Pooled libraries were split and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using 2 × 100-bp pairedend reads and 2 × 12-bp index reads with 2 x S4 300-cycle kit (Illumina, 20012861 or 20012860). Data Processing 9 Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.20. Reads were aligned to the GRCm39.p6 (mus musculus) genome with Gencode v.M19 annotations using using STAR version 2.5.2b with parameters TK. Gene counts were produced using HTSEQ version 0.6.1p1 with default parameters, except "stranded" was set to "false", and "mode" was set to "intersection-nonempty". 4 09/17/2019 C ita tio n : C ita tio n : Sasa T (09/17/2019). SmartSeq2 for HTP Generation of Bulk RNA Libraries-with Pipetting plan .
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