGCTTTAACGTGCCTATACGTTCGTATCGCCTTATCTTT -- AGGTAACTTGCGGTCAATAGAAGGGTGGATTAATGTACGATCTCA -- TGCGTGGTTGCCTAGGCTCTAGGGAACCCTAGTCTCATTATATGC -- TTCGCTCACGGGGTCTACGCGTACCGGACAATTTTGCTTCACATG



  Univariate comparison of methods used in 43 SELEX publications by number of rounds. p. 5 Figure S1. Box plot comparing the estimated number of sequences in the initial library (i.e. library size) for selection experiments incorporating alkaline treatment or other single-strand generating methods. p. 6 Figure S2. Box plot comparing size of the random region in the library used for selection experiments incorporating alkaline treatment or other single-strand generating methods. 


Figure S1 .

 S1 Figure S1. Box plot comparing the estimated number of sequences in the initial library (i.e. library size) for selection experiments incorporating alkaline treatment or other single-strand generating methods. Data was curated from the literature as described in TableS2. Values for each experiment are available in TableS4. Most publications did not provide the estimates, so we calculated the number of sequences based on the experimental conditions. No significant difference was observed. 


Table S2 . Profile of literature analyzed. No. of Papers Condition Table S3. Univariate comparison of methods used in 43 SELEX publications by number of rounds.

 S2 
	Characteristics		Efficient (≤10 rounds)	Inefficient (≥15 rounds)	p-value*
	Alkaline use Average K d (M) : mean (range) Target type Cells Protein sequences Estimated in initial number of library	1×10 5 1×10 10 1×10 15 1×10 20 1×10 25	N=30 9 (30.0%) 3.4e-07 (2.1e-11 -5.5e-06) 2 (6.7%) 22 (73.3%) n.s.	N=13 12 (92.3%) 4.3e-07 (1.3e-08 -2.9e-06) 5 (38.5%) 8 (61.5%)	0.0002 0.6061 0.0188
	Other		6 (20.0%) NO	YES	0 (0.0%)
	Partitioning method	Use of alkaline treatment	
	Affinity chromatography Centrifugation and cell wash		21 (70%) 1 (3.3%)		5 (38.5%) 6 (46.2%)	0.0053
	Filtration		6 (20.0%)		2 (15.4%)
	Year (range)		2007 (1992-2001)	2006 (1990-2011)	0.9468
	* Fisher's exact test for categorical variables; Wilcoxon rank sum test for numerical variables

papers with incomplete data (e.g. did not report the number of rounds or single-strand recovery method) 41 papers using Capillary Electrophoresis-SELEX, Automated SELEX, Non-SELEX or Microfluidic SELEX 42 papers that selected for small molecule targets 1 paper retracted 17 papers describing SELEX experiments of intermediate length (11-14 rounds) 43 Analyzed 

Table S1. Sequences of selected aptamers. *Total reads analyzed from lambda and alkaline SELEX were 378,439 and 965,748 respectively All SELEX experiments from 1990 to 2013 reporting K d values (Ref: http://www.ncbi.nlm.nih.gov/pubmed/26530075) 325 papers performing SELEX with RNA, dsDNA, or modified nucleic acids 


Supplementary Information


High-efficiency enrichment enables identification of aptamers to circulating

 S2. Values for each experiment are available in Table S4. No significant difference was observed.
Eugene K Oteng, Wenjuan Gu, Maureen Mckeague