Transcript Slide 1

Barry et al. Figure S1
A.
B.
Step 1: Degenerate primers designed to DBLa conserved amino
Step 5: Remove vector contamination and edit raw sequence
data (“reads”)
acid blocks D and H [26]
D
H
Forward primer
Individual
reads
Reverse primer
Step 2: PCR of P. falciparum genomic DNA with degenerate primers
results in a pool of PCR products containing distinct sequences from
different genes
Step 6: Align reads with a 96% DNA sequence identity cutoff
Reads
aligned
into
contigs
Pooled
PCR
products
Step 3: Ligate PCR products with Topo-TA vector (Invitrogen) and
clone to separate distinct sequences
Step 7: Remove redundancy by generating consensus
“sequences” (together they form a “repertoire”)
Repertoire
Colonies
Clones
Sequences
Step 4: Culture 96 E. coli colonies in 1ml L-broth plus Kanamycin.
Extract plasmid DNA and sequence using M13 Universal primers
96 well plate
Step 8: Alignment of sequences with a 96% DNA sequence identity cutoff
defines distinct sequences (“types”) in the population.
Types (1-7)
Repertoires
E.coli
transformation
A
B
C
D