RNA-Seq of C. elegans early embryos
CEL-Seq2 with samples of 30 1-2 cell embryos instead of single cells. Otherwise as published. Note: all samples are pooled into a single Illumina library, and the first of the paired end reads contains CEL-Seq barcodes for demultiplexing and a Unique Molecular Identifier (UMI) sequence. Demultiplexing with tools from the CEL-Seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) outputs individual single FASTQ files for each sample with the transcript-identifying sequence information from the second paired end read along with UMI information.