title: scRNAseq of P9.5 brain and dura ILCs: Brain  2
design: Library construction protocol: FACS-sorted cells were stored in 384-well cell-capture plates containing barcoded primers and mineral oil and, immediately stored at -80C. Plates were shipped on dry ice to Single Cell Discoveries, where single-cellRNA sequencing wasperformedaccording toan adapted version ofthe SORT-seq protocol (Muraroet al.,2016)with primers described in vanden Brinket al.,2017).Cells were heat-lysedat 65C followed bycDNA synthesis.After second-strandcDNA synthesis, all the barcoded material from one platewaspooledinto one library and amplified usingin vitro transcription (IVT). Following amplification, library preparation was done following the CEL-Seq2 protocol (Hashimshony et al., 2016) to prepare a cDNA library for sequencing usingTruSeqsmall RNA primers (Illumina).The DNA librarywaspaired-endsequenced on an Illumina Nextseq 500, high output, with a 175 bp Illumina kit(read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles).