title: GSM9203514: WT_D6HetDif_RNA_rep1; Mus musculus; RNA-Seq
library_construction_protocol: Total RNA was isolated with the NZY Total RNA Isolation Kit (NZYTech, MB13402) following the manufacturer's protocol. For RNA-seq applications, 7.5 µg of RNA were treated using the TURBO DNA-free Kit (Thermo Fisher Scientific, AM1907), and RNA integrity (RIN) was assessed on an Agilent 4200 TapeStation. Only samples with RIN > 8 were used for sequencing. Total RNA from D0 (n=3), D3 (n=4), D5 (n=4) and D6 (n=3) WT and Zic2-/- (Z2KO) cells and Zic2FKBPV36 D6 DMSO-treated and dTAG13-treated D6 (n=3 for all conditions, except for the DMSO 48h treatment where n=2) was purified and DNAse-treated. Libraries for WT and Z2KO D3 and D5 samples, as well as Z3K0 D0 samples, were prepared using stranded mRNA-seq protocols and sequenced on an Illumina NovaSeq platform at CNAG (Barcelona, Spain) with 50 bp PE reads (>40M reads/sample), while the rest of the samples were processed (i.e. quality control and library preparation) and sequenced by Macrogen Inc. (Korea) using the TruSeq Stranded mRNA protocol (150 bp PE reads). For the analyses performed on the heterozygous Zic2+/- AntNPCs (Z2HET), an independent dataset composed by WT (n=3), Z2KO (n=3) and Z2HET (n=3) belonging to an independent differentiation was used. These samples were also processed and sequenced by Macrogen Inc. (Korea) as previously described.