title: GSM8453510: e11_5_rep1; Mus musculus; RNA-Seq
library_construction_protocol: Pou5f1-ΔPE-eGFP embryos were somite counted and age-matched. After microdissecting out the migratory region, samples were dissociated. After dissociation, cells were submitted for FACS to concentrate GFP+ migratory germ cells. Samples were reecombined with Oct4-GFP- somatic cells. These cell populations were used to create two 10X Chromium Single Cell 3' (v2 Chemistry) single cell RNA sequencing libraries. 10X ChromiumTM Single Cell 3' Reagent Kits v2 User Guide Rev A. Briefly, we used Single-Cell 3′ Reagent Version 2 Kit (10X Genomics) and used fluidics to create individual cells in gel bead-in-emulsions (GEMS). Samples were prepared directly according to the protocol, with the following steps tailored to maximize library yield: at the cDNA amplification step, we used 14 cycles, and at the sample index PCR step, we used 14 cycles. Samples were tested for quality on an Agilent Bioanalyzer High Sensitivity chip before sequencing. E9.5 and E11.5 libraries were sequenced on HiSeq 4000 (Illumina) with paired-end sequencing parameters: Read1, 98 cycles; Index1, 14 cycles; Index2, 8 cycles; and Read2, 10 cycles. E10.5 libraries were sequenced on Novaseq (Illumina) with paired-end sequencing parameters: Read1, 150 cycles; i7 Index, 8 cycles; i5 index, 0 cycles; and Read2, 150 cycles.