title: GSM6761456: hashed HSPC samples +-APEX1 inhibitors, HTO-derived cDNA; Mus musculus; RNA-Seq
library_construction_protocol: Bone marrow lin-Sca1+ckit+ (LSK) cells were cultured for 7 days in presence or not of APEX1 inhibitors Cells stained for the ADT and HTO tags, were pooled together and resuspended  at an estimated final concentration of 1000 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using the GemCode Single Cell 3' Gel Bead and Library kit, version NextGEM 3.1 (10x Genomics) according to the manufacturer's instructions with the addition of amplification primers (3nM, 5'CCTTGGCACCCGAGAATT*C*C and 5'GTGACTGGAGTTCAGACGTGTGC*T*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein and hashtag oligos.  Size selection with SPRIselect Reagent Kit (Beckman Coulter, B23318) was used to separate amplified cDNA molecules for 3' gene expression and cell surface protein construction. TotalSeq-A protein library construction including sample index PCR using Illumina's Truseq Small RNA primer sets and SPRIselect size selection was performed according to the manufacturer's instructions. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent). Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics core with sequencing settings according to the recommendations of 10x Genomics, pooled in a 80:25 ratio for the combined 3' gene expression and cell surface protein samples, respectively. OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)