Transcriptomic analysis of left-right differences in human embryonic forebrain and midbrain

Abstract

Left-right asymmetry is subtle but pervasive in the human central nervous system. This asymmetry is initiated early during development, but its mechanisms are poorly known. Forebrains and midbrains were dissected from six human embryos at Carnegie stages 15 or 16, one of which was female. The structures were divided into left and right sides, and RNA was isolated. RNA was sequenced with 100 base-pair paired ends using Illumina Hiseq 4000. After quality control, five paired brain sides were available for midbrain and forebrain. A paired analysis between left- and right sides of a given brain structure across the embryos identified left-right differences. The dataset, consisting of Fastq files and a read count table, can be further used to study early development of the human brain.

Figure 1. Experimental design.

Six human embryos at Carnegie stages 15 or 16. Forebrain and midbrain were dissected and divided into left and right. RNA was isolated from the complete tissue sample. Paired end sequencing (100 bp) was done at BGI, China. Alignment and read counts were performed against GrCh38 with RefSeq gene definitions. Adapted from Version 8.25 from the Textbook OpenStax Anatomy and Physiology Published May 18, 2016, licensed under the Creative Commons Attribution 4.0 International license.

Figure 2. FastQC quality scores for a representative sample.

Figure 3. MDS-plot based on gene expression in midbrain and forebrain samples at 5-5.5pcw.

Forebrain samples are shown in black, midbrain samples in red. Unique symbols refer to individual embryos. The smaller squares show the female embryo.