GSM5861306: TrifKO_Vehicle_rep2; Mus musculus; RNA-Seq
24 hours after treatment, dams were sacrificed and embryonic day (E)13.5 embryos were collected. Fetal brains were dissected, minced, triturated, and digested in order to obtain a single-cell suspension. Embryo tails were taken for SRY genotyping. Whenever possible, equal number of male and female brain suspensions were pooled before myeloid cell staining. Cells were stained using Cd11b and Cd45.2 antibodies. Cd11b and Cd45.2 double positive cells were sorted and concentrated prior to maximally loading onto the 10X Chromium Single Cell 3' Regent Kit chip (v3 chemistry). Libraries were prepared according to 10X Chromium Single Cell 3' Reagent Kit (v3 chemistry) vendor specifications at the Functional Genomics Lab at the University of California, Berkeley. Each library corresponds to a replicate with a unique set of 4 barcodes. N=2 independent biological replicates per genotype per treatment are included in the study (8 total libraries). Four single-cell RNA-sequencing libraries corresponding to genotype were pooled (N=2 treatment replicates) for sequencing on one S4 lane of the NovaSeq 6000 platform (2 lanes total) at the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley and the University of California, San Francisco Center for Advanced Technology. There are 12 raw fastq files for Samples 1 through 4 (WT libraries) and 48 raw fastq files for Samples 5 through 8 (Trif KO libraries) due to different de-multiplexing strategies at the aforementioned sequencing facilities.