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The cDNA library (two independent biological replicates) was sequenced on the Illumina sequencing platform (HiSeqTM 2000).
Three lanes of HiSeq were used and each biological replicates was sequenced in different lanes according to proper blocking and randomization procedures [ 34].
Although each sample (composed of 6 pooled biological replicates) was sequenced once, DESeq was able to estimate gene expression dispersion by assuming that most genes have similar expression across treatments.
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The same four biological replicates were sequenced for small subunit (SSU) rRNA genes using high-throughput amplicon pyrosequencing.
Two biological replicates were sequenced for each inoculation and timepoint.
Two independent biological replicates were sequenced in parallel.
Two biological replicates were sequenced for each experiment.
Three biological replicates were sequenced for the TRAP-IP and total RNA samples.
Three biological replicates were sequenced for each treatment and at least three plants were pooled for each biological replicate.
Three biological replicates were sequenced (see supplementary material Table S1 for statistics), with each biological replicate consisting of ∼100 pooled embryos (∼15 µl).
A total of 14 biological replicates were sequenced from two conditions: 7 replicates for the control group and 7 replicates for E2-treated MCF-7 cells.
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