Single-cell transcriptomic effects of LOX knockdown on tumor cell xenografts implanted on aged mouse breast dECM scaffolds

We profiled the single-cell transcriptomic effects of LOX (lysyl oxidase) knockdown on MCF10DCIS.com human breast tumor cells and on CD11b+ tumor-associated myeloid cells in an aged-microenvironment xenograft model. GFP-reporting MCF10DCIS.com cells transduced with either pLKO empty-vector (control) or pLKO-LOX shRNA were seeded onto decellularized/delipidized breast dECM scaffolds derived from aged C57BL/6 mice, cultured for 12 days, and implanted bilaterally into Rag1-/- (B6.129S7-Rag1tm1Mom/J) host mice (right flank = pLKO ctrl, left flank = shLOX, matched within-mouse pairing). Tumors grew for 7 weeks. Three biological replicate pairs (n=3 pLKO + n=3 shLOX, from 3 host mice) were selected for Parse Biosciences Evercode WT v2 single-cell RNA-seq. Each tumor was dissociated and split into a CD11b- tumor-cell fraction and a CD11b+ tumor-associated myeloid fraction, yielding 12 biological samples total (6 tumor + 6 immune). All 12 samples were combinatorially barcoded together and split into 8 sublibraries. Deposited FASTQs are per-biological-sample read groups: after split-pipe v1.0.6p combinatorial demultiplexing, reads were partitioned by assigned sample identity and concatenated across all 8 sublibraries and both sequencing runs, producing one R1/R2 pair per biological sample.