bulk and single-cell RNA-seq on bone marrow derived early T cells

The single cell and bulk expression profiles of early pro T-cell progenitors generated from purified mouse bone marrow, cultured on different stromal cell systems Examination of expression profiles of thymic DN1-DN2 population with bulk RNAseq and single cell RNAseq. 10X V2: Droplet-based 3′ end massively parallel single-cell RNA sequencing droplets were prepared using Chromium Single Cell 3′ Reagent Kits v2 according to manufacturer’s protocol (10x Genomics). Bulk: Bulk RNAseq from FACS sorted early T cell populations were performed. RNAeasy MicroKit (Qiagen) were used to purify the total RNA according to manufacturer’s recommendations. Purified RNA samples were constructed into sequencing library using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) from ~1 μg of total RNA following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50-51 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.