library_construction_protocol: Individual organoids cultured in LEO and from ground control, both with and without added microglia, were snap-frozen and stored at -80°C. RNA was extracted using the Qiagen RNeasy Micro kit (QIAGEN) and eluted into 12μL of ultrapure DI water. RNA quality and concentration was assessed on Bioanalyzer Pico with RIN reported. The RNA was sequenced by Novogene using an ultra-low input preparation of samples with a minimum of 10ng of RNA. A pilot subset of samples were cDNA amplified before sequencing with the Clontech SMART kit employing Clontech SMART CDS Primer IIA. Remaining samples used Nextera library preparation. All samples were then sequenced using the Illumina NovaSeq Platform for high-throughput PE150 sequencing.