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Table 1 The algorithm for small RNA processing for the EhAGO2-2 IP small RNA library from E. histolytica HM-1:IMSS

From: Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes

Procedures

Output

5-P independent cloning (5CIP+PNK method)

HM-1:IMSS AGO2-2 IP library

Total reads by Pyrosequencing

362,445 reads

Primer trimming, size-limiting (15–40nt)

340,280 reads

Unique sequences (percentage)

209,513 unique sequences (158,904 cloned only once; 75.8%) (50,609 cloned more than once; 24.2%)

Scan for tRNA, rRNA

tRNA: 1,640 sequences rRNA: 3,456 sequences

Scan for SINE/LINE, EhERE elements

8,073 sequences

Map to E. histolytica genome

140,943 sequences

Map to E. histolytica predicted ORFs

100,190 sequences

  1. One pyrophosphate sequencing run was performed. Unix tools were used to remove adaptor and linker sequences. The Bowtie alignment tool was used to scan for structural RNAs, repetitive elements and for the final genome mapping. The numbers of reads that map to the genome sequence at each step are listed.