GSM6500888: 9p21+/- BM-MSCs-1, Day 0 [287M_0d_S25]; Mus musculus; RNA-Seq
For bulk RNA-seq, total RNA were extracted using TRIzol Plus purification kit (ThermoFisher), and cDNA libraries were prepared with TruSeq Stranded Total RNA with Ribo-Zero Globin.RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. For CITE-seq, Post staining and sorting, cells were run through the standard 10x Chromium (v3) protocol up until cDNA amplification, with the following modification: during cDNA PCR and 1 pmol of hashtagging oligonucleotide (HTO) additive primer were added to the cDNA amplification master mix. Post cDNA amplification, a 0.6X Solid Phase Reversible Immobilisation (SPRI) bead clean-up was performed to separate the cDNA fraction (on beads) from HTO fraction (in supernatant). The cDNA fraction was converted into a 3' tag gene expression library according to the 10x Genomics Single Cell Genomics Protocol (v3). Supernatant from cleanup was kept for ADT and HTO preparation. To the supernatant, another 1.4X SPRI was added to bring the total SPRI concentration to 2X. After washing the beads in 80% ethanol and eluting in water, a second round of 2X SPRI cleanup was performed to remove any residual primer carryover from the cDNA PCR. RNA and DNA  libraries were prepared for sequencing using standard Illumina protocols