GSM5733596: 134kb SynHoxA assemblon in WT mESCs, 96h of RA+SAG differentiation, replicate 1, RNA-Seq; Mus musculus; RNA-Seq
Cells were collected at 0h or 24h, 48h, or 96h after RA/SAG treatment. RNA was extracted with the TRIzol LS Reagent (Life Technologies) followed by purification with the RNAeasy mini kit (Qiagen). RNA integrity was checked with the Agilent High Sensitivity RNA Screentape (Agilent, 5067-5579). 500 ng of RNA was used to prepare libraries and spiked-in with ERCC Exfold Spike-in mixes (Thermo Fisher 4456739). The TruSeq Stranded mRNA Library Preparation kit (Illumina 20020594) was used to prepare RNA-seq libraries. Library size was checked on the High Sensitivity DNA ScreenTape (Agilent 5067-5584). The KAPA library amplification kit was used to quantify libraries on the Bio-Rad CFX96 or the Roche Lightcycler 480 before pooling libraries. Libraries were sequenced on the Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75 bp) or on the Illumina NovaSeq 6000 using the SP Reagent Kit (100 cycles, single-end 100bp) at the Genomics Core Facility at NYU.