title: GSM3209191: TamCre ETP-3; Mus musculus; RNA-Seq
library_construction_protocol: Total RNA was extracted from 100K-400K DN3 cells and 5K-20K ETP cells using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer's protocol. ΔMxCre, MxCre, Anti-NRR antibody, and Control IgG antibody sequencing libraries for DN3 and ETP cells were prepped from 10 ng of total RNA using the Takara RiboGone kit (634846) and the Clontech SMARTer Ultra low input RNA kit (6348493) using a modified protocol allowing for low input for anti-Notch1 and pI-pC treated cells. ΔTamCre and TamCre sequencing libraries for DN3 cells were prepped from 100 ng of total RNA using the Illumina TruSeq mRNA Sample Prep v2 kit (RS-122-2001, RS-122-2002). ΔTamCre and TamCre sequencing libraries for ETP cells were prepped from 1 ng of total RNA using the Takara SMARTer STranded Total RNA-Seq Pico Input Mammalian kit (635005, 635006, 635007). Library preparation was performed according to the manufacturer's protocol by the University of Michigan Sequencing Core. Libraries from ΔMxCre, MxCre, Anti-NRR antibody, and Control IgG antibody treated cells were amplified using 16 cycles of PCR. Libraries from tamoxifen treated cells were amplified using 12 cycles of PCR for DN3 cells and 15 cycles for ETP cells. RNA-Seq results generated from different kits were not directly compared against each other. Libraries were checked for size on the TapeStation and quantified using the Kapa Biosystems library quantification kit (KK4835) for Illumina adapters.