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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).
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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].
One single biological sample was sequenced for each time point and treatment.
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]).
During PCR, unique index sequences (Illumina) were incorporated into each biological sample to allow identification of reads from each sample when multiple samples were sequenced on a single lane of the flow cell.
All Helicobacter PCR-positive samples were sequenced.
Multiple samples were sequenced together using barcodes.
Positive samples were sequenced.
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