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One single biological sample was sequenced for each time point and treatment.
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Since only one biological samples was sequenced, in order to avoid possible high false positive rates we first used trimmed mean of M values (TMM) to standardize data processing [ 48], then took advantage of DEGseq to analyze differentially expressed genes; the analysis conditions were qvalue <0.005 & log2 (foldchange) >1 [ 49– 51].
Two different biological samples were sequenced for each genotype.
Two biological samples were sequenced for each stage (two separate parasite and RNA preparations from different sections of the small intestine as well as two different tachyzoite cultures).
Three clones per sample were sequenced.
For evaluating the technical reproducibility, two replicates for the each biological replicate of cellulose samples were sequenced on GA-IIx, which demonstrated reproducibility (Additional file 9: Figure S3C, D, E).
Twin-DS-iPSC and Twin-N-iPSC samples were sequenced in three and four biological replicates, respectively, starting from different RNA preparations.
For the greenhouse grown Li 2 plants samples were sequenced in two biological replicates (sequencing and data were described elsewhere [ 9]).
Samples were sequenced on a HiSeq2000 sequencer (Illumina Inc.).
While Chinese_Study_2 samples were sequenced on Illumina, other studies including the Indian samples were sequenced on 454 FLX platform.
All Helicobacter PCR-positive samples were sequenced.
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